COPASI's Use In Research

2024
Akune-Taylor Y, Kon A, Aoki-Kinoshita KF (2024) In silico simulation of glycosylation and related pathways. Analytical and Bioanalytical Chemistry. https://doi.org/10.1007/s00216-024-05331-8 Biochemistry 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, 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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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 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
Rettenbacher LA (2024) Quantifying oxidative folding. Ph.D. Thesis, University of Kent, U.K. 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
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
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
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
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

39 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 B 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 A: Chemistry 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 A 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. The 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
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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

99 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
Großeholz R, Wanke F, Rohr L, Glöckner N, Rausch L, Scholl S, Scacchi E, Spazierer A-J, Shabala L, Shabala S, Schumacher K, Kummer U, Harter K (2022) Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root. eLife 11:e73031 Signaling Physiology Plant Biology Link
Guimera AM, Clark P, Wordsworth J, Anugula S, Rasmussen LJ, Shanley DP (2022) Systems modelling predicts chronic inflammation and genomic instability prevent effective mitochondrial regulation during biological ageing. Experimental Gerontology 166:111889 Signaling Link
Gulhane P, Nimsarkar P, Kharat K, Singh S (2022) Deciphering miR-520c-3p as a probable target for immunometabolism in non-small cell lung cancer using systems biology approach. Oncotarget 13:725–746 Genetics Link
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
He Y, Li K, Wang J, Xu L, Yan J, Yang M, Yan Y (2022) A novel strategy for biodiesel production by combination of liquid lipase, deep eutectic solvent and ultrasonic-assistance in scaled-up reactor: Optimization and kinetics. Journal of Cleaner Production 372:133740 Enzymology Biotechnology Link
Holman SDL, Wills AG, Fazakerley NJ, Poole DL, Coe DM, Berlouis LA, Reid M (2022) Electrochemical Synthesis of Isoxazolines: Method and Mechanism. Chemistry 28:e202103728 Chemistry Link
Huang Q, Lee GY, Li J, Wang C, Zhao RL, Deng Z, Houk KN, Zhao Y-L (2022) Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation. Proceedings of the National Academy of Sciences USA 119:e2119032119 Chemistry Link
Irgen-Gioro S, Yoshida SR, Walling V, Chong S (2022) Fixation can change the appearance of phase separation in living cells. eLife 11:e79903 Cell Biology Biophysics Link
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
Lee JY, Styczynski MP (2022) Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework. Scientific Reports 12:762 Computational Method Metabolism Link
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
Lo-Thong-Viramoutou O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2022) Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model. Frontiers in Artificial Intelligence 5:744755 Computational Method Link
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
Maestri S, Merelli E, Pettini M (2022) Agent-based models for detecting the driving forces of biomolecular interactions. Scientific Reports 12:1878 Computational Method Metabolism Link
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
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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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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
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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
Wang M (2022) Bottom-up synthesis of Nicotinamide Adenine Dinucleotide (NAD) regeneration modules for artificial cells. Ph.D. Thesis, Otto von Guericke Universität Magdeburg, Germany Synthetic Biology Chemistry Link
White C, Rottschäfer V, Bridge LJ (2022) Insights into the dynamics of ligand-induced dimerisation via mathematical modelling and analysis. Journal of Theoretical Biology 538:110996 Signaling Biochemistry Link
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
Xu Q, Rose JJ, Chen X, Wang L, DeMartino AW, Dent MR, Tiwari S, Bocian K, Huang XN, Tong Q, McTiernan CF, Guo L, Alipour E, Jones TC, Ucer KB, Kim-Shapiro DB, Tejero J, Gladwin MT (2022) Cell-free and alkylated hemoproteins improve survival in mouse models of carbon monoxide poisoning. JCI Insight 7:e153296 Biochemistry Toxicology Physiology Link
Yuan L, Wu C, Guo X, Yang C (2022) ParaCopasi: A package for parallel biochemical simulation and analysis. Journal of Computational Chemistry 43:144–154 Computational Method Software Link
Zhang Y-Q, Li Y-Y, Maseras F, Liao R-Z (2022) Mechanism and selectivity of photocatalyzed CO2 reduction by a function-integrated Ru catalyst. Dalton Transactions 51:3747–3759 Chemistry Link
Zondervan NA (2022) Patterns in pathogenesis: elucidating bacterial host interaction. Ph.D. Thesis, Wageningen University, The Netherlands. Microbiology Metabolism Link

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 A: Chemistry 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
Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S (2021) An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Communications Biology 4:1236 Macromolecular Biochemistry Link
Haque MA, Morozova K, Lawrence N, Ferrentino G, Scampicchio M (2021) Radical Scavenging Activity of Antioxidants by Cyclic Voltammetry. Electroanalysis 33:23–28 Chemistry Biophysics Link
Hellgren J (2021) Engineering central carbon metabolism with phosphoketolase pathways in Saccharomyces cerevisiae. Ph.D. Thesis, Chalmers University of Technology, Sweden. Metabolism Biotechnology Link
Héron JDJ (2021) C-H Activation and CuAAC Reactions with 1,8-Naphthyridine Based Dicopper Complexes from a Computational Perspective. Ph.D. Thesis, University of Oslo, Norway. Chemistry Link
Hetmanski JHR, Jones MC, Chunara F, Schwartz J-M, Caswell PT (2021) Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration. PLoS Computational Biology 17:e1008213 Cell Biology Signaling Link
Holzheu P, Großeholz R, Kummer U (2021) Impact of explicit area scaling on kinetic models involving multiple compartments. BMC Bioinformatics 22:21 Theory Link
Huysmans GHM, Ciftci D, Wang X, Blanchard SC, Boudker O (2021) The high-energy transition state of the glutamate transporter homologue GltPh. EMBO Journal 40:e105415 Enzymology Link
Ibáňez Gaspar V, Catozzi S, Ternet C, Luthert PJ, Kiel C (2021) Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Small GTPases 12:209–225 Signaling Link
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
Koch D, Alexandrovich A, Funk F, Kho AL, Schmitt JP, Gautel M (2021) Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers. Cell Reports 36:109448 Signaling Link
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
Scott KE, Fraley SI, Rangamani P (2021) A spatial model of YAP/TAZ signaling reveals how stiffness, dimensionality, and shape contribute to emergent outcomes. Proceedings of the National Academy of Sciences USA 118:e2021571118 Signaling Link
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
Yamada TG, Ii K, König M, Feierabend M, Dräger A, Funahashi A (2021) SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes 9:1830 Software Link
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
Yeom J-S, Georgouli K, Blake R, Navid A (2021) Towards dynamic simulation of a whole cell model. In: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 1–4, 2021, Gainesville, FL, USA, pp. 1–10. DOI:10.1145/3459930.3471161 Computational Method Link
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
Zaccaria F, Zuccaccia C, Macchioni A (2021) Hemi-metallocene Ti(IV) η3-allyl-type complexes: Structure, dynamics in solution and exploration of reactivity. Inorganica Chimica Acta 527:120565 Chemistry Link
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
Zang J, Gesemann M, Keim J, Samardzija M, Grimm C, Neuhauss SC (2021) Circadian regulation of vertebrate cone photoreceptor function. eLife 10:e68903 Signaling Link
Zhu N, Hu X, Fang Z, Guo K (2021) Chemoselective Polymerizations. Progress in Polymer Science 117:101397 Chemistry Link
Zweifel ME, Sherer LA, Mahanta B, Courtemanche N (2021) Nucleation limits the lengths of actin filaments assembled by formin. Biophysical Journal 120:4442–4456 Macromolecular Biochemistry Cell Biology Link

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
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 B: Biology 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
Tenner B, Getz M, Ross B, Ohadi D, Bohrer CH, Greenwald E, Mehta S, Xiao J, Rangamani P, Zhang J (2020) Spatially compartmentalized phase regulation of a Ca2+-cAMP-PKA oscillatory circuit. eLife 9:e55013 Signaling Link
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
Zhou Q, Liu Y, Yuan W (2020) Kinetic modeling of butyric acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. New Biotechnology 55:118–126 Biotechnology Microbiology Link
Zhu H, Poojary MM, Andersen ML, Lund MN (2020) The effect of molecular structure of polyphenols on the kinetics of the trapping reactions with methylglyoxal. Food Chemistry 319:126500 Biochemistry Link
Zweifel ME, Courtemanche N (2020) Profilin’s Affinity for Formin Regulates the Availability of Filament Ends for Actin Monomer Binding. Journal of Molecular Biology 432:166688 Cell Biology Link

112 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
Iancu B, Sanwal U, Gratie C, Petre I (2019) Refinement-based modeling of the ErbB signaling pathway. Computers in Biology and Medicine 106:91–96 Signaling Computational Method Link
Jahagirdar S, Suarez-Diez M, Saccenti E (2019) Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms. Journal of Proteome Research 18:1099–1113 Computational Method Metabolism Link
Jaime JC, Mesa-Álvarez MD, Martin RR, Betancourt-Mar JA, Cocho G, Mansilla R, Nieto-Villar JM (2019) Chronotherapy of cancer: periodic perturbations in vascular growth and metastasis. Biological Rhythm Research 50:495–504 Physiology Link
Jayanthi BEK, Zhao W, Segatori L (2019) Input-dependent post-translational control of the reporter output enhances dynamic resolution of mammalian signaling systems. Methods in Enzymology 622:1–27 Signaling Synthetic Biology Link
Kalra P, Brandl J, Gaub T, Niederalt C, Lippert J, Sahle S, Küpfer L, Kummer U (2019) Quantitative systems pharmacology of interferon alpha administration: A multi-scale approach. PLoS One 14:e0209587 Pharmacology Signaling Link
Kaspar S (2019) The role of promoter architecture in transduction, integration and multiplexing of environmental signals in bacteria. Ph.D. Thesis, University of Heidelberg, Germany Signaling Microbiology Link
Kaushik AC, Mao X, Li C-D, Li Y, Wei D-Q, Sahi S (2019) G-protein-coupled receptors function as logic gates for nanoparticle binding using systems and synthetic biology approach. Journal of Materials Research 34:1854–1867 Signaling Synthetic Biology Link
Kennedy CR, Zhong H, Macaulay RL, Chirik PJ (2019) Regio- and Diastereoselective Iron-Catalyzed [4+4]-Cycloaddition of 1,3-Dienes. Journal of the American Chemical Society 141:8557–8573 Chemistry Link
Knight-Schrijver V (2019) Towards systems pharmacology models of druggable targets and disease mechanisms. Thesis, University of Cambridge, UK Pharmacology Physiology Signaling Link
Koeman M, Engel J, Jansen J, Buydens L (2019) Critical comparison of methods for fault diagnosis in metabolomics data. Scientific Reports 9:1123 Metabolism Computational Method Link
Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ (2019) Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. FEBS Letters 593:319–338 Physiology Link
Kumar A, Chauhan N, Singh S (2019) Understanding the Cross-Talk of Redox Metabolism and Fe-S Cluster Biogenesis in Leishmania Through Systems Biology Approach. Frontiers in Cellular and Infection Microbiology 9:15 Metabolism Link
Kuoka T, Akase S, Karlsson NG, Aoki-Kinoshita KF (2019) 252. In-silico simulation of o-linked glycan biosynthesis in cho cells. Glycoconjugate Journal 36:267–397 (Glyco25, XXV International Symposium on Glycoconjugates) Metabolism Link
Kühn C, Checa S (2019) Computational Modeling to Quantify the Contributions of VEGFR1, VEGFR2, and Lateral Inhibition in Sprouting Angiogenesis. Frontiers in Physiology 10:288 Signaling Physiology Link
Lang SN, Germerodt S, Glock C, Skerka C, Zipfel PF, Schuster S (2019) Molecular crypsis by pathogenic fungi using human factor H. A numerical model. PLoS One 14:e0212187 Immunology Microbiology Link
Lebar T, Verbič A, Ljubetič A, Jerala R (2019) Polarized displacement by transcription activator-like effectors for regulatory circuits. Nature Chemical Biology 15:80–87 Synthetic Biology Genetics Link
Leischner T, Suarez LA, Spannenberg A, Junge K, Nova A, Beller M (2019) Highly selective hydrogenation of amides catalysed by a molybdenum pincer complex: scope and mechanism. Chemical Science 10:10566–10576 Chemistry Link
Lombardo SD, Presti M, Mangano K, Petralia MC, Basile MS, Libra M, Candido S, Fagone P, Mazzon E, Nicoletti F, Bramanti A (2019) Prediction of PD-L1 Expression in Neuroblastoma via Computational Modeling. Brain Sciences 9:E221 Signaling Link
Macikova L, Sinica V, Kadkova A, Villette S, Ciaccafava A, Faherty J, Lecomte S, Alves ID, Vlachova V (2019) Putative interaction site for membrane phospholipids controls activation of TRPA1 channel at physiological membrane potentials. FEBS Journal 286:3664–3683 Signaling Biochemistry Link
Madec M (2019) Systemes heterogenes : outils CAO et applications a la biologie. Habilitation Thesis, Universite de Strasbourg, France. Computational 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 Software Computational Method Link
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
McAuley MT (2019) Computer modelling for nutritionists. Cham, Switzerland: Springer Education Link
McKay AI, Bukvic AJ, Tegner BE, Burnage AL, Martínez-Martínez AJ, Rees NH, Macgregor SA, Weller AS (2019) Room Temperature Acceptorless Alkane Dehydrogenation from Molecular σ-Alkane Complexes. Journal of the American Chemical Society 141:11700–11712 Chemistry Link
Mercadante CJ, Prajapati M, Parmar JH, Conboy HL, Dash ME, Pettiglio MA, Herrera C, Bu JT, Stopa EG, Mendes P, Bartnikas TB (2019) Gastrointestinal iron excretion and reversal of iron excess in a mouse model of inherited iron excess. Haematologica 104:678–689 Physiology Link
Meshram RJ, Goundge MB, Kolte BS, Gacche RN (2019) An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitology International 69:59–70 Metabolism Link
Meyer-Almes F-J (2019) Determination of the binding mechanism of histone deacetylase inhibitors. Chemical Biology & Drug Design 93:1214–1250 Enzymology Link
Miller DSJ, Schmierer B, Hill CS (2019) TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation. Journal of Cell Science 132:jcs234039 Signaling Link
Mitchell S, Hoffmann A (2019) Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB. Proceedings of the National Academy of Sciences USA 116:10592–10597 Signaling Link
Mitchell S, Mercado E, Ho J, Cheng Q, Ghosh G, Hoffmann A (2019) An NFκB Activity Calculator to Delineate Signaling Crosstalk: Type I and II Interferons Enhance NFκB via Distinct Mechanisms. Frontiers in Immunology 10:1425 Signaling Link
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
Molleti N, Martinez-Erro S, Carretero Cerdán A, Sanz-Marco A, Gómez-Bengoa E, Martín-Matute B (2019) Base-Catalyzed [1,n]-Proton Shifts in Conjugated Polyenyl Alcohols and Ethers. ACS Catalysis 9:9134–9139 Chemistry Link
Montero G, Silva E, Mansilla R (2019) Do mole-rats follow the same rules in their longevity and aging in nature? MOJ Gerontology & Geriatrics 4:259–263 Physiology Link
Moreno DF, Jenkins K, Morlot S, Charvin G, Csikász-Nagy A, Aldea M (2019) Proteostasis collapse, a hallmark of aging, hinders the chaperone-Start network and arrests cells in G1. eLife 8:e48240 Signaling Cell Biology Link
Moreno DF, Parisi E, Yahya G, Vaggi F, Csikász-Nagy A, Aldea M (2019) Competition in the chaperone-client network subordinates cell-cycle entry to growth and stress. Life Science Alliance 2:e201800277 Signaling Cell Biology Link
Morgan AE (2019) Using Mathematical Modelling and Electrochemical Analysis to Investigate Age‐Associated Disease. Ph.D. Thesis, University of Chester, UK Physiology Link
Möller MN, Denicola A (2019) Acceleration of the autoxidation of nitric oxide by proteins. Nitric Oxide: Biology and Chemistry 85:28–34 Biochemistry Link
Muth M, Jänsch N, Kopranovic A, Krämer A, Wössner N, Jung M, Kirschhöfer F, Brenner-Weiß G, Meyer-Almes F-J (2019) Covalent inhibition of histone deacetylase 8 by 3,4-dihydro-2H-pyrimido[1,2-c][1,3]benzothiazin-6-imine. Biochimica et Biophysica Acta 1863:577–585 Enzymology Biochemistry Link
Nguyen VD, Styevkó G, Madaras E, Haktanirlar G, Tran ATM, Bujna E, Dam MS, Nguyen QD (2019) Immobilization of β-galactosidase on chitosan-coated magnetic nanoparticles and its application for synthesis of lactulose-based galactooligosaccharides. Process Biochemistry 84:30–38 Biotechnology Link
Nielsen CD-T, Mooij WJ, Sale D, Rzepa HS, Burés J, Spivey AC (2019) Reversibility and reactivity in an acid catalyzed cyclocondensation to give furanochromanes - a reaction at the “oxonium-Prins” vs. “ortho-quinone methide cycloaddition” mechanistic nexus. Chemical Science 10:406–412 Chemistry Link
Ohadi D, Schmitt DL, Calabrese B, Halpain S, Zhang J, Rangamani P (2019) Computational modeling reveals frequency modulation of calcium-cAMP/PKA pathway in dendritic spines. bioRxiv Preprint bioRxiv:521740 Signaling Link
Özkar S, Finke RG (2019) Nanoparticle Formation Kinetics and Mechanistic Studies Important to Mechanism-Based Particle-Size Control: Evidence for Ligand-Based Slowing of the Autocatalytic Surface Growth Step Plus Postulated Mechanisms. Journal of Physical Chemistry 123:14047–14057 Chemistry Link
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
Pollice R (2019) A General Fitting Function to Estimate Apparent Reaction Orders of Kinetic Profiles. chemrxiv doi:10.26434/chemrxiv.7885760.v1 Computational Method Link
Rampioni G, Leoni L, Stano P (2019) Molecular Communications in the Context of “Synthetic Cells” Research. IEEE Transactions on NanoBioscience 18:43–50 Synthetic Biology Link
Rawat KS, Mandal SC, Bhauriyal P, Garg P, Pathak B (2019) Catalytic upgrading of ethanol to n-butanol using an aliphatic Mn–PNP complex: theoretical insights into reaction mechanisms and product selectivity. Catalysis Science & Technology 9:2794–2805 Chemistry Link
Reader P (2019) in vitro Characterisation of the Complement Cascade for Predicting Patient Outcome Post-operatively. Ph.D. Thesis, University of Exeter, UK Biochemistry Physiology Link
Revell JD (2019) Parameter inference for stochastic biological models. Ph.D. Thesis, Newcastle University, UK. Computational Method Link
Robinson KJ, Gould IR, Fecteau KM, Hartnett HE, Williams LB, Shock EL (2019) Deamination reaction mechanisms of protonated amines under hydrothermal conditions. Geochimica et Cosmochimica Acta 244:113–128 Chemistry Link
Rodriguez J, Ren G, Day CR, Zhao K, Chow CC, Larson DR (2019) Intrinsic Dynamics of a Human Gene Reveal the Basis of Expression Heterogeneity. Cell 176:213-226.e18 Link
Rogers JA, Popp BV (2019) Operando Infrared Spectroscopy Study of Iron-Catalyzed Hydromagnesiation of Styrene: Explanation of Nonlinear Catalyst and Inhibitory Substrate Dependencies. Organometallics 38:4533–4538 Chemistry Link
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Saavedra E, Encalada R, Vázquez C, Olivos-García A, Michels PAM, Moreno-Sánchez R (2019) Control and regulation of the pyrophosphate-dependent glucose metabolism in Entamoeba histolytica. Molecular and Biochemical Parasitology 229:75–87 Metabolism Link
Saffioti NA, de Sautu M, Ferreira-Gomes MS, Rossi RC, Berlin J, Rossi JPFC, Mangialavori IC (2019) E2P-like states of plasma membrane Ca2+‑ATPase characterization of vanadate and fluoride-stabilized phosphoenzyme analogues. Biochimica et Biophysica Acta 1861:366–379 Enzymology Link
Sangavai C, Bharathi M, Ganesh SP, Chellapandi P (2019) Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. AMB Express 9:82 Metabolism Microbiology Link
Schilling IE, Hess R, Bolotin J, Lal R, Hofstetter TB, Kohler H-PE (2019) Kinetic Isotope Effects of the Enzymatic Transformation of γ-Hexachlorocyclohexane by the Lindane Dehydrochlorinase Variants LinA1 and LinA2. Environmental Science & Technology 53:2353–2363 Enzymology Environmental Sciences Link
Schoch A (2019) Quantitative Analysis of Information Transfer in Signal Transduction. Ph.D. Thesis, University of Heidelberg, Germany Signaling Link
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Shockey WA (2019) Proteolytic network dynamics in breast cancer and tumor associated macrophages. Ph.D. Thesis, Georgia Tech, Atlanta, USA Signaling Immunology Link
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
Stanbury DM, Harshman J (2019) Large-Scale Models of Radiation Chemistry and the Principle of Detailed Balancing. Journal of Physical Chemistry 123:10240–10245 Chemistry Computational Method Link
Taheri M, Nouri K, Asgari Y, Zabihinpour Z, Sadeghi M (2019) The Significance of Noise in the Evolution of Negative and Positive Cooperativity in Protein Complexes. MATCH Communications in Mathematical and Computer Chemistry 81:177–192 Biochemistry Macromolecular Biochemistry Link
Tang J, Gautam P, Gupta A, He L, Timonen S, Akimov Y, Wang W, Szwajda A, Jaiswal A, Turei D, Yadav B, Kankainen M, Saarela J, Saez-Rodriguez J, Wennerberg K, Aittokallio T (2019) Network pharmacology modeling identifies synergistic Aurora B and ZAK interaction in triple-negative breast cancer. npj Systems Biology and Applications 5:20 Pharmacology Signaling Link
Tapia F, Laske T, Wasik MA, Rammhold M, Genzel Y, Reichl U (2019) Production of defective interfering particles of influenza A virus in parallel continuous cultures at two residence times–insights from qPCR measurements and viral dynamics modeling. Frontiers in Bioengineering and Biotechnology 7:275 Biotechnology Link
Taran O, Patel V, Lynn DG (2019) Small molecule reaction networks that model the ROS dynamics of the rhizosphere. Chemical Communications 55:3602–3605 Chemistry Link
Tjendana Tjhin V (2019) Brain iron trafficking in health and disease: a systems approach. Ph.D. Thesis, University of Warwick, UK Physiology Link
Toney MD (2019) Carbon Acidity in Enzyme Active Sites. Frontiers in Bioengineering and Biotechnology 7:25 Enzymology Link
Verma M, Bassaganya-Riera J, Leber A, Tubau-Juni N, Hoops S, Abedi V, Chen X, Hontecillas R (2019) High-resolution computational modeling of immune responses in the gut. GigaScience 8:giz062 Immunology Link
Virtanen O, Valev D, Kruse O, Wobbe L, Tyystjärvi E (2019) Photoinhibition and continuous growth of the wild-type and a high-light tolerant strain of Chlamydomonas reinhardtii. Photosynthetica 57:617–626 Biochemistry Microbiology Link
Wade OK, Woehrstein JB, Nickels PC, Strauss S, Stehr F, Stein J, Schueder F, Strauss MT, Ganji M, Schnitzbauer J, Grabmayr H, Yin P, Schwille P, Jungmann R (2019) 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics. Nano Letters 19:2641–2646 Laboratory Method Link
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2019) Macromolecular crowding and membrane binding proteins: The case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Macromolecular Biochemistry Link
Wheeler LC, Smith SD (2019) Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs. Integrative and Comparative Biology 59:585–598 Metabolism Link
Whitehead CB, Finke RG (2019) Nucleation Kinetics and Molecular Mechanism in Transition-Metal Nanoparticle Formation: The Intriguing, Informative Case of a Bimetallic Precursor, {[(1,5-COD)IrI·HPO4]2}2–. Chemistry of Materials 31:2848–2862 Chemistry 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 (2019) The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR. F1000Research 8:1877 Education Link
Xie Y, Kazmierczyk M, Graham BP, Dutia MB, Stefan MI, Dutia MB (2019) A multi-scale model reveals cellular and physiological mechanisms underlying hyperpolarisation-gated synaptic plasticity. bioRxiv doi:10.1101/418228 Macromolecular Biochemistry Biophysics Link
Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X, Du J, Li P, Ju X, Zheng Y, Chen Y, Liu Y, Jiang H, Yao Y, Ma H, Ma Y (2019) Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metabolic Engineering 56:142–153 Metabolism Synthetic Biology Link
Yeoh JW, Ng KBI, Teh AY, Zhang J, Chee WKD, Poh CL (2019) An Automated Biomodel Selection System (BMSS) for Gene Circuit Designs. ACS Synthetic Biology 8:1484–1497 Synthetic Biology Computational Method Link
Yeung HH-M, Sapnik AF, Massingberd‐Mundy F, Gaultois MW, Wu Y, Fraser DAX, Henke S, Pallach R, Heidenreich N, Magdysyuk OV, Vo NT, Goodwin AL (2019) Control of Metal–Organic Framework Crystallization by Metastable Intermediate Pre-equilibrium Species. Angewandte Chemie International Edition 58:566–571 Chemistry Link
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Yvinec R, Ayoub MA, De Pascali F, Crépieux P, Reiter E, Poupon A (2019) Workflow Description to Dynamically Model β-Arrestin Signaling Networks. Methods in Molecular Biology 1957:195–215 Signaling Computational Method Link
Zarrella I, Matrella S, Fortunato G, Marchettini N, Proto A, Motta O, Rossi F (2019) Optimization of the anaerobic denitrification process mediated by Bacillus cereus in a batch reactor. Environmental Technology & Innovation 16:100456 Microbiology Environmental Sciences Link
Zhang X, Nagai T, Ahammad RU, Kuroda K, Nakamuta S, Nakano T, Yukinawa N, Funahashi Y, Yamahashi Y, Amano M, Yoshimoto J, Yamada K, Kaibuchi K (2019) Balance between dopamine and adenosine signals regulates the PKA/Rap1 pathway in striatal medium spiny neurons. Neurochemistry International 122:8–18 Signaling Link
Zimmer C, Leuba SI, Cohen T, Yaesoubi R (2019) Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Statistical Methods in Medical Research 28:3591–3608 Epidemiology Link

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
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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
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

103 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
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107 publications
2015