COPASI

COPASI's Use In Research

2025
Khlifi H, Parisi F, Sciascia L, Palmisano L, Parrino F (2025) Combining photocatalytic and adsorption units for the partial oxidation of tyrosol to hydroxytyrosol. Catalysis Today 445:115053 Chemistry Link

1 publication
2024
Akune-Taylor Y, Kon A, Aoki-Kinoshita KF (2024) In silico simulation of glycosylation and related pathways. Analytical and Bioanalytical Chemistry. 416:3687-3696 Biochemistry Link
Amichi H, Merouani S, Dehane A, Bouchoucha H, Hamdaoui O (2024) Photo(solar)-Activated Hypochlorite Treatment: Radicals Analysis Using a Validated Model and Assessment of Efficiency in Organic Pollutants Degradation. Processes 12:1853 Environmental Sciences Chemistry Link
An H, Pires JC, Conant GC (2024) Gene expression bias between the subgenomes of allopolyploid hybrids is an emergent property of the kinetics of expression. PLOS Computational Biology 20:e1011803 Genetics Genomics Link
Anderl F, Salvadori G, Veletic M, Balasingham I (2024) Computational Modeling of Bacterial Sensor Dynamics. paper presented at the 8th Workshop on Molecular Communications. Oslo, Norway. Signaling Link
Angeli L, Morozova K, Dawid C, Scampicchio M, Stark TD (2024) UPLC-ESI-TOF MS Profiling Discriminates Biomarkers in Authentic and Adulterated Italian Samples of Saffron (Crocus sativus L.). ACS Food Science & Technology 4:1783–1794 Chemistry Biochemistry Link
Angeli L, Populin F, Morozova K, Ding Y, Asma U, Bolchini S, Cebulj A, Busatto N, Costa F, Ferrentino G, Scampicchio M (2024) Comparative analysis of antioxidant activity and capacity in apple varieties: Insights from stopped flow DPPH• kinetics, mass spectrometry and electrochemistry. Food Bioscience 58:103729 Biochemistry Link
Asma U, Bertotti ML, Zamai S, Arnold M, Amorati R, Scampicchio M (2024) A Kinetic Approach to Oxygen Radical Absorbance Capacity (ORAC): Restoring Order to the Antioxidant Activity of Hydroxycinnamic Acids and Fruit Juices. Antioxidants 13:222 Laboratory Method Biochemistry Link
Bálint D, Póti ÁL, Alexa A, Sok P, Albert K, Torda L, Földesi-Nagy D, Csókás D, Turczel G, Imre T, Szarka E, Fekete F, Bento I, Bojtár M, Palkó R, Szabó P, Monostory K, Pápai I, Soós T, Reményi A (2024) Reversible covalent c-Jun N-terminal kinase inhibitors targeting a specific cysteine by precision-guided Michael-acceptor warheads. Nature Communications 15:8606 Signaling Link
Bennett T, Geue N, Timco G, Whitehead G, Vitorica-Yrezabal I, Barran P, McInnes E, Winpenny R ( (n.d.)) Studying Cation Exchange in Cr7Co Pseudorotaxanes: Preparatory Studies for Hybrid Molecular Machines. Chemistry 30:e202400432 Chemistry Link
Bermejo-López A, Li M, Dharanipragada NVRA, Raeder M, Inge AK, Himo F, Martín-Matute B (2024) A general catalyst for the base-free mono-N-alkylation of aromatic and aliphatic amines with alcohols. Cell Reports Physical Science 5: 101991. Chemistry Link
Biosca M, Szabó KJ, Himo F (2024) Mechanism of Asymmetric Homologation of Alkenylboronic Acids with CF3-Diazomethane via Borotropic Rearrangement. Journal of Organic Chemistry 89:4538–4548 Chemistry Link
Castaño-Cerezo S, Chamas A, Kulyk H, Treitz C, Bellvert F, Tholey A, Galéote V, Camarasa C, Heux S, Garcia-Alles LF, Millard P, Truan G (2024) Combining systems and synthetic biology for in vivo enzymology. EMBO Journal 43:5169–5185 Synthetic Biology Metabolism Laboratory Method Link
Chakrabarti KS, Bakhtiari D, Rezaei-Ghaleh N (2024) Bifurcations in coupled amyloid-β aggregation-inflammation systems. npj Systems Biology and Applications 10:80 Signaling Macromolecular Biochemistry Link
Chen J, Prinsloo R, Ni X (2024) A Kinetic Study of a Photo-Oxidation Reaction between α-Terpinene and Singlet Oxygen in a Novel Oscillatory Baffled Photo Reactor. Technologies 12:29 Chemistry Link
de la Vega-Hernández K, Suero MG, Ballester P (2024) Investing in entropy: the strategy of cucurbit[n]urils to accelerate the intramolecular Diels–Alder cycloaddition reaction of tertiary furfuryl amines. Chemical Science 15:8841–8849 Chemistry Link
Dehane A, Merouani S (2024) A semi-empirical approach for determining the number density and void fraction of acoustic cavitation bubbles in sono-reactors. Vietnam Journal of Chemistry 62:141–150 Chemistry Link
Deng M, Yu J, Blackmond DG (2024) Symmetry breaking and chiral amplification in prebiotic ligation reactions. Nature 626:1019–1024 Chemistry Biochemistry Link
Díaz-Ruiz M, Nieto-Rodríguez M, Maseras F (2024) Revealing the Mechanistic Features of an Electrosynthetic Catalytic Reaction and the Role of Redox Mediators through DFT Calculations and Microkinetic Modeling. ChemPhysChem 25:e202400402 Chemistry Link
Domínguez-Romero E, Mazurenko S, Scheringer M, Martins dos Santos VAP, Evelo CT, Anton M, Hancock JM, Županič A, Suarez-Diez M (2024) Making PBPK models more reproducible in practice. Briefings in Bioinformatics 25:bbae569 Computational Method Link
Durmaz MG, Tulluk N, Aksoy RD, Yilmaz HB, Yang B, Wipat A, Pusane AE, Mısırlı G, Tugcu T (2024) BioRxToolbox: a computational framework to streamline genetic circuit design in molecular data communications. Synthetic Biology 9:ysae015 Synthetic Biology Computational Method Software Link
Eisenhardt KHS, Fiorentini F, Lindeboom W, Williams CK (2024) Quantifying CO2 Insertion Equilibria for Low-Pressure Propene Oxide and Carbon Dioxide Ring Opening Copolymerization Catalysts. Journal of the American Chemical Society 146:10451–10464 Chemistry Link
Eisenhardt KHS, Fiorentini F, Williams CK (2024) Understanding the Effect of M(III) Choice in Heterodinuclear Polymerization Catalysts. Inorganic Chemistry 63:23438–23449 Chemistry Link
Erbez JP, Rangel GH, Davila M, Englade JA, Erbez AD, Rattanpal J, Li H, Chen Y, Toney MD (2024) Activation Heat Capacities in Pyridoxal Phosphate Enzymes. ACS Catalysis 14:11178–11195 Biochemistry Enzymology Link
Espinel-Ríos S, Behrendt G, Bauer J, Morabito B, Pohlodek J, Schütze A, Findeisen R, Bettenbrock K, Klamt S (2024) Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. Process Biochemistry 143:174–185 Experimental Method Computational Method Link
Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway. BMC Plant Biology 24:220 Plant Biology Metabolism Link
Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) OsTH1 is a key player in thiamin biosynthesis in rice. Scientific Reports 14:13591 Biochemistry Metabolism Plant Biology Link
Fedosov SN, Nexo E, Heegaard CW (2024) Kinetics of Cellular Cobalamin Uptake and Conversion: Comparison of Aquo/Hydroxocobalamin to Cyanocobalamin. Nutrients 16:378 Metabolism Link
Galeas DM, Tolbatov I, Colacino E, Maseras F (2024) Computational study on the mechanism for the synthesis of active pharmaceutical ingredients nitrofurantoin and dantrolene in both solution and mechanochemical conditions. Physical Chemistry Chemical Physics. 26:24288–24293 Chemistry Link
Gantseva AR, Gantseva ER, Sveshnikova AN, Panteleev MA, Kovalenko TA (2024) Kinetic analysis of prothrombinase assembly and substrate delivery mechanisms. Journal of Theoretical Biology 594:111925 Macromolecular Biochemistry Link
Goglia I, Węglarz-Tomczak E, Gioia C, Liu Y, Virtuoso A, Bonanomi M, Gaglio D, Salmistraro N, De Luca C, Papa M, Alberghina L, Westerhoff HV, Colangelo AM (2024) Fusion–fission–mitophagy cycling and metabolic reprogramming coordinate nerve growth factor (NGF)-dependent neuronal differentiation. FEBS Journal 291:2811–2835 Signaling Link
Gondre C, Meille V, Ouali M, Postole G, Loridant S, Pinel C, Perret N (2024) Investigation of the bifunctionality of catalysts based on Rh associated with an oxophilic promoter in the hydrogenolysis of tetrahydrofurfuryl alcohol to 1,5-pentanediol. Journal of Catalysis 430:115305 Chemistry Link
Høyland LE, VanLinden MR, Niere M, Strømland Ø, Sharma S, Dietze J, Tolås I, Lucena E, Bifulco E, Sverkeli LJ, Cimadamore-Werthein C, Ashrafi H, Haukanes KF, van der Hoeven B, Dölle C, Davidsen C, Pettersen IKN, Tronstad KJ, Mjøs SA, Hayat F, Makarov MV, Migaud ME, Heiland I, Ziegler M (2024) Subcellular NAD+ pools are interconnected and buffered by mitochondrial NAD+. Nature Metabolism 6:2319–2337 Metabolism Biochemistry Link
Jacopin E (2024) Model-Based Biology Using Soft Real-Time Systems. Ph.D. Thesis, Osaka University, Japan Computational Method Software Link
Jallet D, Soldan V, Shayan R, Stella A, Ismail N, Zenati R, Cahoreau E, Burlet-Schiltz O, Balor S, Millard P, Heux S (2024) Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli. mSystems 9:e0075024 Metabolism Microbiology Link
Kampourakis T, Ponnam S, Campbell KS, Wellette-Hunsucker A, Koch D (2024) Cardiac myosin binding protein-C phosphorylation as a function of multiple protein kinase and phosphatase activities. Nature Communications 15:5111 Signaling Link
Khanijou JK, Hee YT, Selvarajoo K (2024) Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling. In: Bizzarri M (ed) Systems Biology. Springer US: New York, NY, 3–19. Biotechnology Metabolism Link
Khanijou JK, Hee YT, Scipion CPM, Chen X, Selvarajoo K (2024) Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli. npj Systems Biology and Applications. 10:1–14 Biotechnology Synthetic Biology Metabolism Link
Khilwani R, Singh S (2024) Traversing through the Mechanistic Event Analysis in IL-6 and IL-17 Signaling for a New Therapeutic Paradigm in NSCLC. International Journal of Molecular Sciences 25:1216 Signaling Link
King CR, Berezin C-T, Peccoud J (2024) Stochastic model of vesicular stomatitis virus replication reveals mutational effects on virion production. PLOS Computational Biology 20:e1011373 Immunology Link
Kolokotroni E, Abler D, Ghosh A, Tzamali E, Grogan J, Georgiadi E, Büchler P, Radhakrishnan R, Byrne H, Sakkalis V, Nikiforaki K, Karatzanis I, McFarlane NJB, Kaba D, Dong F, Bohle RM, Meese E, Graf N, Stamatakos G (2024) A Multidisciplinary Hyper-Modeling Scheme in Personalized In Silico Oncology: Coupling Cell Kinetics with Metabolism, Signaling Networks, and Biomechanics as Plug-In Component Models of a Cancer Digital Twin. Journal of Personalized Medicine 14:475 Physiology Signaling Link
Korobkina JD, Panteleev MA, Sveshnikova AN (2024) Comparative Investigation of the Mechanisms of Calcium Response in Human and Murine Spermatozoa. Biochemistry (Moscow) 18:110–126 Signaling Cell Biology Biophysics Link
Köster T, Henning P, Warnke T, Uhrmacher A (2024) Expressive rule-based modeling and fast simulation for dynamic compartments. PLoS One 19:e0312813 Computational Method Link
Lancaster HG, Goodall JC, Douglas SP, Ashfield LJ, Duckett SB, Perutz RN, Weller AS (2024) Platinum(II) Phenylpyridyl Schiff Base Complexes as Latent, Photoactivated, Alkene Hydrosilylation Catalysts. ACS Catalysis 14:7492–7505 Chemistry Link
Lang PF, Penas DR, Banga JR, Weindl D, Novak B (2024) Reusable rule-based cell cycle model explains compartment-resolved dynamics of 16 observables in RPE-1 cells. PLOS Computational Biology 20:e1011151 Signaling Link
Li X, Fomitskaya P, Smaliak VA, Smith BS, Skorb EV, Semenov SN (2024) Selenium catalysis enables negative feedback organic oscillators. Nature Communications 15:3316 Chemistry Link
MacHale LT, Whitehead CB, Finke RG (2024) Platinum Nanoparticle Formation Kinetics and Mechanistic Studies: Evidence for an Alternative 4-Step Mechanism Involving Size-Dependent Growth and Chloride Anion and Room-Dust-Dependent Nucleation. The Journal of Physical Chemistry C 128:13083–13096 Chemistry Link
Marchetti T, Roberts BMW, Frezzato D, Prins LJ (2024) A Minimalistic Covalent Bond-Forming Chemical Reaction Cycle that Consumes Adenosine Diphosphate. Angewandte Chemie International Edition 63:e202402965 Chemistry Biochemistry Link
Matzko RO, Konur S (2024) BioNexusSentinel: a visual tool for bioregulatory network and cytohistological RNA-seq genetic expression profiling within the context of multicellular simulation research using ChatGPT-augmented software engineering. Bioinformatics Advances 4:vbae046 Computational Method Software Link
McCloskey NS, Mammedova A, Liberles DA (2024) PEMPS: a phylogenetic software tool to model the evolution of metabolic pathways. BMC Bioinformatics 25:244 Computational Method Software Link
Morgan AE, Salcedo-Sora JE, Mc Auley MT (2024) A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth. BioSystems 235:105088 Metabolism Microbiology Link
Mutsuddy A (2024) Single Cell Pharmacodynamic Modeling of Cancer Cell Lines. Ph.D. Thesis, Clemson University, Clemson, SC, USA Software Computational Method Link
Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, Gupta P, Gupta L, Vijayaraghavan P, Sengupta A (2024) Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. Journal of Biomolecular Structure and Dynamics 42:4379–4394 Metabolism Link
Nashed A, Naidoo KJ (2024) Universal Glycosyltransferase Continuous Assay for Uniform Kinetics and Inhibition Database Development and Mechanistic Studies Illustrated on ST3GAL1, C1GALT1, and FUT1. ACS Omega 9:17518–17532 Enzymology Laboratory Method Link
Nguyen PH, Cui S, Kozarich AM, Rautio A, Roberts AG, Xiong MP (2024) Utilizing surface plasmon resonance as a novel method for monitoring in-vitro P-glycoprotein efflux. Frontiers in Biophysics 2:1367511 Laboratory Method Biochemistry Link
Olsen LF (2024) Stern–Brocot arithmetic in dynamics of a biochemical reaction model. Chaos: An Interdisciplinary Journal of Nonlinear Science 34:123107 Biochemistry Link
Ospina De Los Ríos S, Bastian P, Keegan L, Sahle S, Vermoortele D, Wehling L (2024) DuneCopasi: A multi-compartment reaction-diffusion simulator for systems biology. Journal of Open Source Software 9:6836 Software Link
Patel K, Barter M, Soul J, Clark P, Proctor C, Clark I, Young D, Shanley DP (2024) Systems analysis of miR-199a/b-5p and multiple miR-199a/b-5p targets during chondrogenesis. eLife 12:RP89701 Genetics Link
Peterson KJ, Loew LM (2024) Using SpringSaLaD mesoscale simulations with COPASI ODE parameter optimization to model membrane-associated kinetics based on measured volumetric rate constants. Biophysical Journal 123:22a Biophysics Link
Phégnon L, Pérochon J, Uttenweiler-Joseph S, Cahoreau E, Millard P, Létisse F (2024) 6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway. FEBS Journal 291:4459–4472 Metabolism Link
Pontisso I, Ornelas-Guevara R, Chevet E, Combettes L, Dupont G (2024) Gradual ER calcium depletion induces a progressive and reversible UPR signaling. PNAS Nexus 3:pgae229 Signaling Link
Poprawa SM, Stasi M, Kriebisch BAK, Wenisch M, Sastre J, Boekhoven J (2024) Active droplets through enzyme-free, dynamic phosphorylation. Nature Communications 15:4204 Chemistry Synthetic Biology Signaling Link
Porey A, Fremin SO, Nand S, Trevino R, Hughes WB, Dhakal SK, Nguyen VD, Greco SG, Arman HD, Larionov OV (2024) Multimodal Acridine Photocatalysis Enables Direct Access to Thiols from Carboxylic Acids and Elemental Sulfur. ACS Catalysis 14:6973–6980 Chemistry Link
Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM (2024) Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. Science Advances 10:eadk7283 Biochemistry Plant Biology Metabolism Link
Ramsey K, Britt M, Maramba J, Ushijima B, Moller E, Anishkin A, Häse C, Sukharev S (2024) The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel MscS. iScience 27:110001 Signaling Microbiology Link
Reißenweber L, Uhl E, Hampel F, Mayer P, Dube H (2024) Directionality Reversal and Shift of Rotational Axis in a Hemithioindigo Macrocyclic Molecular Motor. Journal of the American Chemical Society 146:23387–23397 Chemistry Link
Rettenbacher LA (2024) Quantifying oxidative folding. Ph.D. Thesis, University of Kent, U.K. Biochemistry Link
Richards SE, Bradshaw PR, Johnson CH, Stachulski AV, Athersuch TJ, Nicholson JK, Lindon JC, Wilson ID (2024) Transacylation and hydrolysis of the acyl glucuronides of ibuprofen and its α-methyl-substituted analogues investigated by 1H NMR spectroscopy and computational chemistry: Implications for drug design. Journal of Pharmaceutical and Biomedical Analysis 246:116238 Pharmacology Link
Riepl D, Gamiz-Hernandez AP, Kovalova T, Król SM, Mader SL, Sjöstrand D, Högbom M, Brzezinski P, Kaila VRI (2024) Long-range charge transfer mechanism of the III2IV2 mycobacterial supercomplex. Nature Communications 15:5276 Biochemistry Link
Rowett AC, Sweeting SG, Heard DM, Lennox AJJ (2024) A Stoichiometric Haloform Coupling for Ester Synthesis with Secondary Alcohols. Angewandte Chemie 136:e202400570 Chemistry Link
Sánchez-Campillo I, Blanco-Canosa JB (2024) Kinetic and Mechanistic Studies of Native Chemical Ligation with Phenyl α-Selenoester Peptides. JACS Au 4:4374–4382 Chemistry Biochemistry Link
Sannes DK, Pulumati SH, Skúlason E, Nova A, Olsbye U (2024) CO 2 hydrogenation to methanol over Pt functionalized Hf-UiO-67 versus Zr-UiO-67. Philosophical Transactions of the Royal Society A 382:20230269 Chemistry Link
Sharma AK, Maseras F (2024) The Subtle Mechanism of Nickel-Photocatalyzed C(sp3)–H Cross-Coupling. Inorganic Chemistry 63:13801–13806 Chemistry Link
Seno C, Pokratath R, Unniram Parambil AR, Van den Eynden D, Dhaene E, Prescimone A, De Roo J (2024) Complexation and disproportionation of group 4 metal (alkoxy) halides with phosphine oxides. Dalton Transactions 53:9862–9873 Chemistry Link
Sigg A, Klimacek M, Nidetzky B (2024) Pushing the boundaries of phosphorylase cascade reaction for cellobiose production I: Kinetic model development. Biotechnology and Bioengineering 121:580–592 Biotechnology Metabolism Link
Sigg A, Klimacek M, Nidetzky B (2024) Pushing the boundaries of phosphorylase cascade reaction for cellobiose production II: Model-based multiobjective optimization. Biotechnology and Bioengineering 121:566–579 Biotechnology Metabolism Link
Silberberg M, Hermjakob H, Malik-Sheriff RS, Grecco HE (2024) Poincaré and SimBio: a versatile and extensible Python ecosystem for modeling systems. Bioinformatics 40:btae465 Software Computational Method Link
Sneddon D (2024) The Anhydride-HDDA Reaction and Further Expansion of Hexadehydro-Diels–Alder-based Reaction Methodologies. PhD Thesis, University of Minnesota, Twin Cities, MN, USA. Chemistry Link
Sollin M, Hosseininasab S, Malenfant J, El-Akhrass M, Lopez de Arbina A, Montulet A, Frenette M (2024) Oxidation of secondary hydroperoxides via αC–H abstraction to form ketones and hydroxyl radicals: fluorene autoxidation as a model system. Canadian Journal of Chemistry 102:1–6 Chemistry Link
Steiner MR, Schmallegger M, Donner L, Hlina JA, Marschner C, Baumgartner J, Slugovc C (2024) Using the phospha-Michael reaction for making phosphonium phenolate zwitterions. Beilstein Journal of Organic Chemistry 20:41–51 Chemistry Link
Stindt CN, Crespi S, Feringa BL (2024) Synthesis of Styrylbenzazole Photoswitches and Evaluation of their Photochemical Properties. Chemistry 30:e202401409 Chemistry Link
Su P, Liang H, Li Y, Ke Z (2024) Insight into Roles of Rare-Earth Metals in Heterobimetallic Ni–Y Bifunctional Catalysis for Alkyne Semihydrogenation. ACS Catalysis 14:18278–18291 Chemistry Link
Sumi T, Harada K (2024) Vaccine and antiviral drug promise for preventing post-acute sequelae of COVID-19, and their combination for its treatment. Frontiers in Immunology 15:1329162 Immunology Link
Sveshnikova AN, Shibeko AM, Kovalenko TA, Panteleev MA (2024) Kinetics and regulation of coagulation factor X activation by intrinsic tenase on phospholipid membranes. Journal of Theoretical Biology 582:111757 Signaling Biophysics Link
Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G, Sieber V (2024) Development of a Highly Selective NAD+-Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. ChemSusChem 17:e202301132 Metabolism Enzymology Link
Tonis E, Tzouras NV, Bracho Pozsoni N, Saab M, Bhandary S, Van Hecke K, Nelson DJ, Nahra F, Nolan SP, Vougioukalakis GC (2024) Modular Synthesis of Azines Bearing a Guanidine Core from N-Heterocyclic Carbene (NHC)-Derived Selenoureas and Diazo Reagents. Chemistry – A European Journal 30:e202401816 Chemistry Link
Tseng Y-Y (2024) Comparative mathematical modeling reveals the differential effects of high-fat diet and ketogenic diet on the PI3K-Akt signaling pathway in heart. Nutrition & Metabolism 21:65 Metabolism Signaling Link
Uttley M, Horne G, Tsigkinopoulou A, Del Carratore F, Hawari A, Kiezel-Tsugunova M, Kendall AC, Jones J, Messenger D, Bhogal RK, Breitling R, Nicolaou A (2024) An adaptable in silico ensemble model of the arachidonic acid cascade. Molecular Omics 20:453–468 Metabolism Immunology Link
Veliz López I, Mansilla R, Nieto-Villar JM (2024) Economía circular: una mirada desde la termodinámica y las ciencias de la complejidad. INTER DISCIPLINA 12:297–313 Other Link
Vidal PJ, Pérez AP, Yahya G, Aldea M (2024) Transcriptomic balance and optimal growth are determined by cell size. Molecular Cell 84:3288-3301.e3 Cell Biology Link
Węgrzyn E, Mejdrová I, Müller FM, Nainytė M, Escobar L, Carell T (2024) RNA-Templated Peptide Bond Formation Promotes L-Homochirality. Angewandte Chemie International Edition 63:e202319235 Biochemistry Link
Wei X, Yang X, Hu C, Li Q, Liu Q, Wu Y, Xie L, Ning X, Li F, Cai T, Zhu Z, Zhang Y-HPJ, Zhang Y, Chen X, You C (2024) ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA. Nature Communications 15:3267 Metabolism Biotechnology Link
Yabut KCB, Martynova A, Nath A, Zercher BP, Bush MF, Isoherranen N (2024) Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein (FABP1) and FABP1 Binding Alters Drug Metabolism. Molecular Pharmacology 105:395–410 Metabolism Pharmacology Link
Yang Y, Stanbury DM (2024) Oxidation of Methanesulfinate by Hexachloroiridate(IV) and the Standard Electrode Potential of the Aqueous Methanesulfonyl Radical. Inorganic Chemistry 63:1625–1632 Chemistry Link
Yin F, Song T, Wang Z, Liu J, Zhang H, Tang Y, Zhang Z (2024) Hsp70-Bim incoherent feedforward loop contributes to cell-fate heterogeneity and fractional killing. British Journal of Pharmacology 181:659–669 Signaling Link

94 publications
2023
Absalyamov DZ, Vitkovskaya NM, Orel VB, Schmidt EYu, Trofimov BA (2023) Quantum-Chemical Insight into Self-Organization of Complex Molecules from Acetylene and Anilines Catalyzed by Superbase KOH/DMSO: One-Pot Cascade Assembly of 1,3-Bis(arylamines). Asian Journal of Organic Chemistry 12:e202300042 Chemistry Link
Abraha BW, Marchisio MA (2023) Design of Gene Boolean Gates and Circuits with Convergent Promoters. In: Selvarajoo K (ed) Computational Biology and Machine Learning for Metabolic Engineering and Synthetic Biology. New York, NY: Springer US, 121–154. Synthetic Biology Link
Angeli L, Morozova K, Scampicchio M (2023) A kinetic-based stopped-flow DPPH• method. Scientific Reports 13:7621 Laboratory Method Biochemistry Link
Bartosh AV, Sotnikov DV, Zherdev AV, Dzantiev BB (2023) Handling Detection Limits of Multiplex Lateral Flow Immunoassay by Choosing the Order of Binding Zones. Micromachines 14:333 Laboratory Method Immunology Link
Bazylyak LI, Kytsya AR, Lyutyy PY, Korets’ka NI, Pilyuk YaV, Kuntyi OI (2023) Silver nanoparticles produced via a green synthesis using the rhamnolipid as a reducing agent and stabilizer. Applied Nanoscience 13:5251–5263 Laboratory Method Nanotechnology Link
Bendig T, Ulmer A, Luzia L, Müller S, Sahle S, Bergmann FT, Lösch M, Erdemann F, Zeidan AA, Mendoza SN, Teusink B, Takors R, Kummer U, Figueiredo AS (2023) The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. Journal of Biotechnology 374:90–100 Metabolism Microbiology Link
Bergmann FT (2023) BASICO: A simplified Python interface to COPASI. Journal of Open Source Software 8:5553 Software Link
Berko ER, Witek GM, Matkar S, Petrova ZO, Wu MA, Smith CM, Daniels A, Kalna J, Kennedy A, Gostuski I, Casey C, Krytska K, Gerelus M, Pavlick D, Ghazarian S, Park JR, Marachelian A, Maris JM, Goldsmith KC, Radhakrishnan R, Lemmon MA, Mossé YP (2023) Circulating tumor DNA reveals mechanisms of lorlatinib resistance in patients with relapsed/refractory ALK-driven neuroblastoma. Nature Communications 14:2601 Pharmacology Link
Bloomer BJ, Natoli SN, Garcia-Borràs M, Pereira JH, Hu DB, Adams PD, Houk KN, Clark DS, Hartwig JF (2023) Mechanistic and structural characterization of an iridium-containing cytochrome reveals kinetically relevant cofactor dynamics. Nature Catalysis 6:39–51 Enzymology Link
Bukvic AJ, Kesselring V, Aeschlimann M, Albrecht M (2023) Pincer Platinum(II) Hydrides: High Stability Imparted by Donor-Flexible Pyridylidene Amide Ligands and Evidence for Adduct Formation before Protonation. Inorganic Chemistry 62:2905–2912 Chemistry Link
Campeau D, Pommainville A, Gorodnichy M, Gagosz F (2023) Copper and Silver Catalysis in the (3 + 2) Cycloaddition of Neutral Three-Atom Components with Terminal Alkynes. Journal of the American Chemical Society 145:19018–19029 Chemistry Link
Cardozo G, Mastrogiovanni M, Zeida A, Viera N, Radi R, Reyes AM, Trujillo M (2023) Mitochondrial Peroxiredoxin 3 Is Rapidly Oxidized and Hyperoxidized by Fatty Acid Hydroperoxides. Antioxidants 12:408 Biochemistry Link
Chilmeran M, Hodges M, Ni X-W (2023) A kinetic study of biotransformation from valencene to nootkatone in an oscillatory baffled reactor. Journal of Chemical Technology & Biotechnology 98:1356–1364 Biotechnology Link
Collins S, Linnolahti M (2023) Ionization of Cp2ZrMe2 and Lewis Bases by Methylaluminoxane: Computational Insights. ChemPhysChem 24:e202200759 Chemistry Link
Cook I, Leyh TS (2023) Sterol-activated amyloid beta fibril formation. Journal of Biological Chemistry 299:105445 Macromolecular Biochemistry Link
Cruz E, Montoya A, Ágreda J (2023) Linear stability analysis of chemical mechanism, Listanalchem: A tool for the search of spontaneous mirror symmetry breaking. MethodsX 11:102307 Chemistry Software Link
Czarnievicz N, Rubanu MG, Iturralde M, Albarran-Velo J, Diamanti E, Gotor-Fernandez V, Skolimowski M, López-Gallego F (2023) A Multiplex Assay to Assess the Transaminase Activity toward Chemically Diverse Amine Donors. ChemBioChem 24:e202200614 Laboratory Method Enzymology Link
Dalligos DM, Pilling MJ, Dimitrakis G, Ball LT (2023) Coaxial Dielectric Spectroscopy as an In-Line Process Analytical Technique for Reaction Monitoring. Organic Process Research & Development 27:1094–1103 Laboratory Method Chemistry Link
Das N, Das A, Das S, Bhatawadekar V, Pandey P, Choure K, Damare S, Pandey P (2023) Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. Fermentation 9:196 Biotechnology Environmental Sciences Link
Davies C, Morgan AE, Mc Auley MT (2023) Computationally Modelling Cholesterol Metabolism and Atherosclerosis. Biology 12:1133 Metabolism Physiology Link
Decros G, Dussarrat T, Baldet P, Cassan C, Cabasson C, Dieuaide-Noubhani M, Destailleur A, Flandin A, Prigent S, Mori K, Colombié S, Jorly J, Gibon Y, Beauvoit B, Pétriacq P (2023) Enzyme-based kinetic modelling of ASC–GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability. New Phytologist 240:242–257 Metabolism Plant Biology Link
Deem M (2023) Application of time course-based kinetic methods to complex catalytic systems. Ph.D. Thesis, University of British Columbia, Vancouver, Canada Chemistry Link
Diamataris IG, Peristeras LD, Papavasileiou KD, Melissas VS, Boulougouris GC (2023) Statistical Inference of Rate Constants in Chemical and Biochemical Reaction Networks Using an “Inverse” Event-Driven Kinetic Monte Carlo Method. Journal of Physical Chemistry 127:9132–9143 Computational Method Link
Doellerer D, Pooler DRS, Guinart A, Crespi S, Feringa BL (2023) Highly Efficient Oxindole-Based Molecular Photoswitches. Chemistry 29:e202301634 Chemistry Link
Dougher M, Soh L, Bala AM (2023) Techno-Economic Analysis of Interesterification for Biodiesel Production. Energy & Fuels 37:2912–2925 Chemistry Link
Eisele N (2023) Electrospray-Ionization Mass Spectrometry for the Analysis and Quantification of Carbanions. Ph.D. Thesis, Georg-August University, Göttingen, Germany Chemistry Laboratory Method Link
Eisele NF, Peters M, Koszinowski K (2023) Live Monitoring of Anionic Living Polymerizations by Electrospray-Ionization Mass Spectrometry. Chemistry – A European Journal 29:e202203762 Chemistry Link
Espinel Ríos S (2023) Modeling, optimization, and predictive control for metabolic cybergenetics. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany Biotechnology Metabolism Link
Ferreira MJ, Rodrigues TA, Pedrosa AG, Gales L, Salvador A, Francisco T, Azevedo JE (2023) The mammalian peroxisomal membrane is permeable to both GSH and GSSG – Implications for intraperoxisomal redox homeostasis. Redox Biology 63:102764 Biochemistry Link
Friedhoff VN (2023) Stochastic Modelling of Calcium Dynamics. Ph. D. Thesis, Humboldt-Universität zu Berlin, Germany. Signaling Link
Garay Ruiz D (2023) Unweaving complex reactivity: graph-based tools to handle chemical reaction networks. TDX (Tesis Doctorals en Xarxa). Ph.D. Thesis, Universitat Rovira i Virgili, Tarragona, Spain Computational Method Link
Huber N, Alcalá-Orozco EA, Rexer T, Reichl U, Klamt S (2023) Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 81:10–25 Biotechnology Metabolism Link
Jabbari-Hichri A, Bourouina A, Biard P-F, Denicourt-Nowicki A, Roucoux A, Zanota M-L, Campoli F, De Bellefon C, Meille V (2023) Open cell foam materials as Pd reservoirs for Suzuki-Miyaura coupling catalysis at ppb level. Reaction Chemistry & Engineering 8:1799–1804 Chemistry Link
Jannsen N, Jurrat J, Neumann H, Fischer C, Thede R, Heller D (2023) Major–minor concept revisited: causes for the reversal of thermodynamically determined intermediate ratios under reaction conditions. Catalysis Science & Technology 13:4498–4505 Chemistry Biochemistry Link
Jawale D, Khandibharad S, Singh S (2023) Decoding systems immunological model of sphingolipids with IL-6/IL-17/IL-23 axes in L. major infection. Biochimica et Biophysica Acta 1868:159261 Signaling Immunology Link
Katsyv A, Kumar A, Saura P, Pöverlein MC, Freibert SA, Stripp ST, Jain S, Gamiz-Hernandez AP, Kaila VRI, Müller V, Schuller JM (2023) Molecular Basis of the Electron Bifurcation Mechanism in the [FeFe]-Hydrogenase Complex HydABC. Journal of the American Chemical Society 145:5696–5709 Enzymology Biochemistry Link
Kaya HE, Naidoo KJ (2023) CytoCopasi: A Chemical Systems Biology Target and Drug Discovery Visual Data Analytics Platform. Bioinformatics 39:btad745 Software Link
Keypour H, Kouhdareh J, Alavinia S, Rabiei K, Mohammadi M, Maryamabadi A, Babaei S (2023) Post-synthetic modification of dual-porous UMCM-1-NH2 with palladacycle complex as an effective heterogeneous catalyst in Suzuki and Heck coupling reactions. Journal of Organometallic Chemistry 989:122646 Chemistry Link
Korkola NC, Stillman MJ (2023) Structural Role of Cadmium and Zinc in Metallothionein Oxidation by Hydrogen Peroxide: The Resilience of Metal–Thiolate Clusters. Journal of the American Chemical Society 145:6383–6397 Biochemistry Link
Kyrimis S (2023) Towards realistic large-scale simulations of fixed bed chemical reactors: Bridging the gap between discrete element and porous media computational fluid dynamics models. Ph.D. Thesis, University of Southampton, UK Chemistry Link
Land MA, Ren J, Roberts NJ, Bamford KL, Shayan M, Kutulska A, George T, Masuda JD, Chitnis SS (2023) An Improved Synthesis of PN-adamantanoid Cages P4(NR)6 and a Mechanistic Study of their Fourfold Oxidation. Chemistry – An Asian Journal 18:e202300561 Chemistry Link
Larbi Djaballah M, Belghit A, Dehane A, Merouani S, Hamdaoui O, Ashokkumar M (2023) Radicals (●OH, Cl●, ClO● and Cl2●–) concentration profiles in the intensified degradation of reactive green 12 by UV/chlorine process: Chemical kinetic analysis using a validated model. Journal of Photochemistry and Photobiology 439:114557 Chemistry Link
Lauterbach S, Dienhart H, Range J, Malzacher S, Spöring J-D, Rother D, Pinto MF, Martins P, Lagerman CE, Bommarius AS, Høst AV, Woodley JM, Ngubane S, Kudanga T, Bergmann FT, Rohwer JM, Iglezakis D, Weidemann A, Wittig U, Kettner C, Swainston N, Schnell S, Pleiss J (2023) EnzymeML: seamless data flow and modeling of enzymatic data. Nature Methods 20:400–402 Computational Method Enzymology Link
Lems CM, Burger GA, Beltman JB (2023) Tumor-mediated immunosuppression and cytokine spreading affects the relation between EMT and PD-L1 status. Frontiers in Immunology 14:1219669 Immunology Link
Li Y, Liang H, Liu Y, Lin J, Ke Z (2023) Unraveling the Role of Silyl and Silane in Si–Ni Catalysts for Hydrogenation. ACS Catalysis 13:13008–13020 Chemistry Link
Liang H, Borys AM, Hevia E, Perrin M-EL, Payard P-A (2023) Shedding Light on the Hidden Roles of Lithium in the Nickel-Catalyzed Cross-Coupling of Aryl Ethers. Journal of the American Chemical Society 145:19989–19999 Chemistry Link
Liska O, Boross G, Rocabert C, Szappanos B, Tengölics R, Papp B (2023) Principles of metabolome conservation in animals. Proceedings of the National Academy of Sciences USA 120:e2302147120 Metabolism Link
Liu E, Cherraben S, Boulo L, Troufflard C, Hasenknopf B, Vives G, Sollogoub M (2023) A molecular information ratchet using a cone-shaped macrocycle. Chem 9:1147–1163 Chemistry Link
Liu S, Conley MP, Schrock RR (2023) Synthesis of Mo(IV) para-Substituted Styrene Complexes and an Exploration of Their Conversion to 1-Phenethylidene Complexes. Organometallics 42:1087–1093 Chemistry Link
Liu Y, Westerhoff HV (2023) ‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis. npj Systems Biology and Applications 9:1–13 Metabolism Link
Loman TE, Ma Y, Ilin V, Gowda S, Korsbo N, Yewale N, Rackauckas C, Isaacson SA (2023) Catalyst: Fast and flexible modeling of reaction networks. PLOS Computational Biology 19:e1011530 Software Link
Maeda K, Kurata H (2023) Automatic Generation of SBML Kinetic Models from Natural Language Texts Using GPT. International Journal of Molecular Sciences 24:7296 Computational Method Link
Maheshvare M D, Raha S, König M, Pal D (2023) A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell. Frontiers in Endocrinology 14:1185656 Metabolism Link
Marcos-Ayuso G, Peñas de Frutos MN, Gallego AM, García-Melchor M, Martínez-Ilarduya JM, Espinet P (2023) Problematic ArF-Alkynyl Coupling with Fluorinated Aryls. From Partial Success with Alkynyl Stannanes to Efficient Solutions via Mechanistic Understanding of the Hidden Complexity. Journal of the American Chemical Society 145:527–536 Chemistry Link
Martyanov AA, Stepanyan MG, Sveshnikova AN (2023) Theoretical Explanation for the Variability in Platelet Activation through the GPVI Receptor. Biochemistry (Moscow) 17:83–91 Immunology Link
Masison J, Mendes P (2023) Modeling the iron storage protein ferritin reveals how residual ferrihydrite iron determines initial ferritin iron sequestration kinetics. PLoS One 18:e0281401 Biochemistry Link
Mattila H, Mishra S, Tyystjärvi T, Tyystjärvi E (2023) Singlet oxygen production by photosystem II is caused by misses of the oxygen evolving complex. The New Phytologist 237:113–125 Biochemistry Plant Biology Link
Medasani B, Kasiraju S, Vlachos DG (2023) OpenMKM: An Open-Source C++ Multiscale Modeling Simulator for Homogeneous and Heterogeneous Catalytic Reactions. Journal of Chemical Information and Modeling 63:3377–3391 Software Chemistry Link
Mekic M, Schaefer T, Hoffmann EH, Aiyuk MBE, Tilgner A, Herrmann H (2023) Temperature-Dependent Oxidation of Hydroxylated Aldehydes by •OH, SO4•–, and NO3• Radicals in the Atmospheric Aqueous Phase. The Journal of Physical Chemistry 127:6495–6508 Chemistry Environmental Sciences Link
Mendes P (2023) Reproducibility and FAIR principles: the case of a segment polarity network model. Frontiers in Cell and Developmental Biology 11:1201673 Genetics Signaling Computational Method Link
Millard P, Gosselin-Monplaisir T, Uttenweiler-Joseph S, Enjalbert B (2023) Acetate is a beneficial nutrient for E. coli at low glycolytic flux. EMBO Journal 42:e113079 Metabolism Microbiology Link
Mutsuddy A, Erdem C, Huggins JR, Salim M, Cook D, Hobbs N, Feltus FA, Birtwistle MR (2023) Computational speed-up of large-scale, single-cell model simulations via a fully integrated SBML-based format. Bioinformatics Advances 3:vbad039 Computational Method Link
Nabintu Kajoka C, Gasperi J, Brosillon S, Caupos E, Mebold E, Oliveira M, Rocher V, Chebbo G, Le Roux J (2023) Reactivity of Performic Acid with Organic and Inorganic Compounds: From Oxidation Kinetics to Reaction Pathways. ACS EST Water 3:3121–3131 Environmental Sciences Chemistry Link
Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, Gupta P, Gupta L, Vijayaraghavan P, Sengupta A (2023) Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. Journal of Biomolecular Structure and Dynamics doi:10.1080/07391102.2023.2223726 Metabolism Link
Naumov VV, Trofimov AV, Fedorova GF, Yablonskaya OI, Vasil’ev RF (2023) Kinetic Intricacies of the Light Emission and Antiradical Influence of Exogenous Bioantioxidants Transformation Products in the Chemiluminescence Bioantioxidant Assay. International Journal of Molecular Sciences 24:8486 Biochemistry Biophysics Link
Neiburga KD, Muiznieks R, Zake DM, Pentjuss A, Komasilovs V, Rohwer JM, Tissier A, Stalidzans E (2023) Total optimization potential (TOP) approach based constrained design of isoprene and cis-abienol production in A. thaliana. Biochemical Engineering Journal 190:108723 Metabolism Biotechnology Plant Biology Link
Niehren J, Lhoussaine C, Vaginay A (2023) Core SBML and its Formal Semantics. Paper presented at the CMSB 2023 - 21th International Conference on Formal Methods in Systems Biology. Luxembourg. Computational Method Link
Olavarria K, Becker MV, Sousa DZ, van Loosdrecht MCM, Wahl SA (2023) Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synthetic and Systems Biotechnology 8:629–639 Synthetic Biology Microbiology Metabolism Link
Olsen LF (2023) Complex dynamics in an unexplored simple model of the peroxidase–oxidase reaction. Chaos 33:023102 Biochemistry Enzymology Link
Osypenko A, Cabot R, Armao IV JJ, Kovaříček P, Santoro A, Lehn J-M (2023) Behavior of Constitutional Dynamic Networks: Competition, Selection, Self-sorting in Cryptate Systems. ChemistryEurope 1:e202300017 Chemistry Link
Oughou M, Biot E, Arnaud N, Maugarny-Calès A, Laufs P, Andrey P, Burguet J (2023) Model-based reconstruction of whole organ growth dynamics reveals invariant patterns in leaf morphogenesis. Quantitative Plant Biology 4:E1 Plant Biology Link
Ouyang X, Liu G, Ji S, Luo S, Shi T, Xu P, Zhao Y-L, Tang H (2023) Dioxetane and lactone pathways in dioxygenolytic ring cleavage catalyzed by 2,5-dihydroxypyridine dioxygenase. Chem Catalysis 3:100480 Enzymology Link
Palermo JC, Carllinni Colombo M, Semelak JA, Scocozza MF, Boubeta FM, Murgida DH, Estrin DA, Bari SE (2023) Autocatalytic Mechanism in the Anaerobic Reduction of Metmyoglobin by Sulfide Species. Inorganic Chemistry 62:11304–11317 Chemistry Link
Palermo JC, Colombo MC, Scocozza MF, Murgida DH, Estrín DA, Bari SE (2023) Reduction of metmyoglobin by inorganic disulfide species. Journal of Inorganic Biochemistry 245:112256 Biochemistry Link
Pokratath R, Lermusiaux L, Checchia S, Mathew JP, Cooper SR, Mathiesen JK, Landaburu G, Banerjee S, Tao S, Reichholf N, Billinge SJL, Abécassis B, Jensen KMØ, De Roo J (2023) An Amorphous Phase Precedes Crystallization: Unraveling the Colloidal Synthesis of Zirconium Oxide Nanocrystals. ACS Nano 17:8796–8806 Chemistry Link
Pozdnyakov EM, Korneichuk AD, Rogacheva AV, Vasilev GA (2023) Polymerase β Limits the Rate of DNA Single-Strand Break Repair. Mathematical Biology and Bioinformatics 18:294–307 Genetics Biochemistry Link
Rama RJ, Maya C, Molina F, Nova A, Nicasio MC (2023) Important Role of NH-Carbazole in Aryl Amination Reactions Catalyzed by 2-Aminobiphenyl Palladacycles. ACS Catalysis 13:3934–3948 Link
Ramesh V, Krishnan J (2023) A unified approach to dissecting biphasic responses in cell signaling. eLife 12:e86520 Signaling Link
Ramesh V, Suwanmajo T, Krishnan J (2023) Network regulation meets substrate modification chemistry. Journal of the Royal Society Interface 20:20220510 Signaling Link
Rowett BC (2023) A Stoichiometric Haloform Coupling for Ester Synthesis. Ph.D. Thesis, The University of Bristol, UK Chemistry Link
Ruiter FAA, King J, Swapnasrita S, Giselbrecht S, Truckenmüller R, LaPointe VLS, Baker MB, Carlier A (2023) Optimization of Media Change Intervals through Hydrogels Using Mathematical Models. Biomacromolecules 24:604–612 Laboratory Method Link
Saffioti NA, Alvarez CL, Bazzi Z, Gentilini MV, Gondolesi GE, Schwarzbaum PJ, Schachter J (2023) Dynamic recycling of extracellular ATP in human epithelial intestinal cells. PLOS Computational Biology 19:e1011196 Biochemistry Link
Sader S (2023) Quantum Chemical Studies on the Catalytic Potential of Anionic Transition Metal Compounds in Methane to Methanol and Carbon Dioxide Carboxylation Reactions. Ph.D. Thesis, Auburn University, Alabama. Chemistry Link
Sagmeister P, Schiller C, Weiss P, Silber K, Knoll S, Horn M, Hone CA, Williams JD, Kappe CO (2023) Accelerating reaction modeling using dynamic flow experiments, part 1: design space exploration. Reaction Chemistry & Engineering 8:2818–2825 Chemistry Link
Sarang K, Otto T, Gagan S, Rudzinski K, Schaefer T, Brüggemann M, Grgić I, Kubas A, Herrmann H, Szmigielski R (2023) Aqueous-phase photo-oxidation of selected green leaf volatiles initiated by OH radicals: Products and atmospheric implications. Science of The Total Environment 879:162622 Environmental Sciences Link
Schaumburger N, Pally J, Moraru II, Kositsawat J, Kuchel GA, Blinov ML (2023) Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology 3:1079070 Signaling Physiology Link
Schuster M, Li C, Smith P, Kuttler C (2023) Parameters, architecture and emergent properties of the Pseudomonas aeruginosa LasI/LasR quorum-sensing circuit. Journal of the Royal Society Interface 20:20220825 Microbiology Signaling Link
Siedentop R, Dziennus M, Lütz S, Rosenthal K (2023) Debottlenecking of an In Vitro Enzyme Cascade Using a Combined Model- and Experiment-Based Approach. Chemie Ingenieur Technik 95:543–548 Biochemistry Metabolism Link
Šimek J (2023) Is there a difference between 14-3-3 homo- and heterodimer? Diploma Thesis, Masaryk University, Brno, Czech Republic Macromolecular Biochemistry Biophysics Link
Sotnikov DV, Barshevskaya LV, Zherdev AV, Dzantiev BB (2023) Enhanced Lateral Flow Immunoassay with Double Competition and Two Kinds of Nanoparticles Conjugates for Control of Insecticide Imidacloprid in Honey. Biosensors 13:525 Laboratory Method Link
Stanton DA, Ellis EA, Cruse MR, Jedlinski R, Kraut DA (2023) The importance of proteasome grip depends on substrate stability. Biochemical and Biophysical Research Communications 677:162–167 Macromolecular Biochemistry Link
Suárez H, Guerra A, Mansilla R, Nieto-Villar JM (2023) Ferroptosis as a biological Phase transition II: Chronotherapy of avascular and vascular tumor growth. Biological Rhythm Research 54:722–731 Biochemistry Signaling Link
Sumi T, Harada K (2023) Muscarinic acetylcholine receptor-dependent and NMDA receptor-dependent LTP and LTD share the common AMPAR trafficking pathway. iScience 26:106133 Signaling Link
Szigetvari PD, Patil S, Birkeland E, Kleppe R, Haavik J (2023) The effects of phenylalanine and tyrosine levels on dopamine production in rat PC12 cells. Implications for treatment of phenylketonuria, tyrosinemia type 1 and comorbid neurodevelopmental disorders. Neurochemistry International 171:105629 Metabolism Link
Tare P, Bhowmick T, Katagi G, China A, Nagaraja V (2023) Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS Omega 8:47510–47519 Genetics Macromolecular Biochemistry Link
van den Enk T (2023) Light-Powered Work driven by Molecular Motors. Ph.D. Thesis, University of Groningen, The Netherlands. Nanotechnology Link
Yalçınkaya BH, Genc S, Yılmaz B, Özilgen M (2023) How does exercise affect energy metabolism? An in silico approach for cardiac muscle. Heliyon 9:e17164 Biochemistry Physiology Link
Yuan AT, Stillman MJ (2023) Arsenic binding to human metallothionein-3. Chemical Science 14:5756–5767 Biochemistry Link
Yuan AT, Korkola NC, Stillman MJ (2023) Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. Journal of Biological Chemistry 299:102899 Biochemistry Biophysics Link
Yuan S, Chen S, Yang Y (2023) Dimension Reduction for Dynamic Analysis of Gene Expression Data Using Variational Autoencoder. 2023 IEEE 13th International Conference on CYBER Technology in Automation, Control, and Intelligent Systems (CYBER), 988–991. Computational Method Link

100 publications
2022
Abraha BW, Marchisio MA (2022) NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3—Comp Package. Frontiers in Bioengineering and Biotechnology 10:845240 Synthetic Biology Link
Akbulut D, Özkar S (2022) A review of the catalytic conversion of glycerol to lactic acid in the presence of aqueous base. RSC Advances 12:18864–18883 Chemistry Link
Altus K (2022) Synthesis and characterisation of platinum(II) methyl complexes and their reactivity towards carbon-hydrogen (C-H) and carbon-halogen bonds (C-X). Ph.D. Thesis, University of British Columbia, Vancouver, Canada. Chemistry Link
Anand S, Padmanabhan P, Sahu SS, Mukherjee K (2022) ANN based process optimization for the growth kinetic study of Nostoc ellipsosporum NCIM 2786. IFAC-PapersOnLine 55:423–428 Microbiology Biotechnology Link
Angelini AAR, Gache SAM, Lurdes Sabeckis M, Melian NA, Flecha FLG (2022) On the role of citrate in 12-molybdophosphoric-acid methods for quantification of phosphate in the presence of ATP. New Journal of Chemistry 46:12401–12409 Chemistry Biochemistry Link
Azevedo LG (2022) Priorização em larga-escala de proteínas-alvo para o desenvolvimento de novos compostos antileishmaniais através de integração de dados multi-ômicos e imuno-informática. MS Thesis, Fundação Oswaldo Cruz, Salvador, Brazil. Parasitology Link
Baggett DW, Nath A (2022) Structure–Activity Relationships of Novel Tau Ligands: Passive Fibril Binders and Active Aggregation Inhibitors. ACS Chemical Biology 17:701–708 Macromolecular Biochemistry Link
Barh A, Sharma K, Bhatt P, Annepu SK, Nath M, Shirur M, Kumari B, Kaundal K, Kamal S, Sharma VP, Gupta S, Sharma A, Gupta M, Dutta U (2022) Identification of Key Regulatory Pathways of Basidiocarp Formation in Pleurotus spp. Using Modeling, Simulation and System Biology Studies. Journal of Fungi 8:1073 Metabolism Microbiology Link
Bauerstätter P (2022) Compartment Modeling of Overweight in Toddler Age: Modeling and Simulating a Diets Effect with COPASI. SNE Simulation Notes Europe 32:221–224 Physiology Computational Method Link
Bell M (2022) Mechanochemical modeling of structural plasticity in synapses. Ph.D. Thesis, University of California San Diego, USA. Signaling Link
Bergman D, Marazzi L, Chowkwale M, Maheshvare M D, Bidanta S, Mapder T, Li J (2022) PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell. Gigabyte 2022:1–11 Computational Method Pharmacology Link
Berzins K, Muiznieks R, Baumanis MR, Strazdina I, Shvirksts K, Prikule S, Galvanauskas V, Pleissner D, Pentjuss A, Grube M, Kalnenieks U, Stalidzans E (2022) Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by Crypthecodinium cohnii from Glycerol, Glucose and Ethanol. Marine Drugs 20:115 Metabolism Microbiology Biotechnology Environmental Sciences Link
Boldova AE, Korobkin JD, Nechipurenko YD, Sveshnikova AN (2022) Theoretical Explanation for the Rarity of Antibody-Dependent Enhancement of Infection (ADE) in COVID-19. International Journal of Molecular Sciences 23:11364 Immunology Link
Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder M den, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran J-M, Bakker BM, Daran-Lapujade P (2022) Full humanization of the glycolytic pathway in Saccharomyces cerevisiae. Cell Reports 39:111010 Metabolism Link
Borg Y, Alsford S, Pavlika V, Zaikin A, Nesbeth DN (2022) Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei. Heliyon 8:e08891 Synthetic Biology Link
Bourdon-García RD, Ágreda J, Burgos-Salcedo J, Hochberg D, Ribó JM, Bargueño P, Salamanca AE (2022) Stoichiometric network analysis in reaction networks yielding spontaneous mirror symmetry breaking in a prebiotic atmosphere. Physical Chemistry Chemical Physics 24:20788–20802 Biochemistry Chemistry Link
Burger GA, Nesenberend DN, Lems CM, Hille SC, Beltman JB (2022) Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumour progression. Royal Society Open Science 9:220186 Signaling Link
Chatzinikolaou PN, Margaritelis NV, Chatzinikolaou AN, Paschalis V, Theodorou AA, Vrabas IS, Kyparos A, Nikolaidis MG (2022) Oxygen Transport: A Redox O2dyssey. In: Cobley JN and Davison GW (eds) Oxidative Eustress in Exercise Physiology. CRC Press Metabolism Link
Chedere A, Mishra M, Kulkarni O, Sriraman S, Chandra N (2022) Personalized quantitative models of NAD metabolism in hepatocellular carcinoma identify a subgroup with poor prognosis. Frontiers in Oncology 12:954512 Metabolism Physiology Link
Cho D-J, Függer M, Hopper C, Kushwaha M, Nowak T, Soubeyran Q (2022) Distributed computation with continual population growth. Distributed Computing 35:547–569 Synthetic Biology Link
Daas JCJ, Förster J, Pahle J (2022) Dynamic publication media with the COPASI R Connector (CoRC). Mathematical Biosciences 348:108822 Computational Method Link
Das A, Mandal SC, Pathak B (2022) Mechanistic exploration of CO2 conversion to dimethoxymethane (DMM) using transition metal (Co, Ru) catalysts: an energy span model. Physical Chemistry Chemical Physics 24:8387–8397 Chemistry Link
de la Sovera V, Martínez S, Umpiérrez D, Vila MA, Gonzalez D, Seoane G, Veiga N, Carrera I (2022) Synthesis of Azido-Dienediols by Enzymatic Dioxygenation of Benzylazides: An Experimental and Theoretical Study. European Journal of Organic Chemistry 2022:e202101156 Chemistry Enzymology Link
Deem MC, Derasp JS, Malig TC, Legard K, Berlinguette CP, Hein JE (2022) Ring walking as a regioselectivity control element in Pd-catalyzed C-N cross-coupling. Nature Communications 13:2869 Chemistry Link
Dotsenko OI (2022) The whole-cell kinetic metabolic model of the pH regulation mechanisms in human erythrocytes. Regulatory Mechanisms in Biosystems 13:272–280 Metabolism Whole-Cell Models Link
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR (2022) A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications 13:3555 Computational Method Signaling Link
Esposito M, Picchiami L (2022) A Comparative Study of AI Search Methods for Personalised Cancer Therapy Synthesis in COPASI. In: Bandini S, Gasparini F, Mascardi V, Palmonari M and Vizzari G (eds) AIxIA 2021 – Advances in Artificial Intelligence. Lecture Notes in Computer Science 13196:638–654 Pharmacology Physiology Computational Method Link
Faraj SE, Valsecchi WM, Ferreira-Gomes MS, Centeno M, Saint Martin EM, Fedosova NU, Rossi JPFC, Montes MR, Rossi RC (2022) Measurements of Na+-occluded intermediates during the catalytic cycle of the Na+/K+-ATPase provide novel insights into the mechanism of Na+ transport. Journal of Biological Chemistry 299:102811 Biochemistry Biophysics Link
Fernández Moyano S (2022) Análisis de los procesos de intercambio arilo/haluro en AuIII y revisión de los conceptos retrodonación e influencia trans en sistemas MIIICp*. Ph.D. Thesis, Universidad de Valladolid, Spain. Chemistry Link
Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE, Glazier JA (2022) Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2. Viruses 14:605 Epidemiology Pharmacology Link
Franco R, Serrano-Marín J (2022) Robustness of the Krebs Cycle under Physiological Conditions and in Cancer: New Clues for Evaluating Metabolism-Modifying Drug Therapies. Biomedicines 10:1199 Metabolism Link
Fueyo-González F, McGinty M, Ningoo M, Anderson L, Cantarelli C, Andrea Angeletti null, Demir M, Llaudó I, Purroy C, Marjanovic N, Heja D, Sealfon SC, Heeger PS, Cravedi P, Fribourg M (2022) Interferon-β acts directly on T cells to prolong allograft survival by enhancing regulatory T cell induction through Foxp3 acetylation. Immunity 55:459-474.e7 Immunology Link
Gallas JAC, Olsen LF (2022) Complexity in subnetworks of a peroxidase-oxidase reaction model. Chaos 32:063122 Biochemistry Enzymology Link
Garay-Ruiz D, Bo C (2022) Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal of Cheminformatics 14:29 Software Computational Method Link
Greenyer H (2022) Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets. MS Thesis, University of Victoria, Canada. Computational Method Metabolism Link
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Hamsath A, Lederberg OL, Cui Q, Shieh M, Lam Y, Brummett BJ, Xu S, Robinson JR, Xian M (2022) Intramolecular tetrazine-acryloyl cycloaddition: chemistry and applications. Chemical Science 13:10336–10341 Chemistry Link
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Jad A-C, Ricardo C-M, Rodrigo M-R (2022) mi-RNA129-1 and mi-RNA24-2 as regulators of over-expressed genes in lung typical carcinoid tumors: Potential targets for molecular therapy. Proceedings of the 2022 IEEE 4th International Conference on BioInspired Processing (BIP), 1–8 Genetics Link
Jin Q, Wu Q, Shapiro BM, McKernan SE (2022) Limited Mechanistic Link Between the Monod Equation and Methanogen Growth: a Perspective from Metabolic Modeling. Microbiology Spectrum 10:e0225921 Microbiology Metabolism Link
Juarez A, Vega IA, Mayorga LS, Guevara SR, Arribére MA (2022) An Arsenic-76 radiotracer to study the routes of assimilation, hemolymph distribution, and tissue inventories in the bioindicator organism Pomacea canaliculata. Science of the Total Environment 815:152760 Environmental Sciences Link
Kathan M, Crespi S, Thiel NO, Stares DL, Morsa D, de Boer J, Pacella G, van den Enk T, Kobauri P, Portale G, Schalley CA, Feringa BL (2022) A light-fuelled nanoratchet shifts a coupled chemical equilibrium. Nature Nanotechnology 17:159–165 Chemistry Biotechnology Macromolecular Biochemistry Link
Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ (2022) Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 602:343–348 Biochemistry Enzymology Link
Kouka T, Akase S, Sogabe I, Jin C, Karlsson NG, Aoki-Kinoshita KF (2022) Computational Modeling of O-Linked Glycan Biosynthesis in CHO Cells. Molecules 27:1766 Metabolism Link
Kumar S (2022) Compact, Causal and Multivariate Functional Statistics in Model-Free Discrete Pattern Discovery. Ph.D. Thesis, New Mexico State University, USA. Computational Method Link
Kumar A, Nimsarkar P, Singh S (2022) Systems pharmacology aiding benzimidazole scaffold as potential lead compounds against leishmaniasis for functional therapeutics. Life Sciences 308:120960 Pharmacology Link
Kurlovics J, Zake DM, Zaharenko L, Berzins K, Klovins J, Stalidzans E (2022) Metformin Transport Rates Between Plasma and Red Blood Cells in Humans. Clinical Pharmacokinetics 61:133–142 Pharmacology Link
Kurokhtina AA, Larina EV, Lagoda NA, Schmidt AF (2022) The Role of Catalyst Formation–Deactivation Processes and Evidence for a Nonlinear Mechanism in the Mizoroki–Heck Reaction with Aryl Chlorides. Kinetics and Catalysis 63:543–554 Chemistry Link
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Li G-Q, Huo Z-Y, Wu Q-Y, Chen Z, Wu Y-H, Lu Y, Hu H-Y (2022) Photolysis of free chlorine and production of reactive radicals in the UV/chlorine system using polychromatic spectrum LEDs as UV sources. Chemosphere 286:131828 Chemistry Link
Li M, Liao R-Z (2022) Water Oxidation Catalyzed by a Bioinspired Tetranuclear Manganese Complex: Mechanistic Study and Prediction. ChemSusChem 15:e202200187 Chemistry Link
Li Y, Cheng H (2022) Autocatalytic effect of in situ formed (hydro)quinone intermediates in Fenton and photo-Fenton degradation of non-phenolic aromatic pollutants and chemical kinetic modeling. Chemical Engineering Journal 449:137812 Chemistry Link
Liu Y, Wang W, Zeng A-P (2022) Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nature Communications 13:1595 Biotechnology Synthetic Biology Link
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Lucido A, Basallo O, Sorribas A, Marin-Sanguino A, Vilaprinyo E, Alves R (2022) A mathematical model for strigolactone biosynthesis in plants. Frontiers in Plant Science 13:979162 Metabolism Plant Biology Link
Lueckheide MJ, Ertem MZ, Michon MA, Chmielniak P, Robinson JR (2022) Peroxide-Selective Reduction of O2 at Redox-Inactive Rare-Earth(III) Triflates Generates an Ambiphilic Peroxide. Journal of the American Chemical Society 144:17295–17306 Chemistry Link
MacKeown H, von Gunten U, Criquet J (2022) Iodide sources in the aquatic environment and its fate during oxidative water treatment - A critical review. Water Research 217:118417 Chemistry Environmental Sciences Link
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Maier BD, Aguilera LU, Sahle S, Mutz P, Kalra P, Dächert C, Bartenschlager R, Binder M, Kummer U (2022) Stochastic dynamics of Type-I interferon responses. PLoS Computational Biology 18:e1010623 Immunology Signaling Link
Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-Licona P (2022) NETISCE: a network-based tool for cell fate reprogramming. npj Systems Biology and Applications 8:21 Computational Method Link
Mattila H, Tyystjärvi E (2022) Light-induced damage to photosystem II at a very low temperature (195 K) depends on singlet oxygen. Physiologia Plantarum 174:e13824 Plant Biology Biochemistry Link
Mayer RJ, Hampel N, Ofial AR, Mayr H (2022) Resolving the Mechanistic Complexity in Triarylborane-Induced Conjugate Additions. ACS Catalysis 12:15298–15309 Chemistry Link
Mayr S, Zipse H (2022) Annelated Pyridine Bases for the Selective Acylation of 1,2-Diols. European Journal of Organic Chemistry 2022:e202101521 Chemistry Link
McDaniel T, Smith NE, Cueny ES, Landis CR (2022) Dual-Chain Polymerization at an Early Transition-Metal Single-Site Catalyst. ACS Catalysis 12:10680–10689 Chemistry Link
Mirabella CFM, Aragay G, Ballester P (2022) Influence of the solvent in the self-assembly and binding properties of [1 + 1] tetra-imine bis-calix[4]pyrrole cages. Chemical Science 14:186–195 Chemistry Link
Mokry RL, O’Brien BS, Adelman JW, Rosas S, Schumacher ML, Ebert AD, Terhune SS (2022) Nitric Oxide Attenuates Human Cytomegalovirus Infection yet Disrupts Neural Cell Differentiation and Tissue Organization. Journal of Virology 96:e0012622 Microbiology Immunology Link
Momma TY, Ottaviani JI (2022) There is no direct competition between arginase and nitric oxide synthase for the common substrate l-arginine. Nitric Oxide: Biology and Chemistry 129:16–24 Metabolism Link
Nelson TF, Baumgartner R, Jaggi M, Bernasconi SM, Battagliarin G, Sinkel C, Künkel A, Kohler H-PE, McNeill K, Sander M (2022) Biodegradation of poly(butylene succinate) in soil laboratory incubations assessed by stable carbon isotope labelling. Nature Communications 13:5691 Link
Német N, Miele Y, Shuszter G, Tóth EL, Maróti JE, Szabó PJ, Rossi F, Lagzi I (2022) Inhibition of the urea-urease reaction by the components of the zeolite imidazole frameworks-8 and the formation of urease-zinc-imidazole hybrid compound. Reaction Kinetics, Mechanisms and Catalysis 135:15–28 Chemistry Link
Nieto F, Garrido F, Dinamarca S, Cebrian I, Mayorga LS (2022) Kinetics of antigen cross-presentation assessed experimentally and by a model of the complete endomembrane system. Cellular Immunology 382:104636 Immunology Link
Orrico F, Lopez AC, Saliwonczyk D, Acosta C, Rodriguez-Grecco I, Mouro-Chanteloup I, Ostuni MA, Denicola A, Thomson L, Möller MN (2022) The permeability of human red blood cell membranes to hydrogen peroxide is independent of aquaporins. Journal of Biological Chemistry 298:101503 Biophysics Biochemistry Link
Pallu J, Rabin C, Hui P, Moreira TS, Creste G, Calvet C, Limoges B, Mavré F, Branca M (2022) Exponential amplification by redox cross-catalysis and unmasking of doubly protected molecular probes. Chemical Science 13:2764–2777 Chemistry Link
Paranaiba O, Oliveira P, Marks R, Novy G, Vieira M, Luz LO, Silva PA, Ferreira R, Ramirez J, Nacif JA, Caporali G (2022) Design Automation for Emerging Technologies. Journal of Integrated Circuits and Systems 17:1–11 Biotechnology Nanotechnology Link
Pérez-Saavedra B, Velasco-Rubio Á, Rivera-Chao E, Varela JA, Saá C, Fañanás-Mastral M (2022) Catalytic Lewis Base Additive Enables Selective Copper-Catalyzed Borylative α-C-H Allylation of Alicyclic Amines. Journal of the American Chemical Society 144:16206–16216 Chemistry Link
Pini F, Francés-Soriano L, Peruffo N, Barbon A, Hildebrandt N, Natile MM (2022) Spatial and Temporal Resolution of Luminescence Quenching in Small Upconversion Nanocrystals. ACS Applied Materials & Interfaces 14:11883–11894 Chemistry Link
Poucet T, Beauvoit B, González-Moro MB, Cabasson C, Pétriacq P, Flandin A, Gibon Y, Marino D, Dieuaide-Noubhani M (2022) Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves. The Plant Journal 112:1014–1028 Physiology Plant Biology Link
Ramachandran K, König M, Scharm M, Nguyen TVN, Hermjakob H, Waltemath D, Sheriff RSM (2022) FAIR Sharing of Reproducible Models of Epidemic and Pandemic Forecast. Preprints 2022060137 Computational Method Epidemiology Link
Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F (2022) Protein-Protein Communication Mediated by an Antibody-Responsive DNA Nanodevice. Angewandte Chemie 61:e202115680 Laboratory Method Link
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Rietmeyer L (2022) Étude fonctionnelle et structurale des transférases de la famille Fem de Staphylococcus aureus. Ph.D. Thesis, Sorbonne Université, Paris, France Enzymology Link
Rivas FJ (2022) Monopersulfate in water treatment: Kinetics. Journal of Hazardous Materials 430:128383 Chemistry Link
Rettenbacher LA, von der Haar T (2022) A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microbial Cell Factories 21:268 Biochemistry Microbiology Link
Sader S, Miliordos E (2022) Being negative can be positive: metal oxide anions promise more selective methane to methanol conversion. Physical Chemistry Chemical Physics 24:21583–21587 Chemistry Link
Samarth NH, Singh S (2022) Chapter 37 - Methods to study systems biology of signaling networks: A case study of NSCLC. In: Tripathi T and Dubey VK (eds) Advances in Protein Molecular and Structural Biology Methods. Academic Press, 625–634. Signaling Link
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Sarang K (2022) Atmospheric Secondary Organic Aerosol: Kinetic and Chemical Studies of in-Cloud Reactions of Selected Plant Volatiles. Ph.D. Thesis, Institute of Physical Chemistry of the Polish Academy of Sciences, Warsaw, Poland. Chemistry Environmental Sciences Link
Schälte Y, Klinger E, Alamoudi E, Hasenauer J (2022) pyABC: Efficient and robust easy-to-use approximate Bayesian computation. Journal of Open Source Software 7:4304 Software Link
Schmallegger M, Grützmacher H, Gescheidt G (2022) Bis(acyl)phosphine Oxides as Stoichiometric Photo-Reductants for Copper Nanoparticle Synthesis: Efficiency and Kinetics. ChemPhotoChem 6:e202200155 Chemistry Link
Shaikh B, Smith LP, Vasilescu D, Marupilla G, Wilson M, Agmon E, Agnew H, Andrews SS, Anwar A, Beber ME, Bergmann FT, Brooks D, Brusch L, Calzone L, Choi K, Cooper J, Detloff J, Drawert B, Dumontier M, Ermentrout GB, Faeder JR, Freiburger AP, Fröhlich F, Funahashi A, Garny A, Gennari JH, Gleeson P, Goelzer A, Haiman Z, Hasenauer J, Hellerstein JL, Hermjakob H, Hoops S, Ison JC, Jahn D, Jakubowski HV, Jordan R, Kalaš M, König M, Liebermeister W, Malik-Sheriff RS, Mandal S, McDougal R, Medley JK, Mendes P, Müller R, Myers CJ, Naldi A, Nguyen TVN, Nickerson DP, Olivier BG, Patoliya D, Paulevé L, Petzold LR, Priya A, Rampadarath AK, Rohwer JM, Saglam AS, Singh D, Sinha A, Snoep JL, Sorby H, Spangler R, Starruß J, Thomas PJ, van Niekerk DD, Weindl D, Zhang F, Zhukova A, Goldberg AP, Schaff JC, Blinov ML, Sauro HM, Moraru II, Karr JR (2022) BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Research 50: W108–W114 Computational Method Link
Sharma S, Hsieh Y-C, Dietze J, Bockwoldt M, Strømland Ø, Ziegler M, Heiland I (2022) Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria. Metabolites 12:569 Metabolism Microbiology Link
Shelton MG, Kerns KA, Castora FJ, Coleman RA (2022) Incorporating Mitochondrial Gene Expression Changes Within a Testable Mathematical Model for Alzheimer’s Disease: Stress Response Modulation Predicts Potential Therapeutic Targets. Journal of Alzheimer’s Disease 90:109–117 Signaling Metabolism Link
Sinner EK, Townsend CA (2022) Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis. Methods in Enzymology 669:29–44 Enzymology Link
Sotnikov DV, Barshevskaya LV, Bartosh AV, Zherdev AV, Dzantiev BB (2022) Double Competitive Immunodetection of Small Analyte: Realization for Highly Sensitive Lateral Flow Immunoassay of Chloramphenicol. Biosensors 12:343 Laboratory Method Link
Sumi T, Harada K (2022) Immune response to SARS-CoV-2 in severe disease and long COVID-19. iScience 25:104723 Immunology Link
Sun Y, Zhou P, Zhang P, Meng S, Zhou C, Liu Y, Zhang H, Xiong Z, Duan X, Lai B (2022) New insight into carbon materials enhanced Fenton oxidation: A strategy for green iron(III)/iron(II) cycles. Chemical Engineering Journal 450:138423 Chemistry Link
Tamosiunaite N, Logie LC, Neale SE, Singh K, Davies DL, Macgregor SA (2022) Experimental and Computational Studies on the Acetate-Assisted C–H Activation of N-Aryl Imidazolium Salts at Rhodium and Iridium: A Chloride Additive Changes the Selectivity of C–H Activation. Journal of Organic Chemistry 87:1445–1456 Chemistry Link
Tokarev A, Mozokhina A, Volpert V (2022) Competition of SARS-CoV-2 Variants in Cell Culture and Tissue: Wins the Fastest Viral Autowave. Vaccines 10:995 Immunology Link
Toyoda R, Hoang NV, Moghaddam KG, Crespi S, Pooler DRS, Faraji S, Pshenichnikov MS, Feringa BL (2022) Synergistic interplay between photoisomerization and photoluminescence in a light-driven rotary molecular motor. Nature Communications 13:5765 Biophysics Link
Trošanová Z, Louša P, Kozeleková A, Brom T, Gašparik N, Tungli J, Weisová V, Župa E, Žoldák G, Hritz J (2022) Quantitation of Human 14-3-3ζ Dimerization and the Effect of Phosphorylation on Dimer-monomer Equilibria. Journal of Molecular Biology 434:167479 Signaling Macromolecular Biochemistry Link
Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka K-I, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S (2022) Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. iScience 25:103787 Metabolism Link
Ulrich EC, Drennan CL (2022) The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. Journal of the American Chemical Society 144:5673–5684 Biochemistry Link
Valverde MB, Rodríguez RM (2022) miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament. 2022 IEEE 4th International Conference on BioInspired Processing (BIP), Cartago, Costa Rica: 1–6 Genetics Link
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Wysocka EM, Page M, Snowden J, Simpson TI (2022) Comparison of rule- and ordinary differential equation-based dynamic model of DARPP-32 signalling network. PeerJ 10:e14516 Computational Method Link
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114 publications
2021
Abdallah P, Dossier-Berne F, Karpel Vel Leitner N, Deborde M (2021) Methylparaben chlorination in the presence of bromide ions and ammonia: kinetic study and modeling. Environmental Science and Pollution Research 28:31256–31267 Chemistry Environmental Sciences Link
Acón M, Geiß C, Torres-Calvo J, Bravo-Estupiñan D, Oviedo G, Arias-Arias JL, Rojas-Matey LA, Baez E, Vásquez-Vargas G, Oses-Vargas Y, Guevara-Coto J, Segura-Castillo A, Siles-Canales F, Quirós-Barrantes S, Régnier-Vigouroux A, Mendes P, Mora-Rodríguez R (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience 24:103407 Genetics Biochemistry Computational Method Link
Angeli L, Imperiale S, Ding Y, Scampicchio M, Morozova K (2021) A Novel Stoichio-Kinetic Model for the DPPH• Assay: The Importance of the Side Reaction and Application to Complex Mixtures. Antioxidants 10:1019 Laboratory Method Link
Arya S, Williams A, Reina SV, Knapp CW, Kreft J-U, Hobman JL, Stekel DJ (2021) Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids. Environmental Pollution 275:116602 Microbiology Biotechnology Environmental Sciences Link
Berezovets V, Kytsya A, Zavaliy I, Yartys VA (2021) Kinetics and mechanism of MgH2 hydrolysis in MgCl2 solutions. International Journal of Hydrogen Energy 46:40278–40293 Chemistry Link
Berlina AN, Sotnikov DV, Komova NS, Zherdev AV, Dzantiev BB (2021) Limitations for colorimetric aggregation assay of metal ions and ways of their overcoming. Analytical Methods 13:250–257 Laboratory Method Link
Berezovets V, Kytsya A, Verbovytskyy Yu, Zavaliy I, Yartys VA (2021) Hydrolysis of MgH2 in MgCl2 solutions as an effective way for hydrogen generation. In: Hydrogen Based Energy Storage: Status and Recent Developments. Institute for Problems in Materials Science, 38–52. Chemistry Link
Bhalla US (2021) HillTau: A fast, compact abstraction for model reduction in biochemical signaling networks. PLoS Computational Biology 17:e1009621 Computational Method Link
Biswas S, Blessent MJ, Gordon BM, Zhou T, Malakar S, Wang DY, Krogh-Jespersen K, Goldman AS (2021) Origin of Regioselectivity in the Dehydrogenation of Alkanes by Pincer–Iridium Complexes: A Combined Experimental and Computational Study. ACS Catalysis 11:12038–12051 Chemistry Link
Boecker S, Slaviero G, Schramm T, Szymanski W, Steuer R, Link H, Klamt S (2021) Deciphering the physiological response of Escherichia coli under high ATP demand. Molecular Systems Biology 17:e10504 Metabolism Microbiology Link
Castro M, Lythe G, Smit J, Molina-París C (2021) Fusion and fission events regulate endosome maturation and viral escape. Scientific Reports 11:7845 Cell Biology Link
Carrasco D, Casares JA (2021) Experimental study of the [ZnCl2(THF)2] catalyzed cis/trans-isomerization of [Pd(C6Cl2F3)Me(PPh3)2] and of the transmetalation of trans-[PdCl(C6Cl2F3)(PPh3)2] with [ZnMeCl(THF)2]. Inorganica Chimica Acta 517:120206 Chemistry Link
Chen X, Ouyang X, Li J, Zhao Y-L (2021) Natural Syringyl Mediators Accelerate Laccase-Catalyzed β-O-4 Cleavage and Cα-Oxidation of a Guaiacyl Model Substrate via an Aggregation Mechanism. ACS Omega 6:22578–22588 Enzymology Link
Chushak Y, Harbaugh S, Zimlich K, Alfred B, Chávez J, Kelley-Loughnane N (2021) Characterization of synthetic riboswitch in cell-free protein expression systems. RNA Biology 18:1727-1738 Biochemistry Genetics Link
Collins S, Joshi A, Linnolahti M (2021) Formation and Structure of Hydrolytic Methylaluminoxane Activators. Chemistry 27:15460–15471 Chemistry Link
Coste SC, Brezny AC, Koronkiewicz B, Mayer JM (2021) C-H oxidation in fluorenyl benzoates does not proceed through a stepwise pathway: revisiting asynchronous proton-coupled electron transfer. Chemical Science 12:13127–13136 Chemistry Link
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2021) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131–1141 Cell Biology Signaling Link
Das A, Mandal SC, Pathak B (2021) Unraveling the catalytically preferential pathway between the direct and indirect hydrogenation of CO2 to CH3OH using N-heterocyclic carbene-based Mn(I) catalysts: a theoretical approach. Catalysis Science & Technology 11:1375–1385 Chemistry Link
de Barros HR, Tanaka LY, da Silva RTP, Santiago-Arcos J, de Torresi SIC, López-Gallego F (2021) Assembly of Nano-Biocatalyst for the Tandem Hydrolysis and Reduction of p-Nitrophenol Esters. Particle & Particle Systems Characterization 38:2100136 Chemistry Link
de Gracia Retamosa M, Ruiz-Olalla A, Agirre M, de Cózar A, Bello T, Cossío FP (2021) Additive and Emergent Catalytic Properties of Dimeric Unnatural Amino Acid Derivatives: Aldol and Conjugate Additions. Chemistry 27:15671–15687 Chemistry Link
Del Giudice D, Spatola E, Valentini M, Bombelli C, Ercolani G, Di Stefano S (2021) Time-programmable pH: decarboxylation of nitroacetic acid allows the time-controlled rising of pH to a definite value. Chemical Science 12:7460–7466 Chemistry Laboratory Method Link
Djaballah ML, Merouani S, Bendjama H, Hamdaoui O (2021) Development of a free radical-based kinetics model for the oxidative degradation of chlorazol black in aqueous solution using periodate photoactivated process. Journal of Photochemistry and Photobiology 408:113102 Chemistry Link
Erlendsson S, Teilum K (2021) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Biochemistry Immunology Link
Escala DM (2021) Hydrodynamic instabilities coupled with complex chemical reactions: control, characterization and their modeling. Ph.D. Thesis, Universidad de Santiago de Compostela, Spain. Chemistry Link
Esposito M, Picchiami L (2021) Intelligent Search for Personalized Cancer Therapy Synthesis: an Experimental Comparison. In: Benedictis RD, Maratea M, Micheli A, Scala E, Serina I, Vallati M, et al. (eds) Proceedings of the 9th Italian workshop on Planning and Scheduling (IPS’21) and the 28th International Workshop on “Experimental Evaluation of Algorithms for Solving Problems with Combinatorial Explosion” (RCRA’21) with CEUR-WS. Milan, Italy. Physiology Computational Method Link
Farinelli G, Di Luca A, Kaila VRI, MacLachlan MJ, Tiraferri A (2021) Fe-chitosan complexes for oxidative degradation of emerging contaminants in water: Structure, activity, and reaction mechanism. Journal of Hazardous Materials 408:124662 Biotechnology Chemistry Link
Felber T, Schaefer T, He L, Herrmann H (2021) Aromatic Carbonyl and Nitro Compounds as Photosensitizers and Their Photophysical Properties in the Tropospheric Aqueous Phase. Journal of Physical Chemistry 125:5078–5095 Link
Fenech M, Amorim-Silva V, Esteban Del Valle A, Arnaud D, Ruiz-Lopez N, Castillo AG, Smirnoff N, Botella MA (2021) The role of GDP-l-galactose phosphorylase in the control of ascorbate biosynthesis. Plant Physiology 185:1574–1594 Metabolism Plant Biology Link
Fischer S, Dinh M, Henry V, Robert P, Goelzer A, Fromion V (2021) BiPSim: a flexible and generic stochastic simulator for polymerization processes. Scientific Reports 11:14112 Computational Method Link
Förster J, Bergmann FT, Pahle J (2021) CoRC - the COPASI R Connector. Bioinformatics 37:2778–2779 Software Link
Friedhoff VN, Antunes G, Falcke M, Simões de Souza FM (2021) Stochastic reaction-diffusion modeling of calcium dynamics in 3D dendritic spines of Purkinje cells. Biophysical Journal 120:2112–2123 Signaling Link
Frolova AY, Pakhomov AA, Martynov VI (2021) Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. Russian Journal of Bioorganic Chemistry 47:244–251 Chemistry Link
Gallas JAC, Hauser MJB, Olsen LF (2021) Complexity of a peroxidase-oxidase reaction model. Physical Chemistry Chemical Physics 23:1943–1955 Enzymology Link
Genovese D, Baschieri A, Vona D, Baboi RE, Mollica F, Prodi L, Amorati R, Zaccheroni N (2021) Nitroxides as Building Blocks for Nanoantioxidants. ACS Applied Materials & Interfaces 13:31996–32004 Chemistry Materials Science Link
Guhe V, Soni B, Ingale P, Singh S (2021) Autophagy proteins and its homeostasis in cellular environment. Advances in Protein Chemistry and Structural Biology 123:73–93 Cell Biology Signaling Link
Gupta A, Mendes P (2021) ShinyCOPASI: a web-based exploratory interface for COPASI models. arXiv:2110.03796. Software Link
Guo Y, Baschieri A, Mollica F, Valgimigli L, Cedrowski J, Litwinienko G, Amorati R (2021) Hydrogen Atom Transfer from HOO. to ortho-Quinones Explains the Antioxidant Activity of Polydopamine. Angewandte Chemie International Edition 60:15220–15224 Chemistry Link
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Kalkman ED, Hartwig JF (2021) Direct Observation of Diastereomeric α-C-Bound Enolates during Enantioselective α-Arylations: Synthesis, Characterization, and Reactivity of Arylpalladium Fluorooxindole Complexes. Journal of the American Chemical Society 143:11741–11750 Chemistry Link
King J, Mihaila SM, Ahmed S, Truckenmüller R, Giselbrecht S, Masereeuw R, Carlier A (2021) The Influence of OAT1 Density and Functionality on Indoxyl Sulfate Transport in the Human Proximal Tubule: An Integrated Computational and In Vitro Study. Toxins 13:674 Toxicology Physiology Link
Kleineberg C (2021) Bottom-up assembly of a light-driven ATP regeneration module in lipid, polymer and hybrid vesicles. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany. Synthetic Biology Biochemistry Link
Klimacek M, Zhong C, Nidetzky B (2021) Kinetic modeling of phosphorylase-catalyzed iterative β-1,4-glycosylation for degree of polymerization-controlled synthesis of soluble cello-oligosaccharides. Biotechnology for Biofuels and Bioproducts 14:134 Biotechnology Enzymology Link
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Korobkin JD, Balabin FA, Yakovenko SA, Simonenko EY, Sveshnikova AN (2021) Occurrence of Calcium Oscillations in Human Spermatozoa Is Based on Spatial Signaling Enzymes Distribution. International Journal of Molecular Sciences 22:8018 Signaling Link
Koshy-Chenthittayil S, Dimitrova E, Jenkins EW, Dean BC (2021) A computational framework for finding parameter sets associated with chaotic dynamics. In Silico Biology 14:41–51 Computational Method Link
Lakhova TN, Kazantsev FV, Lashin SA, Matushkin YG (2021) The finding and researching algorithm for potentially oscillating enzymatic systems. Vavilov Journal of Genetics and Breeding 25:318–330 Computational Method Metabolism Link
Leopold M, Siebert M, Siegle AF, Trapp O (2021) Reaction Network Analysis of the Ruthenium-Catalyzed Reduction of Carbon Dioxide to Dimethoxymethane. ChemCatChem 13:2807–2814 Chemistry Link
Li Y, Cheng H (2021) Chemical kinetic modeling of organic pollutant degradation in Fenton and solar photo-Fenton processes. Journal of the Taiwan Institute of Chemical Engineers 123:175–184 Chemistry Environmental Sciences Link
Lin Q, Fu Y, Liu P, Diao T (2021) Monovalent Nickel-Mediated Radical Formation: A Concerted Halogen-Atom Dissociation Pathway Determined by Electroanalytical Studies. Journal of the American Chemical Society 143:14196–14206 Chemistry Link
Liu S, Boudjelel M, Schrock RR, Conley MP, Tsay C (2021) Interconversion of Molybdenum or Tungsten d2 Styrene Complexes with d0 1-Phenethylidene Analogues. Journal of the American Chemical Society 143:17209–17218 Chemistry Link
Long BM, Förster B, Pulsford SB, Price GD, Badger MR (2021) Rubisco proton production can drive the elevation of CO2 within condensates and carboxysomes. Proceedings of the National Academy of Sciences USA 118:e2014406118 Metabolism Biophysics Plant Biology Link
Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG (2021) Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. Journal of Biological Chemistry 297:101175 Macromolecular Biochemistry Microbiology Link
Marchisio MA (2021) Modular Modeling of Genetic Circuits in SBML Level 3. Methods in Molecular Biology 2189:45–63 Synthethic Biology Computational Method Link
Matsuura R, Karunananda MK, Liu M, Nguyen N, Blackmond DG, Engle KM (2021) Mechanistic Studies of Pd(II)-Catalyzed E/Z Isomerization of Unactivated Alkenes: Evidence for a Monometallic Nucleopalladation Pathway. ACS Catalysis 11:4239–4246 Chemistry Link
Mazat J-P, Devin A, Yoboue E, Ransac S (2021) A Theoretical Model of Mitochondrial ATP Synthase Deficiencies. The Role of Mitochondrial Carriers. Processes 9:1424 Metabolism Link
McBane GC (2021) SIR (Susceptible–Infectious–Removed) Model of Epidemiology as an Extended Example for Chemical Kinetics Students. Journal of Chemical Education 98:2906–2911 Education Epidemiology Link
Meftah Y, Boumedjane Y, Fleurat-Lessard P, Delbecq F, Michel C (2021) Enantioselective reduction of prochiral ketones promoted by amino amide ruthenium complexes: A DFT study. Journal of Organometallic Chemistry 939:121765 Chemistry Link
Millard P, Enjalbert B, Uttenweiler-Joseph S, Portais J-C, Letisse F (2021) Control and regulation of acetate overflow in Escherichia coli. eLife 10:e63661 Metabolism Microbiology Link
Mısırlı G, Yang B, James K, Wipat A (2021) Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology 10:3304–3315 Computational Method Synthetic Biology Link
Mohapatra SR, Sadik A, Sharma S, Poschet G, Gegner HM, Lanz TV, Lucarelli P, Klingmüller U, Platten M, Heiland I, Opitz CA (2021) Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine Production. Frontiers in Immunology 12:590532 Metabolism Physiology Link
Monti M, Guiducci G, Paone A, Rinaldo S, Giardina G, Liberati FR, Cutruzzolá F, Tartaglia GG (2021) Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments. Computational and Structural Biotechnology Journal 19:3034–3041 Macromolecular Biochemistry Link
Novichkov AI, Hanopolskyi AI, Miao X, Shimon LJW, Diskin-Posner Y, Semenov SN (2021) Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nature Communications 12:2994 Biochemistry Link
Nuamah MF (2021) The Study of Troglitazone Liver Toxicity via in vitro and in silico Approaches. Ph.D. Thesis, University of Nottingham, UK Toxicology Link
Oliveira A, Rodrigues J, Ferreira EC, Rodrigues L, Dias O (2021) A kinetic model of the central carbon metabolism for acrylic acid production in Escherichia coli. PLoS Computational Biology 17:e1008704 Biotechnology Metabolism Link
Panitz V, Končarević S, Sadik A, Friedel D, Bausbacher T, Trump S, Farztdinov V, Schulz S, Sievers P, Schmidt S, Jürgenson I, Jung S, Kuhn K, Pflüger I, Sharma S, Wick A, Pfänder P, Selzer S, Vollmuth P, Sahm F, von Deimling A, Heiland I, Hopf C, Schulz-Knappe P, Pike I, Platten M, Wick W, Opitz CA (2021) Tryptophan metabolism is inversely regulated in the tumor and blood of patients with glioblastoma. Theranostics 11:9217–9233 Metabolism Link
Patsatzis DG (2021) On the relation of the COVID-19 reproduction number to the explosive timescales: the case of Italy. arXiv:2101.06101 [physics, q-bio]. Epidemiology Link
Pham J, Jarczyk CE, Reynolds EF, Kelly SE, Kim T, He T, Keith JM, Chianese AR (2021) The key role of the latent N–H group in Milstein’s catalyst for ester hydrogenation. Chemical Science 12:8477–8492 Chemistry Link
Quiros DN, Nieto F, Mayorga LS (2021) From cartoons to quantitative models in Golgi transport. Biology of the Cell 113:146–164 Cell Biology Link
Quiros-Fernandez I, Figueroa-Protti L, Arias-Arias JL, Brenes-Cordero N, Siles-Canales F, Mora J, Mora-Rodríguez R (2021) Perturbation-Based Modeling Unveils the Autophagic Modulation of Chemosensitivity and Immunogenicity in Breast Cancer Cells. Metabolites 11:637 Signaling Link
Ramesh V, Krishnan J (2021) Symmetry breaking meets multisite modification. eLife 10:e65358 Signaling Link
Rampadarath AK, Nickerson DP (2021) Automated Execution of Simulation Studies in Systems Medicine Using SED-ML and COMBINE Archive. Systems Medicine 3:423–430 Computational Method Link
Ribeiro de Barros H, García I, Kuttner C, Zeballos N, Camargo PHC, de Torresi SIC, López-Gallego F, Liz-Marzán LM (2021) Mechanistic Insights into the Light-Driven Catalysis of an Immobilized Lipase on Plasmonic Nanomaterials. ACS Catalysis 11:414–423 Enzymology Materials Science Link
Ritis D (2021) Dynamical modeling in biological networks. Masters Thesis, Democritus University of Thrace, Greece. Biochemistry Link
Ritis D, Boulougouris GC (2021) On the hierarchical design of biochemical-based digital computations. Computers in Biology and Medicine 135:104630 Computational Method Theory Link
Rosenbloom AD (2021) Mechanism of Actin Filament Nucleation. Ph.D. Thesis, Yale University, New Haven, CT, USA. Macromolecular Biochemistry Cell Biology Link
Rosenbloom AD, Kovar EW, Kovar DR, Loew LM, Pollard TD (2021) Mechanism of actin filament nucleation. Biophysical Journal 120:4399–4417 Macromolecular Biochemistry Biophysics Link
Rutkis R, Strazdina I, Lasa Z, Bruheim P, Kalnenieks U (2021) Ethanologenesis and respiration in a pyruvate decarboxylase-deficient Zymomonas mobilis. BMC Research Notes 14:208 Metabolism Microbiology Link
Salamanca V, Albéniz AC (2021) Faster palladium-catalyzed arylation of simple arenes in the presence of a methylketone: beneficial effect of an a priori interfering solvent in C–H activation. Organic Chemistry Frontiers 8:1941-1951 Chemistry Link
Sánchez Pladevall B (2021) Beyond conventional DFT catalysis: Mechanochemistry and solid reductants. Ph.D. Thesis, Universitat Rovira i Virgili, Tarragona, Spain. Chemistry Link
Sarang K, Otto T, Rudzinski K, Schaefer T, Grgić I, Nestorowicz K, Herrmann H, Szmigielski R (2021) Reaction Kinetics of Green Leaf Volatiles with Sulfate, Hydroxyl, and Nitrate Radicals in Tropospheric Aqueous Phase. Environmental Science & Technology 55:13666–13676 Chemistry Environmental Sciences Link
Schmiester L, Schälte Y, Bergmann FT, Camba T, Dudkin E, Egert J, Fröhlich F, Fuhrmann L, Hauber AL, Kemmer S, Lakrisenko P, Loos C, Merkt S, Müller W, Pathirana D, Raimúndez E, Refisch L, Rosenblatt M, Stapor PL, Städter P, Wang D, Wieland F-G, Banga JR, Timmer J, Villaverde AF, Sahle S, Kreutz C, Hasenauer J, Weindl D (2021) PEtab-Interoperable specification of parameter estimation problems in systems biology. PLoS Computational Biology 17:e1008646 Computational Method Link
Shaikh B, Marupilla G, Wilson M, Blinov ML, Moraru II, Karr JR (2021) RunBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats. Nucleic Acids Research 49:W597–W602 Software Link
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Sigg A, Klimacek M, Nidetzky B (2021) Three-level hybrid modeling for systematic optimization of biocatalytic synthesis: α-glucosyl glycerol production by enzymatic trans-glycosylation from sucrose. Biotechnology and Bioengineering 118:4028–4040 Biotechnology Metabolism Link
Silva PJ (2021) Response to “Molecular-level understanding of biological energy coupling and transduction: Response to ‘Chemiosmotic misunderstandings’”. Biophysical Chemistry 269:106512 Biochemistry Link
Sollin M (2021) Analyse quantitative de l’oxydation radicalaire de matériaux organiques : étude cinétique et théorique de l’oxydation des hydroperoxydes. Masters Thesis, Université Du Québec À Montréal, Canada. Chemistry Link
Soni B, Singh S (2021) COVID-19 co-infection mathematical model as guided through signaling structural framework. Computational and Structural Biotechnology Journal 19:1672–1683 Signaling Immunology Link
Sotnikov DV, Berlina AN, Zherdev AV, Dzantiev BB (2021) Theoretical limitations for aggregation methods of analysis based on affine interactions. AIP Conference Proceedings 2371:070001 Biophysics Link
Städter P, Schälte Y, Schmiester L, Hasenauer J, Stapor PL (2021) Benchmarking of numerical integration methods for ODE models of biological systems. Scientific Reports 11:2696 Computational Method Link
Suàrez LA (2021) Computational Study on the Deaminative Hydrogenation of Amides Catalyzed by Base Metal Complexes. Ph.D. Thesis, University of Oslo, Norway. Chemistry Link
Sumi T, Harada K (2021) Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea. Communications Chemistry 4:1–9 Metabolism Link
Teilum K, Olsen JG, Kragelund BB (2021) On the specificity of protein-protein interactions in the context of disorder. Biochemical Journal 478:2035–2050 Signaling Macromolecular Biochemistry Link
Tisi R, Spinelli M, Palmioli A, Airoldi C, Cazzaniga P, Besozzi D, Nobile MS, Mazzoleni E, Arnhold S, De Gioia L, Grandori R, Peri F, Vanoni M, Sacco E (2021) The Multi-Level Mechanism of Action of a Pan-Ras Inhibitor Explains its Antiproliferative Activity on Cetuximab-Resistant Cancer Cells. Frontiers in Molecular Biosciences 8:625979 Signaling Cell Biology Link
Tiwari K, Kananathan S, Roberts MG, Meyer JP, Sharif Shohan MU, Xavier A, Maire M, Zyoud A, Men J, Ng S, Nguyen TVN, Glont M, Hermjakob H, Malik-Sheriff RS (2021) Reproducibility in systems biology modelling. Molecular Systems Biology 17:e9982 Computational Method Link
Tomasoni D, Paris A, Giampiccolo S, Reali F, Simoni G, Marchetti L, Kaddi C, Neves-Zaph S, Priami C, Azer K, Lombardo R (2021) QSPcc reduces bottlenecks in computational model simulations. Communications Biology 4:1022 Computational Method Software Link
Vaginay A, Boukhobza T, Smaïl-Tabbone M (2021) From quantitative SBML models to boolean networks. CNA 2021 - 10th International Conference on Complex Networks and their Applications, Nov 2021, Madrid, Spain. Computational Method Link
Valletti N, Budroni MA, Lagzi I, Marchettini N, Sanchez-Dominguez M, Rossi F (2021) Interfacial Mass Transfer in Trichloroethylene/Surfactants/ Water Systems: Implications for Remediation Strategies. Reactions 2:312–322 Chemistry Environmental Sciences Link
Vasilev GA, Filkova AA, Sveshnikova AN (2021) Study of Reversible Platelet Aggregation Model by Nonlinear Dynamics. Mathematics 9:759 Immunology Link
Virtanen O, Khorobrykh S, Tyystjärvi E (2021) Acclimation of Chlamydomonas reinhardtii to extremely strong light. Photosynthesis Research 147:91–106 Biophysics Microbiology Link
Wang JY, Choi K, Zuend SJ, Borate K, Shinde H, Goetz R, Hartwig JF (2021) Cross-Coupling between Hydrazine and Aryl Halides with Hydroxide Base at Low Loadings of Palladium by Rate-Determining Deprotonation of Bound Hydrazine. Angewandte Chemie International Edition 60:399–408 Chemistry Link
Whitehead CB, Handwerk DR, Shipman PD, Li Y, Frenkel AI, Ingham B, Kirby NM, Finke RG (2021) Nanoparticle Formation Kinetics, Mechanisms, and Accurate Rate Constants: Examination of a Second-Generation Ir(0)n Particle Formation System by Five Monitoring Methods Plus Initial Mechanism-Enabled Population Balance Modeling. Journal of Physical Chemistry 125:13449–13476 Chemistry Link
Yahya G, Pérez AP, Mendoza MB, Parisi E, Moreno DF, Artés MH, Gallego C, Aldea M (2021) Stress granules display bistable dynamics modulated by Cdk. Journal of Cell Biology 220:jcb202005102 Cell Biology Signaling Link
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Yang Y, Filipovic D, Bhattacharya S (2021) A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver. Hepatology Communications 6:750-764 Signaling Physiology Toxicology Link
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Yin Q, Xu Z, Lian T, Musaev DG, Hill CL, Geletii YV (2021) Tafel Slope Analyses for Homogeneous Catalytic Reactions. Catalysts 11:87 Chemistry Link
Younas SL, Streuff J (2021) Kinetic Analysis Uncovers Hidden Autocatalysis and Inhibition Pathways in Titanium(III)-Catalyzed Ketone-Nitrile Couplings. ACS Catalysis 11:11451–11458 Chemistry Link
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Zake DM, Kurlovics J, Zaharenko L, Komasilovs V, Klovins J, Stalidzans E (2021) Physiologically based metformin pharmacokinetics model of mice and scale-up to humans for the estimation of concentrations in various tissues. PLoS One 16:e0249594 Pharmacology Physiology Link
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119 publications
2020
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Sharma RP, Westerhoff HV (2020) Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Frontiers in Immunology 10:3091 Immunology Signaling Link
Ajjolli Nagaraja A, Charton P, Cadet XF, Fontaine N, Delsaut M, Wiltschi B, Voit A, Offmann B, Damour C, Grondin-Perez B, Cadet F (2020) A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization. Catalysts 10:291 Computational Method Metabolism Link
Alexander JR, Packard MH, Hildebrandt AM, Ott AA, Topczewski JJ (2020) Divergent Mechanisms of the Banert Cascade with Propargyl Azides. Journal of Organic Chemistry 85:3174–3181 Chemistry Link
Artús Suàrez L, Jayarathne U, Balcells D, Bernskoetter WH, Hazari N, Jaraíz M, Nova A (2020) Rational selection of co-catalysts for the deaminative hydrogenation of amides. Chemical Science 11:2225–2230 Chemistry Link
Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft J-U, Hobman JL, Stekel DJ (2020) A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology 96:fiaa100 Microbiology Genetics Link
Balasubramanian S, Chandrasekran P, Yesudhas AJR, Ganapathyraman P, Eiteman MA, Subramanian R (2020) In vivo interpretation of model predicted inhibition in acrylate pathway engineered Lactococcus lactis. Biotechnology and Bioengineering 117:3785–3798 Microbiology Metabolism Biotechnology Link
Balzer CJ, James ML, Narvaez-Ortiz HY, Helgeson LA, Sirotkin V, Nolen BJ (2020) Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks. eLife 9:e60419 Cell Biology Macromolecular Biochemistry Link
Barrett TM (2020) Thioamides and proteolysis: Examining the effects and applications of a single-atom substitution. Ph.D. Thesis, University of Pennsylvania, USA. Biochemistry Link
Bartoli V, Meaker GA, di Bernardo M, Gorochowski TE (2020) Tunable genetic devices through simultaneous control of transcription and translation. Nature Communications 11:2095 Synthetic Biology Link
Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B (2020) Acidity and nucleophilic reactivity of glutathione persulfide. Journal of Biological Chemistry 295:15466–15481 Biochemistry Link
Benedek Z, Papp M, Oláh J, Szilvási T (2020) Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catalysis 10:12555–12568 Biochemistry Link
Bora N, Jha AN (2020) In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach. Frontiers in Genetics 11:179 Parasitology Metabolism Link
Bourouina A, Oswald A, Lido V, Dong L, Rataboul F, Djakovitch L, de Bellefon C, Meille V (2020) Kinetic Study of the Herrmann–Beller Palladacycle-Catalyzed Suzuki–Miyaura Coupling of 4-Iodoacetophenone and Phenylboronic Acid. Catalysts 10:989 Chemistry Link
Bragança CE, Kraut DA (2020) Mode of targeting to the proteasome determines GFP fate. Journal of Biological Chemistry 295:15892–15901 Biochemistry Link
Cabré A, Rafael S, Sciortino G, Ujaque G, Verdaguer X, Lledós A, Riera A (2020) Catalytic Regioselective Isomerization of 2,2-Disubstituted Oxetanes to Homoallylic Alcohols. Angewandte Chemie International Edition 59:7521–7527 Chemistry Link
Carlson-Stevermer J, Das A, Abdeen AA, Fiflis D, Grindel BI, Saxena S, Akcan T, Alam T, Kletzien H, Kohlenberg L, Goedland M, Dombroe MJ, Saha K (2020) Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nature Communications 11:6277 Laboratory Method Genetics Link
Chauhan N, Singh S (2020) Multiscale Process Modelling in Translational Systems Biology of Leishmania major: A Holistic view. Scientific Reports 10:785 Metabolism Parasitology Link
Cho D-J, Függer M, Hopper C, Kushwaha M, Nowak T, Soubeyran Q (2020) Distributed Computation with Continual Population Growth. In: Attiya H (ed) 34th International Symposium on Distributed Computing (DISC 2020). Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 7:1-7:17. Theory Link
Clark TJ, Guo L, Morgan J, Schwender J (2020) Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models. Annual Review of Plant Biology 71:303–326 Metabolism Plant Biology Link
Ćorović M, Milivojević A, Simović M, Banjanac K, Pjanović R, Bezbradica D (2020) Enzymatically derived oil-based L-ascorbyl esters: Synthesis, antioxidant properties and controlled release from cosmetic formulations. Sustainable Chemistry and Pharmacy 15:100231 Biotechnology Link
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2020) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131-1141 Cell Biology Link
Desoeuvres A, Trombettoni G, Radulescu O (2020) Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity. In: Abate A, Petrov T and Wolf V (eds.) Computational Methods in Systems Biology. Springer International Publishing, 79–101 Computational Method Link
Dhasmana A, Uniyal S, Anukriti, Kashyap VK, Somvanshi P, Gupta M, Bhardwaj U, Jaggi M, Yallapu MM, Haque S, Chauhan SC (2020) Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin. Scientific Reports 10:12045 Signaling Link
Dooley III CJ, Burtea A, Mitilian C, Dao WT, Qu B, Salzameda NT, Rychnovsky SD (2020) Using the Competing Enantioselective Conversion Method to Assign the Absolute Configuration of Cyclic Amines with Bode’s Acylation Reagents. Journal of Organic Chemistry 85:10750–10759 Chemistry Link
Dromms RA, Lee JY, Styczynski MP (2020) LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. BMC Bioinformatics 21:93 Computational Method Metabolism Link
Eastwood JB, Hammarback LA, McRobie MT, Clark IP, Towrie M, Fairlamb IJS, Lynam JM (2020) Time-resolved infra-red spectroscopy reveals competitive water and dinitrogen coordination to a manganese(I) carbonyl complex. Dalton Transactions 49:5463–5470 Chemistry Link
Erlendsson S, Teilum K (2020) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Signaling Theory Link
Ferrall-Fairbanks MC, Kieslich CA, Platt MO (2020) Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks. Proceedings of the National Academy of Sciences USA 117:3307–3318 Enzymology Link
Finke RG, Watzky MA, Whitehead CB (2020) Response to “Particle Size Is a Primary Determinant for Sigmoidal Kinetics of Nanoparticle Formation: A ‘Disproof’ of the Finke–Watzky (F-W) Nanoparticle Nucleation and Growth Mechanism”. Chemistry of Materials 32:3657–3672 Chemistry Materials Science Link
Firczuk H, Teahan J, Mendes P, McCarthy JEG (2020) Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. FEBS Journal 287:925940 Macromolecular Biochemistry Link
Foth PJ, Malig TC, Yu H, Bolduc TG, Hein JE, Sammis GM (2020) Halide-Accelerated Acyl Fluoride Formation Using Sulfuryl Fluoride. Organic Letters 22:6682–6686 Chemistry Link
Fournié M, Truan G (2020) Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments. Scientific Reports 10:21106 Biochemistry Metabolism Link
Fribourg M (2020) A case for the reuse and adaptation of mechanistic computational models to study transplant immunology. American Journal of Transplantation 20:355–361 Immunology Link
Frühwirt P, Kregar A, Törring JT, Katrašnik T, Gescheidt G (2020) Holistic approach to chemical degradation of Nafion membranes in fuel cells: modelling and predictions. Physical Chemistry Chemical Physics 22:5647–5666 Chemistry Link
Fuchino K, Kalnenieks U, Rutkis R, Grube M, Bruheim P (2020) Metabolic Profiling of Glucose-Fed Metabolically Active Resting Zymomonas mobilis Strains. Metabolites 10:E81 Metabolism Microbiology Biotechnology Link
Gallego AM, Peñas de Frutos MN, Marcos-Ayuso G, Martin-Alvarez JM, Martínez-Ilarduya JM, Espinet P (2020) Experimental study of speciation and mechanistic implications when using chelating ligands in aryl-alkynyl Stille coupling. Dalton Transactions 49:11336–11345 Chemistry Link
Garde R, Ewald J, Kovács ÁT, Schuster S (2020) Modelling population dynamics in a unicellular social organism community using a minimal model and evolutionary game theory. Open Biology 10:200206 Microbiology Metabolism Ecology Link
Garde R, Ibrahim B, Schuster S (2020) Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms. Scientific Reports 10:5579 Microbiology Metabolism Link
Garde R, Ibrahim B, Kovács ÁT, Schuster S (2020) Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms. Royal Society Open Science 7:190810 Microbiology Metabolism Link
Garzon Dasgupta AK, Martyanov AA, Filkova AA, Panteleev MA, Sveshnikova AN (2020) Development of a Simple Kinetic Mathematical Model of Aggregation of Particles or Clustering of Receptors. Life 10:E97 Biophysics Link
Ghorbani S, Szigetvari PD, Haavik J, Kleppe R (2020) Serine 19 phosphorylation and 14-3-3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. Journal of Neurochemistry 152:29–47 Signaling Link
Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS (2020) BioModels Parameters: a treasure trove of parameter values from published systems biology models. Bioinformatics 36:4649–4654 Computational Method Link
Greiss F, Daube SS, Noireaux V, Bar-Ziv R (2020) From deterministic to fuzzy decision-making in artificial cells. Nature Communications 11:5648 Synthetic Biology Genetics Link
Guerra A, Silva E, Mansilla R, Nieto-Villar JM (2020) Mathematical modeling of metastasis, a feasible way to detect the weakness. bioRxiv 2020.08.19.257931 Cell Biology Link
Gutterød ES, Pulumati SH, Kaur G, Lazzarini A, Solemsli BG, Gunnæs AE, Ahoba-Sam C, Kalyva ME, Sannes JA, Svelle S, Skúlason E, Nova A, Olsbye U (2020) Influence of Defects and H2O on the Hydrogenation of CO2 to Methanol over Pt Nanoparticles in UiO-67 Metal-Organic Framework. Journal of the American Chemical Society 142:17105–17118 Chemistry Link
Handwerk DR, Shipman PD, Özkar S, Finke RG (2020) Dust Effects on Ir(0)n Nanoparticle Formation Nucleation and Growth Kinetics and Particle Size-Distributions: Analysis by and Insights from Mechanism-Enabled Population Balance Modeling. Langmuir 36:1496–1506 Chemistry Materials Science Link
Hellgren J, Godina A, Nielsen J, Siewers V (2020) Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metabolic Engineering 62:150–160 Metabolism Link
Herrmann HA, Schwartz J-M, Johnson GN (2020) From empirical to theoretical models of light response curves - linking photosynthetic and metabolic acclimation. Photosynthesis Research 145:5–14 Metabolism Link
Hinze T (2020) Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis. Journal of Membrane Computing 2:281–289 Computational Method Link
Horváth D, Taricska N, Keszei E, Stráner P, Farkas V, Tóth GK, Perczel A (2020) Compactness of Protein Folds Alters Disulfide-Bond Reducibility by Three Orders of Magnitude: A Comprehensive Kinetic Case Study on the Reduction of Differently Sized Tryptophan Cage Model Proteins. ChemBioChem 21:681–695 Biochemistry Link
Howell RSM, Klemm C, Thorpe PH, Csikász-Nagy A (2020) Unifying the mechanism of mitotic exit control in a spatiotemporal logical model. PLoS Biology 18:e3000917 Cell Biology Link
Iwasaki T, Takiguchi R, Hiraiwa T, Yamada TG, Yamazaki K, Hiroi NF, Funahashi A (2020) Neural Differentiation Dynamics Controlled by Multiple Feedback Loops in a Comprehensive Molecular Interaction Network. Processes 8:166 Signaling Link
Jones SM, Heppner DE, Vu K, Kosman DJ, Solomon EI (2020) Rapid Decay of the Native Intermediate in the Metallooxidase Fet3p Enables Controlled FeII Oxidation for Efficient Metabolism. Journal of the American Chemical Society 142:10087–10101 Chemistry Link
Karakhim SO, Zhuk PF, Kosterin SO (2020) Kinetics simulation of transmembrane transport of ions and molecules through a semipermeable membrane. Journal of Bioenergetics and Biomembranes 52:47–60 Biophysics Link
Karlstaedt A, Khanna R, Thangam M, Taegtmeyer H (2020) Glucose 6-Phosphate Accumulates via Phosphoglucose Isomerase Inhibition in Heart Muscle. Circulation Research 126:60–74 Metabolism Link
Khaliq W, Großmann P, Neugebauer S, Kleyman A, Domizi R, Calcinaro S, Brealey D, Gräler M, Kiehntopf M, Schäuble S, Singer M, Panagiotou G, Bauer M (2020) Lipid metabolic signatures deviate in sepsis survivors compared to non-survivors. Computational and Structural Biotechnology Journal 18:3678–3691 Metabolism Link
Khurshid G, Abbassi AZ, Khalid MF, Gondal MN, Naqvi TA, Shah MM, Chaudhary SU, Ahmad R (2020) A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants. Scientific Reports 10:20879 Metabolism Link
Kolodkin AN, Sharma RP, Colangelo AM, Ignatenko A, Martorana F, Jennen D, Briedé JJ, Brady NR, Barberis M, Mondeel TDGA, Papa M, Kumar V, Peters B, Skupin A, Alberghina L, Balling R, Westerhoff HV (2020) ROS networks: designs, aging, Parkinson’s disease and precision therapies. npj Systems Biology and Applications 6:34 Biochemistry Link
Leuba SI, Yaesoubi R, Antillon M, Cohen T, Zimmer C (2020) Tracking and predicting U.S. influenza activity with a real-time surveillance network. PLoS Computational Biology 16:e1008180 Epidemiology Link
Li L, Lai M, Cole S, Le Novère N, Edelstein SJ (2020) Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. PLoS Computational Biology 16:e1006991 Signaling Link
Lo-Thong O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2020) Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches. Scientific Reports 10:13446 Metabolism Link
Malig TC, Tan Y, Wisniewski SR, Higman CS, Carrasquillo-Flores R, Ortiz A, Purdum GE, Kolotuchin S, Hein JE (2020) Development of a telescoped synthesis of 4-(1H)-cyanoimidazole core accelerated by orthogonal reaction monitoring. Reaction Chemistry & Engineering 5:1421–1428 Chemistry Laboratory Method Link
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Computational Method Link
Maquilón C, Limburg B, Laserna V, Garay-Ruiz D, González-Fabra J, Bo C, Martínez Belmonte M, Escudero-Adán EC, Kleij AW (2020) Effect of an Al(III) Complex on the Regio- and Stereoisomeric Formation of Bicyclic Organic Carbonates. Organometallics 39:1642–1651 Chemistry Link
Marín-Hernández Á, Gallardo-Pérez JC, Reyes-García MA, Sosa-Garrocho M, Macías-Silva M, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2020) Kinetic modeling of glucose central metabolism in hepatocytes and hepatoma cells. Biochimica et Biophysica Acta 1864:129687 Metabolism Link
Martin DJ, Wise CF, Pegis ML, Mayer JM (2020) Developing Scaling Relationships for Molecular Electrocatalysis through Studies of Fe-Porphyrin-Catalyzed O2 Reduction. Accounts of Chemical Research 53:1056–1065 Chemistry Link
Martyanov AA, Balabin FA, Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN (2020) Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling. Biophysical Journal 118:2641–2655 Immunology Signaling Link
Martyanov AA, Morozova DS, Sorokina MA, Filkova AA, Fedorova DV, Uzueva SS, Suntsova EV, Novichkova GA, Zharkov PA, Panteleev MA, Sveshnikova AN (2020) Heterogeneity of Integrin αIIbβ3 Function in Pediatric Immune Thrombocytopenia Revealed by Continuous Flow Cytometry Analysis. International Journal of Molecular Sciences 21:3035 Immunology Link
Mayorga L, Samartino CG, Flores G, Masuelli S, Sánchez MV, Sánchez CG, Mayorga LS (2020) COVID-19 lockdown: if, when and how. medRxiv, 2020.06.20.20136325 Epidemiology Link
Mazet F, Tindall MJ, Gibbins JM, Fry MJ (2020) A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data. Scientific Reports 10:13244 Signaling Link
Mendes P, Girardi E, Superti-Furga G, Kell DB (2020) Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters. bioRxiv. 2020.01.16.909507 Microbiology Link
Merk LN, Shur AS, Pandey A, Murray RM, Green LN (2020) Engineering Logical Inflammation Sensing Circuit for Gut Modulation. bioRxiv 2020.11.10.377085 Immunology Link
Meyer K, Morales-Navarrete H, Seifert S, Wilsch-Braeuninger M, Dahmen U, Tanaka EM, Brusch L, Kalaidzidis Y, Zerial M (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985 Signaling Cell Biology Link
Mochão H, Barahona P, Costa RS (2020) KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. Database 2020:baaa093 Computational Method Link
Mokry RL, Schumacher ML, Hogg N, Terhune SS (2020) Nitric Oxide Circumvents Virus-Mediated Metabolic Regulation during Human Cytomegalovirus Infection. mBio 11:e02630-20 Immunology Link
Mondeel TDGA, Ivanov O, Westerhoff HV, Liebermeister W, Barberis M (2020) Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. npj Systems Biology and Applications 6:8 Cell Biology Link
Morgan AE, McAuley MT (2020) Cholesterol Homeostasis: An In Silico Investigation into How Aging Disrupts Its Key Hepatic Regulatory Mechanisms. Biology 9:E314 Metabolism Link
Noga MJ, Büke F, van den Broek NJF, Imholz NCE, Scherer N, Yang F, Bokinsky G (2020) Posttranslational Control of PlsB Is Sufficient To Coordinate Membrane Synthesis with Growth in Escherichia coli. mBio 11:e02703-19 Microbiology Metabolism Link
Padayachee L, Rohwer JM, Pillay CS (2020) The thioredoxin redox potential and redox charge are surrogate measures for flux in the thioredoxin system. Archives of Biochemistry and Biophysics 680:108231 Biochemistry Metabolism Link
Pakhomov AA, Frolova AY, Tabakmakher VM, Chugunov AO, Efremov RG, Martynov VI (2020) Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. Journal of Photochemistry and Photobiology 206:111853 Biophysics Link
Panigrahi A, Whitaker D, Vitorica-Yrezabal IJ, Larrosa I (2020) Ag/Pd Cocatalyzed Direct Arylation of Fluoroarene Derivatives with Aryl Bromides. ACS Catalysis 10:2100–2107 Chemistry Link
Pappalardo F, Russo G, Pennisi M, Parasiliti Palumbo GA, Sgroi G, Motta S, Maimone D (2020) The Potential of Computational Modeling to Predict Disease Course and Treatment Response in Patients with Relapsing Multiple Sclerosis. Cells 9:586 Immunology Link
Peñas de Frutos MN (2020) Combining modern tools in the study of physical properties, reaction processes and mechanisms. Ph.D. Thesis, Universidad de Valladolid, Spain Chemistry Link
Potter ME, Armstrong L-M, Carravetta M, Mezza TM, Raja R (2020) Designing Multi-Dopant Species in Microporous Architectures to Probe Reaction Pathways in Solid-Acid Catalysis. Frontiers in Chemistry 8:171 Chemistry Link
Rana P (2020) Mathematical models of cellular signaling and supramolecular self-assembly. Ph.D. Thesis, Virginia Commonwealth University, USA. Signaling Macromolecular Biochemistry Link
Ribó JM, Hochberg D (2020) Spontaneous mirror symmetry breaking: an entropy production survey of the racemate instability and the emergence of stable scalemic stationary states. Physical Chemistry Chemical Physics 22:14013–14025 Chemistry Theory Link
Sanders JN, Jun H, Yu RA, Gleason JL, Houk KN (2020) Mechanism of an Organocatalytic Cope Rearrangement Involving Iminium Intermediates: Elucidating the Role of Catalyst Ring Size. Journal of the American Chemical Society 142:16877–16886 Chemistry Link
Schluschaß B (2020) N2 Splitting and Functionalization in the Coordination Sphere of Tungsten. Ph.D. Thesis, Georg-August University Göttingen, Germany. Chemistry Link
Schmallegger M, Barbon A, Bortolus M, Chemelli A, Bilkis I, Gescheidt G, Weiner L (2020) Systematic Quantification of Electron Transfer in a Bare Phospholipid Membrane Using Nitroxide-Labeled Stearic Acids: Distance Dependence, Kinetics, and Activation Parameters. Langmuir 36:10429–10437 Biophysics Biochemistry Link
Septian A, Shin WS (2020) Slow-release persulfate candle-assisted electrochemical oxidation of 2-methylnaphthalene: Effects of chloride, sulfate, and bicarbonate. Journal of Hazardous Materials 400:123196 Chemistry Link
Shelton M, Castora FJ, Kerns KA, Coleman RA (2020) Modeling the effects of respirasome supercomplex formation on AD progression by incorporation of mitochondrial gene expression data. Alzheimer’s & Dementia 16:e046371 Metabolism Link
Soares DMM, Gonçalves LCP, Machado CO, Esteves LC, Stevani CV, Oliveira CC, Dörr FA, Pinto E, Adachi FMM, Hotta CT, Bastos EL (2020) L-DOPA dioxygenase of the fly agaric toadstool: revision of the dodA gene sequence and mechanism of enzymatic pigment production. bioRxiv 2020.08.03.235077 Biochemistry Link
Solís RR, Rivas FJ, Chávez AM, Dionysiou DD (2020) Peroxymonosulfate/solar radiation process for the removal of aqueous microcontaminants. Kinetic modeling, influence of variables and matrix constituents. Journal of Hazardous Materials 400:123118 Chemistry Link
Song X, Yu Y, Shen C, Wang Y, Wang N (2020) Dimerization/oligomerization of the extracellular domain of the GLP-1 receptor and the negative cooperativity in its ligand binding revealed by the improved NanoBiT. FASEB Journal 34:4348–4368 Macromolecular Biochemistry Signaling Link
Sotnikov DV, Byzova NA, Zvereva EA, Bartosh AV, Zherdev AV, Dzantiev BB (2020) Mathematical modeling of immunochromatographic test systems in a competitive format: Analytical and numerical approaches. Biochemical Engineering Journal 164:107763 Computational Method Laboratory Method Link
Sotnikov DV, Zherdev AV, Dzantiev BB (2020) Lateral Flow Serodiagnosis in the Double-Antigen Sandwich Format: Theoretical Consideration and Confirmation of Advantages. Sensors 21:39 Laboratory Method Link
Sotorríos L (2020) Computational Methods Applied to Transition Metal Catalysis and Pericyclic Reactions. Ph.D. Thesis, Universidad del Pais Vasco, Spain. Chemistry Link
Stanbury DM (2020) Mechanisms of Advanced Oxidation Processes, the Principle of Detailed Balancing, and Specifics of the UV/Chloramine Process. Environmental Science & Technology 54:4658–4663 Chemistry Environmental Sciences Link
Stines-Chaumeil C, Mavré F, Kauffmann B, Mano N, Limoges B (2020) Mechanism of Reconstitution/Activation of the Soluble PQQ-Dependent Glucose Dehydrogenase from Acinetobacter calcoaceticus: A Comprehensive Study. ACS Omega 5:2015–2026 Enzymology Link
Sumi T, Harada K (2020) Mechanism underlying hippocampal long-term potentiation and depression based on competition between endocytosis and exocytosis of AMPA receptors. Scientific Reports 10:14711 Signaling Cell Biology Link
Suwanmajo T, Ramesh V, Krishnan J (2020) Exploring cyclic networks of multisite modification reveals origins of information processing characteristics. Scientific Reports 10:16542 Signaling Link
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Tian S, Jones SM, Solomon EI (2020) Role of a Tyrosine Radical in Human Ceruloplasmin Catalysis. ACS Central Science 6:1835–1843 Enzymology Link
Townrow OPE, Chung C, Macgregor SA, Weller AS, Goicoechea JM (2020) A Neutral Heteroatomic Zintl Cluster for the Catalytic Hydrogenation of Cyclic Alkenes. Journal of the American Chemical Society 142:18330–18335 Chemistry Link
Tsamba L, Cimetière N, Wolbert D, Correc O, Le Cloirec P (2020) Body fluid analog chlorination: Application to the determination of disinfection byproduct formation kinetics in swimming pool water. Journal of Environmental Sciences 87:112–122 Chemistry Environmental Sciences Link
Vargas-Villamil LM, Tedeschi LO, Medina-Peralta S, Izquierdo-Reyes F, Navarro-Alberto J, González-Garduño R (2020) A multi-inverse approach for a holistic understanding of applied animal science systems. Animal 14:s238–s249 Computational Method Physiology Link
Vasil’ev RF, Kancheva VD, Naumov VV, Slavova-Kazakova AK, Trofimov AV, Fedorova GF, Yablonskaya OI (2020) Extreme Kinetics of Chemiluminescence in the Initiated Oxidation of Vegetable Lipids. Russian Journal of Physical Chemistry 14:479–482 Biochemistry Link
Westerhoff HV, Kolodkin AN (2020) Advice from a systems-biology model of the corona epidemics. npj Systems Biology and Applications 6:18 Epidemiology Link
Wibberg D, Batut B, Belmann P, Blom J, Glöckner FO, Grüning B, Hoffmann N, Kleinbölting N, Rahn R, Rey M, Scholz U, Sharan M, Tauch A, Trojahn U, Usadel B, Kohlbacher O (2020) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8:1877 Education Link
Yang J, Postils V, Lipschutz MI, Fasulo M, Raynaud C, Clot E, Eisenstein O, Tilley TD (2020) Efficient Alkene Hydrosilation with Bis(8-quinolyl)phosphine (NPN) Nickel Catalysts. The Dominant Role of Silyl- over Hydrido-Nickel Catalytic Intermediates. Chemical Science 11:5043–5051 Chemistry Link
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113 publications
2019
Adelson CN, Johnston EM, Hilmer KM, Watts H, Dey SG, Brown DE, Broderick JB, Shepard EM, Dooley DM, Solomon EI (2019) Characterization of the Preprocessed Copper Site Equilibrium in Amine Oxidase and Assignment of the Reactive Copper Site in Topaquinone Biogenesis. Journal of the American Chemical Society 141:8877–8890 Enzymology Biochemistry Link
Aguilera LU, Bergmann FT, Dalmasso G, Elmas S, Elsässer T, Großeholz R, Holzheu P, Kalra P, Kummer U, Sahle S, Veith N (2019) Robustness of frequency vs. amplitude coding of calcium oscillations during changing temperatures. Biophysical Chemistry 245:17–24 Signaling Biophysics Link
Aguilera LU, Rodríguez-González J (2019) Modeling the effect of tat inhibitors on HIV latency. Journal of Theoretical Biology 473:20–27 Immunology Link
Anderson R, Lagnado A, Maggiorani D, Walaszczyk A, Dookun E, Chapman J, Birch J, Salmonowicz H, Ogrodnik M, Jurk D, Proctor CJ, Correia-Melo C, Victorelli S, Fielder E, Berlinguer-Palmini R, Owens A, Greaves LC, Kolsky KL, Parini A, Douin-Echinard V, LeBrasseur NK, Arthur HM, Tual-Chalot S, Schafer MJ, Roos CM, Miller JD, Robertson N, Mann J, Adams PD, Tchkonia T, Kirkland JL, Mialet-Perez J, Richardson GD, Passos JF (2019) Length-independent telomere damage drives post-mitotic cardiomyocyte senescence. EMBO Journal 38:e100492 Genetics Physiology Link
Bagaev AV, Garaeva AY, Lebedeva ES, Pichugin AV, Ataullakhanov RI, Ataullakhanov FI (2019) Elevated pre-activation basal level of nuclear NF-κB in native macrophages accelerates LPS-induced translocation of cytosolic NF-κB into the cell nucleus. Scientific Reports 9:4563 Signaling Immunology Link
Bakewell C, White AJP, Crimmin MR (2019) Reversible alkene binding and allylic C-H activation with an aluminium(i) complex. Chemical Science 10:2452–2458 Chemistry Link
Barber AL (2019) Metabolic reprogramming to optimise breast cancer treatment. Ph.D. Thesis, University of Surrey, Guilford, UK. Metabolism Link
Bartoli V, di Bernardo M, Gorochowski TE (2019) Tunable genetic devices through simultaneous control of transcription and translation. bioRxiv Preprint bioRxiv:711275 Synthetic Biology Link
Beal DM, Bastow EL, Staniforth GL, von der Haar T, Freedman RB, Tuite MF (2019) Quantitative Analyses of the Yeast Oxidative Protein Folding Pathway In Vitro and In Vivo. Antioxidants & Redox Signaling 31:261–274 Macromolecular Biochemistry Link
Bell M, Bartol T, Sejnowski T, Rangamani P (2019) Dendritic spine geometry and spine apparatus organization govern the spatiotemporal dynamics of calcium. Journal of General Physiology 151:1017–1034 Cell Biology Biophysics Signaling Link
Belli RG, Wu Y, Ji H, Joshi A, Yunker LP, McIndoe JS, Rosenberg L (2019) Competitive Ligand Exchange and Dissociation in Ru Indenyl Complexes. Inorganic Chemistry 58:747–755 Chemistry Link
Bhatt P, Pal K, Bhandari G, Barh A (2019) Modelling of the methyl halide biodegradation in bacteria and its effect on environmental systems. Pesticide Biochemistry and Physiology 158:88–100 Metabolism Environmental Sciences Link
Boba P (2019) Graphenrekonstruktion anhand abhängiger Zeitreihen in biologischen Netzwerken. Ph.D. Thesis, Technische Universität Darmstadt, Germany. Computational Method Link
Bockisch C, Lorance ED, Shaver G, Williams LB, Hartnett HE, Shock EL, Gould IR (2019) Selective hydrothermal reductions using geomimicry. Green Chemistry 21:4159–4168 Chemistry Link
Bockwoldt M, Houry D, Niere M, Gossmann TI, Reinartz I, Schug A, Ziegler M, Heiland I (2019) Identification of evolutionary and kinetic drivers of NAD-dependent signaling. Proceedings of the National Academy of Sciences USA 116:15957–15966 Signaling Metabolism Link
Broto Vispe JM (2019) Adding new functionality to COPASI, a software for simulation of biological circuits in systems biology. Bachelors Thesis, Universitat de Lleida, Spain. Computational Method Link
Bollu A, Sharma NK (2019) Cleavable Amide Bond: Mechanistic Insight into Cleavable 4-Aminopyrazolyloxy Acetamide at Low pH. Journal of Organic Chemistry 84:5596–5602 Chemistry Link
Cababie LA, Incicco JJ, González-Lebrero RM, Roman EA, Gebhard LG, Gamarnik AV, Kaufman SB (2019) Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA. Scientific Reports 9:10569 Biophysics Macromolecular Biochemistry Link
Carbonell P, Faulon J-L, Breitling R (2019) Efficient learning in metabolic pathway designs through optimal assembling. IFAC-PapersOnLine 52:7–12 Synthetic Biology Link
Chauhan N, Singh S (2019) Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania. Frontiers in Bioengineering and Biotechnology 7:336 Metabolism Parasitology Link
Chum AP, Shoemaker SR, Fleming PJ, Fleming KG (2019) Plasticity and transient binding are key ingredients of the periplasmic chaperone network. Protein Science 28:1340–1349 Macromolecular Biochemistry Microbiology Link
Diccianni JB, Katigbak J, Hu C, Diao T (2019) Mechanistic Characterization of (Xantphos)Ni(I)-Mediated Alkyl Bromide Activation: Oxidative Addition, Electron Transfer, or Halogen-Atom Abstraction. Journal of the American Chemical Society 141:1788–1796 Chemistry Link
Dietz M, Johnson A, Martínez-Martínez AJ, Weller AS (2019) The [Rh(Xantphos)]+ catalyzed hydroboration of diphenylacetylene using trimethylamine-borane. Inorganica Chimica Acta 491:9–13 Chemistry Link
Erlendsson S, Thorsen TS, Vauquelin G, Ammendrup-Johnsen I, Wirth V, Martinez KL, Teilum K, Gether U, Madsen KL (2019) Mechanisms of PDZ domain scaffold assembly illuminated by use of supported cell membrane sheets. eLife 8:e39180 Macromolecular Biochemistry Cell Biology Link
Escala DM, Muñuzuri AP (2019) Interface Fingering Instability Triggered by a Density-Coupled Oscillatory Chemical Reaction via Precipitation. Langmuir 35:13769–13781 Chemistry Link
Faraj SE, Centeno M, Rossi RC, Montes MR (2019) A kinetic comparison between E2P and the E2P-like state induced by a beryllium fluoride complex in the Na,K-ATPase. Interactions with Rb. Biochimica Et Biophysica Acta. Biomembranes 1861:355–365 Enzymology Link
Faraj SE, Noguera ME, Delfino JM, Santos J (2019) Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Scientific Reports 9:1–12 Biochemistry Link
Fecteau KM, Gould IR, Glein CR, Williams LB, Hartnett HE, Shock EL (2019) Production of Carboxylic Acids from Aldehydes under Hydrothermal Conditions: A Kinetics Study of Benzaldehyde. ACS Earth and Space Chemistry 3:170–191 Chemistry Link
Fedorova GF, Lapina VA, Menshov VA, Naumov VV, Trofimov AV, Tsaplev YB, Vasil’ev RF, Yablonskaya OI (2019) Updating the Chemiluminescence Oxygen-Aftereffect Method for Determining the Rate Constant of the Peroxy-Radical Self-Reaction: Oxidation of Cyclohexene. Photochemistry and Photobiology 95:780–786 Chemistry Link
Feldman-Salit A, Veith N, Wirtz M, Hell R, Kummer U (2019) Distribution of control in the sulfur assimilation in Arabidopsis thaliana depends on environmental conditions. New Phytologist 222:1392–1404 Metabolism Link
Filkova AA, Martyanov AA, Dasgupta AK, Panteleev MA, Sveshnikova AN (2019) Quantitative dynamics of reversible platelet aggregation: mathematical modelling and experiments. Scientific Reports 9:1–9 Physiology Link
Georgi V, Dubrovskiy A, Steigele S, Fernández‐Montalván AE (2019) Considerations for improved performance of competition association assays analysed with the Motulsky–Mahan’s “kinetics of competitive binding” model. British Journal of Pharmacology 176:4731-4744 Pharmacology Link
Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P (2019) A predictive computational model reveals that GIV/girdin serves as a tunable valve for EGFR-stimulated cyclic AMP signals. Molecular Biology of the Cell 30:1621–1633 Signaling Cell Biology Link
Ghorbani S, Szigetvari PD, Haavik J, Kleppe R (2020) Serine 19 phosphorylation and 14-3-3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. Journal of Neurochemistry 152:29–47 Signaling Link
Ghosh A, Radhakrishnan R (2019) Time-dependent antagonist-agonist switching in receptor tyrosine kinase-mediated signaling. BMC Bioinformatics 20:242 Signaling Link
Gianì F, Russo G, Pennisi M, Sciacca L, Frasca F, Pappalardo F (2019) Computational modeling reveals MAP3K8 as mediator of resistance to vemurafenib in thyroid cancer stem cells. Bioinformatics 35:2267–2275 Signaling Pharmacology Link
González-Chávez Z, Vázquez C, Mejia-Tlachi M, Márquez-Dueñas C, Manning-Cela R, Encalada R, Rodríguez-Enríquez S, Michels PAM, Moreno-Sánchez R, Saavedra E (2019) Gamma-glutamylcysteine synthetase and tryparedoxin 1 exert high control on the antioxidant system in Trypanosoma cruzi contributing to drug resistance and infectivity. Redox Biology 26:101231 Metabolism Link
Green K-A, Hoover JM (2019) Intermediacy of Copper(I) under Oxidative Conditions in the Aerobic Copper-Catalyzed Decarboxylative Thiolation of Benzoic Acids. ACS Catalysis 10:1769–1782 Chemistry Link
Hetmanski JHR, de Belly H, Busnelli I, Waring T, Nair RV, Sokleva V, Dobre O, Cameron A, Gauthier N, Lamaze C, Swift J, del Campo A, Starborg T, Zech T, Goetz JG, Paluch EK, Schwartz J-M, Caswell PT (2019) Membrane Tension Orchestrates Rear Retraction in Matrix-Directed Cell Migration. Developmental Cell 51:460-475.e10 Cell Biology Biophysics Link
Hochberg D, Ribó JM (2019) Entropic Analysis of Mirror Symmetry Breaking in Chiral Hypercycles. Life 9:28 Biochemistry Link
Hodgson D, Rowan AD, Falciani F, Proctor CJ (2019) Systems biology reveals how altered TGFβ signalling with age reduces protection against pro-inflammatory stimuli. PLoS Computational Biology 15:e1006685 Signaling Link
Houston MT, Gutierrez JB (2019) The FRiND Model: A Mathematical Model for Representing Macrophage Plasticity in Muscular Dystrophy Pathogenesis. Bulletin of Mathematical Biology 81:3976–3997 Immunology Link
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Mandal M, Luke AM, Dereli B, Elwell CE, Reineke TM, Tolman WB, Cramer CJ (2019) Computational Prediction and Experimental Verification of ε-Caprolactone Ring-Opening Polymerization Activity by an Aluminum Complex of an Indolide/Schiff-Base Ligand. ACS Catalysis 9:885–889 Chemistry Link
Mandal SC, Rawat KS, Nandi S, Pathak B (2019) Theoretical insights into CO 2 hydrogenation to methanol by a Mn–PNP complex. Catalysis Science & Technology 9:1867–1878 Chemistry Link
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Meyer-Almes F-J (2019) Determination of the binding mechanism of histone deacetylase inhibitors. Chemical Biology & Drug Design 93:1214–1250 Enzymology Link
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Mohapatra SR, Sadik A, Tykocinski L-O, Dietze J, Poschet G, Heiland I, Opitz CA (2019) Hypoxia Inducible Factor 1α Inhibits the Expression of Immunosuppressive Tryptophan-2,3-Dioxygenase in Glioblastoma. Frontiers in Immunology 10:2762 Immunology Signaling Link
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Pallu J, Rabin C, Creste G, Branca M, Mavré F, Limoges B (2019) Exponential Molecular Amplification by H2O2-Mediated Autocatalytic Deprotection of Boronic Ester Probes to Redox Cyclers. Chemistry 25:7534–7546 Chemistry Link
Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA (2019) Efficiently Encoding Complex Biochemical Models with the Multistate Model Builder (MSMB). Methods in Molecular Biology 1945:119–139 Computational Method Link
Parmar JH, Mendes P (2019) A computational model to understand mouse iron physiology and disease. PLoS Computational Biology 15:e1006680 Physiology Link
Pawłowski PH, Szczęsny P, Rempoła B, Poznańska A, Poznański J (2019) Combined in silico and 19F NMR analysis of 5-fluorouracil metabolism in yeast at low ATP conditions. Bioscience Reports 39:BSR20192847 Biochemistry Link
Pegis ML, Martin DJ, Wise CF, Brezny AC, Johnson SI, Johnson LE, Kumar N, Raugei S, Mayer JM (2019) Mechanism of Catalytic O2 Reduction by Iron Tetraphenylporphyrin. Journal of the American Chemical Society 141:8315–8326 Chemistry Link
Peñas de Frutos MN, Bartolomé C, García-Melchor M, Espinet P (2019) RhIAr/AuIAr′ Transmetalation: A Case of Group Exchange Pivoting on the Formation of M−M′ Bonds through Oxidative Insertion. Angewandte Chemie 131:3539–3543 Chemistry Link
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Silva E, Martin RR, Pomuceno JP, Mansilla R, Betancourt-Mar JA, Cocho G, Nieto-Villar JM (2019) Dose and frequency in cancer therapy. Theoretical non-autonomous model of p53 network. Biological Rhythm Research 50:483–489 Signaling Link
Sinica V, Zimova L, Barvikova K, Macikova L, Barvik I, Vlachova V (2019) Human and Mouse TRPA1 Are Heat and Cold Sensors Differentially Tuned by Voltage. Cells 9:57 Biophysics Link
Singh A, Marcoline FV, Veshaguri S, Kao AW, Bruchez M, Mindell JA, Stamou D, Grabe M (2019) Protons in small spaces: Discrete simulations of vesicle acidification. PLoS Computational Biology 15:e1007539 Physiology Link
Sinner EK, Lichstrahl MS, Li R, Marous DR, Townsend CA (2019) Methylations in complex carbapenem biosynthesis are catalyzed by a single cobalamin-dependent radical S-adenosylmethionine enzyme. Chemical Communications 55:14934–14937 Enzymology Link
Smith NE, Bernskoetter WH, Hazari N (2019) The Role of Proton Shuttles in the Reversible Activation of Hydrogen via Metal-Ligand Cooperation. Journal of the American Chemical Society 141:17350–17360 Chemistry Link
Sotorríos L, Demertzidou VP, Zografos AL, Gómez-Bengoa E (2019) DFT studies on metal-catalyzed cycloisomerization of trans -1,5-enynes to cyclopropane sesquiterpenoids. Organic & Biomolecular Chemistry 17:5112–5120 Chemistry Link
Stalidzans E, Landmane K, Sulins J, Sahle S (2019) Misinterpretation risks of global stochastic optimisation of kinetic models revealed by multiple optimisation runs. Mathematical Biosciences 307:25–32 Computational Method Link
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Tjendana Tjhin V (2019) Brain iron trafficking in health and disease: a systems approach. Ph.D. Thesis, University of Warwick, UK Physiology Link
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139 publications
2018
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Westerhoff HV (2018) Predictable Irreversible Switching Between Acute and Chronic Inflammation. Frontiers in Immunology 9:1596 Signaling Immunology Link
Acón M, Siles-Canales F, Mora-Rodríguez R (2018) Modeling Gene Dosage Compensation Mediated by Sensor Loops in Large-Scale Mathematical Models of MicroRNA-Transcription Factor Networks. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464210 Genomics Link
Arora D, Singh A (2018) Systems biology approach deciphering the biochemical signaling pathway and pharmacokinetic study of PI3K/mTOR/p53-Mdm2 module involved in neoplastic transformation. Network Modeling Analysis in Health Informatics and Bioinformatics 7:2 Signaling Link
Artús Suàrez L, Culakova Z, Balcells D, Bernskoetter WH, Eisenstein O, Goldberg KI, Hazari N, Tilset M, Nova A (2018) The Key Role of the Hemiaminal Intermediate in the Iron-Catalyzed Deaminative Hydrogenation of Amides. ACS Catalysis 8:8751–8762 Chemistry Link
Baschieri A, Valgimigli L, Gabbanini S, DiLabio GA, Romero-Montalvo E, Amorati R (2018) Extremely Fast Hydrogen Atom Transfer between Nitroxides and HOO· Radicals and Implication for Catalytic Coantioxidant Systems. Journal of the American Chemical Society 140:10354–10362 Chemistry Link
Behinaein B, Rudie K, Sangrar W (2018) Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer. IEEE/ACM Transactions on Computational Biology and Bioinformatics 15:231–243 Signaling Link
Beneš N, Brim L, Pastva S, Šafránek D, Troják M, Červenỳ J, Šalagovič J (2018) Fully Automated Attractor Analysis of Cyanobacteria Models. 2018 22nd International Conference on System Theory, Control and Computing (ICSTCC). pp. 354–359 doi:doi.org/10.1109/ICSTCC.2018.8540762 Computational Method Link
Bhardwaj T, Somvanshi P (2018) A computational approach using mathematical modeling to assess the peptidoglycan biosynthesis of Clostridium botulinum ATCC 3502 for potential drug targets. Gene Reports 12:179–186 Metabolism Microbiology Link
Blumhardt P, Stein J, Mücksch J, Stehr F, Bauer J, Jungmann R, Schwille P (2018) Photo-Induced Depletion of Binding Sites in DNA-PAINT Microscopy. Molecules 23:3165 Laboratory Method Link
Bockisch C, Lorance ED, Hartnett HE, Shock EL, Gould IR (2018) Kinetics and Mechanisms of Dehydration of Secondary Alcohols Under Hydrothermal Conditions. ACS Earth and Space Chemistry 2:821–832 Chemistry Link
Bogantes-Vidal MA, Mora-Rodríguez R, Aeón MS (2018) In-Silico Modeling for the Identification of Regulatory Microrna Targets in Epithelial Mesenchymal Transition. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464202 Genomics Link
Burford RJ, Castro L, Maron L, Hein JE, Fryzuk MD (2018) Dinitrogen functionalization at a ditantalum center. Balancing N 2 displacement and N 2 functionalization in the reaction of coordinated N 2 with CS 2. Dalton Transactions 47:7983–7991 Chemistry Link
Buriticá DCC, Mejía BV, Rojas LM, Sáenz L, Yosa J (2018) Análisis determinístico de la red de regulación génica involucrada en la expresión y función del factor de transcripción σ^ 32 en E. coli. Revista Cuarzo 23:7–15 Genetics Microbiology Link
Carpine R, Raganati F, Olivieri G, Hellingwerf KJ, Pollio A, Salatino P, Marzocchella A (2018) Poly-β-hydroxybutyrate (PHB) production by Synechocystis PCC6803 from CO2: Model development. Algal Research 29:49–60 Microbiology Biochemistry Link
Chen C, Bai Z, Cui Y, Cong Y, Pan X, Wu J (2018) ppm-Level Thermally Switchable Yttrium Phenoxide Catalysts for Moisture-Insensitive and Controllably Immortal Polymerization of rac-Lactide. Macromolecules 51:6800–6809 Chemistry Link
Costa RS, Vinga S (2018) Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data. Biotechnology Progress 34:1344–1354 Metabolism Link
Coulthard SA, McGarrity S, Sahota K, Berry P, Redfern C (2018) Three Faces of Mercaptopurine Cytotoxicity in vitro: Methylation, Nucleotide Homeostasis and Deoxythioguanosine in DNA. Drug Metabolism and Disposition 46:1191–1199 Toxicology Biochemistry Link
Dalle Pezze P, Karanasios E, Kandia V, Walker SA, Ktistakis NT, Le Novère N (2018) Dynamic modelling suggests differential mechanisms for initiation of non-selective autophagy and mitophagy. bioRxiv Preprint bioRxiv:370114 Cell Biology Link
Das A, Grosser R, Velazquez Albino A, Saha K, Capitani CM (2018) Mathematical modeling of CAR T cell therapy outcomes to develop design specifications for CAR T cell engineering. Journal for ImmunoTherapy of Cancer 6:434 Immunology Link
Diedrichs DR, Gomez JA, Huang C-S, Rutkowski DT, Curtu R (2018) A data-entrained computational model for testing the regulatory logic of the vertebrate unfolded protein response. Molecular Biology of the Cell 29:1502–1517 Signaling Link
Eibel A, Fast DE, Gescheidt G (2018) Choosing the ideal photoinitiator for free radical photopolymerizations: predictions based on simulations using established data. Polymer Chemistry 9:5107–5115 Chemistry Link
Fiebig D, Storka J, Roeder M, Meyners C, Schmelz S, Blankenfeldt W, Scrima A, Kolmar H, Fuchsbauer H-L (2018) Destructive twisting of neutral metalloproteases: the catalysis mechanism of the Dispase autolysis-inducing protein from Streptomyces mobaraensis DSM 40487. FEBS Journal 285:4246–4264 Biochemistry Link
Folch-Fortuny A, Teusink B, Hoefsloot HC, Smilde AK, Ferrer A (2018) Dynamic elementary mode modelling of non-steady state flux data. BMC Systems Biology 12:71 Computational Method Link
Földes T (2018) Computational Mechanistic Studies on Organocatalytic Addition Reactions. Ph.D. Thesis, Eötvös Loránd University, Hungary. Chemistry Link
Gagnon J-S, Hochberg D, Pérez-Mercader J (2018) Selection and control of pathways by using externally adjustable noise on a stochastic cubic autocatalytic chemical system. Physical Review E 98:062216 Chemistry Link
Gao Y (2018) Functionalization of alkanes and other hydrocarbons by high-oxidation state iridium: catalyst design and mechanistic study. Ph.D. Thesis, Rutgers University, New Jersey, USA Chemistry Link
Getz M, Swanson L, Sahoo D, Ghosh P, Rangamani P (2018) Guanine-nucleotide Exchange Modulator, GIV/Girdin, Serves as a Tunable Valve for Growth Factor-Stimulated Cyclic AMP Signals. bioRxiv Preprint bioRxiv:149781 Signaling Link
Griesser M, Shah R, Van Kessel AT, Zilka O, Haidasz EA, Pratt DA (2018) The Catalytic Reaction of Nitroxides with Peroxyl Radicals and Its Relevance to Their Cytoprotective Properties. Journal of the American Chemical Society 140:3798–3808 Chemistry Link
Guerra A, Rodriguez DJ, Montero S, Betancourt-Mar JA, Martin RR, Silva E, Bizzarri M, Cocho G, Mansilla R, Nieto-Villar JM (2018) Phase transitions in tumor growth VI: Epithelial–Mesenchymal transition. Physica A 499:208–215 Physiology Cell Biology Link
Guimera AM (2018) Investigating homeostatic disruption by constitutive signals during biological ageing. Thesis, Newcastle University Signaling Physiology Link
Guimera AM, Welsh CM, Proctor CJ, McArdle A, Shanley DP (2018) ‘Molecular habituation’as a potential mechanism of gradual homeostatic loss with age. Mechanisms of Ageing and Development 169:53–62 Physiology Link
Gupta A, Mendes P (2018) An overview of network-based and-free approaches for stochastic simulation of biochemical systems. Computation 6:9 Computational Method Link
Haffez H, Chisholm DR, Tatum NJ, Valentine R, Redfern C, Pohl E, Whiting A, Przyborski SA (2018) Probing biological activity through structural modelling of ligand-receptor interactions of 2,4-disubstituted thiazole retinoids. Bioorganic & Medicinal Chemistry 26:1560–1572 Biochemistry Link
Hantusch A (2018) Systems Biological Analysis of Bcl-2 Family Interactions and Effector Oligomerization. Ph.D. Thesis, University of Konstanz, Germany Cell Biology Macromolecular Biochemistry Link
Hill DE, Pei Q, Zhang E, Gage JR, Yu J-Q, Blackmond DG (2018) A General Protocol for Addressing Speciation of the Active Catalyst Applied to Ligand-Accelerated Enantioselective C(sp3)–H Bond Arylation. ACS Catalysis 8:1528–1531 Chemistry Link
Hodgson D (2018) Using systems biology to investigate how age-related changes in TGFβ signalling alter pro-inflammatory stimuli. Ph.D. Thesis, Newcastle University, UK. Signaling Immunology Link
Jiménez-Vargas D, Acón M, Sahin Ö, Eyüpoğlu E, Riazalhosseini Y, Molina-Mora JA, Guevara-Coto J, Mora-Rodríguez R (2018) Modules of Correlated Genes in a Gene Expression Regulatory Network of CDDP-Resistant Cancer Cells. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI). doi:10.1109/IWOBI.2018.8464190 Genomics Link
Johnson HC, Cueny ES, Landis CR (2018) Chain Transfer with Dialkyl Zinc During Hafnium–Pyridyl Amido-Catalyzed Polymerization of 1-Octene: Relative Rates, Reversibility, and Kinetic Models. ACS Catalysis 8:4178–4188 Chemistry Link
Jones Jr TC, Hoops S, Watson LT, Palmisano A, Tyson JJ, Shaffer CA (2018) JigCell Model Connector: building large molecular network models from components. SIMULATION 94:993–1008 Computational Method Software Link
Jung J, Nidetzky B (2018) Evidence of a sequestered imine intermediate during reduction of nitrile to amine by the nitrile reductase QueF from Escherichia coli. Journal of Biological Chemistry 293:3720–3733 Link
Kaliamurthi S, Selvaraj G, Kaushik AC, Gu K-R, Wei D-Q (2018) Designing of cD8+ and cD8+-overlapped cD4+ epitope vaccine by targeting late and early proteins of human papillomavirus. Biologics: Targets & Therapy 12:107–125 Immunology Link
Kaushik AC, Kumar A, Dwivedi VD, Bharadwaj S, Kumar S, Bharti K, Kumar P, Chaudhary RK, Mishra SK (2018) Deciphering the Biochemical Pathway and Pharmacokinetic Study of Amyloid βeta-42 with Superparamagnetic Iron Oxide Nanoparticles (SPIONs) Using Systems Biology Approach. Molecular Neurobiology 55:3224–3236 Biochemistry Pharmacology Laboratory Method Link
Khan S, Bhardwaj T, Somvanshi P, Mandal RK, Dar SA, Jawed A, Wahid M, Akhter N, Lohani M, Alouffi S, Haque S (2018) Inhibition of C298S mutant of human aldose reductase for antidiabetic applications: Evidence from in silico elementary mode analysis of biological network model. Journal of Cellular Biochemistry 119:6961–6973 Metabolism Link
Khan S, Somvanshi P, Bhardwaj T, Mandal RK, Dar SA, Wahid M, Jawed A, Lohani M, Khan M, Areeshi MY, Haque S (2018) Aspartate-β-semialdeyhyde dehydrogenase as a potential therapeutic target of Mycobacterium tuberculosis H37Rv: Evidence from in silico elementary mode analysis of biological network model. Journal of Cellular Biochemistry 119:2832–2842 Metabolism Microbiology Link
Kim C, Ahn J-Y, Kim TY, Shin WS, Hwang I (2018) Activation of Persulfate by Nanosized Zero-Valent Iron (NZVI): Mechanisms and Transformation Products of NZVI. Environmental Science & Technology 52:3625–3633 Chemistry Environmental Sciences Link
Kim J, Woo SS, Sarpeshkar R (2018) Fast and precise emulation of stochastic biochemical reaction networks with amplified thermal noise in silicon chips. IEEE Transactions on Biomedical Circuits and Systems 12:379–389 Computational Method Link
Kleppe R, Jonassen I, Døskeland SO, Selheim F (2018) Mathematical Modelling of Nitric Oxide/Cyclic GMP/Cyclic AMP Signalling in Platelets. International Journal of Molecular Sciences 19:612 Signaling Link
Kosey D, Soni B, Nimsarkar P, Singh S (2018) Infection dynamics in L. major autophagic machinery is regulated by ATG9-PI3P negative feedback loop. bioRxiv Preprint bioRxiv:398545 Cell Biology Immunology Link
Kwon JS, Wang X, Yao G (2018) Study Quiescence Heterogeneity by Coupling Single-Cell Measurements and Computer Modeling. Methods in Molecular Biology 1686:287–299 Cell Biology Education Link
Lease N, Pelczar EM, Zhou T, Malakar S, Emge TJ, Hasanayn F, Krogh-Jespersen K, Goldman AS (2018) PNP-Pincer Complexes of Osmium: Comparison with Isoelectronic (PCP) Ir and (PNP) Ir+ Units. Organometallics 37:314–326 Chemistry Link
Leedale J, Sharkey KJ, Colley HE, Norton ÁM, Peeney D, Mason CL, Sathish JG, Murdoch C, Sharma P, Webb SD (2018) A Combined In Vitro/In Silico Approach to Identifying Off-Target Receptor Toxicity. iScience 4:84–96 Toxicology Link
Li X, Holmes WR (2018) Biophysical attributes that affect CaMKII activation deduced with a novel spatial stochastic simulation approach. PLoS Computational Biology 14:e1005946 Biophysics Signaling Link
Liang Q, Salmon A, Kim PJ, Yan L, Song D (2018) Unusual Rearrangement of an N-Donor-Functionalized N-Heterocyclic Carbene Ligand on Group 8 Metals. Journal of the American Chemical Society 140:1263–1266 Chemistry Link
Lutjen AB, Quirk MA, Barbera AM, Kolonko EM (2018) Synthesis of (E)-cinnamyl ester derivatives via a greener Steglich esterification. Bioorganic & Medicinal Chemistry 26:5291–5298 Chemistry Link
Macaranas JA, Luke AM, Mandal M, Neisen BD, Marell DJ, Cramer CJ, Tolman WB (2018) Sterically Induced Ligand Framework Distortion Effects on Catalytic Cyclic Ester Polymerizations. Inorganic Chemistry 57:3451–3457 Chemistry Link
Maiorov AS, Shepelyuk TO, Balabin FA, Martyanov AA, Nechipurenko DY, Sveshnikova AN (2018) Modeling of Granule Secretion upon Platelet Activation through the TLR4-Receptor. Biophysics 63:357–364 Signaling Immunology Link
Maldonado EM, Fisher CP, Mazzatti DJ, Barber AL, Tindall MJ, Plant NJ, Kierzek AM, Moore JB (2018) Multi-scale, whole-system models of liver metabolic adaptation to fat and sugar in non-alcoholic fatty liver disease. npj Systems Biology and Applications 4:33 Metabolism Link
Mayorga LS, Cebrian I, Verma M, Hoops S, Bassaganya-Riera J (2018) Reconstruction of endosomal organization and function by a combination of ODE and agent-based modeling strategies. Biology Direct 13:25 Cell Biology Link
McDonald NW (2018) Exploring the mechanistic effects of life extending treatments on the mTOR network : a combined computational and experimental approach. Ph.D. Thesis, Newcastle University Signaling Link
Mishra M, Jayal P, Karande AA, Chandra N (2018) Identification of a co-target for enhancing efficacy of sorafenib in HCC through a quantitative modeling approach. FEBS Journal 285:3977–3992 Metabolism Signaling Link
Molina-Mora JA, Kop-Montero M, Quirós-Fernández I, Quirós-Barrantes S, Crespo-Mariño JL, Mora-Rodríguez R (2018) A hybrid mathematical modeling approach of the metabolic fate of a fluorescent sphingolipid analogue to predict cancer chemosensitivity. Computers in Biology and Medicine 97:8–20 Biochemistry Pharmacology Link
Moreno-Sánchez R, Marín-Hernández Á, Gallardo-Pérez JC, Vázquez C, Rodríguez-Enríquez S, Saavedra E (2018) Control of the NADPH supply and GSH recycling for oxidative stress management in hepatoma and liver mitochondria. Biochimica et Biophysica Acta 1859:1138–1150 Metabolism Link
Muñoz-Flores C, Astuya A, Roa F, Romero A, Acosta J, Sánchez O, Toledo J (2018) Activation of membrane-bound and soluble Toll-like Receptors 5 in Salmo salar depends on the MyD88 signalling pathway. Biochimica et Biophysica Acta 1862:2215 Siganling Link
Nguyen VD, Styevkó G, Ta LP, Tran ATM, Bujna E, Orbán P, Dam MS, Nguyen QD (2018) Immobilization and some properties of commercial enzyme preparation for production of lactulose-based oligosaccharides. Food and Bioproducts Processing 107:97–103 Biotechnology Enzymology Link
Oh S, Boudker O (2018) Kinetic mechanism of coupled binding in sodium-aspartate symporter GltPh. eLife 7:e37291 Enzymology Link
Orrico F, Möller MN, Cassina A, Denicola A, Thomson L (2018) Kinetic and stoichiometric constraints determine the pathway of H2O2 consumption by red blood cells. Free Radical Biology and Medicine 121:231–239 Metabolism Link
Palai T, Bhattacharya PK (2018) Bioconjugates from smart polymers and β-galactosidase: Synthesis, characterization and application in producing galacto-oligosaccharides from lactose. Journal of Indian Chemical Society 95:917–924 Biotechnology Link
Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology 110:357–369 Microbiology Link
Potter ME, Armstrong L-M, Raja R (2018) Combining catalysis and computational fluid dynamics towards improved process design for ethanol dehydration. Catalysis Science & Technology 8:6163–6172 Chemistry Link
Revell JD, Zuliani P (2018) Stochastic Rate Parameter Inference Using the Cross-Entropy Method. In: Češka M., Šafránek D. (eds.) Computational Methods in Systems Biology. CMSB2018. Lecture Notes in Computer Science, vol 11095. Springer, Cham pp.146–164 Computational Method Link
Rosas Lemus M, Roussarie E, Hammad N, Mougeolle A, Ransac S, Issa R, Mazat J-P, Uribe-Carvajal S, Rigoulet M, Devin A (2018) The role of glycolysis-derived hexose phosphates in the induction of the Crabtree effect. Journal of Biological Chemistry 293:12843–12854 Metabolism Link
Rossi F, Torbensen K, Ristori S, Abou-Hassan A (2018) Signal Transduction and Communication Through Model Membranes in Networks of Coupled Chemical Oscillators. In: Pelillo M, Poli I, Roli A, Serra R, Slanzi D, Villani M (eds.) Artificial Life and Evolutionary Computation. WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer Biochemistry Signaling Link
Šalagovič J (2018) Computational analysis and model integration of biorhythmic systems. Masters Thesis, Masaryk University, Faculty of Informatics, Czech Republic Metabolism Microbiology Computational Method Link
Schams A, Britt M, Rowe I, Cetiner U, Anishkin A, Sukharev S (2018) Dissecting the Fast Hypoosmotic Permeability Response in E. coli. Biophysical Journal 114:112a–113a Biophysics Link
Scharm M (2018) Improving Reproducibility and Reuse of Modelling Results in the Life Sciences. Ph.D. Thesis, University of Rostock, Germany Computational Method Link
Semenov SN, Ainla A, Skorb EV, Postma SGJ (2018) Four-Variable Model of an Enzymatic Oscillator Based on Trypsin. Israel Journal of Chemistry 58:781–786 Biochemistry Link
Silva BVR, Rad M, Cui J, McCabe M, Pan K (2018) A Mobile-Based Diet Monitoring System for Obesity Management. Journal of Health & Medical Informatics 9:307 Computational method Link
Silva E, Martin R, Pomuceno JP, Mansilla R, Betancourt-Mar JA, Cocho G, Nieto-Villar JM (2018) Dose and frequency in cancer therapy. Theoretical non-autonomous model of p53 network. Biological Rhythm Research 50:483-489 Signaling Link
Silva LHG (2018) Self-Replication and Non-enzymatic Catalytic Networks subject to Open Flow. MS Thesis, University of Porto, Portugal. Biochemistry Theory Link
Silva LHG, Hochberg D (2018) Open flow non-enzymatic template catalysis and replication. Physical Chemistry Chemical Physics 20:14864–14875 Biochemistry Link
Soni B, Saha B, Singh S (2018) Systems cues governing IL6 signaling in leishmaniasis. Cytokine 106:169–175 Signaling Immunology Link
Suwanmajo T, Krishnan J (2018) Exploring the intrinsic behaviour of multisite phosphorylation systems as part of signalling pathways. Journal of the Royal Society Interface 15:1520180109 Signaling Link
Vargas-Mora C, Acón M, Mora-Rodríguez R, Quirós-Barrantes S (2018) A Transcriptional Regulatory Network Model Reveals miR-34a as a Potential Regulator of Proliferation in Cancer Cell Lines. 2018 IEEE International Work Conference on Bioinspired Intelligence (IWOBI) doi:10.1109/IWOBI.2018.8464205 Genomics Link
Vögeli B (2018) Control of reactive intermediates in enzymes and enzyme complexes. Ph.D. Thesis, Philipps-Universität Marburg, Germany. Enzymology Link
Vranish JN, Ancona MG, Oh E, Susumu K, Lasarte Aragonés G, Breger JC, Walper SA, Medintz IL (2018) Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates. ACS Nano 12:7911–7926 Biotechnology Enzymology Link
Wang M, Park C, Woehl TJ (2018) Quantifying the Nucleation and Growth Kinetics of Electron Beam Nanochemistry with Liquid Cell Scanning Transmission Electron Microscopy. Chemistry of Materials 30:7727–7736 Chemistry Link
Wang M, Wölfer C, Otrin L, Ivanov I, Vidaković-Koch T, Sundmacher K (2018) Transmembrane NADH Oxidation with Tetracyanoquinodimethane. Langmuir 34:5435–5443 Biochemistry Biotechnology Link
Wei D, Sadek O, Dorcet V, Roisnel T, Darcel C, Gras E, Clot E, Sortais J-B (2018) Selective mono N-methylation of anilines with methanol catalyzed by rhenium complexes: An experimental and theoretical study. Journal of Catalysis 366:300–309 Chemistry Link
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2018) Macromolecular crowding and membrane binding proteins: the case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Biochemistry Biophysics Link
Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP (2018) PyCoTools: A Python Toolbox for COPASI. Bioinformatics 34:3702–3710 Computational Method Software Link
Weyder M, Prudhomme M, Bergé M, Polard P, Fichant G (2018) Dynamic modeling of Streptococcus pneumoniae competence provides regulatory mechanistic insights into its tight temporal regulation. Frontiers in Microbiology 9:1637 Microbiology Link
Wiebe HA (2018) Mechanistic applications of volume profiles for chemical and biochemical processes. Ph.D. Thesis, Simon Fraser University, Canada Chemistry Link
Winter F, Bludszuweit-Philipp C, Wolkenhauer O (2018) Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer’s disease. Journal of Cerebral Blood Flow & Metabolism 38:304–316 Physiology Metabolism Biophysics Link
Woller A, Gonze D (2018) Modeling clock-related metabolic syndrome due to conflicting light and food cues. Scientific Reports 8:13641 Physiology Metabolism Link
Woo SS, Kim J, Sarpeshkar R (2018) A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks. IEEE Transactions on Biomedical Circuits and Systems 12:360–378 Computational Method Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. Ph.D. Thesis, Ohio University, USA Signaling Biochemistry Link
Xu H, Curtis TY, Powers SJ, Raffan S, Gao R, Huang J, Heiner M, Gilbert DR, Halford NG (2018) Genomic, biochemical and modelling analyses of asparagine synthetases from wheat. Frontiers in Plant Science 8:2237 Biochemistry Plant Biology Link
Yeom K-H, Mitchell S, Linares AJ, Zheng S, Lin C-H, Wang X-J, Hoffmann A, Black DL (2018) Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proceedings of the National Academy of Sciences USA 115:E11061–E11070 Genetics Biochemistry Link
Yu Y, Rebek Jr J (2018) Reactions of Folded Molecules in Water. Accounts of Chemical Research 51:3031–3040 Chemistry Link
Zhou Q (2018) Kinetic Modeling of Inhibitor Effects on Butanol Synthesis by Clostridium saccharoperbutylacetonicum. Ph.D. Thesis, North Carolina State University, USA Metabolism Microbiology Link
Zhou Q, Liu Y, Yuan W (2018) Kinetic modeling of lactic acid and acetic acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. Fuel 226:181–189 Metabolism Microbiology Biotechnology Link
Zhou Q, Zheng H, Yuan W (2018) Modeling Butanol Synthesis in Xylose by Clostridium saccharoperbutylacetonicum. BioResources 13:7270–7280 Metabolism Microbiology Link
Zimmer C, Leuba SI, Cohen T, Yaesoubi R (2018) Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Statistical Methods in Medical Research 28:3591-3608 Epidemiology Link

103 publications
2017
Agrawal R, Kalmady SV, Venkatasubramanian G (2017) In Silico Model-driven Assessment of the Effects of Brain-derived Neurotrophic Factor Deficiency on Glutamate and Gamma-Aminobutyric Acid: Implications for Understanding Schizophrenia Pathophysiology. Clinical Psychopharmacology and Neuroscience 15:115 Physiology Signaling Link
Aguilera LU, Zimmer C, Kummer U (2017) A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. BMC Systems Biology 11:26 Computational Method Immunology Link
Amdahl MB, Sparacino-Watkins CE, Corti P, Gladwin MT, Tejero J (2017) Efficient Reduction of Vertebrate Cytoglobins by the Cytochrome b 5/Cytochrome b 5 Reductase/NADH System. Biochemistry 56:3993–4004 Biochemistry Enzymology Link
Appleton E, Madsen C, Roehner N, Densmore D (2017) Design Automation in Synthetic Biology. Cold Spring Harbor Perspectives in Biology 9:a023978 Synthetic Biology Computational Method Link
Aullón G, Crespo M, Jover J, Martínez M (2017) Diarylplatinum (II) Scaffolds for Kinetic and Mechanistic Studies on the Formation of Platinacycles via an Oxidative Addition/Reductive Elimination/Oxidative Addition Sequence. Advances in Inorganic Chemistry 70:195–242 Chemistry Link
Badet T, Peyraud R, Mbengue M, Navaud O, Derbyshire M, Oliver RP, Barbacci A, Raffaele S (2017) Codon optimization underpins generalist parasitism in fungi. eLife 6:e22472 Genomics Theory Macromolecular Biochemistry Link
Barry JK (2017) Mathematical Modelling of the HIV Life Cycle: Identifying Optimal Treatment Strategies. Ph.D. Thesis, Universitätsmedizin der Ernst-Moritz-Arndt-Universität Greifswald, Germany. Microbiology Immunology Link
Baumgart L, Mather W, Hasty J (2017) Synchronized DNA cycling across a bacterial population. Nature Genetics 49:1282–128 Synthetic Biology Microbiology Link
Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S (2017) COPASI and its applications in biotechnology. Journal of Biotechnology 261:215–220 Software Link
Beuke K, Schildberg FA, Pinna F, Albrecht U, Liebe R, Bissinger M, Schirmacher P, Dooley S, Bode JG, Knolle PA, Kummer U, Breuhahn K, Sahle S (2017) Quantitative and integrative analysis of paracrine hepatocyte activation by non-parenchymal cells upon lipopolysaccharide induction. FEBS Journal 284:796–813 Immunology Link
Bleicken S, Hantusch A, Das KK, Frickey T, García-Sáez AJ (2017) Quantitative interactome of a membrane Bcl-2 network identifies a hierarchy of complexes for apoptosis regulation. Nature Communications 8:73 Signaling Link
Brezny AC, Landis CR (2017) Unexpected CO Dependencies, Catalyst Speciation, and Single-Turnover Hydrogenolysis Studies of Hydroformylation via High Pressure NMR Spectroscopy. Journal of the American Chemical Society 139:2778–2785 Chemistry Link
Cabezas Pérez RJ (2017) Mecanismos de protección frente a rotenona por PDGF-BB en un modelo astrocitario. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia. http://repository.javeriana.edu.co/handle/10554/38509 Toxicology Biochemistry Link
Chelushkin MA, Panteleev MA, Sveshnikova AN (2017) Activation of the contact pathway of blood coagulation on the circulating microparticles may explain blood plasma coagulation induced by dilution. Biochemistry (Moscow) 11:130–143 Biophysics Link
Chizzolini F, Forlin M, Yeh Martín N, Berloffa G, Cecchi D, Mansy SS (2017) Cell-free translation is more variable than transcription. ACS Synthetic Biology 6:638–647 Macromolecular Biochemistry Synthetic Biology Link
Chua HE, Bhowmick SS, Tucker-Kellogg L (2017) Synergistic target combination prediction from curated signaling networks: Machine learning meets systems biology and pharmacology. Methods 129:60–80 Computational Method Software Link
Chung R, Hein JE (2017) The More, The Better: Simultaneous In Situ Reaction Monitoring Provides Rapid Mechanistic and Kinetic Insight. Topics in Catalysis 60:594–608 Chemistry Laboratory Method Link
Colletto C, Whitaker D, Larrosa I (2017) Determination of 2H KIEs from Competition Experiments: Increased Accuracy via Isotopic Enrichment. Topics in Catalysis 60:589–593 Chemistry Laboratory Method Link
Dacheux E, Malys N, Meng X, Ramachandran V, Mendes P, McCarthy JEG (2017) Translation initiation events on structured eukaryotic mRNAs generate gene expression noise. Nucleic Acids Research 45:6981–6992 Macromolecular Biochemistry Link
Dalle Pezze P, Le Novère N (2017) SBpipe: a collection of pipelines for automating repetitive simulation and analysis tasks. BMC Systems Biology 11:46 Computational Method Software Link
Dunn AL, Landis CR (2017) Progress toward reaction monitoring at variable temperatures: a new stopped-flow NMR probe design. Magnetic Resonance in Chemistry 55:329–336 Chemistry Link
Dunn AL, Landis CR (2017) Stopped-Flow NMR and Quantitative GPC Reveal Unexpected Complexities for the Mechanism of NHC-Catalyzed Lactide Polymerization. Macromolecules 50:2267–2275 Chemistry Link
Elsts A, Pentjuss A, Stalidzans E (2017) SpaceScanner: COPASI wrapper for automated management of global stochastic optimization experiments. Bioinformatics 33:2966–2967 Software Computational Method Link
Fieser ME, Sanford MJ, Mitchell LA, Dunbar CR, Mandal M, Van Zee NJ, Urness DM, Cramer CJ, Coates GW, Tolman WB (2017) Mechanistic Insights into the Alternating Copolymerization of Epoxides and Cyclic Anhydrides Using a (Salph) AlCl and Iminium Salt Catalytic System. Journal of the American Chemical Society 139:15222–15231 Chemistry Link
Finney EE, Finke RG (2017) Catalyst Sintering Kinetics Data: Is There a Minimal Chemical Mechanism Underlying Kinetics Previously Fit by Empirical Power-Law Expressions—and if So, What Are Its Implications? Industrial & Engineering Chemistry Research 56:10271–10286 Chemistry Link
Földes T, Madarász Á, Révész Á, Dobi Z, Varga S, Hamza A, Nagy PR, Pihko PM, Pápai I (2017) Stereocontrol in Diphenylprolinol Silyl Ether Catalyzed Michael Additions: Steric Shielding or Curtin–Hammett Scenario? Journal of the American Chemical Society 139:17052–17063 Chemistry Link
Fortuny AF (2017) Chemometric Approaches for Systems Biology. Ph.D. Thesis, Universitat Politècnica de València, Spain. Computational Method Link
Fribourg M, Logothetis DE, González-Maeso J, Sealfon SC, Galocha-Iragüen B, Andrés FL-H, Brezina V (2017) Elucidation of molecular kinetic schemes from macroscopic traces using system identification. PLoS Computational Biology 13:e1005376 Computational Method Link
Funes-Ardoiz I, Nelson DJ, Maseras F (2017) Halide Abstraction Competes with Oxidative Addition in the Reactions of Aryl Halides with [Ni (PMenPh (3-n)) 4]. Chemistry 23:16728–16733 Chemistry Link
Galochkina T, Chelushkin M, Sveshnikova A (2017) Activation of Contact Pathway of Blood Coagulation on the Lipopolysaccharide Aggregates. Mathematical Modelling of Natural Phenomena 12:196–207 Signaling Link
Gao Y, Guan C, Zhou M, Kumar A, Emge TJ, Wright AM, Goldberg KI, Krogh-Jespersen K, Goldman AS (2017) β-Hydride Elimination and C–H Activation by an Iridium Acetate Complex, Catalyzed by Lewis Acids. Alkane Dehydrogenation Cocatalyzed by Lewis Acids and [2, 6-Bis (4, 4-dimethyloxazolinyl)-3, 5-dimethylphenyl] iridium. Journal of the American Chemical Society 139:6338–6350 Chemistry Link
Gil-Lozano C, Davila AF, Losa-Adams E, Fairen AG, Gago-Duport L (2017) Quantifying Fenton reaction pathways driven by self-generated H2O2 on pyrite surfaces. Scientific Reports 7:43703 Chemistry Link
Ghosh D, De RK (2017) In Silico Modeling of Crabtree Effect. Endocrine, Metabolic & Immune Disorders Drug Targets 17:182–188 Metabolism Link
Greene JL, Wäechter A, Tyo KE, Broadbelt LJ (2017) Acceleration Strategies to Enhance Metabolic Ensemble Modeling Performance. Biophysical Journal 113:1150–1162 Computational Method Link
Haanstra JR, Gerding A, Dolga AM, Sorgdrager FJ, Buist-Homan M, du Toit F, Faber KN, Holzhütter H-G, Szöör B, Matthews KR, Snoep JL, Westerhoff HV, Bakker BM (2017) Targeting pathogen metabolism without collateral damage to the host. Scientific Reports 7:40406 Microbiology Parasitology Metabolism Link
Haffez H, Chisholm DR, Valentine R, Pohl E, Redfern C, Whiting A (2017) The molecular basis of the interactions between synthetic retinoic acid analogues and the retinoic acid receptors. MedChemComm 8:578 Biochemistry Pharmacology Link
Hagen SJ, Son M (2017) Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Physical Biology 14:015001 Signaling Microbiology Link
Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, Wilson AJ, Beeby M, Schaber J, Albers S-V (2017) ArnS, a kinase involved in starvation-induced archaellum expression. Molecular Microbiology 103:181–194 Microbiology Signaling Link
Hay S (2017) Extracting Kinetic Isotope Effects From a Global Analysis of Reaction Progress Curves. Methods in Enzymology 596:85–111 Enzymology Link
Hendrickx DM, Souza T, Jennen DG, Kleinjans JC (2017) DTNI: a novel toxicogenomics data analysis tool for identifying the molecular mechanisms underlying the adverse effects of toxic compounds. Archives of Toxicology 91:2343–2352 Computational Method Toxicology Link
Henze R, Dittrich P, Ibrahim B (2017) A Dynamical Model for Activating and Silencing the Mitotic Checkpoint. Scientific Reports 7:3865 Cell Biology Link
Hill DE, Bay KL, Yang Y-F, Plata RE, Takise R, Houk KN, Yu J-Q, Blackmond DG (2017) Dynamic Ligand Exchange as a Mechanistic Probe in Pd-Catalyzed Enantioselective C–H Functionalization Reactions Using Monoprotected Amino Acid Ligands. Journal of the American Chemical Society 139:18500–18503 Chemistry Link
Hochberg D, García RDB, Bastidas JAÁ, Ribó JM (2017) Stoichiometric network analysis of spontaneous mirror symmetry breaking in chemical reactions. Physical Chemistry Chemical Physics 19:17618–17636 Chemistry Link
Houwman JA (2017) The ribosome regulates flavodoxin folding. Ph.D. Thesis, Wageningen University, The Netherlands. Biophysics Biochemistry Link
Ismail AM, Mohamad MS, Abdul Majid H, Abas KH, Deris S, Zaki N, Mohd Hashim SZ, Ibrahim Z, Remli MA (2017) An improved hybrid of particle swarm optimization and the gravitational search algorithm to produce a kinetic parameter estimation of aspartate biochemical pathways. BioSystems 162:81–89 Computational Method Link
Jaraíz M, Enríquez L, Pinacho R, Rubio JE, Lesarri A, López-Pérez JL (2017) A DFT-Based Computational-Experimental Methodology for Synthetic Chemistry: Example of Application to the Catalytic Opening of Epoxides by Titanocene. Journal of Organic Chemistry 82:3760–3766 Chemistry Link
Jiang Y, AkhavanAghdam Z, Tsimring LS, Hao N (2017) Coupled feedback loops control the stimulus-dependent dynamics of the yeast transcription factor Msn2. Journal of Biological Chemistry 292:12366–12372 Signaling Link
Jordão G, Tavares JN (2017) Mathematical models in cancer therapy. BioSystems 162:12–23 Signaling Link
Jover J (2017) Quantitative DFT modeling of product concentration in organometallic reactions: Cu-mediated pentafluoroethylation of benzoic acid chlorides as a case study. Physical Chemistry Chemical Physics 19:29344–29353 Chemistry Link
Kagan VE, Mao G, Qu F, Angeli JPF, Doll S, St Croix C, Dar HH, Liu B, Tyurin VA, Ritov VB, Kapralov AA, Amoscato AA, Jiang J, Anthonymuthu T, Mohammadyani D, Yang Q, Proneth B, Klein-Seetharaman J, Watkins S, Bahar I, Greenberger J, Mallampalli RK, Stockwell BR, Tyurina YY, Conrad M, Bayır H (2017) Oxidized arachidonic and adrenic PEs navigate cells to ferroptosis. Nature Chemical Biology 13:81–90 Signaling Cell Biology Link
Kale SD, Ayubi T, Chung D, Tubau-Juni N, Leber A, Dang HX, Karyala S, Hontecillas R, Lawrence CB, Cramer RA, Bassaganya-Riera J (2017) Modulation of Immune Signaling and Metabolism Highlights Host and Fungal Transcriptional Responses in Mouse Models of Invasive Pulmonary Aspergillosis. Scientific Reports 7:17096 Immunology Link
Kalek M, Himo F (2017) Mechanism and Selectivity of Cooperatively Catalyzed Meyer–Schuster Rearrangement/Tsuji-Trost Allylic Substitution. Evaluation of Synergistic Catalysis by Means of Combined DFT and Kinetics Simulations. Journal of the American Chemical Society 139:10250–10266 Chemistry Link
Karasik A, Ledwitch KV, Arányi T, Váradi A, Roberts AG, Szeri F (2017) Boosted coupling of ATP hydrolysis to substrate transport upon cooperative estradiol-17-β-D-glucuronide binding in a Drosophila ATP binding cassette type-C transporter. FASEB Journal 32:fj–201700606R Enzymology Link
Komasilovs V, Pentjuss A, Elsts A, Stalidzans E (2017) Total enzyme activity constraint and homeostatic constraint impact on the optimization potential of a kinetic model. BioSystems 162:128-134 Computational Method Biotechnology Link
Korman TP, Opgenorth PH, Bowie JU (2017) A synthetic biochemistry platform for cell free production of monoterpenes from glucose. Nature Communications 8:15526 Synthetic Biology Metabolism Link
Kosey D, Singh S (2017) Computational design of molecular motors as nanocircuits in Leishmaniasis. F1000Research 6:94 Synthetic Biology Link
Kwon JS, Everetts NJ, Wang X, Wang W, Della Croce K, Xing J, Yao G (2017) Controlling Depth of Cellular Quiescence by an Rb-E2F Network Switch. Cell Reports 20:3223–3235 Signaling Link
Leber A, Hontecillas R, Abedi V, Tubau-Juni N, Zoccoli-Rodriguez V, Stewart C, Bassaganya-Riera J (2017) Modeling new immunoregulatory therapeutics as antimicrobial alternatives for treating Clostridium difficile infection. Artificial Intelligence in Medicine 78:1–13 Immunology Link
Man-Sai A, Siles-Canales F, Mora-Rodríguez R (2017) A biocomputational platform for the automated construction of large-scale mathematical models of miRNA-transcription factor networks for studies on gene dosage compensation. 2016 IEEE 36th Central American and Panama Convention (CONCAPAN XXXVI), San Jose, 2016, pp. 1-7 Genomics Link
Madec M, Lallement C, Haiech J (2017) Modeling and simulation of biological systems using SPICE language. PLoS One 12:e0182385 Software Link
Malek M, Kielkowska A, Chessa T, Anderson KE, Barneda D, Pir P, Nakanishi H, Eguchi S, Koizumi A, Sasaki J, Juvin V, Kiselev VY, Niewczas I, Gray A, Valayer A, Spensberger D, Imbert M, Felisbino S, Habuchi T, Beinke S, Cosulich S, Le Novère N, Sasaki T, Clark J, Hawkins PT, Stephens LR (2017) PTEN Regulates PI(3,4)P2 Signaling Downstream of Class I PI3K. Molecular Cell 68:566-580.e10 Signaling Link
Marchetti L, Lombardo R, Priami C (2017) HSimulator: Hybrid Stochastic/Deterministic Simulation of Biochemical Reaction Networks. Complexity 2017:1–12 Computational Method Link
Martin RR, Montero S, Silva E, Bizzarri M, Cocho G, Mansilla R, Nieto-Villar JM (2017) Phase transitions in tumor growth: V what can be expected from cancer glycolytic oscillations? Physica A 486:762–771 Metabolism Theory Link
Meng X, Firczuk H, Pietroni P, Westbrook R, Dacheux E, Mendes P, McCarthy JEG (2017) Minimum-noise production of translation factor eIF4G maps to a mechanistically determined optimal rate control window for protein synthesis. Nucleic Acids Research 45:1015–1025 Macromolecular Biochemistry Link
Meyners C, Meyer-Almes F-J (2017) Impact of binding mechanism on selective inhibition of histone deacetylase isoforms. Chemical Biology & Drug Design 90:1215–1225 Enzymology Pharmacology Link
Milivojević A, Ćorović M, Carević M, Banjanac K, Vujisić L, Veličković D, Bezbradica D (2017) Highly efficient enzymatic acetylation of flavonoids: Development of solvent-free process and kinetic evaluation. Biochemical Engineering Journal 128:106–115 Biotechnology Enzymology Link
Millard P, Smallbone K, Mendes P (2017) Metabolic regulation is sufficient for global and robust coordination of glucose uptake, catabolism, energy production and growth in Escherichia coli. PLoS Computational Biology 13:e1005396 Metabolism Microbiology Link
Musante V, Li L, Kanyo J, Lam TT, Colangelo CM, Cheng SK, Brody AH, Greengard P, Le Novère N, Nairn AC (2017) Reciprocal regulation of ARPP-16 by PKA and MAST3 kinases provides a cAMP-regulated switch in protein phosphatase 2A inhibition. eLife 6:e24998 Signaling Link
Nakatani-Webster E, Nath A (2017) Inferring Mechanistic Parameters from Amyloid Formation Kinetics by Approximate Bayesian Computation. Biophysical Journal 112:868–880 Macromolecular Biochemistry Computational Method Link
Opgenorth PH, Korman TP, Iancu L, Bowie JU (2017) A molecular rheostat maintains ATP levels to drive a synthetic biochemistry system. Nature Chemical Biology 13:938–942 Synthetic Biology Link
Orlenko A, Chi PB, Liberles DA (2017) Characterizing the roles of changing population size and selection on the evolution of flux control in metabolic pathways. BMC Evolutionary Biology 17:117 Biochemistry Genetics Link
Oroszlán G, Dani R, Szilágyi A, Závodszky P, Thiel S, Gál P, Dobó J (2017) Extensive basal level activation of complement mannose-binding lectin-associated serine protease (MASP)-3: kinetic modeling of lectin pathway activation provides possible mechanism. Frontiers in Immunology 8:1821 Immunology Signaling Link
Parmar JH, Davis G, Shevchuk H, Mendes P (2017) Modeling the dynamics of mouse iron body distribution: hepcidin is necessary but not sufficient. BMC Systems Biology 11:57 Physiology Link
Pinna F, Bissinger M, Beuke K, Huber N, Longerich T, Kummer U, Schirmacher P, Sahle S, Breuhahn K (2017) A20/TNFAIP3 Discriminates Tumor Necrosis Factor (TNF)-Induced NF-κB from JNK Pathway Activation in Hepatocytes. Frontiers in Physiology 8:610 Signaling Link
Postma SGJ, te Brinke D, Vialshin IN, Wong ASY, Huck WTS (2017) A trypsin-based bistable switch. Tetrahedron 73:4896–4900 Macromolecular Biochemistry Link
Proctor CJ, Goljanek-Whysall K (2017) Using computer simulation models to investigate the most promising microRNAs to improve muscle regeneration during ageing. Scientific Reports 7:12314 Genetics Signaling Link
Proctor CJ, Smith GR (2017) Computer simulation models as a tool to investigate the role of microRNAs in osteoarthritis. PLoS One 12:e0187568 Genetics Signaling Link
Rodesney CA, Roman B, Dehamani N, Cooley BJ, Katira P, Touhami A, Gordon VD (2017) Mechanosensing of shear by Pseudomonas aeruginosa leads to increased levels of the cyclic-di-GMP signal initiating biofilm development. Proceedings of the National Academy of Sciences USA 114:5906–5911 Microbiology Signaling Link
Roy RD, Rosenmund C, Stefan MI (2017) Cooperative binding mitigates the high-dose hook effect. BMC Systems Biology 11:74 Theory Macromolecular Biochemistry Link
Schäuble S, Stavrum A-K, Bockwoldt M, Puntervoll P, Heiland I (2017) SBMLmod: a Python-based web application and web service for efficient data integration and model simulation. BMC Bioinformatics 18:314 Software Link
Schmölzer K, Eibinger M, Nidetzky B (2017) Active-Site His85 of Pasteurella dagmatis Sialyltransferase Facilitates Productive Sialyl Transfer and So Prevents Futile Hydrolysis of CMP-Neu5Ac. ChemBioChem 18:1544–1550 Enzymology Link
Seitter H (2017) Retinal function of the voltage-gated calcium channel subunit α2δ-3 / Light-dependent effects in α2δ-3 mutant and in wild type retina. Ph.D. Thesis, Universität Tübingen, Germany. Biochemistry Biophysics Physiology Link
Selvarajoo K (2017) A systems biology approach to overcome TRAIL resistance in cancer treatment. Progress in Biophysics and Molecular Biology 128:142–154 Signaling Link
Shrivastava N, Macwan AS, Kohler H-PE, Kumar A (2017) Important amino acid residues of hexachlorocyclohexane dehydrochlorinases (LinA) for enantioselective transformation of hexachlorocyclohexane isomers. Biodegradation 28:171–180 Chemistry Link
Sier JH, Thumser AE, Plant NJ (2017) Linking physiologically-based pharmacokinetic and genome-scale metabolic networks to understand estradiol biology. BMC Systems Biology 11:141 Physiology Pharmacology Link
Simak M, Yeang C-H, Lu HH-S (2017) Exploring candidate biological functions by Boolean Function Networks for Saccharomyces cerevisiae. PLoS One 12:e0185475 Computational Method Link
Stalidzans E, Mozga I, Sulins J, Zikmanis P (2017) Search for a Minimal Set of Parameters by Assessing the Total Optimization Potential for a Dynamic Model of a Biochemical Network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 14:978–985 Computational Method Biotechnology Link
Stasiw DE, Luke AM, Rosen T, League AB, Mandal M, Neisen BD, Cramer CJ, Kol M, Tolman WB (2017) Mechanism of the Polymerization of rac-Lactide by Fast Zinc Alkoxide Catalysts. Inorganic Chemistry 56:14366–14372 Chemistry Link
Stasiw DE, Mandal M, Neisen BD, Mitchell LA, Cramer CJ, Tolman WB (2017) Why So Slow? Mechanistic Insights from Studies of a Poor Catalyst for Polymerization of ε-Caprolactone. Inorganic Chemistry 56:725–728 Chemistry Link
Sveshnikova AN, Panteleev MA, Dreval AV, Shestakova TP, Medvedev OS, Dreval OA (2017) Theoretical evaluation of the parameters of glucose metabolism on the basis of continuous glycemia monitoring data using mathematical modeling. Biophysics 62:842–847 Metabolism Physiology Link
Tatham MH, Cole C, Scullion P, Wilkie R, Westwood NJ, Stark LA, Hay RT (2017) A proteomic approach to analyse the aspirin-mediated lysine acetylome. Molecular & Cellular Proteomics 16:310–326 Pharmacology Biochemistry Laboratory Method Link
Tikidji-Hamburyan A, Reinhard K, Storchi R, Dietter J, Seitter H, Davis KE, Idrees S, Mutter M, Walmsley L, Bedford RA, Ueffing M, Ala-Laurila P, Brown TM, Lucas RJ, Münch TA (2017) Rods progressively escape saturation to drive visual responses in daylight conditions. Nature Communications 8:1813 Biochemistry Biophysics Physiology Link
Tolleter D, Chochois V, Poiré R, Price GD, Badger MR (2017) Measuring CO2 and HCO3- permeabilities of isolated chloroplasts using a MIMS-18O approach. Journal of Experimental Botany 68:3915–3924 Laboratory Method Physiology Link
Torbensen K, Ristori S, Rossi F, Abou-Hassan A (2017) Tuning the Chemical Communication of Oscillating Microdroplets by Means of Membrane Composition. Journal of Physical Chemistry 121:13256–13264 Chemistry Biophysics Link
Trieu MM, Devine EL, Lamarche LB, Ammerman AE, Greco JA, Birge RR, Theobald DL, Oprian DD (2017) Expression, purification, and spectral tuning of RhoGC, a retinylidene/guanylyl cyclase fusion protein and optogenetics tool from the aquatic fungus Blastocladiella emersonii. Journal of Biological Chemistry 292:10379–10389 Enzymology Laboratory Method Link
Vranish JN, Ancona MG, Oh E, Susumu K, Medintz IL (2017) Enhancing coupled enzymatic activity by conjugating one enzyme to a nanoparticle. Nanoscale 9:5172–5187 Enzymology Biotechnology Link
Wagner AJ, Zubarev DY, Aspuru-Guzik A, Blackmond DG (2017) Chiral Sugars Drive Enantioenrichment in Prebiotic Amino Acid Synthesis. ACS Central Science 3:322–328 Chemistry Link
Wang H, Ray JCJ (2017) Dynamical predictors of an imminent phenotypic switch in bacteria. Physical Biology 14:045007 Microbiology Biochemistry Link
Wei D, Roisnel T, Darcel C, Clot E, Sortais J-B (2017) Hydrogenation of Carbonyl Derivatives with a Well-Defined Rhenium Precatalyst. ChemCatChem 9:80–83 Chemistry Link
Wong ASY, Huck WTS (2017) Grip on complexity in chemical reaction networks. Beilstein Journal of Organic Chemistry 13:1486–1497 Chemistry Theory Link
Zaccarin M, Bosello-Travain V, Di Paolo ML, Falda M, Maiorino M, Miotto G, Piccolo S, Roveri A, Ursini F, Venerando R, Toppo S (2017) Redox status in a model of cancer stem cells. Archives of Biochemistry and Biophysics 617:120–128 Biochemistry Cell Biology Link
Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV (2017) The peculiar glycolytic pathway in hyperthermophylic archaea: understanding its whims by experimentation in silico. International Journal of Molecular Sciences 18:876 Metabolism Microbiology Enzymology Link
Zhao W, Pferdehirt L, Segatori L (2017) Quantitatively predictable control of cellular protein levels through proteasomal degradation. ACS Synthetic Biology 7:540–552 Synthetic Biology Macromolecular Biochemistry Link
Zimmer C, Yaesoubi R, Cohen T (2017) A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLoS Computational Biology 13:e1005257 Computational Method Link

104 publications
2016
Altıntaş A, Davidsen K, Garde C, Mortensen UH, Brasen JC, Sams T, Workman CT (2016) High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells. Free Radical Biology and Medicine 101:143–153 Metabolism Link
Andrews SS, Peria WJ, Richard CY, Colman-Lerner A, Brent R (2016) Push-pull and feedback mechanisms can align signaling system outputs with inputs. Cell Systems 3:444–455 Signaling Link
Balabin FA, Sveshnikova AN (2016) Computational biology analysis of platelet signaling reveals roles of feedbacks through phospholipase C and inositol 1,4,5-trisphosphate 3-kinase in controlling amplitude and duration of calcium oscillations. Mathematical Biosciences 276:67–74 Signaling Link
Barbon A, Bortolus M, Isse AA, Reznikov VA, Weiner L (2016) Electron transfer in pH-sensitive nitroxide radicals. Chemical Physics Letters 665:137–140 Chemistry Link
Bergmann FT, Sahle S, Zimmer C (2016) Piecewise parameter estimation for stochastic models in COPASI. Bioinformatics 32:1586–1588 Computational Method Link
Beuke K (2016) TNF-induced NF-κB Signal Transduction in the Liver. Ph.D. Thesis, Heidelberg University, Germany. Immunology Signaling Link
Boross G, Papp B (2016) No evidence that protein noise-induced epigenetic epistasis constrains gene expression evolution. Molecular Biology and Evolution 34:380–390 Metabolism Genetics Link
Burés J (2016) A Simple Graphical Method to Determine the Order in Catalyst. Angewandte Chemie 55:2028-31 Chemistry Link
Bush A, Vasen G, Constantinou A, Dunayevich P, Patop IL, Blaustein M, Colman-Lerner A (2016) Yeast GPCR signaling reflects the fraction of occupied receptors, not the number. Molecular Systems Biology 12:898 Signaling Link
Chizzolini F (2016) The relationship between genotype and phenotype in cell-free transcription-translation reactions. Ph.D. Thesis, University of Trento, Italy Genetics Link
Claudino M, Zhang X, Alim MD, Podgórski M, Bowman CN (2016) Mechanistic Kinetic Modeling of Thiol–Michael Addition Photopolymerizations via Photocaged “Superbase” Generators: An Analytical Approach. Macromolecules 49:8061–8074 Chemistry Link
Coakley S, Richmond P, Gheorghe M, Chin S, Worth D, Holcombe M, Greenough C (2016) Large-Scale Simulations with FLAME. In Intelligent Agents in Data-intensive Computing (Kolodziej J, Correia L, Molina JM eds.), Springer pp.123-142 Software Link
Coletta C (2016) Study of growth mechanism of conducting polymers by pulse radiolysis. Ph.D. Thesis, Université Paris Saclay, France Chemistry Link
Compel WS (2016) The use of coordinating solvents in gold cluster synthesis. Ph.D. Thesis, Colorado State University, USA. Chemistry Link
Costa RS, Vinga S (2016) Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochemical Engineering Journal 110:59–70 Metabolism Link
Dalle Pezze P, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PR, van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Horvatovich P, Shanley DP, Thedieck K (2016) A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nature Communications 7:13254 Signaling Link
del Pozo J, Salas G, Álvarez R, Casares JA, Espinet P (2016) The Negishi Catalysis: Full Study of the Complications in the Transmetalation Step and Consequences for the Coupling Products. Organometallics 35:3604–3611 Chemistry Link
delToro D, Ortiz D, Ordyan M, Sippy J, Oh C-S, Keller N, Feiss M, Catalano CE, Smith DE (2016) Walker-A Motif Acts to Coordinate ATP Hydrolysis with Motor Output in Viral DNA Packaging. Journal of Molecular Biology 428:2709–2729 Biochemistry Link
Di Camillo B, Carlon A, Eduati F, Toffolo GM (2016) A rule-based model of insulin signalling pathway. BMC Systems Biology 10:38 Signaling Link
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances 2:e1600823 Biochemistry Signaling Link
Emiola A, Andrews SS, Heller C, George J (2016) Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proceedings of the National Academy of Sciences USA 113:3108–3113 Signaling Cell Biology Link
Espejo Mojica ÁJ (2016) Producción, purificación y caracterización de tres hexosaminidasas lisosomales recombinantes en pichia pastoris. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia Enzymology Metabolism Link
Firdaus MY, Brask J, Nielsen PM, Guo Z, Fedosov SN (2016) Kinetic model of biodiesel production catalyzed by free liquid lipase from Thermomyces lanuginosus. Journal of Molecular Catalysis B: Enzymatic 133:55–64 Biotechnology Enzymology Link
Firdaus MY, Guo Z, Fedosov SN (2016) Development of kinetic model for biodiesel production using liquid lipase as a biocatalyst, esterification step. Biochemical Engineering Journal 105:52–61 Biotechnology Link
Froese RD, Whiteker GT, Peterson TH, Arriola DJ, Renga JM, Shearer JW (2016) Computational and Experimental Studies of Regioselective SNAr Halide Exchange (Halex) Reactions of Pentachloropyridine. Journal of Organic Chemistry 81:10672–10682 Chemistry Link
Furrow SD, Cervellati R, Greco E (2016) Study of the transition to higher iodide in the malonic acid Briggs–Rauscher oscillator. Reaction Kinetics, Mechanisms and Catalysis 118:59–71 Chemistry Link
Gallimore AR, Aricescu AR, Yuzaki M, Calinescu R (2016) A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression. PLoS Computational Biology 12:e1004664 Signaling Link
Ganesan N, Li J, Sharma V, Jiang H, Compagnoni A (2016) Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13:365–379 Computational Method Link
Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E (2016) A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLoS Computational Biology 12:e1004703 Metabolism Physiology Link
Haffez HRS (2016) Design, synthesis and biological evaluation of small molecules for controlling cellular development. Ph.D. Thesis, Durham University, UK. Biochemistry Pharmacology Link
Hamgini BB (2016) Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways. Ph.D. Thesis, Queen’s University, Kingston, Ontario, Canada Computational Method Link
Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Briefings in Bioinformatics 19:77–88 Computational Method Link
Hoops S, Hontecillas R, Abedi V, Leber A, Philipson CW, Carbo A, Bassaganya-Riera J (2016) Chapter 5 - Ordinary Differential Equations (ODEs) Based Modeling. In: Bassaganya-Riera J (ed) Computational Immunology. Academic Press, 63–78. Computational Method Software Link
Ihekwaba AEC, Mura I, Walshaw J, Peck MW, Barker GC (2016) An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production. PLoS Computational Biology 12:e1005205 Microbiology Link
Julien-Laferrière A (2016) Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia. Ph.D. Thesis, Université Lyon 1-Claude Bernard, France Computational Method Metabolism Microbiology Link
Jablonsky J, Papacek S, Hagemann M (2016) Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control. Scientific Reports 6:33024 Microbiology Metabolism Link
Jung J, Czabany T, Wilding B, Klempier N, Nidetzky B (2016) Kinetic analysis and probing with substrate analogues of the reaction pathway of the nitrile reductase QueF from Escherichia coli. Journal of Biological Chemistry 291:25411–25426 Enzymology Link
Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P (2016) Quantitative super-resolution imaging with qPAINT. Nature Methods 13:439–442 Laboratory Method Macromolecular Biochemistry Link
Kilner J, Corfe BM, McAuley MT, Wilkinson SJ (2016) A deterministic oscillatory model of microtubule growth and shrinkage for differential actions of short chain fatty acids. Molecular BioSystems 12:93-101 Cell Biology Link
Kollarovic G, Studencka M, Ivanova L, Lauenstein C, Heinze K, Lapytsko A, Talemi SR, Figueiredo AS, Schaber J (2016) To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage. Aging 8:158 Cell Biology Link
Laviska DA, Zhou T, Kumar A, Emge TJ, Krogh-Jespersen K, Goldman AS (2016) Single and Double C–H Activation of Biphenyl or Phenanthrene. An Example of C–H Addition to Ir(III) More Facile than Addition to Ir(I). Organometallics 35:1613–1623 Chemistry Link
Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J (2016) Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of Theoretical Biology 398:74–84 Immunology Link
Leber A, Bassaganya-Riera J, Tubau-Juni N, Zoccoli-Rodriguez V, Viladomiu M, Abedi V, Lu P, Hontecillas R (2016) Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection. PLoS One 11:e0167440 Immunology Link
Ledwitch KV, Barnes RW, Roberts AG (2016) Unravelling the complex drug–drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Bioscience Reports 36:e00309 Pharmacology Biochemistry Link
Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG (2016) Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology 118:96–108 Pharmacology Biochemistry Link
Levenhagen MA, Ferreira GA, Pereira GM, Santos AR (2016) A computer simulation model for Strongyloides infection. PeerJ Preprints 4:e2399v1 Immunology Parasitology Link
Levin MD, Kaphan DM, Hong CM, Bergman RG, Raymond KN, Toste FD (2016) Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis. Journal of the American Chemical Society 138:9682–9693 Enzymology Chemistry Link
Lima AP, Baixinho V, Machado D, Rocha I (2016) A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli. IFAC-PapersOnLine 49:270–276 Metabolism Link
Llanos-Pérez JA, Betancourt-Mar JA, Cocho G, Mansilla R, Nieto-Villar JM (2016) Phase transitions in tumor growth: III vascular and metastasis behavior. Physica A 462:560–568 Physiology Link
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen W-H, Bork P, Glass JI, Serrano L, Lluch-Senar M (2016) Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances 2:e1501363 Microbiology Genetics Link
Marlier EE, Macaranas JA, Marell DJ, Dunbar CR, Johnson MA, DePorre Y, Miranda MO, Neisen BD, Cramer CJ, Hillmyer MA, Tolman WB (2016) Mechanistic Studies of ε-Caprolactone Polymerization by (salen)AlOR Complexes and a Predictive Model for Cyclic Ester Polymerizations. ACS Catalysis 6:1215–1224 Chemistry Link
Marín-Hernández Á, Rodríguez-Zavala JS, Del Mazo-Monsalvo I, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2016) Inhibition of Non-flux-Controlling Enzymes Deters Cancer Glycolysis by Accumulation of Regulatory Metabolites of Controlling Steps. Frontiers in Physiology 7:412 Metabolism Link
McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. Ph.D. Thesis, Seattle, University of Washington, USA. Biochemistry Macromolecular Biochemistry Link
Michalak P, Sobral BW, Abedi V, Kim YB, Deng X, Philipson CW, Viladomiu M, Lu P, Wendelsdorf K, Hontecillas R, Bassaganya-Riera J (2016) From Big Data Analytics and Network Inference to Systems Modeling. In: Bassaganya-Riera J (ed) Computational Immunology, Academic Press, 113–144. Computational Method Immunology Link
Mizeranschi A, Swain MT, Scona R, Fazilleau Q, Bosak B, Piontek T, Kopta P, Thompson P, Dubitzky W (2016) MultiGrain/MAPPER: A distributed multiscale computing approach to modeling and simulating gene regulation networks. Future Generation Computer Systems 63:1–14 Computational Method Link
Monti M, Matos MR, Choi J-M, Ferry MS, Borek B (2016) A modified galactose network model with implications for growth. arXiv preprint arXiv:1601.03235 Link
Morgan AE, Mooney KM, Wilkinson SJ, Pickles NA, McAuley MT (2016) Mathematically modelling the dynamics of cholesterol metabolism and ageing. BioSystems 145:19–32 Metabolism Link
Obydennyy SI, Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2016) Dynamics of calcium spiking, mitochondrial collapse and phosphatidylserine exposure in platelet subpopulations during activation. Journal of Thrombosis and Haemostasis 14:1867–1881 Signaling Link
Olajuyigbe FM, Demitri N, De Zorzi R, Geremia S (2016) Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 21:1458 Biochemistry Link
Orlenko A, Hermansen RA, Liberles DA (2016) Flux control in glycolysis varies across the tree of life. Journal of Molecular Evolution 82:146–161 Metabolism Link
Orlenko A, Teufel AI, Chi PB, Liberles DA (2016) Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biology Direct 11:31 Genetics Metabolism Link
Ouzounoglou E, Dionysiou D, Stamatakos GS (2016) Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC Systems Biology 10:23 Cell Biology Link
Özkar S, Finke RG (2016) Palladium(0) Nanoparticle Formation, Stabilization, and Mechanistic Studies: Pd(acac) 2 as a Preferred Precursor, [Bu 4 N] 2 HPO 4 Stabilizer, plus the Stoichiometry, Kinetics, and Minimal, Four-Step Mechanism of the Palladium Nanoparticle Formation and Subsequent Agglomeration Reactions. Langmuir 32:3699–3716 Chemistry Link
Palai T, Kumar A, Bhattacharya PK (2016) Enzyme immobilization/bioconjugation in producing galactio-oligosaccharidies from lactose: developments of kinetic models and bio-reactors. Materials Today: Proceedings 3:3568–3586 Biotechnology Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Pappalardo F, Russo G, Candido S, Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra M (2016) Computational Modeling of PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer. PLoS One 11:e0152104 Signaling Link
Pires JC, Conant GC (2016) Robust yet fragile: expression noise, protein misfolding, and gene dosage in the evolution of genomes. Annual Review of Genetics 50:113–131 Genetics Genomics Link
Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ (2016) Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallographica D72:922-932 Biophysics Link
Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil’ev SA, Demina IA, Ataullakhanov FI, Alessi M-C, Panteleev MA (2016) Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. Biochimica et Biophysica Acta 1858:1216–1227 Immunology Biochemistry Biophysics Link
Proctor CJ, Gartland A (2016) Simulated interventions to ameliorate age-related bone loss indicate the importance of timing. Frontiers in Endocrinology 7:61 Physiology Signaling Link
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLoS One 11:e0148320 Genetics Microbiology Synthetic Biology Link
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G (2016) Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Computational Biology 12:e1004825 Microbiology Metabolism Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561 Biochemistry Macromolecular Biochemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link
Rocchigiani L, Busico V, Pastore A, Macchioni A (2016) Comparative NMR Study on the Reactions of Hf(IV) Organometallic Complexes with Al/Zn Alkyls. Organometallics 35:1241–1250 Chemistry Link
Rutkis R, Strazdina I, Balodite E, Lasa Z, Galinina N, Kalnenieks U (2016) The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway. PLoS One 11:e0153866 Metabolism Microbiology Link
Salcedo-Sora JE, McAuley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link
Samal SS (2016) Analysis of biochemical reaction networks using tropical and polyhedral geometry methods. Ph.D. Thesis, Rheinische Friedrich-Wilhelms-Universität Bonn, Germany Computational Method Theory Link
Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano A, Ito Y, Sato M, Suzuki Y, Kuroda S (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Science Signaling 9:ra112–ra112 Signaling Physiology Link
Scharm M, Waltemath D (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5:2421 Computational Method Link
Semenov SN, Kraft LJ, Ainla A, Zhao M, Baghbanzadeh M, Campbell VE, Kang K, Fox JM, Whitesides GM (2016) Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537:656–660 Chemistry Biochemistry Link
Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T (2016) Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP+ oxidoreductase with NADP+/NADPH and ferredoxin. Biochimica et Biophysica Acta 1857:678–687 Microbiology Enzymology Link
Shepelyuk TO, Panteleev MA, Sveshnikova AN (2016) Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover. Mathematical Modelling of Natural Phenomena 11:91–101 Metabolism Physiology Link
Shi Q, Mower MP, Blackmond DG, Rebek Jr J (2016) Water-soluble cavitands promote hydrolyses of long-chain diesters. Proceedings of the National Academy of Sciences USA 113:9199–9203 Chemistry Link
Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA (2016) A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PLoS One 11:e0162428 Physiology Pharmacology Link
Stanger FV, Burmann BM, Harms A, Aragão H, Mazur A, Sharpe T, Dehio C, Hiller S, Schirmer T (2016) Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Proceedings of the National Academy of Sciences USA 113:E529–E537 Enzymology Link
Sung S, Sale D, Braddock DC, Armstrong A, Brennan C, Davies RP (2016) Mechanistic Studies on the Copper-Catalyzed N-Arylation of Alkylamines Promoted by Organic Soluble Ionic Bases. ACS Catalysis 6:3965–74 Chemistry Link
Sveshnikova AN, Balatskiy AV, Demianova AS, Shepelyuk TO, Shakhidzhanov SS, Balatskaya MN, Pichugin AV, Ataullakhanov FI, Panteleev MA (2016) Systems biology insights into the meaning of the platelet’s dual-receptor thrombin signaling. Journal of Thrombosis and Haemostasis 14:2045–2057 Physiology Signaling Link
Talemi SR, Tiger C-F, Andersson M, Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J (2016) Systems Level Analysis of the Yeast Osmo-Stat. Scientific Reports 6:30950 Signaling Link
Thiaville JJ, Frelin O, García-Salinas C, Harrison K, Hasnain G, Horenstein NA, de la Garza RID, Henry CS, Hanson AD, de Crécy-Lagard V (2016) Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). Frontiers in Microbiology 7:431 Metabolism Link
Tomalin LE, Day AM, Underwood ZE, Smith GR, Dalle Pezze P, Rallis C, Patel W, Dickinson BC, Bähler J, Brewer TF, Chang CJ-L, Shanley DP, Veal EA (2016) Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2, with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed. Free Radical Biology and Medicine 95:333–348 Metabolism Link
Tootoonchi MH, Sharma G, Calles J, Prabhakar R, Kaifer AE (2016) Cooperative Self-Assembly of a Quaternary Complex Formed by Two Cucurbit [7] uril Hosts, Cyclobis (paraquat-p-phenylene), and a “Designer” Guest. Angewandte Chemie 128:11679–83 Chemistry Link
Troják M, Šafránek D, Hrabec J, Šalagovič J, Romanovská F, Červenỳ J (2016) E-Cyanobacterium. org: A Web-Based Platform for Systems Biology of Cyanobacteria. International Conference on Computational Methods in Systems Biology. Springer, 316–322. Software Link
Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA (2016) The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Systems Biology 10:20 Microbiology Immunology Signaling Link
Valero E, Macià H, Ildefonso M, Hernández J-A, González-Sánchez M-I, García-Carmona F (2016) Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. BMC Systems Biology 10:11 Metabolism Physiology Link
van Eunen K, Volker-Touw CM, Gerding A, Bleeker A, Wolters JC, van Rijt WJ, Martines A-CM, Niezen-Koning KE, Heiner RM, Permentier H, Groen AK, Reijngoud D-J, Derks TGJ, Bakker BM (2016) Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. BMC Biology 14:107 Metabolism Link
Vinciotti V, Augugliaro L, Abbruzzo A, Wit EC (2016) Model selection for factorial Gaussian graphical models with an application to dynamic regulatory networks. Statistical Applications in Genetics and Molecular Biology 15:193–212 Computational Method Link
Vranish JN, Das D, Barondeau DP (2016) Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe–S Cluster Biosynthetic Pathways. ACS Chemical Biology 11:3114–3121 Enzymology Biochemistry Link
Walker MA, Madduri R, Rodriguez A, Greenstein JL, Winslow RL (2016) Models and Simulations as a Service: Exploring the Use of Galaxy for Delivering Computational Models. Biophysical Journal 110:1038–1043 Computational Method Link
Waltemath D, Karr JR, Bergmann FT, Chelliah V, Hucka M, Krantz M, Liebermeister W, Mendes P, Myers CJ, Pir P, Alaybeyoglu B, Aranganathan NK, Baghalian K, Bittig AT, Burke PEP, Cantarelli M, Chew YH, Costa RS, Cursons J, Czauderna T, Goldberg AP, Gomez HF, Hahn J, Hameri T, Gardiol DFH, Kazakiewicz D, Kiselev I, Knight-Schrijver V, Knüpfer C, König M, Lee D, Lloret-Villas A, Mandrik N, Medley JK, Moreau B, Naderi-Meshkin H, Palaniappan SK, Priego-Espinosa D, Scharm M, Sharma M, Smallbone K, Stanford NJ, Song J-H, Theile T, Tokic M, Tomar N, Toure V, Uhlendorf J, Varusai TM, Watanabe LH, Wendland F, Wolfien M, Yurkovich JT, Zhu Y, Zardilis A, Zhukova A, Schreiber F (2016) Toward Community Standards and Software for Whole-Cell Modeling. IEEE Transactions on Biomedical Engineering 63:2007–2014 Computational Method Whole-Cell Models Link
Woller A, Duez H, Staels B, Lefranc M (2016) A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Reports 17:1087–1097 Metabolism Physiology Signaling Link
Woo SS (2016) Fast simulation of stochastic biochemical reaction networks on cytomorphic chips. Ph.D. Thesis, Massachusetts Institute of Technology, Cambridge MA, USA Computational Method Link
Woods ML, Barnes CP (2016) Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Computational Biology 12:e1005131 Computational Method Link
Xie Y (2016) Multi-scale modelling of the cellular and molecular mechanisms of hyperpolarisation mediated synaptic plasticity in the vestibular nuclei. MSc Thesis, The University of Edinburgh, UK Signaling Physiology Link
Xu H, Diccianni JB, Katigbak J, Hu C, Zhang Y, Diao T (2016) Bimetallic C–C Bond-Forming Reductive Elimination from Nickel. Journal of the American Chemical Society 138:4779–4786 Chemistry Link
Zimmer C, Bergmann FT, Sahle S (2016) Reducing local minima in fitness landscapes of parameter estimation by using piecewise evaluation and state estimation. arXiv preprint arXiv:1601.04458 Computational Method Link
Zimmer C (2016) Experimental Design for Stochastic Models of Nonlinear Signaling Pathways Using an Interval-Wise Linear Noise Approximation and State Estimation. PLoS One 11:e0159902 Computational Method Link
Zimmer C, Sahle S (2016) Comparison of approaches for parameter estimation on stochastic models: Generic least squares versus specialized approaches. Computational Biology and Chemistry 61:75–85 Computational Method Link

108 publications
2015
Abdallah P, Deborde M, Dossier-Berne F, Karpel Vel Leitner N (2015) Kinetics of Chlorination of Benzophenone-3 in the Presence of Bromide and Ammonia. Environmental Science & Technology 49:14359–14367 Environmental Sciences Chemistry Link
Amemiya T, Honma M, Kariya Y, Ghosh S, Kitano H, Kurachi Y, Fujita K, Sasaki Y, Homma Y, Abernethy DR, Kume H, Suzuki H (2015) Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. npj Systems Biology and Applications 1:15005 Toxicology Signaling Link
Aullón G, Crespo M, Font-Bardia M, Jover J, Martínez M, Pike J (2015) A combined kinetico-mechanistic and computational study on the competitive formation of seven- versus five-membered platinacycles; the relevance of spectator halide ligands. Dalton Transactions 44:17968-79 Chemistry Link
Azimi S, Czeizler E, Gratie C, Gratie D, Iancu B, Ibssa N, Petre I, Rogojin V, Shadbahr T, Shokri F (2015) An Excursion Through Quantitative Model Refinement. Lecture Notes in Computer Science 9504:25-47 Computational Method Software Link
Azizi M, Biard P-F, Couvert A, Ben Amor M (2015) Competitive kinetics study of sulfide oxidation by chlorine using sulfite as reference compound. Chemical Engineering Research and Design 94:141–152 Chemistry Link
Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A (2015) On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry 56:98-1089 Computational Method Link
Castello MA (2015) Lipid Regulation as a Critical Factor in the Development of Alzheimer’s Disease. Ph.D. Thesis, Loma Linda University, California, USA. Metabolism Link
Compel WS, Wong OA, Chen X, Yi C, Geiss R, Häkkinen H, Knappenberger KL Jr, Ackerson CJ (2015) Dynamic Diglyme-Mediated Self-Assembly of Gold Nanoclusters. ACS Nano 9:11690-8. Chemistry Link
Czabany T, Schmölzer K, Luley-Goedl C, Ribitsch D, Nidetzky B (2015) All-in-one assay for beta-D-galactoside sialyltransferases: quantification of productive turnover, error hydrolysis and site selectivity. Analytical Biochemistry 483:47-53 Laboratory Method Enzymology Link
D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL (2015) Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life 5:969-96 Synthetic Biology Link
Dacheux E, Firczuk H, McCarthy JEG (2015) Rate control in yeast protein synthesis at the population and single-cell levels. Biochemical Society Transactions 43:1266-70 Macromolecular Biochemistry Link
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. Journal of Cell Biology 208:23-32 Macromolecular Biochemistry Cell Biology Link
della Sala F, Kay ER (2015) Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange. Angewandte Chemie 127:4261-5 Chemistry Link
Donovan S, Eaton CD, Gower ST, Jenkins KP, LaMar MD, Poli DB, Sheehy R, Wojdak JM (2015) QUBES: a community focused on supporting teaching and learning in quantitative biology. Letters in Biomathematics 2:46-55 Education Link
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucleic Acids Research 43:10623-32. Macromolecular Biochemistry Genetics Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLoS One 10:e0116616 Physiology Macromolecular Biochemistry Link
Emiola A, George J, Andrews SS (2015) A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli. PLoS One 10:e0121216 Metabolism Microbiology Link
Everetts NJ (2015) Computational Analysis of the Control of Cell Cycle Entry. Bachelor's Thesis, Department of Molecular and Cellular Biology, University of Arizona, USA Cell Biology Signaling Link
Gladkovskaya O, Greaney P, Gun'ko YK, O'Connor GM, Meere M, Rochev Y (2015) An experimental and theoretical assessment of quantum dot cytotoxicity. Toxicology Research 4:1409-15 Toxicology Link
Hamacher-Brady A, Brady NR (2015) Bax/Bak-Dependent, Drp1-Independent Targeting of XIAP into Inner-Mitochondrial Compartments Counteracts Smac-Dependent Effector Caspase Activation. Journal of Biological Chemistry 290:22005-18. Signaling Link
Hinze T, Kirkici K, Sauer P, Sauer P, Behre J (2015) Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. Lecture Notes in Computer Science 9504:215-235 Computational Method Link
Hristova-Neeley D, Neshchadin D, Gescheidt G (2015) Time-Resolved EPR as a Tool to Investigate Oxygen Quenching in Photoinitiated Radical Polymerizations. Journal of Physical Chemistry 119:13883-7 Chemistry Link
Hudson DA, Gannon SA, Thorpe C, (2015) Oxidative protein folding: From thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radical Biology and Medicine 80:171-182 Macromolecular Biochemistry Link
Ihekwaba AEC, Mura I, Peck MW, Barker GC (2015) The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective. Pathogens and Disease 73:ftv084 Microbiology Link
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H (2015) Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC Systems Biology 9:81. Immunology Cell Biology Signaling Link
Jeong H, John JM, Schrock RR (2015) Formation of Alternating trans-A-alt-B Copolymers through Ring-Opening Metathesis Polymerization Initiated by Molybdenum Imido Alkylidene Complexes. Organometallics 34:5136–5145 Chemistry Link
Jeong H, John JM, Schrock RR, Hoveyda AH (2015) Synthesis of Alternating trans-AB Copolymers through Ring-Opening Metathesis Polymerization Initiated by Molybdenum Alkylidenes. Journal of the American Chemical Society 137:2239-42 Chemistry Link
Ji Y, Benkovics T, Beutner GL, Sfouggatakis C, Eastgate MD, Blackmond DG (2015) Mechanistic Insights into the Vanadium-Catalyzed Achmatowicz Rearrangement of Furfurol. Journal of Organic Chemistry 80:1696-1702 Chemistry Link
Jones AR, Rentergent J, Scrutton NS, Hay S (2015) Probing reversible chemistry in coenzyme B12-dependent ethanolamine amonnia lyase with kinetic isotope effects. Chemistry 21:8826-31 Enzymology Link
Juty N, Ali R, Glont M, Keating SM, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V (2015) BioModels: Content, Features, Functionality, and Use. CPT:Pharmacometrics & Systems Pharmacology 4:1-14 Software Link
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Review E 92:062712 Macromolecular Biochemistry Theory Link
Kashyap R, Palai T, Bhattacharya PK (2015) Kinetics and model development for enzymatic synthesis of fructo-oligosaccharides using fructosyltransferase. Bioprocess and Biosystems Engineering 38:2417-26 Biotechnology Metabolism Link
Kesten D, Kummer U, Sahle S, Hübner K (2015) A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse. Biophysical Chemistry 206:40-57. Metabolism Link
Koutsouradis E, Provelengios G, Kouskoumvekakis E, Manolakos ES (2015) Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks. in 2015 Euromicro Conference on Digital System Design (DSD) pp.583-590 Computational Method Link
Lai M, Brun D, Edelstein SJ, Le Novère N (2015) Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLoS Computational Biology 11:e1004063 Biochemistry Enzymology Link
Laurell Nash A, Hertzberg R, Wen YQ, Dahlgren B, Brinck T, Moberg C (2015) Dual Lewis Acid-Lewis Base Catalyzed Acylcyanation of Aldehydes: A Mechanistic Study. Chemistry 22:3821-3829 Chemistry Link
Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson CW, Hoops S, Howard B, Bassaganya-Riera J (2015) Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLoS One 10:e0134849 Immunology Link
Lee TW, Yang AS-P, Brittain T, Birch NP (2015) An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins: Structure, Function, and Bioinformatics 83:135-52 Macromolecular Biochemistry Link
Li L, Gervasi N, Girault J-A (2015) Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications 6:6319 Cell Biology Signaling Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Luna A, McFadden GB, Aladjem MI, Kohn KW (2015) Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Computational Biology 11:e1004144 Cell Biology Link
Luo J, Theron R, Sewell LJ, Hooper TN, Weller AS, Oliver AG, McIndoe JS (2015) Rhodium-Catalyzed Selective Partial Hydrogenation of Alkynes. Organometallics 34:3021-8 Chemistry Link
Madsen C, Shmarov F, Zuliani P (2015) BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Proceedings 13th International Conference, CMSB 2015 (Roux O, Bourdon J, Eds.), Springer pp182-94 Computational Method Link
Maggi M, Chiarelli LR, Valentini G, Scotti C (2015) Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 10:e0117025 Microbiology Biotechnology Enzymology Link
Mandlik V, Gurav M, Singh S (2015) Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach. Journal of Biomolecular Structure and Dynamics 33:2554-62 Synthetic Biology Genetics Metabolism Link
Marwaha S (2015) A Genomics and Mathematical Modeling Approach for the study of Helicobacter pylori associated Gastritis and Gastric Cancer. Ph.D. Thesis, University of Cincinnati, Ohio, USA Immunology Signaling Link
Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson CW, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J (2015) Multiscale modeling of mucosal immune responses. BMC Bioinformatics 16:Supp12:S2 Immunology Link
Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J (2015) ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12:289-97 Software Link
Mendes P, Oliver SG, Kell DB (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences 36:710-23 Physiology Pharmacology Link
Montes MR, Ferreira-Gomes MS, Centeno M, Rossi RC (2015) The E2P-like state induced by magnesium fluoride complexes in the Na, K-ATPase. Kinetics of formation and interaction with Rb+. Biochimica et Biophysica Acta 1848:1514-23 Enzymology Link
Müller JM, Risse JM, Friehs K, Flaschel E (2015) Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Engineering in Life Sciences 15:627-639 Laboratory Method Link
Nelsen ER, Brezny AC, Landis CR (2015) Interception and Characterization of Catalyst Species in Rhodium Bis(diazaphospholane)-Catalyzed Hydroformylation of Octene, Vinyl Acetate, Allyl Cyanide, and 1-Phenyl-1,3-butadiene. Journal of the American Chemical Society 137:14208-219 Chemistry Link
Palai T, Kumar A, Bhattacharya PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme and Microbial Technology 70:42-49 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA (2015) JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biology 9:95 Software Link
Patschinski P (2015) Chemoselective Silylation of Alcohols Through Lewis Base-catalyzed Reactions. Experimental and Theoretical Studies. Ph.D. Thesis, Ludwig-Maximilians University of Munich, Germany Chemistry Link
Paul D, Dasgupta A, De RK (2015) Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach. PLoS One 10:e0137728. Theory Link
Penkler GP, du Toit F, Adams W, Rautenbach M, Palm DC, van Niekerk DD, Snoep JL (2015) Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS Journal 282:1481-511 Metabolism Link
Peñarrubia L, Romero P, Carrió-Seguí A, Andrés-Bordería A, Moreno J, Sanz A (2015) Temporal aspects of copper homeostasis and its crosstalk with hormones. Frontiers in Plant Science 6:255. Physiology Plant Biology Link
Phelix CF, Feltus FA (2015) Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome(TTM) technology-effects of drought stress on rice. Plant Biology 17:63-73 Computational Method Plant Biology Link
Philipson CW (2015) Systems analysis and characterization of mucosal immunity. Ph.D. Thesis, Virginia Tech, USA Immunology Link
Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R (2015) Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLoS One 10:e0137839 Immunology Link
Pineda E, Encalada R, Vázquez C, González Z, Moreno-Sánchez R, Saavedra E (2015) Glucose Metabolism and Its Controlling Mechanisms in Entamoeba histolytica. In Amebiasis. Part IV Biology and Pathogenesis of Entamoeba (Nozaki T, Bhattacharya A eds.) Springer pp.351-372 Metabolism Microbiology Link
Prieto C, González Delgado JA, Arteaga JF, Jaraíz M, López-Pérez JL, Barrero AF (2015) Homocoupling versus reduction of radicals: an experimental and theoretical study of Ti(III)-mediated deoxygenation of activated alcohols. Organic & Biomolecular Chemistry 13:3462–3469 Chemistry Link
Raganati F, Procentese A, Olivieri G, Götzc P, Salatino P, Marzocchella A (2015) Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model. Biochemical Engineering Journal 99:156-66. Biotechnology Metabolism Microbiology Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Scientific Reports 5:13540 Genetics Macromolecular Biochemistry Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link
Rosenthal RG, Vögeli B, Quade N, Capitani G, Kiefer P, Vorholt JA, Ebert MO, Erb TJ (2015) The use of ene adducts to study and engineer enoyl-thioester reductases. Nature Chemical Biology 11:398-400. Enzymology Link
Šalagovič J (2015) Formální modely oscilací v biologii a jejich analýza. Ph.D. Thesis, Masarykova univerzita, Czech Republic. Computational Method Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bulletin of Mathematical Biology 77:2180-211. Computational Method Theory Link
Sander ZH, West ZJ, Ervin JS, Zabarnick S (2015) Experimental and Modeling Studies of Heat Transfer, Fluid Dynamics, and Autoxidation Chemistry in the Jet Fuel ThermalOxidation Tester (JFTOT). Energy & Fuels 29:7036-47. Chemistry Chemical Engineering Link
Sapra A, Ramadan D, Thorpe C (2015) Multivalency in the inhibition of oxidative protein folding by arsenic(III) species. Biochemistry 54:612–621 Macromolecular Biochemistry Link
Sengupta A, Grover M, Chakraborty A, Saxena S (2015) HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual. PLoS One 10:e0127918 Metabolism Link
Sier JH (2015) Investigation of the impact of MRP3 and MRP4 on the disposition of drugs and conjugates in rat and human. Doctoral Thesis, University of Surrey, UK Physiology Link
Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ (2015) Toxicity of an alpha-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging. Journal of Biological Chemistry 290:4856-4865 Macromolecular Biochemistry Link
Subramanian A, Sarkar RR (2015) Dynamics Of GLI Regulation And A Strategy To Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. Journal of Biological Systems 23:681-719 Signaling Link
Subramanian A, Singh V, Sarkar RR (2015) Understanding Visceral Leishmaniasis Disease Transmission and its Control - A Study Based on Mathematical Modeling. Mathematics 3:913-944 Epidemiology Link
Suwanmajo T, Krishnan J (2015) Mixed mechanisms of multi-site phosphorylation. Journal of the Royal Society Interface 12:20141405 Signaling Link
Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2015) Compartmentalized calcium signaling triggers subpopulation formation upon platelet activation through PAR1. Molecular BioSystems 11:1052-60 Signaling Link
Talawar B (2015) A Crossbar Interconnection Network in DNA. Proceedings of 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, pp. 342-5 Synthetic Biology Link
Terentyeva VA, Sveshnikova AN, Panteleev MA (2015) Kinetics and mechanisms of surface-dependent coagulation factor XII activation. Journal of Theoretical Biology 382:235–243 Physiology Biophysics Link
Torbensen K, Rossi F, Pantani OL, Ristori S, Abou-Hassan A (2015) Interaction of the Belousov-Zhabotinsky Reaction with Phospholipid Engineered Membranes. Journal of Physical Chemistry 119:10224-30 Chemistry Link
Trausinger G, Gruber C, Krahulec S, Magnes C, Nidetzky B, Klimacek M (2015) Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts. Biotechnology for Biofuels and Bioproducts 8:157 Biotechnology Metabolism Link
Tummler K, Kühn C, Klipp E (2015) Dynamic metabolic models in context: biomass backtracking. Integrative Biology 7:940-51 Computational Method Link
Twycross J, Bennett M, Krasnogor N (2015) A High-Performance Multicompartment Stochastic Simulator for Executable Biology. Preprint Link
Tóth A, Brózik A, Szakács G, Sarkadi B, Hegedüs T (2015) A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System. PLoS One 10:e0115533 Toxicology Link
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology 9:8 Computational Method Link
Wang H-Y, Huang Y-X, Zheng L-H, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Sun Y, Wang G-N, Ma Z-Q, Li Y-X (2015) Modelling Coupled Oscillations in the Notch, Wnt, and FGF Signaling Pathways during Somitogenesis: A Comprehensive Mathematical Model. Computational Intelligence and Neuroscience 2015:387409 Signaling Link
Willems PH, Pahle J, Stalpers XL, Mugahid D, Nikolaew A, Koopman WJ, Kummer U (2015) PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals. FEBS Journal 282:2187-201 Signaling Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Computational Biology 11:e1004593 Macromolecular Biochemistry Cell Biology Link
Zimmer C (2015) Reconstructing the hidden states in time course data of stochastic models. Mathematical Biosciences 269:117-29 Computational Method Link
Zimmer C, Sahle S (2015) A termination criterion for parameter estimation in stochastic models in systems biology. BioSystems 9:181-92 Computational Method Link

92 publications
2014
Antunes G, Sebastião AM, de Souza FMS (2014) Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 9:e105531 Signaling Pharmacology Link
Arnold A, Nikoloski Z (2014) In search for an accurate model of the photosynthetic carbon metabolism. Mathematics and Computers in Simulation 96:171–194 Plant Biology Metabolism Link
Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y (2014) Computer-assisted design for scaling up systems based on DNA reaction networks. Journal of the Royal Society Interface 11:20131167 Software Link
Beauvoit B, Colombié S, Monier A, Andrieu M-H, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat J-P, Gibon Y (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell 26:3224-42 Metabolism Plant Biology Link
Bellini M, Besozzi D, Cazzaniga P, Mauri G, Nobile MS (2014) Simulation and analysis of the blood coagulation cascade accelerated on GPU. 2014 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, 590–593 Computational Method Link
Benfeitas R, Selvaggio G, Antunes F, Coelho PMBM, Salvador A (2014) Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II. Free Radical Biology and Medicine 74:35-49 Metabolism Link
Bhosle A, Chandra N (2014) Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 209-213 Metabolism Link
Boba P, Gries S, Hamacher K (2014) R as an Integration Tool in High Performance Computing - Lessons Learned. GI-Jahrestagung. Lecture Notes in Informatics 232:138–148 Computational Method Software Link
Carbo A, Olivares-Villagómez D, Hontecillas R, Bassaganya-Riera J, Chaturvedi R, Piazuelo MB, Delgado A, Washington MK, Wilson KT, Algood HMS (2014) Systems modeling of the role of IL-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection. mBio 5:e01243-14 Immunology Link
Carrasco D, Pérez-Temprano MH, Casares JA, Espinet P (2014) Cross Alkyl-Aryl versus Homo Aryl-Aryl Coupling in Palladium-Catalyzed Coupling of Alkyl-Gold (I) and Aryl-Halide. Organometallics 33:3540-3545 Chemistry Link
Castaldi DF (2014) Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation. Ph.D. Thesis, University of Milano-Bicocca, Milan, Italy. Computational Method Link
Cazzaniga P, Nobile MS, Besozzi D, Bellini M, Mauri G (2014) Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Research International 2014:863298 Computational Method Link
Claudino M, Jonsson M, Johansson M (2014) Utilizing thiol-ene coupling kinetics in the design of renewable thermoset resins based on D-limonene and polyfunctional thiols. RSC Advances 4:10317-10329 Chemistry Link
Clough JM, Sijbesma RP (2014) Dioxetane scission products unchanged by mechanical force. ChemPhysChem 15:3565–3571 Chemistry Link
Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S (2014) An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production. Molecular BioSystems 10:628-639 Microbiology Metabolism Link
Cui Y, Murphy B, Gentilcore A, Sharma Y, Minasian LM, Kramer BS, Coates PM, Gohagan JK, Klenk J, Tidor B (2014) Multilevel modeling and value of information in clinical trial decision support. BMC Systems Biology 8:6 Metabolism Link
Dalle Pezze P, Nelson G, Otten EG, Korolchuk VI, Kirkwood TBL, von Zglinicki T, Shanley DP (2014) Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. PLoS Computational Biology 10:e1003728. Signaling Link
Drees B, Reiger M, Jung K, Bischofs IB (2014) A modular view of the diversity of cell-density-encoding schemes in bacterial quorum-sensing systems. Biophysical Journal 107:266-277 Microbiology Link
Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews KR, Clayton C (2014) Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Molecular Microbiology 94:307-326 Microbiology Genomics Link
Figueredo GP, Siebers P-O, Owen MR, Reps J, Aickelin U (2014) Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer. PLoS One 9:e95150 Computational Method Link
Gautam VK, Czeizler E, Haddow PC, Kuiper M (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. In: Dediu AH, Lozano M, Martín-Vide C (eds) Theory and Practice of Natural Computing. TPNC 2014. Lecture Notes in Computer Science 8890:119-133 Synthetic Biology Link
Gianni S, Dogan J, Jemth P (2014) Distinguishing induced fit from conformational selection. Biophysical Chemistry 189:33–39 Macromolecular Biochemistry Link
Godfrey L, Yamada-Fowler N, Smith J, Thornalley PJ, Rabbani N (2014) Arginine-directed glycation and decreased HDL plasma concentration and functionality. Nutrition & Diabetes 4:e134 Physiology Link
Graybill C, Prehoda KE (2014) Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 53:4931-7 Signaling Link
Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E (2014) Superoxide production by cytochrome bc 1 complex: A mathematical model. Biochimica et Biophysica Acta 1837:1643–1652 Enzymology Link
Hallinan JS, Gilfellon O, Misirli G, Wipat A (2014) Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. Proceedings of the 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8 Synthetic Biology Link
Helgeson LA (2014) Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex. Ph.D. Thesis, University of Oregon, USA. Cell Biology Link
Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ (2014) Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. Annals of the Rheumatic Diseases 75:449–458 Signaling Immunology Link
Ihekwaba AEC, Mura I, Barker GC (2014) Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. BMC Systems Biology 8:119 Microbiology Link
Irving JA, Haq I, Dickens JA, Faull SV, Lomas DA (2014) Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization. Biochemical Journal 460:103–119 Macromolecular Biochemistry Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. Ph.D. Thesis, University of Tokyo, Japan. Synthetic Biology Computational Method Link
Jakubík J, Zimčík P, Randáková A, Fuksová K, El-Fakahany EE, Doležal V (2014) Molecular mechanisms of methoctramine binding and selectivity at muscarinic acetylcholine receptors. Molecular Pharmacology 86:180–192 Pharmacology Link
James AI, Imran HAQ, Jennifer AD, Sarah VF, David AL (2014) Altered native stability is the dominant basis for susceptibility of alpha1-antitrypsin mutants to polymerization. Biochemical Journal 460:103-115 Macromolecular Biochemistry Link
Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R (2014) A Mathematical Model of Skeletal Muscle Disease and Immune Response in the mdx Mouse. BioMed Research International 2014:871810 Immunology Link
Jones AX (2014) Mechanistic studies of enantioselective alkene bromolactonisation reactions. Ph.D. Thesis, Imperial College London, UK. Chemistry Link
Karonen M, Mattila H, Huang P, Mamedov F, Styring S, Tyystjärvi E (2014) A tandem mass spectrometric method for singlet oxygen measurement. Photochemistry and Photobiology 90:965-971 Laboratory Method Link
Kefalidis CE, Davi M, Holstein PM, Clot E, Baudoin O (2014) Mechanistic Study of the Selectivity of Olefin versus Cyclobutene Formation by Palladium (0)-Catalyzed Intramolecular C (sp3)-H Activation. Journal of Organic Chemistry 79:11903-11910 Chemistry Link
Kent PD, Mondloch JE, Finke RG (2014) A Four-Step Mechanism for the Formation of Supported-Nanoparticle Heterogenous Catalysts in Contact with Solution: The Conversion of Ir (1, 5-COD) Cl/gamma-Al2O3 to Ir (0) 170/gamma-Al2O3. Journal of the American Chemical Society 136:1930-41 Chemistry Link
Khandekar DC, Palai T, Agarwal A, Bhattacharya PK (2014) Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition. Bioprocess and Biosystems Engineering 37:2529–2537 Enzymology Biotechnology Link
Kleppe R, Ghorbani S, Fossbakk A, Martinez A, Haavik J (2014) Modeling the Dynamics of Dopamine Biosynthesis and its Regulation by Tyrosine Hydroxylase. In: Eiden LE (ed) Catecholamine Research in the 21st Century. Boston: Academic Press, 30. Metabolism Link
Kleppe R, Ghorbani S, Martinez A, Haavik J (2014) Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Letters 588:92–98 Signaling Link
Lakin MR, Minnich A, Lane T, Stefanovic D (2014) Design of a biochemical circuit motif for learning linear functions. Journal of the Royal Society Interface 11:20140902 Synthetic Biology Link
Le Muzic M, Parulek J, Stavrum A-K, Viola I (2014) Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33:141-150 Software Link
Leal Denis MF (2014) Homeostasis de ATP extracelular en eritrocitos: interregulación y consecuencias funcionales. Ph.D. Thesis, Universidad de Buenos Aires, Argentina. Physiology Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds.) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Ligon TS, Leonhardt C, Rädler JO (2014) Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLoS One 9:e107148 Cell Biology Genomics Link
Luo J (2014) Mechanistic investigation of catalytic organometallic reactions using ESI MS. Ph.D. Thesis, University of Victoria, British Columbia, Canada. Chemistry Link
Lutz A, Sanwald J, Thomas M, Feuer R, Sawodny O, Ederer M, Borner C, Humar M, Merfort I (2014) Interleukin-1beta Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes. PLoS One 9:e115603. Immunology Link
Machado D, Rodrigues L, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. BioSystems 125:16-21 Synthetic Biology Metabolism Link
Marwaha S, Schumacher MA, Zavros Y, Eghbalnia HR (2014) Crosstalks between Cytokines and Sonic Hedgehog in Helicobacter pylori Infection: A Mathematical Model. PLoS One 9:e111338. Immunology Signaling Link
Marín-Hernández Á, López-Ramírez SY, Del Mazo-Monsalvo I, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Modeling cancer glycolysis under hypoglycemia, and the role played by the differential expression of glycolytic isoforms. FEBS Journal 281:3325–3345 Metabolism Link
Marín-Hernández Á, López-Ramírez SY, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Systems biology approaches to cancer energy metabolism. in M.A. Aon et al. (eds.), Systems Biology of Metabolic and Signaling Networks, Springer-Verlag pp.213-239 Metabolism Link
Matsuoka Y, Funahashi A, Ghosh S, Kitano H (2014) Modeling and simulation using CellDesigner. Methods in Molecular Biology 1164:121-145 Software Link
McAuley MT, Khalil R, Stockton DJ, Schilstra MJ (2014) Modelling the flagellar motor assembly process to help improve industrial operations systems design. Preprint Signaling Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson CW, Bassaganya-Riera J (2014) ENISI MSM: A novel multi-scale modeling platform for computational immunology. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 391-396 Software Link
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh P-R, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J (2014) Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology 8:13 Computational Method Link
Miller AJM, Kaminsky W, Goldberg KI (2014) Arene Activation at Iridium Facilitates C-O Bond Cleavage of Aryl Ethers. Organometallics 33:1245-1252 Chemistry Link
Mol M, Patole MS, Singh S (2014) Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion. Biochimica et Biophysica Acta 1840:71–79 Signaling Immunology Link
Mozga I, Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing 150:150–159 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Mauri G (2014) GPU-accelerated simulations of mass-action kinetics models with cupSODA. Journal of Supercomputing 69:17-24 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G (2014) cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS One 9:e91963. Computational Method Link
Ouzounoglou E, Kalamatianos D, Emmanouilidou E, Xilouri M, Stefanis L, Vekrellis K, Manolakos ES (2014) In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Systems Biology 8:54 Physiology Cell Biology Link
Palai T, Singh AK, Bhattacharya PK (2014) Enzyme, beta-galactosidase immobilized on membrane surface for galacto-oligosaccharides formation from lactose: kinetic study with feed flow under recirculation loop. Biochemical Engineering Journal 88:68-76 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA (2014) Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology 8:42 Software Computational Method Link
Pandey V (2014) Metabolic modeling of different degrees of steatohepatitis in mice. Ph.D. Thesis, Department of Mathematics and Computer Science, Free University of Berlin, Germany. Metabolism Link
Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo M-L, Sültmann H, Trauner M, Denk M, Zatloukal K, Lehrach H, Wierling C (2014) Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains. PLoS One 9:e111006. Metabolism Link
Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z (2014) Towards a computational model of a methane producing archaeum. Archaea 2014:898453 Metabolism Microbiology Whole-Cell Models Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2014) Biomarkers from biosimulations: Transcriptome-to-reactome™ Technology for individualized medicine. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 3452–3455 Computational Method Link
Phelix CF, Villareal G, LeBaron R, Perry G, Roberson DJ (2014) Precision medicine using individualized biosimulations of drug dosing: Alzheimer’s disease. Healthcare Innovation Conference (HIC), IEEE, 292–295 Pharmacology Link
Proctor CJ, Macdonald C, Milner JM, Rowan AD, Cawston TE (2014) A Computer Simulation Approach to Assessing Therapeutic Intervention Points for the Prevention of Cytokine-Induced Cartilage Breakdown. Arthritis & Rheumatology 66:979-989 Immunology Link
Rabbani N, Xue M, Thornalley PJ (2014) Activity, regulation, copy number and function in the glyoxalase system. Biochemical Society Transactions 42:419–424 Metabolism Link
Raganati F (2014) Butanol production by fermentation of renewable feedstocks. Ph.D. Thesis, Università di Napoli Federico II, Naples, Italy Biotechnology Link
Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B (2014) A model reduction method for biochemical reaction networks. BMC Systems Biology 8:52 Computational Method Link
Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. Journal of Biological Chemistry 289:14448–14457 Macromolecular Biochemistry Biophysics Microbiology Link
Rossi F, Ristori S, Marchettini N, Pantani OL (2014) Functionalized clay microparticles as catalysts for chemical oscillators. Journal of Physical Chemistry 118:24389–24396 Chemistry Link
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S (2014) A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. BioSystems 124:26–38 Metabolism Signaling Genetics Link
Sakkalis V, Sfakianakis S, Tzamali E, Marias K, Stamatakos G, Misichroni F, Ouzounoglou E, Kolokotroni E, Dionysiou D, Johnson D, McKeever S, Graf N (2014) Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models. IEEE Journal of Biomededical Health Informatics 18:824-31 Software Link
Saller S, Kunz L, Berg D, Berg U, Lara H, Urra J, Hecht S, Pavlik R, Thaler CJ, Mayerhofer A (2014) Dopamine in human follicular fluid is associated with cellular uptake and metabolism-dependent generation of reactive oxygen species in granulosa cells: implications for physiology and pathology. Human Reproduction 29:555-67 Physiology Metabolism Link
Sapra A, Ramadan D, Thorpe C (2014) Multivalency in the inhibition of oxidative protein folding by arsenic (III) species. Biochemistry 54:612–621 Biochemistry Link
Schaber J, Lapytsko A, Flockerzi D (2014) Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. Journal of the Royal Society Interface 11:20130971 Signaling Link
Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhütter H-G, Schuster S (2014) A theoretical study of lipid accumulation in the liver—Implications for nonalcoholic fatty liver disease. Biochimica et Biophysica Acta 1841:62–69 Metabolism Link
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Research 42:7539-7552 Computational Method Link
Shinde S, Mol M, Singh S (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention. Gene 550:214-22. Pharmacology Genomics Link
Smallbone K, Corfe BM (2014) A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. International Journal of Experimental Pathology 95:1–7 Physiology Link
Sosa CM, Pavarotti MA, Zanetti MN, Zoppino FCM, De Blas GA, Mayorga LS (2014) Kinetics of human sperm acrosomal exocytosis. MHR: Basic Science of Reproductive Medicine 21:244–254 Cell Biology Link
Spiaggi AJ (2014) Caracterización de los pasos involucrados en el transporte de K+ por la Na+/K+-ATPasa. Ph.D. Thesis, Universidad de Buenos Aires, Argentina. Enzymology Link
Sugiura M, Azami C, Koyama K, Rutherford AW, Rappaport F, Boussac A (2014) Modification of the pheophytin redox potential in Thermosynechococcus elongatus Photosystem II with PsbA3 as D1. Biochimica et Biophysica Acta 1837:139–148 Metabolism Microbiology Biophysics Link
Talemi SR, Jacobson T, Garla V, Navarrete C, Wagner A, Tamás MJ, Schaber J (2014) Mathematical modelling of arsenic transport, distribution and detoxification processes in yeast. Molecular Microbiology 92:1343–1356 Toxicology Metabolism Link
Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP (2014) Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathogens 10:e1003907 Macromolecular Biochemistry Link
Valero G, Ribó JM, Moyano A (2014) A closer look at spontaneous mirror symmetry breaking in aldol reactions. Chemistry 20:17395–17408 Chemistry Link
Valero G (2014) Estudis mecanístics i metodològics de processos d'autocatàlisi i organocatàlisi asimètriques. Ph.D. Thesis, Department of Organic Chemistry, University of Barcelona, Spain Chemistry Link
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A (2014) Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proceedings of the National Academy of Sciences USA 111:E3860–E3869 Signaling Link
Vickers JW, Sumliner JM, Lv H, Morris M, Geletii YV, Hill CL (2014) Collecting meaningful early-time kinetic data in homogeneous catalytic water oxidation with a sacrificial oxidant. Physical Chemistry Chemical Physics 16:11942-11949 Chemistry Link
Wang CCN, Chang P-C, Ng K-L, Chang C-M, Sheu PCY, Tsai JJP (2014) A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biology 8:15 Signaling Link
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Zikmanis P, Kampenusa I (2014) Relationship between Metabolic Fluxes and Sequence-Derived Properties of Enzymes. International Scholarly Research Notices 2014:817102 Metabolism Link
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97 publications
2013
Altintaş CM (2013) Effects of growth medium conditions on antibiotic production by actinomyces sp. MS Thesis, Dokuz Eylül University, Izmir, Turkey Biotechnology Microbiology Link
Berestovsky N, Nakhleh L (2013) An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PLoS One 8:e66031 Computational Method Link
Bulipopa N, Sulins J (2013) Automatic termination of parallel optimization runs of global stochastic optimization methods by upper limit criterion. Biosystems and Information Technology 2:15-18 Computational Method Link
Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R (2013) Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS One 8:e73365 Immunology Link
Carbo A, Hontecillas R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe M, Eubank S, Bisset K, Wendelsdorf K, Jarrah AS, Mei Y, Bassaganya-Riera J (2013) Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity. PLoS Computational Biology 9:e1003027 Immunology Signaling Link
Challenger JD (2013) The stochastic dynamics of biochemical systems. Ph.D. Thesis, University of Manchester, UK Computational Method Metabolism Link
Chelliah V, Laibe C, Le Novère N (2013) BioModels database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021:189–199 Software Link
Claudino M (2013) Macromolecular design: UV-curable thiol-ene networks based on renewable resources. Ph.D. Thesis, KTH Royal Institute of Technology, Stockholm, Sweden Chemistry Link
Claudino M, Jonsson M, Johansson M (2013) Thiol–ene coupling kinetics of d-limonene: a versatile ‘non-click’free-radical reaction involving a natural terpene. RSC Advances 3:11021–11034 Chemistry Link
Cornish-Bowden A, Piedrafita G, Morán F, Cárdenas ML, Montero F (2013) Simulating a model of metabolic closure. Biological Theory 8:383-390 Theory Link
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G (2013) An online model composition tool for system biology models. BMC Systems Biology 7:88 Computational Method Link
Diao T, Pun D, Stahl SS (2013) Aerobic Dehydrogenation of Cyclohexanone to Cyclohexenone Catalyzed by Pd(DMSO)2(TFA)2: Evidence for Ligand-Controlled Chemoselectivity. Journal of the American Chemical Society 135:8205-8212 Chemistry Link
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link
Fedosov SN, Brask J, Pedersen AK, Nordblad M, Woodley JM, Xu X (2013) Kinetic model of biodiesel production using immobilized lipase Candida antarctica lipase B. Journal of Molecular Catalysis B: Enzymatic 85–86:156–168 Biotechnology Enzymology Link
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff HV, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Fröhlich M (2013) Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis. Ph.D. Thesis, Free University of Berlin, Germany Physiology Link
Galazka M, Hay JO (2013) In silico metabolic control analysis of Brassica napus seeds based on dynamic kinetic modeling. A Compilation of Internship Reports. In (Stegman M, Morris M. and Blackburn N, eds.) A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 75–80 Metabolism Link
Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV (2013) Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochimica et Biophysica Acta 1830:4943- 59 Toxicology Metabolism Link
Genc S, Sorguven E, Ozilgen M, Aksan Kurnaz I (2013) Unsteady exergy destruction of the neuron under dynamic stress conditions. Energy 59:422–431 metabolism Link
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Haq I, Irving JA, Faull SV, Dickens JA, Ordonez A, Belorgey D, Gooptu B, Lomas DA (2013) Reactive centre loop mutants of alpha-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Bioscience Reports 33:499-511 Macromolecular Biochemistry Link
Hayashi K, Piras V, Tabata S, Tomita M, Selvarajoo K (2013) A systems biology approach to suppress TNF-induced proinflammatory gene expressions. Cell Communication and Signaling 11:84 Signaling Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Incicco JJ, Gebhard LG, González-Lebrero RM, Gamarnik AV, Kaufman SB (2013) Steady-State NTPase Activity of Dengue Virus NS3: Number of Catalytic Sites, Nucleotide Specificity and Activation by ssRNA. PLoS One 8:e58508 Macromolecular Biochemistry Link
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Kampenusa I, Zikmanis P (2013) Relationships between metabolic fluxes and enzyme amino acid composition. Central European Journal of Biology 8:107–120 Metabolism Link
Kennedy N, Mizeranschi A, Thompson P, Zheng H, Dubitzky W (2013) Reverse engineering of gene regulation models from multi-condition experiments. Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.112-119 Computational Method Link
Kent E, Neumann S, Kummer U, Mendes P (2013) What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? PLoS One 8:e79244 Computational Method Link
Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybilo M, Driessen NN, Gilbert DR, Breitling R, Bakker BM, Barrett MP (2013) Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Computational Biology 9:e1003371. Metabolism Link
Khan HA (2013) Asymmetric Synthesis of Lactones and Lactams: Rhodium Catalysis in the Hydroacylation of Ketones and the Hydrogenation of Cyclic Dehydropeptides. Ph.D. Thesis, Department of Chemistry, University of Toronto, Canada Chemistry Link
Klement M, Šafránek D, Ded T, Pejznoch A, Nedbal L, Steuer R, Cerveny J, Müller S (2013) A comprehensive web-based platform for domain-specific biological models. Electronic Notes in Theoretical Computer Science 299:61-67 Software Link
Kolodkin AN, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant NJ (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4:1792 Signaling Link
Kourdis PD, Goussis DA (2013) Glycolysis in Saccharomyces cerevisiae: Algorithmic exploration of robustness and origin of oscillations. Mathematical Biosciences 243:190-214 Theory Link
Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. Journal of Biological Chemistry 288:34729-34735 Enzymology Link
LeBaron R, Villareal G, Roberson DJ, Phelix CF (2013) Abstract 5224: Breast cancer biomarkers from biosimulations: transcriptome-to-reactome™ technology. Cancer Research 73:5224 Genomics Computational Method Link
Leroux AE, Haanstra JR, Bakker BM, Krauth-Siegel RL (2013) Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. Journal of Biological Chemistry 288:23751-23764 Metabolism Link
Levering J, Kummer U, Becker K, Sahle S (2013) Glycolytic oscillations in a model of a lactic acid bacterium metabolism. Biophysical Chemistry 172:53-60 Metabolism Link
Lv H, Rudd JA, Zhuk PF, Lee JY, Constable EC, Housecroft CE, Hill CL, Musaev DG, Geletii YV (2013) Bis (4'-(4-pyridyl)-2,2':6',2''-terpyridine)ruthenium (ii) complexes and their N-alkylated derivatives in catalytic light-driven water oxidation. RSC Advances 3:20647-20654 Chemistry Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (2013) Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Systems Biology 7:42 Computational Method Link
Mednis M, Vigants A (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information Technology 2:1-5 Computational Method Link
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Mensonides F, Bakker BM, Cremazy F, Messiha HL, Mendes P, Boogerd FC, Westerhoff HV (2013) A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters 587:2860-7 Metabolism Link
Miah F, Koliwer-Brandl H, Rejzek M, Field RA, Kalscheuer R, Bornemann S (2013) Flux through trehalose synthase flows from trehalose to the alpha anomer of maltose in mycobacteria. Chemical Biology 20:487-493 Metabolism Link
Mitchell S, Mendes P (2013) A Computational Model of Liver Iron Metabolism. PLoS Computational Biology 9:e1003299 Metabolism Link
Mozga I (2013) Determinition of best set of adjustable parameters with full search and limited search methods. Biosystems and Information Technology 2:11–14 Computational Method Link
Nim TH, White JK, Tucker-Kellogg L (2013) SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. Nucleic Acids Research 41:W187-191 Software Link
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Nägele T, Weckwerth W (2013) A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Frontiers in Plant Science 4:541 Metabolism Plant Biology Link
Palai T, Bhattacharya PK (2013) Kinetics of lactose conversion to galacto-oligosaccharides by beta-galactosidase immobilized on PVDF membrane. Journal of Bioscience and Bioengineering 115:668-673 Enzymology Link
Palaniappan SK (2013) Probabilistic verification and analysis of biopathway dynamics. Ph.D. Thesis School of Computing, National University of Singapore Computational Method Link
Penkler GP (2013) A kinetic model of glucose catabolism in Plasmodium falciparum. Ph.D. Thesis, Faculty of Science, University of Stellenbosch, South Africa Metabolism Link
Phelix CF, LeBaron R, Roberson DJ, Villareal G, Perry G (2013) Flux and metabolite pathway mapping in the aging and Alzheimer’s disease hippocampus. Alzheimer’s & Dementia 9:P346–P347 Metabolism Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2013) Molecular neural model recreates electrophysiology: Transcriptome-To-Physiome™ NeurobioSimulations using COPASI® software. Proceedings of the 2013 6th International IEEE/EMBS Conference on Neural Engineering (NER). San Diego, CA, 178–181 Physiology Link
Philipson CW, Bassaganya-Riera J, Hontecillas R (2013) Animal models of enteroaggregative Escherichia coli infection. Gut Microbes 4:281-291 Immunology Link
Proctor CJ, Boche D, Gray DA, Nicoll JAR (2013) Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS One 8:e73631 Macromolecular Biochemistry Link
Pun D, Diao T, Stahl SS (2013) Aerobic dehydrogenation of cyclohexanone to phenol catalyzed by Pd (TFA) 2/2-dimethylaminopyridine: Evidence for the role of Pd nanoparticles. Journal of the American Chemical Society 135:8213–8221 Chemistry Link
Qi Y-F, Huang Y-X, Wang H-Y, Zhang Y, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Zheng L-H, Sun Y, Wang G-N, Li Y-X (2013) Elucidating the crosstalk mechanism between IFN-gamma and IL-6 via mathematical modelling. BMC Bioinformatics 14:41 Signaling Link
Ravichandran S, Rao KVS, Jain S (2013) Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. Molecular BioSystems 9:2498-2511 Signaling Link
Reeves BD, Hilmer JK, Mellmann L, Hartzheim M, Poffenberger K, Johnson K, Joshi N, Singel DJ, Grieco PA (2013) Selective trapping of SNO-BSA and GSNO by benzenesulfinic acid sodium salt: mechanistic study of thiosulfonate formation and feasibility as a protein S-nitrosothiol detection strategy. Tetrahedron Letters 54:5707-10 Chemistry Link
Roberts E, Stone JE, Luthey-Schulten Z (2013) Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. Journal of Computational Chemistry 34:245-255 Computational Method Link
Rutkis R, Kalnenieks U, Stalidzans E, Fell DA (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology 159:2674-2689 Metabolism Microbiology Link
Saeidi N, Arshath M, Chang MW, Poh CL (2013) Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation. Chemical Engineering Science 103:91–99 Synthetic Biology Microbiology Link
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PAR, Hitzmann B, Ueffing M, Paquet-Durand F (2013) Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death & Disease 4:e488 Cell Biology Signaling Link
Sarma U, Gade PM, Saha B (2013) A mathematical model for dynamics of CD40 clustering. Systems and Synthetic Biology 7:197-208 Macromolecular Biochemistry Link
Schäuble S, Stavrum A-K, Puntervoll P, Schuster S, Heiland I (2013) Effect of substrate competition in kinetic models of metabolic networks. FEBS Letters 587:2818-2824 Metabolism Link
Scheller S, Goenrich M, Thauer RK, Jaun B (2013) Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M. Journal of the American Chemical Society 135:14985-14995 Chemistry Enzymology Link
Schokker D, Bannink A, Smits MA, Rebel JMJ (2013) A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue. Journal of Theoretical Biology 330:75–87 Immunology Link
Sharma V (2013) Language design for computational modeling, simulation, and visualization. Proceedings of the 2013 Winter Simulation Conference: Simulation: Making Decisions in a Complex World. Washington, D.C.: IEEE Press, 3934–3935 Computational Method Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Sharp GC (2013) Comprehensive data analysis to study parturition. Ph.D. Thesis, University of Edinburgh, UK. Signaling Link
Sharp GC, Ma H, Saunders PTK, Norman JE (2013) A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour. PLoS One 8:e70180 Signaling Link
Shemirani MI (2013) Construction of metabolic pathway of catecholamine from tyrosine in human fibroblast cell. Degree Project Thesis in Medicine, School of Medicine and Health Science, Orerbo University, Sweden Metabolism Link
Sheng X (2013) Evolutionary and Functional Aspects of Two-Component Signalling Systems. Ph.D. Thesis, Imperial College London, UK. Microbiology Link
Singh VK, Ghosh I (2013) Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Letters 587:2806-2817 Metabolism Link
Skvortsov A, Gray P (2013) A simple model for assessment of anti-toxin antibodies. BioMed Research International 2013:230906 Laboratory Method Link
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Letters 587:2832-41 Metabolism Link
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Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One 8:e79195 Computational Method Whole-Cell Models Link
Stavrum A-K, Heiland I, Schuster S, Puntervoll P, Ziegler M (2013) Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. Journal of Biological Chemistry 288:34555-34566 Metabolism Link
Sundin S, Dahlgren B, Roth O, Jonsson M (2013) H2O2 and radiation induced dissolution of UO2 and SIMFUEL in deficient aqueous solution. Journal of Nuclear Materials 443:291-297 Chemistry Link
Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013) Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics 29:223-9 Software Link
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91 publications
2012
Achcar F, Kerkhoven EJ, The SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R (2012) Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLoS Computational Biology 8:e1002352 Metabolism Link
Adamczyk M, Westerhoff HV (2012) Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal 7:877-883 Metabolism Microbiology Link
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. Journal of Biological Rhythms 27:328–332 Computational Method Link
Adiamah DA, Schwartz J-M (2012) Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations. Metabolites 2:382-397 Metabolism Whole-Cell Models Link
Altintaş CM, Ertas G, Kayali HA (2012) Simulation of Microbial Production of Ramoplanin via Stoichiometric Modeling from Actinoplanes sp. ATCC 33076. New Biotechnology 29:S144–S145 Microbiology Biotechnology Link
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I (2012) Regulation of release factor expression using a translational negative feedback loop: A systems analysis. RNA 18:2320-2334 Signaling Link
Biswas S, Huang Z, Choliy Y, Wang DY, Brookhart M, Krogh-Jespersen K, Goldman AS (2012) Olefin Isomerization by Iridium Pincer Catalysts. Experimental Evidence for an η 3 -Allyl Pathway and an Unconventional Mechanism Predicted by DFT Calculations. Journal of the American Chemical Society 134:13276-13295 Chemistry Link
Bodenstein C, Heiland I, Schuster S (2012) Temperature compensation and entrainment in circadian rhythms. Physical Biology 9:036011 Theory Link
Bortolussi L, Policriti A (2012) Studying cancer-cell populations by programmable models of networks. Network Modeling Analysis in Health Informatics and Bioinformatics 1:117-133 Cell Biology Link
Burés J, Armstrong A, Blackmond DG (2012) Curtin-Hammett Paradigm for Stereocontrol in Organocatalysis by Diarylprolinol Ether Catalysts. Journal of the American Chemical Society 134:6741-6750 Chemistry Link
Challenger JD, McKane AJ, Pahle J (2012) Multi-compartment linear noise approximation. Journal of Statistical Mechanics: Theory and Experiment 2012:P11010 Computational Method Link
Chang J-Y, Chantrathammachart P, Monroe DM, Key NS (2012) Studies on the mechanism of action of the aptamer BAX499, an Inhibitor of tissue factor pathway inhibitor. Thrombosis Research 130:e151-e157 Macromolecular Biochemistry Link
Chua HE, Bhowmick SS, Tucker-Kellogg L, Forbes Dewey C (2012) STEROID: in silico heuristic target combination identification for disease-related signaling networks. Proceedings of the 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine BCB'12 pp. 4-11 Computational Method Link
Criquet J, Allard S, Salhi E, Joll CA, Heitz A, von Gunten U (2012) Iodate and Iodo-Trihalomethane Formation during Chlorination of Iodide-Containing Waters: Role of Bromide. Environmental Science & Technology 46:7350-7357 Chemistry Environmental Sciences Link
Cristovao M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P (2012) Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Research 40:5448-5464 Genomics Link
Czeizler E, Mizera A, Czeizler E, Back R-J, Eriksson JE, Petre I (2012) Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:885-898 Cell Biology Link
Dada JO, Mendes P (2012) ManyCell: A Multiscale Simulator for Cellular Systems. (Gilbert D and Heiner M eds.) Computational Methods in Systems Biology. Berlin, Heidelberg: Springer Berlin Heidelberg, 366-369. Software Link
Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Godel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K (2012) A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation. Science Signaling 5:ra25-ra25 Signaling Link
Davies O, Mendes P, Smallbone K, Malys N (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB reports 45:259-264 Enzymology Metabolism Link
Ding K, Miranda MO, Moscato-Goodpaster B, Ajellal N, Breyfogle LE, Hermes ED, Schaller CP, Roe SE, Cramer CJ, Hillmyer MA, Tolman WB (2012) Roles of Monomer Binding and Alkoxide Nucleophilicity in Aluminum-Catalyzed Polymerization of ε-Caprolactone. Macromolecules 45:5387-5396 Chemistry Link
Friedrich LC, Mendes MA, Silva VO, Zanta CLPS, Machulek Jr. A, Quina FH (2012) Mechanistic implications of zinc(II) ions on the degradation of phenol by the fenton reaction. Journal of the Brazilian Chemical Society 23:1372-1377 Chemistry Link
Gatti DL (2012) Biapenem Inactivation by B2 Metallo β-Lactamases: Energy Landscape of the Post-Hydrolysis Reactions. PLoS One 7:e30079 Enzymology Link
Gebhard LG, Kaufman SB, Gamarnik AV (2012) Novel ATP-Independent RNA Annealing Activity of the Dengue Virus NS3 Helicase. PLoS One 7:e36244 Enzymology Link
Georgoulas A, Clark A, Ocone A, Gilmore S, Sanguinetti G (2012) A subsystems approach for parameter estimation of ODE models of hybrid systems. Electronic Proceedings in Theoretical Computer Science 92:30-41 Computational Method Link
Guo C, Gow C-H, Li Y, Gardner A, Khan S, Zhang J (2012) Regulated Clearance of Histone Deacetylase 3 Protects Independent Formation of Nuclear Receptor Corepressor Complexes. Journal of Biological Chemistry 287:12111-12120 Enzymology Link
Hamberg A, Maurer S, Hult K (2012) Rational engineering of Candida antarctica lipase B for selective monoacylation of diols. Chemical Communications 48:10013 Biochemistry Link
Heiland I, Bodenstein C, Hinze T, Weisheit O, Ebenhoeh O, Mittag M, Schuster S (2012) Modeling temperature entrainment of circadian clocks using the Arrhenius equation and a reconstructed model from Chlamydomonas reinhardtii. Journal of Biological Physics 38:449-464 Signaling Link
Hoffman-Sommer M (2012) Cell-to-cell communication circuits: quantitative analysis of synthetic logic gates. Frontiers in Physiology 3:287 Synthetic Biology Link
Holcombe M, Adra S, Bicak M, Chin S, Coakley S, Graham AI, Green J, Greenough C, Jackson D, Kiran M, MacNeil S, Maleki-Dizaji A, McMinn P, Pogson M, Poole R, Qwarnstrom E, Ratnieks F, Rolfe MD, Smallwood R, Sun T, Worth D (2012) Modelling complex biological systems using an agent-based approach. Integrative Biology 4:53–64 Computational Method Link
Hultqvist G, Punekar AS, Morrone A, Chi CN, Engström Å, Selmer M, Gianni S, Jemth P (2012) Tolerance of Protein Folding to a Circular Permutation in a PDZ Domain. PLoS One 7:e50055 Enzymology Link
Jozefczuk J, Kashofer K, Ummanni R, Henjes F, Rehman S, Geenen S, Wruck W, Regenbrecht C, Daskalaki A, Wierling C, Turano P, Bertini I, Korf U, Zatloukal K, Westerhoff HV, Lehrach H, Adjaye J (2012) A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. Frontiers in Physiology 3:339 Metabolism Link
Kent E, Hoops S, Mendes P (2012) Condor-COPASI: high-throughput computing for biochemical networks. BMC Systems Biology 6:91 Software Link
Kim B, Eggel A, Tarchevskaya SS, Vogel M, Prinz H, Jardetzky TS (2012) Accelerated disassembly of IgE-receptor complexes by a disruptive macromolecular inhibitor. Nature 491:613-617 Immunology Link
Kleessen S, Nikoloski Z (2012) Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6:16 Computational Method Plant Biology Metabolism Link
Kloster A, Olsen LF (2012) Oscillations in glycolysis in Saccharomyces cerevisiae: the role of autocatalysis and intracellular ATPase activity. Biophysical Chemistry 165–166:39–47 Metabolism Link
Kostromins A, Mozga I, Stalidzans E (2012) ConvAn: A convergence analyzing tool for optimization of biochemical networks. BioSystems 108:73-77 Software Computational Method Link
Koval OM, Snyder JS, Wolf RM, Pavlovicz RE, Glynn P, Curran J, Leymaster ND, Dun W, Wright PJ, Cardona N, Qian L, Mitchell CC, Boyden PA, Binkley PF, Li C, Anderson ME, Mohler PJ, Hund TJ (2012) Ca2+/calmodulin-dependent protein kinase II-based regulation of voltage-gated Na+ channel in cardiac disease. Circulation 126:2084–2094 Physiology Signaling Link
Kowald A, Hamann A, Zintel S, Ullrich S, Klipp E, Osiewacz HD (2012) A systems biological analysis links ROS metabolism to mitochondrial protein quality control. Mechanisms of Ageing and Development 133:331-337 Cell Biology Link
Kraut DA, Israeli E, Schrader EK, Patil A, Nakai K, Nanavati D, Inobe T, Matouschek A (2012) Sequence- and Species-Dependence of Proteasomal Processivity. ACS Chemical Biology 7:1444–1453 Biochemistry Macromolecular Biochemistry Link
Leach MD, Tyc KM, Brown AJP, Klipp E (2012) Modelling the Regulation of Thermal Adaptation in Candida albicans, a Major Fungal Pathogen of Humans. PLoS One 7:e32467 Signaling Link
Krey T, Bontems F, Vonrhein C, Vaney M-C, Bricogne G, Rümenapf T, Rey FA (2012) Crystal structure of the pestivirus envelope glycoprotein E(rns) and mechanistic analysis of its ribonuclease activity. Structure 20:862–873 Biochemistry Link
Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B (2012) Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach: Modelling glycolysis of lactic acid bacteria. FEBS Journal 279:1274-1290 Metabolism Link
Li Y, Wang M, Carra C, Cucinotta FA (2012) Modularized Smad-regulated TGFβ signaling pathway. Mathematical Biosciences 240:187-200 Signaling Link
Lindner C (2012) Phosphane in der Organokatalyse: experimentelle und theoretische Studien. Ph.D. Thesis, Ludwig-Maximilians University Munich, Germany. Chemistry Link
Maiwald T (2012) Computational Analysis of The Interferon Alpha Signalling Using a Systems Biology Modelling Approach Pathway. Ph.D. Thesis, Heidelberg University, Germany. Signaling Link
Mayorga LS, Lopez MJ, Becker WM (2012) Molecular Thermodynamics for Cell Biology as Taught with Boxes. Cell Biology Education 11:31-38 Cell Biology Education Link
Mazemondet O, John M, Leye S, Rolfs A, Uhrmacher AM (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS One 7:e42792 Signaling Link
McAuley MT, Wilkinson DJ, Jones JJ, Kirkwood TBL (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link
Micheau J-C, Coudret C, Cruz J-M, Buhse T (2012) Amplification of enantiomeric excess, mirror-image symmetry breaking and kinetic proofreading in Soai reaction models with different oligomeric orders. Physical Chemistry Chemical Physics 14:13239 Chemistry Link
Monge ME, Rosenorn T, Favez O, Muller M, Adler G, Abo Riziq A, Rudich Y, Herrmann H, George C, D’Anna B (2012) Alternative pathway for atmospheric particles growth. Proceedings of the National Academy of Sciences USA 109:6840-6844 Chemistry Link
Moscato BM, Zhu B, Landis CR (2012) Mechanistic Investigations into the Behavior of a Labeled Zirconocene Polymerization Catalyst. Organometallics 31:2097-2107 Chemistry Link
Muntean N, Thuy LB, Kály-Kullai K, Wittmann M, Noszticzius Z, Onel L, Furrow SD (2012) Measurement of Hypoiodous Acid Concentration by a Novel Type Iodide Selective Electrode and a New Method To Prepare HOI. Monitoring HOI Levels in the Briggs-Rauscher Oscillatory Reaction. Journal of Physical Chemistry 116:6630-6642 Chemistry Link
Olin-Sandoval V, González-Chávez Z, Berzunza-Cruz M, Martínez I, Jasso-Chávez R, Becker I, Espinoza B, Moreno-Sánchez R, Saavedra E (2012) Drug target validation of the trypanothione pathway enzymes through metabolic modelling: Kinetic modelling of trypanothione metabolism. FEBS Journal 279:1811-1833 Metabolism Link
Pahle J, Challenger JD, Mendes P, McKane AJ (2012) Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6:86 Computational Method Software Link
Palai T, Mitra S, Bhattacharya PK (2012) Kinetics and design relation for enzymatic conversion of lactose into galacto-oligosaccharides using commercial grade β-galactosidase. Journal of Bioscience and Bioengineering 114:418-423 Metabolism Link
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Phelix CF, Villareal G, Perez-Cordova M, Hernandez S, Perry G, Colom L (2012) P3-395: Reanimating basal forebrain cholinergic neurons in electrophysiology biosimulations using COPASI software. Alzheimer’s & Dementia 8:P593–P594 Physiology Biophysics Link
Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D’Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K (2012) A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Frontiers in Physiology 3:466 Signaling Link
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Ray JCJ, Igoshin OA (2012) Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLoS Computational Biology 8:e1002672 Microbiology Genetics Link
Reyes-Palomares A, Montañez R, Sánchez-Jiménez F, Medina MÁ (2012) A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability. Amino Acids 42:597–610 Metabolism Link
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Sarma U, Ghosh I (2012) Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC Systems Biology 6:82 Signaling Link
Sarma U, Ghosh I (2012) Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Research Notes 5:287 Signaling Link
Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B (2012) Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases. PLoS One 7:e39898 Signaling Link
Schaber J (2012) Easy parameter identifiability analysis with COPASI. BioSystems 110:183-185 Computational Method Link
Schaber J, Baltanas R, Bush A, Klipp E, Colman-Lerner A (2012) Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast. Molecular Systems Biology 8:622 Signaling Link
Schimek C, Vlaic S, Wöstemeyer J, Werner S, Schuster S, Schroeter A (2012) Model of the synthesis of trisporic acid in Mucorales showing bistability. IET Systems Biology 6:207-214 Signaling Link
Singh VK, Das K, Seshadri K (2012) Kinetic Modelling of GlmU Reactions - Prioritization of Reaction for Therapeutic Application. PLoS One 7:e43969 Metabolism Link
Stalidzans E, Kostromins A, Sulins J (2012) Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. 13th IEEE International Symposium on Computational Intelligence and Informatics (CINTI 2012), IEEE, 365–369 Computational Method Link
Stefan MI, Marshall DP, Le Novère N (2012) Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII. PLoS One 7:e29406 Enzymology Link
Steinacher A, Leyser O, Clayton RH (2012) A computational model of auxin and pH dynamics in a single plant cell. Journal of Theoretical Biology 296:84-94 Cell Biology Link
Sulins J, Mednis M (2012) Automatic termination of parallel optimization runs of stochastic global optimization methods in consensus or stagnation cases. Biosystems and Information Technology 1:1-5 Software Computational Method Link
Surovtsova I, Simus N, Hübner K, Sahle S, Kummer U (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Systems Biology 6:14 Software Computational Method Link
Tagore S, De RK (2012) SAGPAR: Structural Grammar-based automated pathway reconstruction. Interdisciplinary Sciences: Computational Life Sciences 4:116-127 Software Computational Method Link
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Usuyama M, Ushida C, Shingai R (2012) A model of the intracellular response of an olfactory neuron in Caenorhabditis elegans to odor stimulation. PLoS One 7:e42907 Signaling Link
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Warren PB, Allen RJ (2012) Steady-state parameter sensitivity in stochastic modeling via trajectory reweighting. Journal of Chemical Physics 136:104106 Computational Method Link
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86 publications
2011
Baez M, Wilson CA, Babul J (2011) Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. FEBS Letters 585:2158–2164 Macromolecular Biochemistry Link
Bairy S, Wong CF (2011) Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models. Proteins: Structure, Function, and Bioinformatics 79:2491–2504 Signaling Link
Baker SM, Poskar CH, Junker BH (2011) Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP Journal on Bioinformatics & Systems Biology 2011:7 Computational Method Link
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. Journal of Computational Biology 18:147-154 Laboratory Method Computational Method Link
Berestovsky N (2011) On the modeling of signaling networks with petri nets. MS Thesis, Rice University, Houston, Texas, USA. Computational Method Link
Casas A, Ramos MJ, Pérez Á (2011) Kinetics of chemical interesterification of sunflower oil with methyl acetate for biodiesel and triacetin production. Chemical Engineering Journal 171:1324–1332 Biotechnology Chemistry Link
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. Ph.D. Thesis, University of Washington, Seattle, USA. Software Synthetic Biology Link
Checkley S (2011) Engineering Tuneable Gene Circuits in Yeast. Ph.D. Thesis, University of Manchester, UK. Synthetic Biology Link
Chen X (2011) Glutathione suppresses the autoxidation of 2’,5’-dihydroxy-4-chlorobiphenyl. MS Thesis, University of Iowa, USA. Toxicology Link
Criquet J, Karpel Vel Leitner N (2011) Electron beam irradiation of aqueous solution of persulfate ions. Chemical Engineering Journal 169:258–262 Chemistry Link
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234 Signaling Microbiology Link
DasGupta B, Vera-Licona P, Sontag E (2011) Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors). John Wiley & Sons, Inc. Computational Method Link
Diao T, Stahl SS (2011) Synthesis of Cyclic Enones via Direct Palladium-Catalyzed Aerobic Dehydrogenation of Ketones. Journal of the American Chemical Society 133:14566–9 Chemistry Link
Fabrini R, Bocedi A, Dawood KF, Turella P, Stella L, Parker MW, Pedersen JZ, Federici G, Antonini G, Ricci G (2011) The extended catalysis of glutathione transferase. FEBS Letters 585:341–345 Enzymology Link
Fedosov SN, Xu X (2011) Enzymatic synthesis of biodiesel from fatty acids. Kinetics of the reaction measured by fluorescent response of Nile Red. Biochemical Engineering Journal 56:172–183 Biotechnology Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. Ph.D. Thesis, Heidelberg University, Germany Software Computational Method Link
Genc S, Kurnaz IA, Ozilgen M (2011) Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions-in silico study supported by in vitro expression data. BMC Systems Biology 5:162 Cell Biology Metabolism Link
Gerber S (2011) In silico modeling of cation homeostasis in Saccharomyces cerevisiae. Ph.D. Thesis, Humboldt-University of Berlin, Germany. Physiology Link
Hein JE, Armstrong A, Blackmond DG (2011) Kinetic profiling of prolinate-catalyzed α-amination of aldehydes. Organic Letters 13:4300–4303 Chemistry Link
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS (2011) Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. Journal of Physical Chemistry 115:4474–4483 Enzymology Link
Hinze T, Schumann M, Bodenstein C, Heiland I, Schuster S (2011) Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems. Computational Intelligence and Neuroscience 2011:1–9 Theory Link
Hoffman-Sommer M, Supady A, Klipp E (2011) Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates. Frontiers in Physiology 3:287–287 Synthetic Biology Link
Hooshangi S, Bentley WE (2011) LsrR quorum sensing “switch” is revealed by a bottom-up approach. PLoS Computational Biology 7:e1002172 Microbiology Signaling Link
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S (2011) The IkB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nature Immunology 12:1167-75 Immunology Signaling Link
Izawa Y, Pun D, Stahl SS (2011) Palladium-Catalyzed Aerobic Dehydrogenation of Substituted Cyclohexanones to Phenols. Science 333:209-213 Chemistry Link
Jablonsky J, Bauwe H, Wolkenhauer O (2011) Modeling the Calvin-Benson cycle. BMC Systems Biology 5:185 Metabolism Plant Biology Link
Johnson KRD, Hayes PG (2011) Kinetic and Mechanistic Investigation of Metallacycle Ring Opening in an Ortho-Metalated Lutetium Aryl Complex. Organometallics 30:58–67 Chemistry Link
Keitz BK, Grubbs RH (2011) Probing the origin of degenerate metathesis selectivity via characterization and dynamics of ruthenacyclobutanes containing variable NHCs. Journal of the American Chemical Society 133:16277-16284 Chemistry Link
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology 22:713–719 Signaling Metabolism Link
Klotz C, Ziegler T, Figueiredo AS, Rausch S, Hepworth MR, Obsivac N, Sers C, Lang R, Hammerstein P, Lucius R, Hartmann S (2011) A Helminth Immunomodulator Exploits Host Signaling Events to Regulate Cytokine Production in Macrophages. PLoS Pathogens 7:e1001248 Immunology Link
Koh G, Hsu D, Thiagarajan PS (2011) Component-based construction of bio-pathway models: The parameter estimation problem. Theoretical Computer Science 412:2840–2853 Computational Method Link
Koh G, Lee D-Y (2011) Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators. Computers in Biology and Medicine 41:512–528 Signaling Link
Kolodkin AN (2011) Emergence of design. Ph.D. Thesis, Vrije Universiteit Amsterdam, The Netherlands. Theory Metabolism Link
Lauro FM, DeMaere MZ, Yau S, Brown MV, Ng C, Wilkins D, Raftery MJ, Gibson JAE, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Thomas T, Cavicchioli R (2011) An integrative study of a meromictic lake ecosystem in Antarctica. ISME Journal 5:879-95 Ecology Link
Le Roux J, Gallard H, Croué J-P (2011) Chloramination of nitrogenous contaminants (pharmaceuticals and pesticides): NDMA and halogenated DBPs formation. Water Research 45:3164–3174 Environmental Sciences Chemistry Link
Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology 7:514 Genomics Link
Li Y, Cucinotta FA (2011) Modeling non-homologous end joining. Journal of Theoretical Biology 283:122–135 Genetics Theory Macromolecular Biochemistry Link
Liu B, Hsu D, Thiagarajan PS (2011) Probabilistic approximations of ODEs based bio-pathway dynamics. Theoretical Computer Science 412:2188–2206 Theory Link
Liu B, Zhang J, Tan PY, Hsu D, Blom AM, Leong B, Sethi S, Ho B, Ding JL, Thiagarajan PS (2011) A computational and experimental study of the regulatory mechanisms of the complement system. PLoS Computational Biology 7:e1001059 Immunology Signaling Link
Marchisio MA, Stelling J (2011) Automatic Design of Digital Synthetic Gene Circuits. PLoS Computational Biology 7:e1001083 Synthetic Biology Link
Matuszak Z (2011) Photodynamic therapy of melanoma. Monte Carlo modeling of light transport in human pigmented skin. Bio Algorithms Med Syst. 7:85–93 Biophysics Link
Mauch S, Stalzer M (2011) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:27-35 Computational Method Link
Mozga I, Stalidzans E (2011) Convergence dynamics of biochemical models to the global optimum. Paper presented at the 2011 E-Health and Bioengineering Conference (EHB). IEEE: Iaşi, Romania, 1–4 Computational Method Metabolism Link
Oh E, Lu M, Park C, Park C, Oh HB, Lee SY, Lee J (2011) Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis. Journal of Microbiology and Biotechnology 21:162–169 Microbiology Metabolism Link
Proctor CJ, Lorimer IAJ (2011) Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis. PLoS One 6:e22038 Macromolecular Biochemistry Link
Qian L, Winfree E (2011) A simple DNA gate motif for synthesizing large-scale circuits. Journal of the Royal Society Interface 8:1281-97 Synthetic Biology Link
Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201 Synthetic Biology Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS One 6:e21925 Cell Biology Macromolecular Biochemistry Link
Schaber J, Flöttmann M, Li J, Tiger C-F, Hohmann S, Klipp E (2011) Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PLoS One 6:e14791 Signaling Computational Method Software Link
Schweizer N (2011) Calcium signaling in fish cells. Ph.D. Thesis, University of Heidelberg, Germany. Signaling Link
Schweizer N, Kummer U, Hercht H, Braunbeck T (2011) Amplitude-encoded calcium oscillations in fish cells. Biophysical Chemistry 159:294–302 Signaling Link
Shivanandan A (2011) Stochastic modelling and identification of arabinose uptake network in Escherichia coli (PDF Download Available). MS Thesis, Université Joseph Fourier, Grenoble, France. Metabolism Microbiology Link
Sorokina O, Corellou F, Dauvillée D, Sorokin A, Goryanin I, Ball S, Bouget F-Y, Millar AJ (2011) Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC Systems Biology 5:36 Metabolism Link
Tsaloglou M-N, Attard GS, Dymond MK (2011) The effect of lipids on the enzymatic activity of 6-phosphofructo-1-kinase from B. stearothermophilus. Chemistry and Physics of Lipids 164:713–721 Enzymology Metabolism Microbiology Link
Waltemath D, Adams RR, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru II, Nickerson DP, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N (2011) Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology 7:e1001122 Computational Method Link
Wendelsdorf K (2011) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis. Ph.D. Thesis, Virginia Tech, USA. Immunology Link
Yang J (2011) Midazolam as a Probe Drug to Study Cytochrome P450 3A Allosterism. Ph.D. Thesis, University of Washington, Seattle, USA. Enzymology Pharmacology Link
Yao G, Tan C, West M, Nevins JR, You L (2011) Origin of bistability underlying mammalian cell cycle entry. Molecular Systems Biology 7:485 Cell Biology Link

58 publications
2010
Adra S, Sun T, MacNeil S, Holcombe M, Smallwood R (2010) Development of a Three Dimensional Multiscale Computational Model of the Human Epidermis. PLoS One 5:e8511. Physiology Link
Andreani A, Burnelli S, Granaiola M, Leoni A, Locatelli A, Morigi R, Rambaldi M, Varoli L, Cremonini MA, Placucci G (2010) New isatin derivatives with antioxidant activity. European Journal of Medicinal Chemistry 45:1374–1378 Chemistry Link
Baker SM, Schallau K, Junker BH (2010) Comparison of different algorithms for simultaneous estimation of multiple parameters in kinetic metabolic models. Journal of Integrative Bioinformatics 7:519-520 Computational Method Link
Brasen JC, Barington T, Olsen LF (2010) On the mechanism of oscillations in neutrophils. Biophysical Chemistry 148:82-92 Cell Biology Link
Chi CN, Bach A, Gottschalk M, Kristensen AS, Stromgaard K, Jemth P (2010) Deciphering the Kinetic Binding Mechanism of Dimeric Ligands Using a Potent Plasma-stable Dimeric Inhibitor of Postsynaptic Density Protein-95 as an Example. Journal of Biological Chemistry 285:28252–28260 Macromolecular Biochemistry Link
Christianson MD, Tan EHP, Landis CR (2010) Stopped-Flow NMR: Determining the Kinetics of [ rac -(C 2 H 4 (1-indenyl) 2 )ZrMe][MeB(C 6 F 5 ) 3 ]-Catalyzed Polymerization of 1-Hexene by Direct Observation. Journal of the American Chemical Society 132:11461–11463 Chemistry Link
Colby DA, Bergman RG, Ellman JA (2010) Rhodium-Catalyzed C−C Bond Formation via Heteroatom-Directed C−H Bond Activation. Chemical Reviews 110:624–655 Link
Costa RS, Machado D, Ferreira EC, Rocha I (2010) Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments. IFAC Proceedings Volumes 43:114–119 Computational Method Metabolism Link
Costa RS, Machado D, Rocha I, Ferreira EC (2010) Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. BioSystems 100:150–157 Metabolism Microbiology Link
Dada JO, Spasić I, Paton NW, Mendes P (2010) SBRML: a markup language for associating systems biology data with models. Bioinformatics 26:932–938 Computational Method Link
Degasperi A, Calder M (2010) Relating PDEs in Cylindrical Coordinates and CTMCs with Levels of Concentration. Electronic Notes in Theoretical Computer Science 268:49–59 Computational Method Link
Dimitrova E, Vera-Licona P, McGee J, Laubenbacher R (2010) Discretization of Time Series Data. Journal of Computational Biology 17:853-68. Computational Method Link
Escuela G, Hinze T, Dittrich P, Schuster S, Moreno-Alvarez M (2010) Modelling Modified Atmosphere Packaging for Fruits and Vegetables using Membrane Systems. In Fred A, Filipe J Gamboa H. (Eds.), Proc. 3rd International Conference on Bio-inspired Systems and Signal Processing BIOSIGNALS 2010, pp. 306-311, INSTICC press Computational Method Biotechnology Link
Flach EH, Schnell S (2010) Stability of open pathways. Mathematical Biosciences 228:147–152 Theory Metabolism Link
Fujita KA, Toyoshima Y, Uda S, Ozaki Y, Kubota H, Kuroda S (2010) Decoupling of Receptor and Downstream Signals in the Akt Pathway by Its Low-Pass Filter Characteristics. Science Signaling 3:ra56-ra56 Signaling Link
Funahashi A, Matsuoka Y, Jouraku A, Takizawa H, Hiroi NF, Ghosh S, Kikuchi N, Kitano H (2010) 細胞シミュレータCellDesignerの設計と実装. Journal of The Society of Instrument and Control Engineers 49:531–536 Software Link
Furrow SD, Aurentz DJ (2010) Reactions of Iodomalonic Acid, Diiodomalonic Acid, and Other Organics in the Briggs−Rauscher Oscillating System. Journal of Physical Chemistry 114:2526–2533 Chemistry Link
Hallinan JS, Misirli G, Wipat A (2010) Evolutionary computation for the design of a stochastic switch for synthetic genetic circuits. Proceedings of the 2010 Annual International Conference of the IEEE Engineering in Medicine and Biology 768–774 Synthetic Biology Link
Hill MP, Carroll EC, Vang MC, Addington TA, Toney MD, Larsen DS (2010) Light-Enhanced Catalysis by Pyridoxal Phosphate-Dependent Aspartate Aminotransferase. Journal of the American Chemical Society 132:16953–16961 Enzymology Link
Huang R, Grabarek Z, Wang C-LA (2010) Differential effects of caldesmon on the intermediate conformational states of polymerizing actin. Journal of Biological Chemistry 285:71-79 Macromolecular Biochemistry Link
Iadevaia S, Lu Y, Morales FC, Mills GB, Ram PT (2010) Identification of optimal drug combinations targeting cellular networks: integrating phospho-proteomics and computational network analysis. Cancer Research 70:6704–6714 Signaling Pharmacology Link
Koh G, Hsu D, Thiagarajan PS (2010) Incremental Signaling Pathway Modeling by Data Integration. In: Berger B (ed) Research in Computational Molecular Biology. Springer: Berlin, Heidelberg, 281–296 Computational Method Signaling Link
Li P, Dada JO, Jameson D, Spasić I, Swainston N, Carroll KM, Dunn WB, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder CL, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11:582 Computational Method Metabolism Link
Liu J, Mehdi S, Topping J, Tarkowski P, Lindsey K (2010) Modelling and experimental analysis of hormonal crosstalk in Arabidopsis. Molecular Systems Biology 6:373 Signaling Plant Biology Link
Maiwald T, Schneider A, Busch H, Sahle S, Gretz N, Weiss TS, Kummer U, Klingmüller U (2010) Combining theoretical analysis and experimental data generation reveals IRF9 as a crucial factor for accelerating interferon α-induced early antiviral signalling: IRF9 accelerates IFNα signal transduction. FEBS Journal 277:4741-4754 Signaling Link
Mazza T, Iaccarino G, Priami C (2010) Snazer: the simulations and networks analyzer. BMC Systems Biology 4:1 Computational Method Software Link
Mellor N, Bligh F, Chandler I, Hodgman C (2010) Reduction of Off-Flavor Generation in Soybean Homogenates: A Mathematical Model. Journal of Food Science 75:R131–R138 Metabolism Biotechnology Link
Mizera A, Gambin B (2010) Stochastic modelling of the eukaryotic heat shock response. Journal of Theoretical Biology 265:455–466 Biochemistry Link
Morrissey ER, Juarez MA, Denby KJ, Burroughs NJ (2010) On reverse engineering of gene interaction networks using time course data with repeated measurements. Bioinformatics 26:2305–2312 Computational Method Link
Nakano T, Doi T, Yoshimoto J, Doya K (2010) A Kinetic Model of Dopamine- and Calcium-Dependent Striatal Synaptic Plasticity. PLoS Computational Biology 6:e1000670. Physiology Link
Orrillo AG, Furlan RLE (2010) Supramolecular Interactions between Library Members Modulate the Behavior of Dynamic Combinatorial Libraries. Journal of Organic Chemistry 75:211–214 Chemistry Link
Pezzola S, Antonini G, Geroni C, Beria I, Colombo M, Broggini M, Mongelli N, Leboffe L, MacArthur R, Mozzi AF, Federici G, Caccuri AM (2010) Role of Glutathione Transferases in the Mechanism of Brostallicin Activation. Biochemistry 49:226–235 Enzymology Link
Piedrafita G, Montero F, Morán F, Cárdenas ML, Cornish-Bowden A (2010) A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability. PLoS Computational Biology 6:e1000872 Metabolism Theory Link
Quaranta M (2010) Mechanistic study of asymmetric amplification in the Soai autocatalytic reaction. Ph.D. Thesis, Imperial College London, UK Chemistry Link
Samorodnitsky E, Pugh BF (2010) Genome-Wide Modeling of Transcription Preinitiation Complex Disassembly Mechanisms using ChIP-chip Data. PLoS Computational Biology 6:e1000733 Macromolecular Biochemistry Genomics Link
Smallbone K, Simeonidis E, Swainston N, Mendes P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology 4:6 Genomics Whole-Cell Models Metabolism Link
Smith GR, Shanley DP (2010) Modelling the Response of FOXO Transcription Factors to Multiple Post-Translational Modifications Made by Ageing-Related Signalling Pathways. PLoS One 5:e11092 Signaling Genetics Link
Swainston N, Jameson D, Li P, Spasić I, Mendes P, Paton NW (2010) Integrative information management for systems biology. Lecture Notes in Computer Science 6254:164–178 Computational Method Link
Tiwari A, Balázsi G, Gennaro ML, Igoshin OA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Physical Biology 7:36005 Microbiology Genetics Link
Watkins AL, Landis CR (2010) Origin of Pressure Effects on Regioselectivity and Enantioselectivity in the Rhodium-Catalyzed Hydroformylation of Styrene with ( S , S , S )-BisDiazaphos. Journal of the American Chemical Society 132:10306–10317 Chemistry Link
Wendelsdorf K, Bassaganya-Riera J, Hontecillas R, Eubank S (2010) Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease. Journal of Theoretical Biology 264:1225-1239 Immunology Link
Yao G, Tan C, West M, Nevins JR, You L (2010) A Minimal Gene Circuit Underlying the Bistable Cell Cycle Entry. Citeseer Preprint Synthetic Biology Link
Zhang R, Monsma F (2010) Binding kinetics and mechanism of action: toward the discovery and development of better and best in class drugs. Expert Opinion on Drug Discovery 5:1023–1029 Enzymology Pharmacology Link
Zhang Y, Song D, Lanni LM, Shimizu KD (2010) Importance of Functional Monomer Dimerization in the Molecular Imprinting Process. Macromolecules 43:6284–6294 Chemistry Link

44 publications
2009
Baralla A, Mentzen WI, De La Fuente A (2009) Inferring Gene Networks: Dream or Nightmare?: Part 1: Challenges 1 and 3. Annals of the New York Academy of Sciences 1158:246-256 Computational Method Link
Bauer-Mehren A, Furlong LI, Rautschka M, Sanz F (2009) From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways. BMC Bioinformatics 10:S6 Signaling Link
Blaquiere N, Shore DG, Rousseaux S, Fagnou K (2009) Decarboxylative Ketone Aldol Reactions: Development and Mechanistic Evaluation under Metal-Free Conditions. Journal of Organic Chemistry 74:6190–6198 Chemistry Link
Cai Y, Lux MW, Adam L, Peccoud J (2009) Modeling Structure-Function Relationships in Synthetic DNA Sequences using Attribute Grammars. PLoS Computational Biology 5:e1000529 Synthetic Biology Computational Method Laboratory Method Link
Chu C-F (2009) Computational characterization of the role of antioxidant potential in the tonifying mechanism of Yang-invigorating Chinese tonifying herbs. Masters Thesis, National Chiao Tung University, Taiwan, Republic of China Biochemistry Link
Cimetière N, Dossier-Berne F, De Laat J (2009) Monochloramination of Resorcinol: Mechanism and Kinetic Modeling. Environmental Science & Technology 43:9380–9385 Chemistry Environmental Sciences Link
Criquet J, Leitner NKV (2009) Degradation of acetic acid with sulfate radical generated by persulfate ions photolysis. Chemosphere 77:194–200 Chemistry Environmental Sciences Link
Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R (2009) Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Molecular Systems Biology 5:271 Metabolism Link
Dell’Acqua G, Castiglione F (2009) Stability and phase transitions in a mathematical model of Duchenne muscular dystrophy. Journal of Theoretical Biology 260:283–289 Immunology Link
Figueiredo AS, Höfer T, Klotz C, Sers C, Hartmann S, Lucius R, Hammerstein P (2009) Modelling and simulating interleukin-10 production and regulation by macrophages after stimulation with an immunomodulator of parasitic nematodes: Modelling interleukin-10 production and regulation. FEBS Journal 276:3454-3469 Signaling Link
Friedrich A, Ghosh R, Kolb R, Herdtweck E, Schneider S (2009) Iridium Olefin Complexes Bearing Dialkylamino/amido PNP Pincer Ligands: Synthesis, Reactivity, and Solution Dynamics. Organometallics 28:708-718 Biochemistry Link
Gallagher SS, Sable JE, Sheetz MP, Cornish VW (2009) An In Vivo Covalent TMP-Tag Based on Proximity-Induced Reactivity. ACS Chemical Biology 4:547-56 Laboratory Method Link
Goyal M, Rizzo M, Schumacher F, Wong CF (2009) Beyond thermodynamics: drug binding kinetics could influence epidermal growth factor signaling. Journal of Medicinal Chemistry 52:5582-5585 Signaling Link
Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV (2009) A general map of iron metabolism and tissue-specific subnetworks. Molecular BioSystems 5:422 Metabolism Link
Ibrahim B, Schmitt E, Dittrich P, Diekmann S (2009) In silico study of kinetochore control, amplification, and inhibition effects in MCC assembly. BioSystems 95:35-50 Signaling Link
Jain P, Bhalla US (2009) Signaling Logic of Activity-Triggered Dendritic Protein Synthesis: An mTOR Gate But Not a Feedback Switch. PLoS Computational Biology 5:e1000287 Signaling Link
Katzberg M, Wechler K, Müller M, Dünkelmann P, Stohrer J, Hummel W, Bertau M (2009). Biocatalytical production of (5S)-hydroxy-2-hexanone. Organic & Biomolecular Chemistry 7:304-314 Biochemistry Link
Knoke B, Textor S, Gershenzon J, Schuster S (2009) Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves. Phytochemistry Reviews 8:39-51 Metabolism Link
Kona F, Tao P, Martin P, Xu X, Gatti DL (2009) Electronic Structure of the Metal Center in the Cd 2+ , Zn 2+ , and Cu 2+ Substituted Forms of KDO8P Synthase: Implications for Catalysis. Biochemistry 48:3610–3630 Enzymology Biochemistry Link
Kovács K, Hurst LD, Papp B (2009) Stochasticity in Protein Levels Drives Colinearity of Gene Order in Metabolic Operons of Escherichia coli. PLoS Biology 7:e1000115 Genetics Link
Liu J, Brazier-Hicks M, Edwards R (2009) A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana. Biophysical Chemistry 143:85–94 Metabolism Link
Ma H, Boogerd FC, Goryanin I (2009) Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. Journal of Biotechnology 144:175–183 Metabolism Microbiology Link
Magarkar A, Banerji A, Kolhi S (2009) Quantification of Biological Robustness at the Systemic Level. arXiv preprint arXiv:0903.4844 Theory Link
Mellmann L (2009) Exogenous ligand effects on S-nitrosohemoglobin formation in reactions of methemoglobin with nitric oxide. Ph.D. Thesis Montana State University-Bozeman, USA Chemistry Link
Mendes P, Messiha HL, Malys N, Hoops S (2009) Enzyme Kinetics and Computational Modeling for Systems Biology. Methods in Enzymology 467:583–599 Enzymology Computational Method Link
Menolascina F, Bellomo D, Maiwald T, Bevilacqua V, Ciminelli C, Paradiso A, Tommasi S (2009) Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering. BMC Bioinformatics 10:S4 Laboratory Method Signaling Link
Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A (2009) Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network. BMC Systems Biology 3:2 Metabolism Link
Orton RJ, Adriaens ME, Gormand A, Sturm OE, Kolch W, Gilbert DR (2009) Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway. BMC Systems Biology 3:100 Signaling Link
Pieper I, Wechler K, Katzberg M, Brusch L, Sørensen PG, Mensonides F, Bertau M (2009) Biosimulation of drug metabolism--a yeast based model. European Journal of Pharmaceutical Sciences 36:157–170 Metabolism Pharmacology Link
Pingoud V, Wende W, Friedhoff P, Reuter M, Alves J, Jeltsch A, Mones L, Fuxreiter M, Pingoud A (2009) On the Divalent Metal Ion Dependence of DNA Cleavage by Restriction Endonucleases of the EcoRI Family. Journal of Molecular Biology 393:140-60 Macromolecular Biochemistry Link
Pokrzywa RM (2009) Systems Biology in an Imperfect World: Modeling Biological Systems with Incomplete Information. Ph.D. Thesis, Virginia Tech, USA. Computational Method Link
Reyes-Palomares A, Sánchez-Jiménez F, Medina MÁ (2009) First steps in computational systems biology: A practical session in metabolic modeling and simulation. Biochemistry and Molecular Biology Education 37:178–181 Education Link
Ricagno S, Caccia S, Sorrentino G, Antonini G, Bolognesi M (2009) Human Neuroserpin: Structure and Time-Dependent Inhibition. Journal of Molecular Biology 388:109–121 Enzymology Macromolecular Biochemistry Link
Rossi F, Simoncini E, Marchettini N, Tiezzi E (2009) Deuterium isotope effect on the induction period of the cerium catalyzed Belousov–Zhabotinsky reaction. Chemical Physics Letters 470:147–150 Chemistry Link
Saffrey P, Orton R (2009) Version control of pathway models using XML patches. BMC Systems Biology 3:34 Computational Method Link
Schulz M, Bakker BM, Klipp E (2009) TIde: a software for the systematic scanning of drug targets in kinetic network models. BMC Bioinformatics 10:344 Software Link
Shen Z, Dornan PK, Khan HA, Woo TK, Dong VM (2009) Mechanistic Insights into the Rhodium-Catalyzed Intramolecular Ketone Hydroacylation. Journal of the American Chemical Society 131:1077-91 Chemistry Link
Shi Y, Varghese SM, Huang S, White J, Pervaiz S, Tucker-Kellogg L (2009) Computational modeling of pathway dynamics for detecting drug effects: paradoxical effects of LYS303511 on TRAIL-induced apoptosis. Proceedings of the LSS Computational Systems Bioinformatics Conference 213–224 Toxicology Link
Stefan MI, Edelstein SJ, Le Novère N (2009) Computing phenomenologic Adair-Klotz constants from microscopic MWC parameters. BMC Systems Biology 3:68 Biochemistry Link
Sun T, Adra S, Smallwood R, Holcombe M, MacNeil S (2009) Exploring Hypotheses of the Actions of TGF-β1 in Epidermal Wound Healing Using a 3D Computational Multiscale Model of the Human Epidermis. PLoS One 4:e8515 Immunology Computational Method Software Link
Sun Y-C (2009) Examination of effects of GSK3β phosphorylation, β-catenin phosphorylation, and β-catenin degradation on kinetics of Wnt signaling pathway using computational method. Theoretical Biology & Medical Modelling 6:13 Signaling Link
Troncoso-Ponce MA, Kruger NJ, Ratcliffe G, Garcés R, Martínez-Force E (2009) Characterization of glycolytic initial metabolites and enzyme activities in developing sunflower (Helianthus annuus L.) seeds. Phytochemistry 70:1117–1122 Metabolism Link
Williamson T, Schwartz J-M, Kell DB, Stateva L (2009) Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. BMC Systems Biology 3:70 Signaling Metabolism Link

43 publications
2008
Ciocchetta F, Hillston J, Kos M, Tollervey D (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408:41–54 Macromolecular Biochemistry Link
Colby DA, Bergman RG, Ellman JA (2008) Synthesis of dihydropyridines and pyridines from imines and alkynes via C- H activation. Journal of the American Chemical Society 130:3645–3651 Chemistry Link
Colvin RA, Bush AI, Volitakis I, Fontaine CP, Thomas D, Kikuchi K, Holmes WR (2008) Insights into Zn2+ homeostasis in neurons from experimental and modeling studies. American Journal of Physiology 294:C726-C742 Physiology Link
Del Conte-Zerial P, Brusch L, Rink JC, Collinet C, Kalaidzidis Y, Zerial M, Deutsch A (2008) Membrane identity and GTPase cascades regulated by toggle and cut-out switches. Molecular Systems Biology 4:206 Signaling Link
Díaz Cuervo H (2008) Analysis of the role of Cdc14/Flp1 in checkpoint response to genotoxic stress in “Schizosaccharomyces pombe.” Ph.D. Thesis, Universidad de Salamanca, Spain. Signaling Link
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kırdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26:1155–1160 Microbiology Computational Method Link
Jordão L, Bleck CKE, Mayorga LS, Griffiths G, Anes E (2008) On the killing of mycobacteria by macrophages. Cellular Microbiology 10:529-48 Immunology Link
Jungmann R, Renner S, Simmel FC (2008) From DNA nanotechnology to synthetic biology. HFSP Journal 2:99-109 Synthetic Biology Link
Koh G, Hsu D, Thiagarajan PS (2008) Composition of signaling pathway models and its application to parameter estimation. ACM International Conference on Computational Biology (RECOMB) Poster Book, Singapore Link
Kühn C, Pe℡enz E, Nordlander B, Schaber J, Hohmann S, Klipp E (2008) Exploring the Impact of Osmoadaptation on Glycolysis Using Time-Varying Response-Coefficients. Genome Informatics 20:77–90 Metabolism Link
Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J (2008) Modelling phagosomal lipid networks that regulate actin assembly. BMC Systems Biology 2:107 Metabolism Macromolecular Biochemistry Link
Lagzdina L, Mozga I, Stalidzans E (2008) Algorithm for bioethanol yield optimisation in Saccharomyces cerevisiae glycolysis using “COPASI.” Paper presented at the International Scientific Conference: Applied Information and Communication Technologies, , Jelgava (Latvia), 10-12 Apr 2008. Latvia University of Agriculture. Biotechnology Link
Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24:132–134 Computational Method Genomics Link
Marchisio MA (2008) How to design synthetic gene circuits with composable parts and pools in the ProMoT framework. CiteSeer Preprint Synthetic Biology Link
Marchisio MA, Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24:1903-10. Synthetic Biology Link
Pahle J (2008) Stochastic simulation and analysis of biochemical networks. Ph.D. Thesis, Humboldt-Universität zu Berlin, Germany Computational Method Link
Roy S, Werner-Washburne M, Lane T (2008) A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics 24:1318-1320 Software Link
Sahle S, Mendes P, Hoops S, Kummer U (2008) A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A 366:3619-3631 Computational Method Link
Schmierer B, Tournier AL, Bates PA, Hill CS (2008) Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proceedings of the National Academy of Sciences USA 105:6608-13 Cell Biology Signaling Link
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proceedings of the National Academy of Sciences USA 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link
Wilkinson SJ, Benson N, Kell DB (2008) Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Molecular BioSystems 4:74–97 Computational Method Link
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22 publications
2007
Camacho D, Vera-Licona P, Mendes P, Laubenbacher R (2007) Comparison of reverse-engineering methods using an in silico network. Annals of the New York Academy of Sciences 1115:73-89. Computational Method Link
Ellman JA, Colby DA, Bergman R (2007) Synthesis of Dihydropyridines and Pyridines from Imines and Alkynes via CH Activation. Technical Report, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, California, USA. Chemistry Link
Kelly MP, Isiegas C, Cheung YF, Tokarczyk J, Yang X, Esposito MF, Rapoport DA, Fabian SA, Siegel SJ, Wand G, Houslay MD, Kanes SJ, Abel T (2007) Constitutive activation of Galphas within forebrain neurons causes deficits in sensorimotor gating because of PKA-dependent decreases in cAMP. Neuropsychopharmacology 32:577-88 Pharmacology Signaling Link
Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J (2007) Systems biology standards - The community speaks. Nature Biotechnology 25:390-1 Computational Method Link
Kummer U, Zobeley J, Brasen JC, Fahmy R, Kindzelskii AL, Petty AR, Clark AJ, Petty HR (2007) Elevated Glucose Concentrations Promote Receptor-Independent Activation of Adherent Human Neutrophils: An Experimental and Computational Approach. Biophysical Journal 92:2597-2607 Immunology Link
Mandel JJ, Fuß H, Palfreyman NM, Dubitzky W (2007) Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 8:103 Computational Method Software Link
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences USA 104:15635-40 Macromolecular Biochemistry Cell Biology Link
Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, Struys EA, Klipp E, Jakobs C, Breitenbach M, Lehrach H, Krobitsch S (2007) Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. Journal of Biology 6:10 Metabolism Link
Uys L, Botha FC, Hofmeyr J-HS, Rohwer JM (2007) Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68:2375-92 Metabolism Link
Xie Z (2007) Modelling genetic regulatory networks: A new model for circadian rhythms in Drosophila and investigation of genetic noise in a viral infection process. Ph.D. Thesis. Lincoln University, New Zealand Cell Biology Link

10 publications
2006
Frein D (2006) Signaling and Redox Regulation by Nitric Oxide, Superoxide and Carbon Monoxide. Ph.D. Thesis, Universität Konstanz, Germany Signaling Link
Manninen T, Mäkiraatikka E, Ylipää A, Pettinen A, Leinonen K, Linne M-L (2006) Discrete stochastic simulation of cell signaling: comparison of computational tools. Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society. 2006:2013–2016 Computational Method Link
Vauquelin G, Fierens F, Van Liefde I (2006) Long-lasting angiotensin type 1 receptor binding and protection by candesartan: comparison with other biphenyl-tetrazole sartans. Journal of Hypertension 24:S23-30 Pharmacology Link
Vauquelin G, Van Liefde I (2006) Slow antagonist dissociation and long-lasting in vivo receptor protection. Trends in Pharmacological Sciences 27:356–359 Signaling Biochemistry Pharmacology Link

4 publications
2005
Kummer U, Krajnc B, Pahle J, Green AK, Dixon CJ, Marhl M (2005) Transition from stochastic to deterministic behavior in calcium oscillations. Biophysical Journal 89:1603–1611 Signaling Link

1 publication