COPASI's Use In Research

2024
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
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 Experimental Method Biochemistry Link
Deng M, Yu J, Blackmond DG (2024) Symmetry breaking and chiral amplification in prebiotic ligation reactions. Nature 626:1019–1024 Chemistry Biochemistry 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
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
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
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
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
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

18 publications
2023
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
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 Experimental 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 Experimental 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 Experimental 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 Experimental Method Link
Stanton DA, Ellis EA, Cruse MR, Jedlinski R, Kraut DA (2023) The importance of proteasome grip depends on substrate stability. Biochemical and Biophysical Research Communications 677:162–167 Macromolecular Biochemistry Link
Suárez H, Guerra A, Mansilla R, Nieto-Villar JM (2023) Ferroptosis as a biological Phase transition II: Chronotherapy of avascular and vascular tumor growth. Biological Rhythm Research 54:722–731 Biochemistry Signaling Link
Sumi T, Harada K (2023) Muscarinic acetylcholine receptor-dependent and NMDA receptor-dependent LTP and LTD share the common AMPAR trafficking pathway. iScience 26:106133 Signaling Link
Szigetvari PD, Patil S, Birkeland E, Kleppe R, Haavik J (2023) The effects of phenylalanine and tyrosine levels on dopamine production in rat PC12 cells. Implications for treatment of phenylketonuria, tyrosinemia type 1 and comorbid neurodevelopmental disorders. Neurochemistry International 171:105629 Metabolism Link
Tare P, Bhowmick T, Katagi G, China A, Nagaraja V (2023) Comparison of Transcription Elongation Rates of Three RNA Polymerases in Real Time. ACS Omega 8:47510–47519 Genetics Macromolecular Biochemistry Link
Yalçınkaya BH, Genc S, Yılmaz B, Özilgen M (2023) How does exercise affect energy metabolism? An in silico approach for cardiac muscle. Heliyon 9:e17164 Biochemistry Physiology Link
Yuan AT, Stillman MJ (2023) Arsenic binding to human metallothionein-3. Chemical Science 14:5756–5767 Biochemistry Link
Yuan AT, Korkola NC, Stillman MJ (2023) Apo-metallothionein-3 cooperatively forms tightly compact structures under physiological conditions. Journal of Biological Chemistry 299:102899 Biochemistry Biophysics Link
Yuan S, Chen S, Yang Y (2023) Dimension Reduction for Dynamic Analysis of Gene Expression Data Using Variational Autoencoder. 2023 IEEE 13th International Conference on CYBER Technology in Automation, Control, and Intelligent Systems (CYBER), 988–991. Computational Method Link

100 publications
2022
Abraha BW, Marchisio MA (2022) NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3—Comp Package. Frontiers in Bioengineering and Biotechnology 10:845240 Synthetic Biology Link
Akbulut D, Özkar S (2022) A review of the catalytic conversion of glycerol to lactic acid in the presence of aqueous base. RSC Advances 12:18864–18883 Chemistry Link
Altus K (2022) Synthesis and characterisation of platinum(II) methyl complexes and their reactivity towards carbon-hydrogen (C-H) and carbon-halogen bonds (C-X). Ph.D. Thesis, University of British Columbia, Vancouver, Canada. Chemistry Link
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114 publications
2021
Abdallah P, Dossier-Berne F, Karpel Vel Leitner N, Deborde M (2021) Methylparaben chlorination in the presence of bromide ions and ammonia: kinetic study and modeling. Environmental Science and Pollution Research 28:31256–31267 Chemistry Environmental Sciences Link
Acón M, Geiß C, Torres-Calvo J, Bravo-Estupiñan D, Oviedo G, Arias-Arias JL, Rojas-Matey LA, Baez E, Vásquez-Vargas G, Oses-Vargas Y, Guevara-Coto J, Segura-Castillo A, Siles-Canales F, Quirós-Barrantes S, Régnier-Vigouroux A, Mendes P, Mora-Rodríguez R (2021) MYC dosage compensation is mediated by miRNA-transcription factor interactions in aneuploid cancer. iScience 24:103407 Genetics Biochemistry Computational Method Link
Angeli L, Imperiale S, Ding Y, Scampicchio M, Morozova K (2021) A Novel Stoichio-Kinetic Model for the DPPH• Assay: The Importance of the Side Reaction and Application to Complex Mixtures. Antioxidants 10:1019 Experimental 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 Experimental 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
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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
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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
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Sigg A, Klimacek M, Nidetzky B (2021) Three-level hybrid modeling for systematic optimization of biocatalytic synthesis: α-glucosyl glycerol production by enzymatic trans-glycosylation from sucrose. Biotechnology and Bioengineering 118:4028–4040 Biotechnology Metabolism Link
Silva PJ (2021) Response to “Molecular-level understanding of biological energy coupling and transduction: Response to ‘Chemiosmotic misunderstandings’”. Biophysical Chemistry 269:106512 Biochemistry Link
Sollin M (2021) Analyse quantitative de l’oxydation radicalaire de matériaux organiques : étude cinétique et théorique de l’oxydation des hydroperoxydes. Masters Thesis, Université Du Québec À Montréal, Canada. Chemistry Link
Soni B, Singh S (2021) COVID-19 co-infection mathematical model as guided through signaling structural framework. Computational and Structural Biotechnology Journal 19:1672–1683 Signaling Immunology Link
Sotnikov DV, Berlina AN, Zherdev AV, Dzantiev BB (2021) Theoretical limitations for aggregation methods of analysis based on affine interactions. AIP Conference Proceedings 2371:070001 Biophysics Link
Städter P, Schälte Y, Schmiester L, Hasenauer J, Stapor PL (2021) Benchmarking of numerical integration methods for ODE models of biological systems. Scientific Reports 11:2696 Computational Method Link
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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
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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
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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
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Zake DM, Kurlovics J, Zaharenko L, Komasilovs V, Klovins J, Stalidzans E (2021) Physiologically based metformin pharmacokinetics model of mice and scale-up to humans for the estimation of concentrations in various tissues. PLoS One 16:e0249594 Pharmacology Physiology Link
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119 publications
2020
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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
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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
Yu T (2019) Oxidative Protein Folding: Investigating New Enzymes, New Assays, and New Locations. Ph.D. Thesis, University of Delaware, USA. Biochemistry Link
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
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Vranish JN, Ancona MG, Oh E, Susumu K, Lasarte Aragonés G, Breger JC, Walper SA, Medintz IL (2018) Enhancing Coupled Enzymatic Activity by Colocalization on Nanoparticle Surfaces: Kinetic Evidence for Directed Channeling of Intermediates. ACS Nano 12:7911–7926 Biotechnology Enzymology Link
Wang M, Park C, Woehl TJ (2018) Quantifying the Nucleation and Growth Kinetics of Electron Beam Nanochemistry with Liquid Cell Scanning Transmission Electron Microscopy. Chemistry of Materials 30:7727–7736 Chemistry Link
Wang M, Wölfer C, Otrin L, Ivanov I, Vidaković-Koch T, Sundmacher K (2018) Transmembrane NADH Oxidation with Tetracyanoquinodimethane. Langmuir 34:5435–5443 Biochemistry Biotechnology Link
Wei D, Sadek O, Dorcet V, Roisnel T, Darcel C, Gras E, Clot E, Sortais J-B (2018) Selective mono N-methylation of anilines with methanol catalyzed by rhenium complexes: An experimental and theoretical study. Journal of Catalysis 366:300–309 Chemistry Link
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2018) Macromolecular crowding and membrane binding proteins: the case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Biochemistry Biophysics Link
Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP (2018) PyCoTools: A Python Toolbox for COPASI. Bioinformatics 34:3702–3710 Computational Method Software Link
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Wiebe HA (2018) Mechanistic applications of volume profiles for chemical and biochemical processes. Ph.D. Thesis, Simon Fraser University, Canada Chemistry Link
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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
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Yu Y, Rebek Jr J (2018) Reactions of Folded Molecules in Water. Accounts of Chemical Research 51:3031–3040 Chemistry Link
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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
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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
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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
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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
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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
Chizzolini F (2016) The relationship between genotype and phenotype in cell-free transcription-translation reactions. Ph.D. Thesis, University of Trento, Italy Genetics Link
Claudino M, Zhang X, Alim MD, Podgórski M, Bowman CN (2016) Mechanistic Kinetic Modeling of Thiol–Michael Addition Photopolymerizations via Photocaged “Superbase” Generators: An Analytical Approach. Macromolecules 49:8061–8074 Chemistry Link
Coakley S, Richmond P, Gheorghe M, Chin S, Worth D, Holcombe M, Greenough C (2016) Large-Scale Simulations with FLAME. In Intelligent Agents in Data-intensive Computing (Kolodziej J, Correia L, Molina JM eds.), Springer pp.123-142 Software Link
Coletta C (2016) Study of growth mechanism of conducting polymers by pulse radiolysis. Ph.D. Thesis, Université Paris Saclay, France Chemistry Link
Compel WS (2016) The use of coordinating solvents in gold cluster synthesis. Ph.D. Thesis, Colorado State University, USA. Chemistry Link
Costa RS, Vinga S (2016) Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochemical Engineering Journal 110:59–70 Metabolism Link
Dalle Pezze P, Ruf S, Sonntag AG, Langelaar-Makkinje M, Hall P, Heberle AM, Navas PR, van Eunen K, Tölle RC, Schwarz JJ, Wiese H, Warscheid B, Deitersen J, Stork B, Fäßler E, Schäuble S, Horvatovich P, Shanley DP, Thedieck K (2016) A systems study reveals concurrent activation of AMPK and mTOR by amino acids. Nature Communications 7:13254 Signaling Link
del Pozo J, Salas G, Álvarez R, Casares JA, Espinet P (2016) The Negishi Catalysis: Full Study of the Complications in the Transmetalation Step and Consequences for the Coupling Products. Organometallics 35:3604–3611 Chemistry Link
delToro D, Ortiz D, Ordyan M, Sippy J, Oh C-S, Keller N, Feiss M, Catalano CE, Smith DE (2016) Walker-A Motif Acts to Coordinate ATP Hydrolysis with Motor Output in Viral DNA Packaging. Journal of Molecular Biology 428:2709–2729 Biochemistry Link
Di Camillo B, Carlon A, Eduati F, Toffolo GM (2016) A rule-based model of insulin signalling pathway. BMC Systems Biology 10:38 Signaling Link
Dubey BN, Lori C, Ozaki S, Fucile G, Plaza-Menacho I, Jenal U, Schirmer T (2016) Cyclic di-GMP mediates a histidine kinase/phosphatase switch by noncovalent domain cross-linking. Science Advances 2:e1600823 Biochemistry Signaling Link
Emiola A, Andrews SS, Heller C, George J (2016) Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli. Proceedings of the National Academy of Sciences USA 113:3108–3113 Signaling Cell Biology Link
Espejo Mojica ÁJ (2016) Producción, purificación y caracterización de tres hexosaminidasas lisosomales recombinantes en pichia pastoris. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia Enzymology Metabolism Link
Firdaus MY, Brask J, Nielsen PM, Guo Z, Fedosov SN (2016) Kinetic model of biodiesel production catalyzed by free liquid lipase from Thermomyces lanuginosus. Journal of Molecular Catalysis B: Enzymatic 133:55–64 Biotechnology Enzymology Link
Firdaus MY, Guo Z, Fedosov SN (2016) Development of kinetic model for biodiesel production using liquid lipase as a biocatalyst, esterification step. Biochemical Engineering Journal 105:52–61 Biotechnology Link
Froese RD, Whiteker GT, Peterson TH, Arriola DJ, Renga JM, Shearer JW (2016) Computational and Experimental Studies of Regioselective SNAr Halide Exchange (Halex) Reactions of Pentachloropyridine. Journal of Organic Chemistry 81:10672–10682 Chemistry Link
Furrow SD, Cervellati R, Greco E (2016) Study of the transition to higher iodide in the malonic acid Briggs–Rauscher oscillator. Reaction Kinetics, Mechanisms and Catalysis 118:59–71 Chemistry Link
Gallimore AR, Aricescu AR, Yuzaki M, Calinescu R (2016) A Computational Model for the AMPA Receptor Phosphorylation Master Switch Regulating Cerebellar Long-Term Depression. PLoS Computational Biology 12:e1004664 Signaling Link
Ganesan N, Li J, Sharma V, Jiang H, Compagnoni A (2016) Process Simulation of Complex Biological Pathways in Physical Reactive Space and Reformulated for Massively Parallel Computing Platforms. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13:365–379 Computational Method Link
Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E (2016) A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLoS Computational Biology 12:e1004703 Metabolism Physiology Link
Haffez HRS (2016) Design, synthesis and biological evaluation of small molecules for controlling cellular development. Ph.D. Thesis, Durham University, UK. Biochemistry Pharmacology Link
Hamgini BB (2016) Petri net siphon analysis and network centrality measures for identifying combination therapies in signaling pathways. Ph.D. Thesis, Queen’s University, Kingston, Ontario, Canada Computational Method Link
Henkel R, Hoehndorf R, Kacprowski T, Knüpfer C, Liebermeister W, Waltemath D (2016) Notions of similarity for systems biology models. Briefings in Bioinformatics 19:77–88 Computational Method Link
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Kilner J, Corfe BM, McAuley MT, Wilkinson SJ (2016) A deterministic oscillatory model of microtubule growth and shrinkage for differential actions of short chain fatty acids. Molecular BioSystems 12:93-101 Cell Biology Link
Kollarovic G, Studencka M, Ivanova L, Lauenstein C, Heinze K, Lapytsko A, Talemi SR, Figueiredo AS, Schaber J (2016) To senesce or not to senesce: how primary human fibroblasts decide their cell fate after DNA damage. Aging 8:158 Cell Biology Link
Laviska DA, Zhou T, Kumar A, Emge TJ, Krogh-Jespersen K, Goldman AS (2016) Single and Double C–H Activation of Biphenyl or Phenanthrene. An Example of C–H Addition to Ir(III) More Facile than Addition to Ir(I). Organometallics 35:1613–1623 Chemistry Link
Leber A, Abedi V, Hontecillas R, Viladomiu M, Hoops S, Ciupe S, Caughman J, Andrew T, Bassaganya-Riera J (2016) Bistability analyses of CD4+ T follicular helper and regulatory cells during Helicobacter pylori infection. Journal of Theoretical Biology 398:74–84 Immunology Link
Leber A, Bassaganya-Riera J, Tubau-Juni N, Zoccoli-Rodriguez V, Viladomiu M, Abedi V, Lu P, Hontecillas R (2016) Modeling the Role of Lanthionine Synthetase C-Like 2 (LANCL2) in the Modulation of Immune Responses to Helicobacter pylori Infection. PLoS One 11:e0167440 Immunology Link
Ledwitch KV, Barnes RW, Roberts AG (2016) Unravelling the complex drug–drug interactions of the cardiovascular drugs, verapamil and digoxin, with P-glycoprotein. Bioscience Reports 36:e00309 Pharmacology Biochemistry Link
Ledwitch KV, Gibbs ME, Barnes RW, Roberts AG (2016) Cooperativity between verapamil and ATP bound to the efflux transporter P-glycoprotein. Biochemical Pharmacology 118:96–108 Pharmacology Biochemistry Link
Levenhagen MA, Ferreira GA, Pereira GM, Santos AR (2016) A computer simulation model for Strongyloides infection. PeerJ Preprints 4:e2399v1 Immunology Parasitology Link
Levin MD, Kaphan DM, Hong CM, Bergman RG, Raymond KN, Toste FD (2016) Scope and Mechanism of Cooperativity at the Intersection of Organometallic and Supramolecular Catalysis. Journal of the American Chemical Society 138:9682–9693 Enzymology Chemistry Link
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McClary WD (2016) Interactions of Cytochrome P450 3A4 with Phospholipid Bilayer Nanodiscs. Ph.D. Thesis, Seattle, University of Washington, USA. Biochemistry Macromolecular Biochemistry Link
Michalak P, Sobral BW, Abedi V, Kim YB, Deng X, Philipson CW, Viladomiu M, Lu P, Wendelsdorf K, Hontecillas R, Bassaganya-Riera J (2016) From Big Data Analytics and Network Inference to Systems Modeling. In: Bassaganya-Riera J (ed) Computational Immunology, Academic Press, 113–144. Computational Method Immunology Link
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Obydennyy SI, Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2016) Dynamics of calcium spiking, mitochondrial collapse and phosphatidylserine exposure in platelet subpopulations during activation. Journal of Thrombosis and Haemostasis 14:1867–1881 Signaling Link
Olajuyigbe FM, Demitri N, De Zorzi R, Geremia S (2016) Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 21:1458 Biochemistry Link
Orlenko A, Hermansen RA, Liberles DA (2016) Flux control in glycolysis varies across the tree of life. Journal of Molecular Evolution 82:146–161 Metabolism Link
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Ouzounoglou E, Dionysiou D, Stamatakos GS (2016) Differentiation resistance through altered retinoblastoma protein function in acute lymphoblastic leukemia: in silico modeling of the deregulations in the G1/S restriction point pathway. BMC Systems Biology 10:23 Cell Biology Link
Özkar S, Finke RG (2016) Palladium(0) Nanoparticle Formation, Stabilization, and Mechanistic Studies: Pd(acac) 2 as a Preferred Precursor, [Bu 4 N] 2 HPO 4 Stabilizer, plus the Stoichiometry, Kinetics, and Minimal, Four-Step Mechanism of the Palladium Nanoparticle Formation and Subsequent Agglomeration Reactions. Langmuir 32:3699–3716 Chemistry Link
Palai T, Kumar A, Bhattacharya PK (2016) Enzyme immobilization/bioconjugation in producing galactio-oligosaccharidies from lactose: developments of kinetic models and bio-reactors. Materials Today: Proceedings 3:3568–3586 Biotechnology Link
Panchal C, Azimi S, Petre I (2016) Generating the Logicome of a Biological Network. International Conference on Algorithms for Computational Biology. Springer, 38–49 Computational Method Signaling Link
Pappalardo F, Russo G, Candido S, Pennisi M, Cavalieri S, Motta S, McCubrey JA, Nicoletti F, Libra M (2016) Computational Modeling of PI3K/AKT and MAPK Signaling Pathways in Melanoma Cancer. PLoS One 11:e0152104 Signaling Link
Pires JC, Conant GC (2016) Robust yet fragile: expression noise, protein misfolding, and gene dosage in the evolution of genomes. Annual Review of Genetics 50:113–131 Genetics Genomics Link
Pletneva NV, Pletnev S, Pakhomov AA, Chertkova RV, Martynov VI, Muslinkina L, Dauter Z, Pletnev VZ (2016) Crystal structure of the fluorescent protein from Dendronephthya sp. in both green and photoconverted red forms. Acta Crystallographica D72:922-932 Biophysics Link
Podoplelova NA, Sveshnikova AN, Kurasawa JH, Sarafanov AG, Chambost H, Vasil’ev SA, Demina IA, Ataullakhanov FI, Alessi M-C, Panteleev MA (2016) Hysteresis-like binding of coagulation factors X/Xa to procoagulant activated platelets and phospholipids results from multistep association and membrane-dependent multimerization. Biochimica et Biophysica Acta 1858:1216–1227 Immunology Biochemistry Biophysics Link
Proctor CJ, Gartland A (2016) Simulated interventions to ameliorate age-related bone loss indicate the importance of timing. Frontiers in Endocrinology 7:61 Physiology Signaling Link
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLoS One 11:e0148320 Genetics Microbiology Synthetic Biology Link
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G (2016) Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Computational Biology 12:e1004825 Microbiology Metabolism Link
Reichard EL, Chirico GG, Dewey WJ, Nassif ND, Bard KE, Millas NE, Kraut DA (2016) Substrate Ubiquitination Controls the Unfolding Ability of the Proteasome. Journal of Biological Chemistry 291:18547–18561 Biochemistry Macromolecular Biochemistry Link
Rentergent J, Driscoll MD, Hay S (2016) Time course analysis of enzyme-catalyzed DNA polymerization. Biochemistry 55:5622–5634 Biochemistry Enzymology Macromolecular Biochemistry Link
Rocchigiani L, Busico V, Pastore A, Macchioni A (2016) Comparative NMR Study on the Reactions of Hf(IV) Organometallic Complexes with Al/Zn Alkyls. Organometallics 35:1241–1250 Chemistry Link
Rutkis R, Strazdina I, Balodite E, Lasa Z, Galinina N, Kalnenieks U (2016) The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway. PLoS One 11:e0153866 Metabolism Microbiology Link
Salcedo-Sora JE, McAuley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link
Sano T, Kawata K, Ohno S, Yugi K, Kakuda H, Kubota H, Uda S, Fujii M, Kunida K, Hoshino D, Hatano A, Ito Y, Sato M, Suzuki Y, Kuroda S (2016) Selective control of up-regulated and down-regulated genes by temporal patterns and doses of insulin. Science Signaling 9:ra112–ra112 Signaling Physiology Link
Scharm M, Waltemath D (2016) A fully featured COMBINE archive of a simulation study on syncytial mitotic cycles in Drosophila embryos. F1000Research 5:2421 Computational Method Link
Semenov SN, Kraft LJ, Ainla A, Zhao M, Baghbanzadeh M, Campbell VE, Kang K, Fox JM, Whitesides GM (2016) Autocatalytic, bistable, oscillatory networks of biologically relevant organic reactions. Nature 537:656–660 Chemistry Biochemistry Link
Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T (2016) Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP+ oxidoreductase with NADP+/NADPH and ferredoxin. Biochimica et Biophysica Acta 1857:678–687 Microbiology Enzymology Link
Shepelyuk TO, Panteleev MA, Sveshnikova AN (2016) Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover. Mathematical Modelling of Natural Phenomena 11:91–101 Metabolism Physiology Link
Shi Q, Mower MP, Blackmond DG, Rebek Jr J (2016) Water-soluble cavitands promote hydrolyses of long-chain diesters. Proceedings of the National Academy of Sciences USA 113:9199–9203 Chemistry Link
Sluka JP, Fu X, Swat M, Belmonte JM, Cosmanescu A, Clendenon SG, Wambaugh JF, Glazier JA (2016) A Liver-Centric Multiscale Modeling Framework for Xenobiotics. PLoS One 11:e0162428 Physiology Pharmacology Link
Stanger FV, Burmann BM, Harms A, Aragão H, Mazur A, Sharpe T, Dehio C, Hiller S, Schirmer T (2016) Intrinsic regulation of FIC-domain AMP-transferases by oligomerization and automodification. Proceedings of the National Academy of Sciences USA 113:E529–E537 Enzymology Link
Sung S, Sale D, Braddock DC, Armstrong A, Brennan C, Davies RP (2016) Mechanistic Studies on the Copper-Catalyzed N-Arylation of Alkylamines Promoted by Organic Soluble Ionic Bases. ACS Catalysis 6:3965–74 Chemistry Link
Sveshnikova AN, Balatskiy AV, Demianova AS, Shepelyuk TO, Shakhidzhanov SS, Balatskaya MN, Pichugin AV, Ataullakhanov FI, Panteleev MA (2016) Systems biology insights into the meaning of the platelet’s dual-receptor thrombin signaling. Journal of Thrombosis and Haemostasis 14:2045–2057 Physiology Signaling Link
Talemi SR, Tiger C-F, Andersson M, Babazadeh R, Welkenhuysen N, Klipp E, Hohmann S, Schaber J (2016) Systems Level Analysis of the Yeast Osmo-Stat. Scientific Reports 6:30950 Signaling Link
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Tomalin LE, Day AM, Underwood ZE, Smith GR, Dalle Pezze P, Rallis C, Patel W, Dickinson BC, Bähler J, Brewer TF, Chang CJ-L, Shanley DP, Veal EA (2016) Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2, with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed. Free Radical Biology and Medicine 95:333–348 Metabolism Link
Tootoonchi MH, Sharma G, Calles J, Prabhakar R, Kaifer AE (2016) Cooperative Self-Assembly of a Quaternary Complex Formed by Two Cucurbit [7] uril Hosts, Cyclobis (paraquat-p-phenylene), and a “Designer” Guest. Angewandte Chemie 128:11679–83 Chemistry Link
Troják M, Šafránek D, Hrabec J, Šalagovič J, Romanovská F, Červenỳ J (2016) E-Cyanobacterium. org: A Web-Based Platform for Systems Biology of Cyanobacteria. International Conference on Computational Methods in Systems Biology. Springer, 316–322. Software Link
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Valero E, Macià H, Ildefonso M, Hernández J-A, González-Sánchez M-I, García-Carmona F (2016) Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. BMC Systems Biology 10:11 Metabolism Physiology Link
van Eunen K, Volker-Touw CM, Gerding A, Bleeker A, Wolters JC, van Rijt WJ, Martines A-CM, Niezen-Koning KE, Heiner RM, Permentier H, Groen AK, Reijngoud D-J, Derks TGJ, Bakker BM (2016) Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. BMC Biology 14:107 Metabolism Link
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Woods ML, Barnes CP (2016) Mechanistic Modelling and Bayesian Inference Elucidates the Variable Dynamics of Double-Strand Break Repair. PLoS Computational Biology 12:e1005131 Computational Method Link
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106 publications
2015
Abdallah P, Deborde M, Dossier-Berne F, Karpel Vel Leitner N (2015) Kinetics of Chlorination of Benzophenone-3 in the Presence of Bromide and Ammonia. Environmental Science & Technology 49:14359–14367 Environmental Sciences Chemistry Link
Amemiya T, Honma M, Kariya Y, Ghosh S, Kitano H, Kurachi Y, Fujita K, Sasaki Y, Homma Y, Abernethy DR, Kume H, Suzuki H (2015) Elucidation of the molecular mechanisms underlying adverse reactions associated with a kinase inhibitor using systems toxicology. npj Systems Biology and Applications 1:15005 Toxicology Signaling Link
Aullón G, Crespo M, Font-Bardia M, Jover J, Martínez M, Pike J (2015) A combined kinetico-mechanistic and computational study on the competitive formation of seven- versus five-membered platinacycles; the relevance of spectator halide ligands. Dalton Transactions 44:17968-79 Chemistry Link
Azimi S, Czeizler E, Gratie C, Gratie D, Iancu B, Ibssa N, Petre I, Rogojin V, Shadbahr T, Shokri F (2015) An Excursion Through Quantitative Model Refinement. Lecture Notes in Computer Science 9504:25-47 Computational Method Software Link
Azizi M, Biard P-F, Couvert A, Ben Amor M (2015) Competitive kinetics study of sulfide oxidation by chlorine using sulfite as reference compound. Chemical Engineering Research and Design 94:141–152 Chemistry Link
Bodei C, Bortolussi L, Chiarugi D, Guerriero ML, Policriti A, Romanel A (2015) On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry 56:98-1089 Computational Method Link
Castello MA (2015) Lipid Regulation as a Critical Factor in the Development of Alzheimer’s Disease. Ph.D. Thesis, Loma Linda University, California, USA. Metabolism Link
Compel WS, Wong OA, Chen X, Yi C, Geiss R, Häkkinen H, Knappenberger KL Jr, Ackerson CJ (2015) Dynamic Diglyme-Mediated Self-Assembly of Gold Nanoclusters. ACS Nano 9:11690-8. Chemistry Link
Czabany T, Schmölzer K, Luley-Goedl C, Ribitsch D, Nidetzky B (2015) All-in-one assay for beta-D-galactoside sialyltransferases: quantification of productive turnover, error hydrolysis and site selectivity. Analytical Biochemistry 483:47-53 Laboratory Method Enzymology Link
D'Aguanno E, Altamura E, Mavelli F, Fahr A, Stano P, Luisi PL (2015) Physical Routes to Primitive Cells: An Experimental Model Based on the Spontaneous Entrapment of Enzymes inside Micrometer-Sized Liposomes. Life 5:969-96 Synthetic Biology Link
Dacheux E, Firczuk H, McCarthy JEG (2015) Rate control in yeast protein synthesis at the population and single-cell levels. Biochemical Society Transactions 43:1266-70 Macromolecular Biochemistry Link
Daneshjou N, Sieracki N, van Nieuw Amerongen GP, Schwartz MA, Komarova YA, Malik AB, Conway DE (2015) Rac1 functions as a reversible tension modulator to stabilize VE-cadherin trans-interaction. Journal of Cell Biology 208:23-32 Macromolecular Biochemistry Cell Biology Link
della Sala F, Kay ER (2015) Reversible Control of Nanoparticle Functionalization and Physicochemical Properties by Dynamic Covalent Exchange. Angewandte Chemie 127:4261-5 Chemistry Link
Donovan S, Eaton CD, Gower ST, Jenkins KP, LaMar MD, Poli DB, Sheehy R, Wojdak JM (2015) QUBES: a community focused on supporting teaching and learning in quantitative biology. Letters in Biomathematics 2:46-55 Education Link
Dornseifer S, Willkomm S, Far RK, Liebschwager J, Beltsiou F, Frank K, Laufer SD, Martinetz T, Sczakiel G, Claussen JC, Restle T (2015) RNAi revised - target mRNA-dependent enhancement of gene silencing. Nucleic Acids Research 43:10623-32. Macromolecular Biochemistry Genetics Link
Dromms RA, Styczynski MP (2015) Improved metabolite profile smoothing for flux estimation. Molecular BioSystems 11:2394-2405 Computational Method Laboratory Method Link
Dutta-Roy R, Rosenmund C, Edelstein SJ, Le Novère N (2015) Ligand-Dependent Opening of the Multiple AMPA Receptor Conductance States: A Concerted Model. PLoS One 10:e0116616 Physiology Macromolecular Biochemistry Link
Emiola A, George J, Andrews SS (2015) A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli. PLoS One 10:e0121216 Metabolism Microbiology Link
Everetts NJ (2015) Computational Analysis of the Control of Cell Cycle Entry. Bachelor's Thesis, Department of Molecular and Cellular Biology, University of Arizona, USA Cell Biology Signaling Link
Gladkovskaya O, Greaney P, Gun'ko YK, O'Connor GM, Meere M, Rochev Y (2015) An experimental and theoretical assessment of quantum dot cytotoxicity. Toxicology Research 4:1409-15 Toxicology Link
Hamacher-Brady A, Brady NR (2015) Bax/Bak-Dependent, Drp1-Independent Targeting of XIAP into Inner-Mitochondrial Compartments Counteracts Smac-Dependent Effector Caspase Activation. Journal of Biological Chemistry 290:22005-18. Signaling Link
Hinze T, Kirkici K, Sauer P, Sauer P, Behre J (2015) Membrane Computing Meets Temperature: A Thermoreceptor Model as Molecular Slide Rule with Evolutionary Potential. Lecture Notes in Computer Science 9504:215-235 Computational Method Link
Hristova-Neeley D, Neshchadin D, Gescheidt G (2015) Time-Resolved EPR as a Tool to Investigate Oxygen Quenching in Photoinitiated Radical Polymerizations. Journal of Physical Chemistry 119:13883-7 Chemistry Link
Hudson DA, Gannon SA, Thorpe C, (2015) Oxidative protein folding: From thiol-disulfide exchange reactions to the redox poise of the endoplasmic reticulum. Free Radical Biology and Medicine 80:171-182 Macromolecular Biochemistry Link
Ihekwaba AEC, Mura I, Peck MW, Barker GC (2015) The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective. Pathogens and Disease 73:ftv084 Microbiology Link
Intosalmi J, Ahlfors H, Rautio S, Mannerstöm H, Chen ZJ, Lahesmaa R, Stockinger B, Lähdesmäki H (2015) Analyzing Th17 cell differentiation dynamics using a novel integrative modeling framework for time-course RNA sequencing data. BMC Systems Biology 9:81. Immunology Cell Biology Signaling Link
Jeong H, John JM, Schrock RR (2015) Formation of Alternating trans-A-alt-B Copolymers through Ring-Opening Metathesis Polymerization Initiated by Molybdenum Imido Alkylidene Complexes. Organometallics 34:5136–5145 Chemistry Link
Jeong H, John JM, Schrock RR, Hoveyda AH (2015) Synthesis of Alternating trans-AB Copolymers through Ring-Opening Metathesis Polymerization Initiated by Molybdenum Alkylidenes. Journal of the American Chemical Society 137:2239-42 Chemistry Link
Ji Y, Benkovics T, Beutner GL, Sfouggatakis C, Eastgate MD, Blackmond DG (2015) Mechanistic Insights into the Vanadium-Catalyzed Achmatowicz Rearrangement of Furfurol. Journal of Organic Chemistry 80:1696-1702 Chemistry Link
Jones AR, Rentergent J, Scrutton NS, Hay S (2015) Probing reversible chemistry in coenzyme B12-dependent ethanolamine amonnia lyase with kinetic isotope effects. Chemistry 21:8826-31 Enzymology Link
Juty N, Ali R, Glont M, Keating SM, Rodriguez N, Swat MJ, Wimalaratne SM, Hermjakob H, Le Novère N, Laibe C, Chelliah V (2015) BioModels: Content, Features, Functionality, and Use. CPT:Pharmacometrics & Systems Pharmacology 4:1-14 Software Link
Karapetyan S, Buchler NE (2015) Role of DNA binding sites and slow unbinding kinetics in titration-based oscillators. Physical Review E 92:062712 Macromolecular Biochemistry Theory Link
Kashyap R, Palai T, Bhattacharya PK (2015) Kinetics and model development for enzymatic synthesis of fructo-oligosaccharides using fructosyltransferase. Bioprocess and Biosystems Engineering 38:2417-26 Biotechnology Metabolism Link
Kesten D, Kummer U, Sahle S, Hübner K (2015) A new model for the aerobic metabolism of yeast allows the detailed analysis of the metabolic regulation during glucose pulse. Biophysical Chemistry 206:40-57. Metabolism Link
Koutsouradis E, Provelengios G, Kouskoumvekakis E, Manolakos ES (2015) Scalable FPGA Accelerator of the NRM Algorithm for Efficient Stochastic Simulation of Large-Scale Biochemical Reaction Networks. in 2015 Euromicro Conference on Digital System Design (DSD) pp.583-590 Computational Method Link
Lai M, Brun D, Edelstein SJ, Le Novère N (2015) Modulation of calmodulin lobes by different targets: an allosteric model with hemiconcerted conformational transitions. PLoS Computational Biology 11:e1004063 Biochemistry Enzymology Link
Laurell Nash A, Hertzberg R, Wen YQ, Dahlgren B, Brinck T, Moberg C (2015) Dual Lewis Acid-Lewis Base Catalyzed Acylcyanation of Aldehydes: A Mechanistic Study. Chemistry 22:3821-3829 Chemistry Link
Leber A, Viladomiu M, Hontecillas R, Abedi V, Philipson CW, Hoops S, Howard B, Bassaganya-Riera J (2015) Systems Modeling of Interactions between Mucosal Immunity and the Gut Microbiome during Clostridium difficile Infection. PLoS One 10:e0134849 Immunology Link
Lee TW, Yang AS-P, Brittain T, Birch NP (2015) An analysis approach to identify specific functional sites in orthologous proteins using sequence and structural information: Application to neuroserpin reveals regions that differentially regulate inhibitory activity. Proteins: Structure, Function, and Bioinformatics 83:135-52 Macromolecular Biochemistry Link
Li L, Gervasi N, Girault J-A (2015) Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications 6:6319 Cell Biology Signaling Link
Lu P, Abedi V, Mei Y, Hontecillas R, Hoops S, Carbo A, Bassaganya-Riera J (2015) Supervised learning methods in modeling of CD4+ T cell heterogeneity. BioData Mining 8:1-21 Computational Method Immunology Link
Luna A, McFadden GB, Aladjem MI, Kohn KW (2015) Predicted Role of NAD Utilization in the Control of Circadian Rhythms during DNA Damage Response. PLoS Computational Biology 11:e1004144 Cell Biology Link
Luo J, Theron R, Sewell LJ, Hooper TN, Weller AS, Oliver AG, McIndoe JS (2015) Rhodium-Catalyzed Selective Partial Hydrogenation of Alkynes. Organometallics 34:3021-8 Chemistry Link
Madsen C, Shmarov F, Zuliani P (2015) BioPSy: An SMT-based Tool for Guaranteed Parameter Set Synthesis of Biological Models. Proceedings 13th International Conference, CMSB 2015 (Roux O, Bourdon J, Eds.), Springer pp182-94 Computational Method Link
Maggi M, Chiarelli LR, Valentini G, Scotti C (2015) Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 10:e0117025 Microbiology Biotechnology Enzymology Link
Mandlik V, Gurav M, Singh S (2015) Regulatory dynamics of network architecture and function in tristable genetic circuit of Leishmania: a mathematical biology approach. Journal of Biomolecular Structure and Dynamics 33:2554-62 Synthetic Biology Genetics Metabolism Link
Marwaha S (2015) A Genomics and Mathematical Modeling Approach for the study of Helicobacter pylori associated Gastritis and Gastric Cancer. Ph.D. Thesis, University of Cincinnati, Ohio, USA Immunology Signaling Link
Mei Y, Abedi V, Carbo A, Zhang X, Lu P, Philipson CW, Hontecillas R, Hoops S, Liles N, Bassaganya-Riera J (2015) Multiscale modeling of mucosal immune responses. BMC Bioinformatics 16:Supp12:S2 Immunology Link
Mei Y, Carbo A, Hoops S, Hontecillas R, Bassaganya-Riera J (2015) ENISI SDE: A New Web-Based Tool for Modeling Stochastic Processes. IEEE/ACM Transactions on Computational Biology and Bioinformatics 12:289-97 Software Link
Mendes P, Oliver SG, Kell DB (2015) Fitting Transporter Activities to Cellular Drug Concentrations and Fluxes: Why the Bumblebee Can Fly. Trends in Pharmacological Sciences 36:710-23 Physiology Pharmacology Link
Montes MR, Ferreira-Gomes MS, Centeno M, Rossi RC (2015) The E2P-like state induced by magnesium fluoride complexes in the Na, K-ATPase. Kinetics of formation and interaction with Rb+. Biochimica et Biophysica Acta 1848:1514-23 Enzymology Link
Müller JM, Risse JM, Friehs K, Flaschel E (2015) Model-based development of an assay for the rapid detection of biotin-blocked binding sites of streptavidin. Engineering in Life Sciences 15:627-639 Laboratory Method Link
Nelsen ER, Brezny AC, Landis CR (2015) Interception and Characterization of Catalyst Species in Rhodium Bis(diazaphospholane)-Catalyzed Hydroformylation of Octene, Vinyl Acetate, Allyl Cyanide, and 1-Phenyl-1,3-butadiene. Journal of the American Chemical Society 137:14208-219 Chemistry Link
Palai T, Kumar A, Bhattacharya PK (2015) Kinetic studies and model development for the formation of galacto-oligosaccharides from lactose using synthesized thermo-responsive bioconjugate. Enzyme and Microbial Technology 70:42-49 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones TC, Tyson JJ, Shaffer CA (2015) JigCell Run Manager (JC-RM): a tool for managing large sets of biochemical model parametrizations. BMC Systems Biology 9:95 Software Link
Patschinski P (2015) Chemoselective Silylation of Alcohols Through Lewis Base-catalyzed Reactions. Experimental and Theoretical Studies. Ph.D. Thesis, Ludwig-Maximilians University of Munich, Germany Chemistry Link
Paul D, Dasgupta A, De RK (2015) Exploring the Altered Dynamics of Mammalian Central Carbon Metabolic Pathway in Cancer Cells: A Classical Control Theoretic Approach. PLoS One 10:e0137728. Theory Link
Penkler GP, du Toit F, Adams W, Rautenbach M, Palm DC, van Niekerk DD, Snoep JL (2015) Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS Journal 282:1481-511 Metabolism Link
Peñarrubia L, Romero P, Carrió-Seguí A, Andrés-Bordería A, Moreno J, Sanz A (2015) Temporal aspects of copper homeostasis and its crosstalk with hormones. Frontiers in Plant Science 6:255. Physiology Plant Biology Link
Phelix CF, Feltus FA (2015) Plant stress biomarkers from biosimulations: the Transcriptome-To-Metabolome(TTM) technology-effects of drought stress on rice. Plant Biology 17:63-73 Computational Method Plant Biology Link
Philipson CW (2015) Systems analysis and characterization of mucosal immunity. Ph.D. Thesis, Virginia Tech, USA Immunology Link
Philipson CW, Bassaganya-Riera J, Viladomiu M, Kronsteiner B, Abedi V, Hoops S, Michalak P, Kang L, Girardin SE, Hontecillas R (2015) Modeling the Regulatory Mechanisms by Which NLRX1 Modulates Innate Immune Responses to Helicobacter pylori Infection. PLoS One 10:e0137839 Immunology Link
Pineda E, Encalada R, Vázquez C, González Z, Moreno-Sánchez R, Saavedra E (2015) Glucose Metabolism and Its Controlling Mechanisms in Entamoeba histolytica. In Amebiasis. Part IV Biology and Pathogenesis of Entamoeba (Nozaki T, Bhattacharya A eds.) Springer pp.351-372 Metabolism Microbiology Link
Prieto C, González Delgado JA, Arteaga JF, Jaraíz M, López-Pérez JL, Barrero AF (2015) Homocoupling versus reduction of radicals: an experimental and theoretical study of Ti(III)-mediated deoxygenation of activated alcohols. Organic & Biomolecular Chemistry 13:3462–3469 Chemistry Link
Raganati F, Procentese A, Olivieri G, Götzc P, Salatino P, Marzocchella A (2015) Kinetic study of butanol production from various sugars by Clostridium acetobutylicum using a dynamic model. Biochemical Engineering Journal 99:156-66. Biotechnology Metabolism Microbiology Link
Rastgou Talemi S, Kollarovic G, Lapytsko A, Schaber J (2015) Development of a robust DNA damage model including persistent telomere-associated damage with application to secondary cancer risk assessment. Scientific Reports 5:13540 Genetics Macromolecular Biochemistry Link
Rezgui A, Madec M, Lallement C, Haiech J (2015) Integration of SBML models for the description of biological system in a lab-on-chip. Proceedings of the 22nd International Conference Mixed Design of Integrated Circuits & Systems 165-70 Computational Method Laboratory Method Link
Rosenthal RG, Vögeli B, Quade N, Capitani G, Kiefer P, Vorholt JA, Ebert MO, Erb TJ (2015) The use of ene adducts to study and engineer enoyl-thioester reductases. Nature Chemical Biology 11:398-400. Enzymology Link
Šalagovič J (2015) Formální modely oscilací v biologii a jejich analýza. Ph.D. Thesis, Masarykova univerzita, Czech Republic. Computational Method Link
Samal SS, Grigoriev D, Fröhlich H, Weber A, Radulescu O (2015) A Geometric Method for Model Reduction of Biochemical Networks with Polynomial Rate Functions. Bulletin of Mathematical Biology 77:2180-211. Computational Method Theory Link
Sander ZH, West ZJ, Ervin JS, Zabarnick S (2015) Experimental and Modeling Studies of Heat Transfer, Fluid Dynamics, and Autoxidation Chemistry in the Jet Fuel ThermalOxidation Tester (JFTOT). Energy & Fuels 29:7036-47. Chemistry Chemical Engineering Link
Sapra A, Ramadan D, Thorpe C (2015) Multivalency in the inhibition of oxidative protein folding by arsenic(III) species. Biochemistry 54:612–621 Macromolecular Biochemistry Link
Sengupta A, Grover M, Chakraborty A, Saxena S (2015) HEPNet: A Knowledge Base Model of Human Energy Pool Network for Predicting the Energy Availability Status of an Individual. PLoS One 10:e0127918 Metabolism Link
Sier JH (2015) Investigation of the impact of MRP3 and MRP4 on the disposition of drugs and conjugates in rat and human. Doctoral Thesis, University of Surrey, UK Physiology Link
Subburaj Y, Ros U, Hermann E, Tong R, García-Sáez AJ (2015) Toxicity of an alpha-Pore-forming Toxin Depends on the Assembly Mechanism on the Target Membrane as Revealed by Single Molecule Imaging. Journal of Biological Chemistry 290:4856-4865 Macromolecular Biochemistry Link
Subramanian A, Sarkar RR (2015) Dynamics Of GLI Regulation And A Strategy To Control Cancerous Situation: Hedgehog Signaling Pathway Revisited. Journal of Biological Systems 23:681-719 Signaling Link
Subramanian A, Singh V, Sarkar RR (2015) Understanding Visceral Leishmaniasis Disease Transmission and its Control - A Study Based on Mathematical Modeling. Mathematics 3:913-944 Epidemiology Link
Suwanmajo T, Krishnan J (2015) Mixed mechanisms of multi-site phosphorylation. Journal of the Royal Society Interface 12:20141405 Signaling Link
Sveshnikova AN, Ataullakhanov FI, Panteleev MA (2015) Compartmentalized calcium signaling triggers subpopulation formation upon platelet activation through PAR1. Molecular BioSystems 11:1052-60 Signaling Link
Talawar B (2015) A Crossbar Interconnection Network in DNA. Proceedings of 2015 IEEE International Parallel and Distributed Processing Symposium Workshop, pp. 342-5 Synthetic Biology Link
Terentyeva VA, Sveshnikova AN, Panteleev MA (2015) Kinetics and mechanisms of surface-dependent coagulation factor XII activation. Journal of Theoretical Biology 382:235–243 Physiology Biophysics Link
Torbensen K, Rossi F, Pantani OL, Ristori S, Abou-Hassan A (2015) Interaction of the Belousov-Zhabotinsky Reaction with Phospholipid Engineered Membranes. Journal of Physical Chemistry 119:10224-30 Chemistry Link
Trausinger G, Gruber C, Krahulec S, Magnes C, Nidetzky B, Klimacek M (2015) Identification of novel metabolic interactions controlling carbon flux from xylose to ethanol in natural and recombinant yeasts. Biotechnology for Biofuels and Bioproducts 8:157 Biotechnology Metabolism Link
Tummler K, Kühn C, Klipp E (2015) Dynamic metabolic models in context: biomass backtracking. Integrative Biology 7:940-51 Computational Method Link
Twycross J, Bennett M, Krasnogor N (2015) A High-Performance Multicompartment Stochastic Simulator for Executable Biology. Preprint Link
Tóth A, Brózik A, Szakács G, Sarkadi B, Hegedüs T (2015) A Novel Mathematical Model Describing Adaptive Cellular Drug Metabolism and Toxicity in the Chemoimmune System. PLoS One 10:e0115533 Toxicology Link
Villaverde AF, Henriques D, Smallbone K, Bongard S, Schmid J, Cicin-Sain D, Crombach A, Saez-Rodriguez J, Mauch K, Balsa-Canto E, Mendes P, Jaeger J, Banga JR (2015) BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology. BMC Systems Biology 9:8 Computational Method Link
Wang H-Y, Huang Y-X, Zheng L-H, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Sun Y, Wang G-N, Ma Z-Q, Li Y-X (2015) Modelling Coupled Oscillations in the Notch, Wnt, and FGF Signaling Pathways during Somitogenesis: A Comprehensive Mathematical Model. Computational Intelligence and Neuroscience 2015:387409 Signaling Link
Willems PH, Pahle J, Stalpers XL, Mugahid D, Nikolaew A, Koopman WJ, Kummer U (2015) PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals. FEBS Journal 282:2187-201 Signaling Link
Zhou J, Aponte-Santamaría C, Sturm S, Bullerjahn JT, Bronowska A, Gräter F (2015) Mechanism of Focal Adhesion Kinase Mechanosensing. PLoS Computational Biology 11:e1004593 Macromolecular Biochemistry Cell Biology Link
Zimmer C (2015) Reconstructing the hidden states in time course data of stochastic models. Mathematical Biosciences 269:117-29 Computational Method Link
Zimmer C, Sahle S (2015) A termination criterion for parameter estimation in stochastic models in systems biology. BioSystems 9:181-92 Computational Method Link

92 publications
2014
Antunes G, Sebastião AM, de Souza FMS (2014) Mechanisms of regulation of olfactory transduction and adaptation in the olfactory cilium. PLoS One 9:e105531 Signaling Pharmacology Link
Arnold A, Nikoloski Z (2014) In search for an accurate model of the photosynthetic carbon metabolism. Mathematics and Computers in Simulation 96:171–194 Plant Biology Metabolism Link
Aubert N, Mosca C, Fujii T, Hagiya M, Rondelez Y (2014) Computer-assisted design for scaling up systems based on DNA reaction networks. Journal of the Royal Society Interface 11:20131167 Software Link
Beauvoit B, Colombié S, Monier A, Andrieu M-H, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat J-P, Gibon Y (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell 26:3224-42 Metabolism Plant Biology Link
Bellini M, Besozzi D, Cazzaniga P, Mauri G, Nobile MS (2014) Simulation and analysis of the blood coagulation cascade accelerated on GPU. 2014 22nd Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP), IEEE, 590–593 Computational Method Link
Benfeitas R, Selvaggio G, Antunes F, Coelho PMBM, Salvador A (2014) Hydrogen peroxide metabolism and sensing in human erythrocytes: a validated kinetic model and reappraisal of the role of peroxiredoxin II. Free Radical Biology and Medicine 74:35-49 Metabolism Link
Bhosle A, Chandra N (2014) Different cancer cell lines resistant to the same drug exhibit differences in folate pathway dynamics. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 209-213 Metabolism Link
Boba P, Gries S, Hamacher K (2014) R as an Integration Tool in High Performance Computing - Lessons Learned. GI-Jahrestagung. Lecture Notes in Informatics 232:138–148 Computational Method Software Link
Carbo A, Olivares-Villagómez D, Hontecillas R, Bassaganya-Riera J, Chaturvedi R, Piazuelo MB, Delgado A, Washington MK, Wilson KT, Algood HMS (2014) Systems modeling of the role of IL-21 in the maintenance of effector CD4+ T cell responses during chronic Helicobacter pylori infection. mBio 5:e01243-14 Immunology Link
Carrasco D, Pérez-Temprano MH, Casares JA, Espinet P (2014) Cross Alkyl-Aryl versus Homo Aryl-Aryl Coupling in Palladium-Catalyzed Coupling of Alkyl-Gold (I) and Aryl-Halide. Organometallics 33:3540-3545 Chemistry Link
Castaldi DF (2014) Network Based Simulation on HPC for Translational Medicine: an Application to Anticoagulation. Ph.D. Thesis, University of Milano-Bicocca, Milan, Italy. Computational Method Link
Cazzaniga P, Nobile MS, Besozzi D, Bellini M, Mauri G (2014) Massive exploration of perturbed conditions of the blood coagulation cascade through GPU parallelization. BioMed Research International 2014:863298 Computational Method Link
Claudino M, Jonsson M, Johansson M (2014) Utilizing thiol-ene coupling kinetics in the design of renewable thermoset resins based on D-limonene and polyfunctional thiols. RSC Advances 4:10317-10329 Chemistry Link
Clough JM, Sijbesma RP (2014) Dioxetane scission products unchanged by mechanical force. ChemPhysChem 15:3565–3571 Chemistry Link
Costa RS, Hartmann A, Gaspar P, Neves AR, Vinga S (2014) An extended dynamic model of Lactococcus lactis metabolism for mannitol and 2,3-butanediol production. Molecular BioSystems 10:628-639 Microbiology Metabolism Link
Cui Y, Murphy B, Gentilcore A, Sharma Y, Minasian LM, Kramer BS, Coates PM, Gohagan JK, Klenk J, Tidor B (2014) Multilevel modeling and value of information in clinical trial decision support. BMC Systems Biology 8:6 Metabolism Link
Dalle Pezze P, Nelson G, Otten EG, Korolchuk VI, Kirkwood TBL, von Zglinicki T, Shanley DP (2014) Dynamic Modelling of Pathways to Cellular Senescence Reveals Strategies for Targeted Interventions. PLoS Computational Biology 10:e1003728. Signaling Link
Drees B, Reiger M, Jung K, Bischofs IB (2014) A modular view of the diversity of cell-density-encoding schemes in bacterial quorum-sensing systems. Biophysical Journal 107:266-277 Microbiology Link
Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews KR, Clayton C (2014) Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Molecular Microbiology 94:307-326 Microbiology Genomics Link
Figueredo GP, Siebers P-O, Owen MR, Reps J, Aickelin U (2014) Comparing stochastic differential equations and agent-based modelling and simulation for early-stage cancer. PLoS One 9:e95150 Computational Method Link
Gautam VK, Czeizler E, Haddow PC, Kuiper M (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. In: Dediu AH, Lozano M, Martín-Vide C (eds) Theory and Practice of Natural Computing. TPNC 2014. Lecture Notes in Computer Science 8890:119-133 Synthetic Biology Link
Gianni S, Dogan J, Jemth P (2014) Distinguishing induced fit from conformational selection. Biophysical Chemistry 189:33–39 Macromolecular Biochemistry Link
Godfrey L, Yamada-Fowler N, Smith J, Thornalley PJ, Rabbani N (2014) Arginine-directed glycation and decreased HDL plasma concentration and functionality. Nutrition & Diabetes 4:e134 Physiology Link
Graybill C, Prehoda KE (2014) Ordered multisite phosphorylation of lethal giant larvae by atypical protein kinase C. Biochemistry 53:4931-7 Signaling Link
Guillaud F, Dröse S, Kowald A, Brandt U, Klipp E (2014) Superoxide production by cytochrome bc 1 complex: A mathematical model. Biochimica et Biophysica Acta 1837:1643–1652 Enzymology Link
Hallinan JS, Gilfellon O, Misirli G, Wipat A (2014) Tuning receiver characteristics in bacterial quorum communication: An evolutionary approach using standard virtual biological parts. Proceedings of the 2014 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 1-8 Synthetic Biology Link
Helgeson LA (2014) Mechanisms of Branched Actin Network Formation through Coordinate Activation of Arp2/3 Complex. Ph.D. Thesis, University of Oregon, USA. Cell Biology Link
Hui W, Young DA, Rowan AD, Xu X, Cawston TE, Proctor CJ (2014) Oxidative changes and signalling pathways are pivotal in initiating age-related changes in articular cartilage. Annals of the Rheumatic Diseases 75:449–458 Signaling Immunology Link
Ihekwaba AEC, Mura I, Barker GC (2014) Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. BMC Systems Biology 8:119 Microbiology Link
Irving JA, Haq I, Dickens JA, Faull SV, Lomas DA (2014) Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization. Biochemical Journal 460:103–119 Macromolecular Biochemistry Link
Ivan ANY (2014) Assisted Design of DNA Computing Systems: the DNA Toolbox and Beyond. Ph.D. Thesis, University of Tokyo, Japan. Synthetic Biology Computational Method Link
Jakubík J, Zimčík P, Randáková A, Fuksová K, El-Fakahany EE, Doležal V (2014) Molecular mechanisms of methoctramine binding and selectivity at muscarinic acetylcholine receptors. Molecular Pharmacology 86:180–192 Pharmacology Link
James AI, Imran HAQ, Jennifer AD, Sarah VF, David AL (2014) Altered native stability is the dominant basis for susceptibility of alpha1-antitrypsin mutants to polymerization. Biochemical Journal 460:103-115 Macromolecular Biochemistry Link
Jarrah AS, Castiglione F, Evans NP, Grange RW, Laubenbacher R (2014) A Mathematical Model of Skeletal Muscle Disease and Immune Response in the mdx Mouse. BioMed Research International 2014:871810 Immunology Link
Jones AX (2014) Mechanistic studies of enantioselective alkene bromolactonisation reactions. Ph.D. Thesis, Imperial College London, UK. Chemistry Link
Karonen M, Mattila H, Huang P, Mamedov F, Styring S, Tyystjärvi E (2014) A tandem mass spectrometric method for singlet oxygen measurement. Photochemistry and Photobiology 90:965-971 Laboratory Method Link
Kefalidis CE, Davi M, Holstein PM, Clot E, Baudoin O (2014) Mechanistic Study of the Selectivity of Olefin versus Cyclobutene Formation by Palladium (0)-Catalyzed Intramolecular C (sp3)-H Activation. Journal of Organic Chemistry 79:11903-11910 Chemistry Link
Kent PD, Mondloch JE, Finke RG (2014) A Four-Step Mechanism for the Formation of Supported-Nanoparticle Heterogenous Catalysts in Contact with Solution: The Conversion of Ir (1, 5-COD) Cl/gamma-Al2O3 to Ir (0) 170/gamma-Al2O3. Journal of the American Chemical Society 136:1930-41 Chemistry Link
Khandekar DC, Palai T, Agarwal A, Bhattacharya PK (2014) Kinetics of sucrose conversion to fructo-oligosaccharides using enzyme (invertase) under free condition. Bioprocess and Biosystems Engineering 37:2529–2537 Enzymology Biotechnology Link
Kleppe R, Ghorbani S, Fossbakk A, Martinez A, Haavik J (2014) Modeling the Dynamics of Dopamine Biosynthesis and its Regulation by Tyrosine Hydroxylase. In: Eiden LE (ed) Catecholamine Research in the 21st Century. Boston: Academic Press, 30. Metabolism Link
Kleppe R, Ghorbani S, Martinez A, Haavik J (2014) Modelling cellular signal communication mediated by phosphorylation dependent interaction with 14-3-3 proteins. FEBS Letters 588:92–98 Signaling Link
Lakin MR, Minnich A, Lane T, Stefanovic D (2014) Design of a biochemical circuit motif for learning linear functions. Journal of the Royal Society Interface 11:20140902 Synthetic Biology Link
Le Muzic M, Parulek J, Stavrum A-K, Viola I (2014) Illustrative visualization of molecular reactions using omniscient intelligence and passive agents. Computer Graphics Forum 33:141-150 Software Link
Leal Denis MF (2014) Homeostasis de ATP extracelular en eritrocitos: interregulación y consecuencias funcionales. Ph.D. Thesis, Universidad de Buenos Aires, Argentina. Physiology Link
Liao C, Cai Y (2014) Towards Modeling Automation for Synthetic Biology. In: Kulkarni V., Stan GB., Raman K. (eds.) A Systems Theoretic Approach to Systems and Synthetic Biology II: Analysis and Design of Cellular Systems. Springer, Dordrecht, 201–217 Synthetic Biology Computational Method Link
Ligon TS, Leonhardt C, Rädler JO (2014) Multi-level kinetic model of mRNA delivery via transfection of lipoplexes. PLoS One 9:e107148 Cell Biology Genomics Link
Luo J (2014) Mechanistic investigation of catalytic organometallic reactions using ESI MS. Ph.D. Thesis, University of Victoria, British Columbia, Canada. Chemistry Link
Lutz A, Sanwald J, Thomas M, Feuer R, Sawodny O, Ederer M, Borner C, Humar M, Merfort I (2014) Interleukin-1beta Enhances FasL-Induced Caspase-3/-7 Activity without Increasing Apoptosis in Primary Mouse Hepatocytes. PLoS One 9:e115603. Immunology Link
Machado D, Rodrigues L, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. BioSystems 125:16-21 Synthetic Biology Metabolism Link
Marwaha S, Schumacher MA, Zavros Y, Eghbalnia HR (2014) Crosstalks between Cytokines and Sonic Hedgehog in Helicobacter pylori Infection: A Mathematical Model. PLoS One 9:e111338. Immunology Signaling Link
Marín-Hernández Á, López-Ramírez SY, Del Mazo-Monsalvo I, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Modeling cancer glycolysis under hypoglycemia, and the role played by the differential expression of glycolytic isoforms. FEBS Journal 281:3325–3345 Metabolism Link
Marín-Hernández Á, López-Ramírez SY, Gallardo-Pérez JC, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2014) Systems biology approaches to cancer energy metabolism. in M.A. Aon et al. (eds.), Systems Biology of Metabolic and Signaling Networks, Springer-Verlag pp.213-239 Metabolism Link
Matsuoka Y, Funahashi A, Ghosh S, Kitano H (2014) Modeling and simulation using CellDesigner. Methods in Molecular Biology 1164:121-145 Software Link
McAuley MT, Khalil R, Stockton DJ, Schilstra MJ (2014) Modelling the flagellar motor assembly process to help improve industrial operations systems design. Preprint Signaling Link
Mei Y, Carbo A, Hontecillas R, Hoops S, Liles N, Lu P, Philipson CW, Bassaganya-Riera J (2014) ENISI MSM: A novel multi-scale modeling platform for computational immunology. Proceedings of the 2014 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 391-396 Software Link
Meyer P, Cokelaer T, Chandran D, Kim KH, Loh P-R, Tucker G, Lipson M, Berger B, Kreutz C, Raue A, Steiert B, Timmer J, Bilal E, Sauro HM, Stolovitzky G, Saez-Rodriguez J (2014) Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology 8:13 Computational Method Link
Miller AJM, Kaminsky W, Goldberg KI (2014) Arene Activation at Iridium Facilitates C-O Bond Cleavage of Aryl Ethers. Organometallics 33:1245-1252 Chemistry Link
Mol M, Patole MS, Singh S (2014) Immune signal transduction in leishmaniasis from natural to artificial systems: role of feedback loop insertion. Biochimica et Biophysica Acta 1840:71–79 Signaling Immunology Link
Mozga I, Stalidzans E (2014) Reduction of Combinatorial Space of Adjustable Kinetic Parameters of Biochemical Network Models in Optimisation Task. Baltic Journal of Modern Computing 150:150–159 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Mauri G (2014) GPU-accelerated simulations of mass-action kinetics models with cupSODA. Journal of Supercomputing 69:17-24 Computational Method Link
Nobile MS, Cazzaniga P, Besozzi D, Pescini D, Mauri G (2014) cuTauLeaping: A GPU-Powered Tau-Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS One 9:e91963. Computational Method Link
Ouzounoglou E, Kalamatianos D, Emmanouilidou E, Xilouri M, Stefanis L, Vekrellis K, Manolakos ES (2014) In silico modeling of the effects of alpha-synuclein oligomerization on dopaminergic neuronal homeostasis. BMC Systems Biology 8:54 Physiology Cell Biology Link
Palai T, Singh AK, Bhattacharya PK (2014) Enzyme, beta-galactosidase immobilized on membrane surface for galacto-oligosaccharides formation from lactose: kinetic study with feed flow under recirculation loop. Biochemical Engineering Journal 88:68-76 Biotechnology Enzymology Link
Palmisano A, Hoops S, Watson LT, Jones Jr TC, Tyson JJ, Shaffer CA (2014) Multistate Model Builder (MSMB): a flexible editor for compact biochemical models. BMC Systems Biology 8:42 Software Computational Method Link
Pandey V (2014) Metabolic modeling of different degrees of steatohepatitis in mice. Ph.D. Thesis, Department of Mathematics and Computer Science, Free University of Berlin, Germany. Metabolism Link
Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo M-L, Sültmann H, Trauner M, Denk M, Zatloukal K, Lehrach H, Wierling C (2014) Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains. PLoS One 9:e111006. Metabolism Link
Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z (2014) Towards a computational model of a methane producing archaeum. Archaea 2014:898453 Metabolism Microbiology Whole-Cell Models Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2014) Biomarkers from biosimulations: Transcriptome-to-reactome™ Technology for individualized medicine. 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 3452–3455 Computational Method Link
Phelix CF, Villareal G, LeBaron R, Perry G, Roberson DJ (2014) Precision medicine using individualized biosimulations of drug dosing: Alzheimer’s disease. Healthcare Innovation Conference (HIC), IEEE, 292–295 Pharmacology Link
Proctor CJ, Macdonald C, Milner JM, Rowan AD, Cawston TE (2014) A Computer Simulation Approach to Assessing Therapeutic Intervention Points for the Prevention of Cytokine-Induced Cartilage Breakdown. Arthritis & Rheumatology 66:979-989 Immunology Link
Rabbani N, Xue M, Thornalley PJ (2014) Activity, regulation, copy number and function in the glyoxalase system. Biochemical Society Transactions 42:419–424 Metabolism Link
Raganati F (2014) Butanol production by fermentation of renewable feedstocks. Ph.D. Thesis, Università di Napoli Federico II, Naples, Italy Biotechnology Link
Rao S, van der Schaft A, van Eunen K, Bakker BM, Jayawardhana B (2014) A model reduction method for biochemical reaction networks. BMC Systems Biology 8:52 Computational Method Link
Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. Journal of Biological Chemistry 289:14448–14457 Macromolecular Biochemistry Biophysics Microbiology Link
Rossi F, Ristori S, Marchettini N, Pantani OL (2014) Functionalized clay microparticles as catalysts for chemical oscillators. Journal of Physical Chemistry 118:24389–24396 Chemistry Link
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S (2014) A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. BioSystems 124:26–38 Metabolism Signaling Genetics Link
Sakkalis V, Sfakianakis S, Tzamali E, Marias K, Stamatakos G, Misichroni F, Ouzounoglou E, Kolokotroni E, Dionysiou D, Johnson D, McKeever S, Graf N (2014) Web-based workflow planning platform supporting the design and execution of complex multiscale cancer models. IEEE Journal of Biomededical Health Informatics 18:824-31 Software Link
Saller S, Kunz L, Berg D, Berg U, Lara H, Urra J, Hecht S, Pavlik R, Thaler CJ, Mayerhofer A (2014) Dopamine in human follicular fluid is associated with cellular uptake and metabolism-dependent generation of reactive oxygen species in granulosa cells: implications for physiology and pathology. Human Reproduction 29:555-67 Physiology Metabolism Link
Sapra A, Ramadan D, Thorpe C (2014) Multivalency in the inhibition of oxidative protein folding by arsenic (III) species. Biochemistry 54:612–621 Biochemistry Link
Schaber J, Lapytsko A, Flockerzi D (2014) Nested autoinhibitory feedbacks alter the resistance of homeostatic adaptive biochemical networks. Journal of the Royal Society Interface 11:20130971 Signaling Link
Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhütter H-G, Schuster S (2014) A theoretical study of lipid accumulation in the liver—Implications for nonalcoholic fatty liver disease. Biochimica et Biophysica Acta 1841:62–69 Metabolism Link
Schmitz U, Lai X, Winter F, Wolkenhauer O, Vera J, Gupta SK (2014) Cooperative gene regulation by microRNA pairs and their identification using a computational workflow. Nucleic Acids Research 42:7539-7552 Computational Method Link
Shinde S, Mol M, Singh S (2014) Regulatory networks, genes and glycerophospholipid biosynthesis pathway in schistosomiasis: A systems biology view for pharmacological intervention. Gene 550:214-22. Pharmacology Genomics Link
Smallbone K, Corfe BM (2014) A mathematical model of the colon crypt capturing compositional dynamic interactions between cell types. International Journal of Experimental Pathology 95:1–7 Physiology Link
Sosa CM, Pavarotti MA, Zanetti MN, Zoppino FCM, De Blas GA, Mayorga LS (2014) Kinetics of human sperm acrosomal exocytosis. MHR: Basic Science of Reproductive Medicine 21:244–254 Cell Biology Link
Spiaggi AJ (2014) Caracterización de los pasos involucrados en el transporte de K+ por la Na+/K+-ATPasa. Ph.D. Thesis, Universidad de Buenos Aires, Argentina. Enzymology Link
Sugiura M, Azami C, Koyama K, Rutherford AW, Rappaport F, Boussac A (2014) Modification of the pheophytin redox potential in Thermosynechococcus elongatus Photosystem II with PsbA3 as D1. Biochimica et Biophysica Acta 1837:139–148 Metabolism Microbiology Biophysics Link
Talemi SR, Jacobson T, Garla V, Navarrete C, Wagner A, Tamás MJ, Schaber J (2014) Mathematical modelling of arsenic transport, distribution and detoxification processes in yeast. Molecular Microbiology 92:1343–1356 Toxicology Metabolism Link
Tunnicliffe RB, Hautbergue GM, Wilson SA, Kalra P, Golovanov AP (2014) Competitive and Cooperative Interactions Mediate RNA Transfer from Herpesvirus Saimiri ORF57 to the Mammalian Export Adaptor ALYREF. PLoS Pathogens 10:e1003907 Macromolecular Biochemistry Link
Valero G, Ribó JM, Moyano A (2014) A closer look at spontaneous mirror symmetry breaking in aldol reactions. Chemistry 20:17395–17408 Chemistry Link
Valero G (2014) Estudis mecanístics i metodològics de processos d'autocatàlisi i organocatàlisi asimètriques. Ph.D. Thesis, Department of Organic Chemistry, University of Barcelona, Spain Chemistry Link
Ventura AC, Bush A, Vasen G, Goldín MA, Burkinshaw B, Bhattacharjee N, Folch A, Brent R, Chernomoretz A, Colman-Lerner A (2014) Utilization of extracellular information before ligand-receptor binding reaches equilibrium expands and shifts the input dynamic range. Proceedings of the National Academy of Sciences USA 111:E3860–E3869 Signaling Link
Vickers JW, Sumliner JM, Lv H, Morris M, Geletii YV, Hill CL (2014) Collecting meaningful early-time kinetic data in homogeneous catalytic water oxidation with a sacrificial oxidant. Physical Chemistry Chemical Physics 16:11942-11949 Chemistry Link
Wang CCN, Chang P-C, Ng K-L, Chang C-M, Sheu PCY, Tsai JJP (2014) A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biology 8:15 Signaling Link
Yang X, Zhang Y, Zheng Y, Ma H (2014) Development and analysis of a kinetic model for Escherichia coli threonine biosynthesis. Chinese Journal of Biotechnology 30:18-29. Metabolism Microbiology Link
Zikmanis P, Kampenusa I (2014) Relationship between Metabolic Fluxes and Sequence-Derived Properties of Enzymes. International Scholarly Research Notices 2014:817102 Metabolism Link
Zimmer C, Sahle S, Pahle J (2014) Exploiting intrinsic fluctuations to identify model parameters. IET Systems Biology 9:64-73 Computational Method Link

97 publications
2013
Altintaş CM (2013) Effects of growth medium conditions on antibiotic production by actinomyces sp. MS Thesis, Dokuz Eylül University, Izmir, Turkey Biotechnology Microbiology Link
Berestovsky N, Nakhleh L (2013) An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data. PLoS One 8:e66031 Computational Method Link
Bulipopa N, Sulins J (2013) Automatic termination of parallel optimization runs of global stochastic optimization methods by upper limit criterion. Biosystems and Information Technology 2:15-18 Computational Method Link
Carbo A, Bassaganya-Riera J, Pedragosa M, Viladomiu M, Marathe M, Eubank S, Wendelsdorf K, Bisset K, Hoops S, Deng X, Alam M, Kronsteiner B, Mei Y, Hontecillas R (2013) Predictive Computational Modeling of the Mucosal Immune Responses during Helicobacter pylori Infection. PLoS One 8:e73365 Immunology Link
Carbo A, Hontecillas R, Kronsteiner B, Viladomiu M, Pedragosa M, Lu P, Philipson CW, Hoops S, Marathe M, Eubank S, Bisset K, Wendelsdorf K, Jarrah AS, Mei Y, Bassaganya-Riera J (2013) Systems modeling of molecular mechanisms controlling cytokine-driven CD4+ T cell differentiation and phenotype plasticity. PLoS Computational Biology 9:e1003027 Immunology Signaling Link
Challenger JD (2013) The stochastic dynamics of biochemical systems. Ph.D. Thesis, University of Manchester, UK Computational Method Metabolism Link
Chelliah V, Laibe C, Le Novère N (2013) BioModels database: a repository of mathematical models of biological processes. Methods in Molecular Biology 1021:189–199 Software Link
Claudino M (2013) Macromolecular design: UV-curable thiol-ene networks based on renewable resources. Ph.D. Thesis, KTH Royal Institute of Technology, Stockholm, Sweden Chemistry Link
Claudino M, Jonsson M, Johansson M (2013) Thiol–ene coupling kinetics of d-limonene: a versatile ‘non-click’free-radical reaction involving a natural terpene. RSC Advances 3:11021–11034 Chemistry Link
Cornish-Bowden A, Piedrafita G, Morán F, Cárdenas ML, Montero F (2013) Simulating a model of metabolic closure. Biological Theory 8:383-390 Theory Link
Coskun SA, Cicek AE, Lai N, Dash RK, Ozsoyoglu ZM, Ozsoyoglu G (2013) An online model composition tool for system biology models. BMC Systems Biology 7:88 Computational Method Link
Diao T, Pun D, Stahl SS (2013) Aerobic Dehydrogenation of Cyclohexanone to Cyclohexenone Catalyzed by Pd(DMSO)2(TFA)2: Evidence for Ligand-Controlled Chemoselectivity. Journal of the American Chemical Society 135:8205-8212 Chemistry Link
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link
Fedosov SN, Brask J, Pedersen AK, Nordblad M, Woodley JM, Xu X (2013) Kinetic model of biodiesel production using immobilized lipase Candida antarctica lipase B. Journal of Molecular Catalysis B: Enzymatic 85–86:156–168 Biotechnology Enzymology Link
Firczuk H, Kannambath S, Pahle J, Claydon A, Beynon R, Duncan J, Westerhoff HV, Mendes P, McCarthy JEG (2013) An in vivo control map for the eukaryotic mRNA translation machinery. Molecular Systems Biology 9:635 Macromolecular Biochemistry Cell Biology Link
Fröhlich M (2013) Computational and experimental investigation of the mechanisms involved in cellular water transport and (cat)ion homeostasis. Ph.D. Thesis, Free University of Berlin, Germany Physiology Link
Galazka M, Hay JO (2013) In silico metabolic control analysis of Brassica napus seeds based on dynamic kinetic modeling. A Compilation of Internship Reports. In (Stegman M, Morris M. and Blackburn N, eds.) A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 75–80 Metabolism Link
Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV (2013) Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochimica et Biophysica Acta 1830:4943- 59 Toxicology Metabolism Link
Genc S, Sorguven E, Ozilgen M, Aksan Kurnaz I (2013) Unsteady exergy destruction of the neuron under dynamic stress conditions. Energy 59:422–431 metabolism Link
Gow C-H (2013) Novel mechanisms of transcriptional regulation by leukemia fusion proteins. Ph.D. Thesis, University of Cincinnati, Ohio, USA. Signaling Link
Haq I, Irving JA, Faull SV, Dickens JA, Ordonez A, Belorgey D, Gooptu B, Lomas DA (2013) Reactive centre loop mutants of alpha-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway. Bioscience Reports 33:499-511 Macromolecular Biochemistry Link
Hayashi K, Piras V, Tabata S, Tomita M, Selvarajoo K (2013) A systems biology approach to suppress TNF-induced proinflammatory gene expressions. Cell Communication and Signaling 11:84 Signaling Link
Helgeson LA, Nolen BJ (2013) Mechanism of synergistic activation of Arp2/3 complex by cortactin and N-WASP. eLife 2:e00884 Macromolecular Biochemistry Signaling Link
Incicco JJ, Gebhard LG, González-Lebrero RM, Gamarnik AV, Kaufman SB (2013) Steady-State NTPase Activity of Dengue Virus NS3: Number of Catalytic Sites, Nucleotide Specificity and Activation by ssRNA. PLoS One 8:e58508 Macromolecular Biochemistry Link
Jensen MV, Hay JO (2013) Systems Biology Markup Language formulation of a dynamic kinetic model and its uses in quantitative and computational metabolic modeling. In (Stegman M, Morris M. and Blackburn N, eds.) A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 108–112 Computational Method Link
Kampenusa I, Zikmanis P (2013) Relationships between metabolic fluxes and enzyme amino acid composition. Central European Journal of Biology 8:107–120 Metabolism Link
Kennedy N, Mizeranschi A, Thompson P, Zheng H, Dubitzky W (2013) Reverse engineering of gene regulation models from multi-condition experiments. Proceedings of the 2013 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), pp.112-119 Computational Method Link
Kent E, Neumann S, Kummer U, Mendes P (2013) What Can We Learn from Global Sensitivity Analysis of Biochemical Systems? PLoS One 8:e79244 Computational Method Link
Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybilo M, Driessen NN, Gilbert DR, Breitling R, Bakker BM, Barrett MP (2013) Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Computational Biology 9:e1003371. Metabolism Link
Khan HA (2013) Asymmetric Synthesis of Lactones and Lactams: Rhodium Catalysis in the Hydroacylation of Ketones and the Hydrogenation of Cyclic Dehydropeptides. Ph.D. Thesis, Department of Chemistry, University of Toronto, Canada Chemistry Link
Klement M, Šafránek D, Ded T, Pejznoch A, Nedbal L, Steuer R, Cerveny J, Müller S (2013) A comprehensive web-based platform for domain-specific biological models. Electronic Notes in Theoretical Computer Science 299:61-67 Software Link
Kolodkin AN, Sahin N, Phillips A, Hood SR, Bruggeman FJ, Westerhoff HV, Plant NJ (2013) Optimization of stress response through the nuclear receptor-mediated cortisol signalling network. Nature Communications 4:1792 Signaling Link
Kourdis PD, Goussis DA (2013) Glycolysis in Saccharomyces cerevisiae: Algorithmic exploration of robustness and origin of oscillations. Mathematical Biosciences 243:190-214 Theory Link
Kraut DA (2013) Slippery substrates impair ATP-dependent protease function by slowing unfolding. Journal of Biological Chemistry 288:34729-34735 Enzymology Link
LeBaron R, Villareal G, Roberson DJ, Phelix CF (2013) Abstract 5224: Breast cancer biomarkers from biosimulations: transcriptome-to-reactome™ technology. Cancer Research 73:5224 Genomics Computational Method Link
Leroux AE, Haanstra JR, Bakker BM, Krauth-Siegel RL (2013) Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. Journal of Biological Chemistry 288:23751-23764 Metabolism Link
Levering J, Kummer U, Becker K, Sahle S (2013) Glycolytic oscillations in a model of a lactic acid bacterium metabolism. Biophysical Chemistry 172:53-60 Metabolism Link
Lv H, Rudd JA, Zhuk PF, Lee JY, Constable EC, Housecroft CE, Hill CL, Musaev DG, Geletii YV (2013) Bis (4'-(4-pyridyl)-2,2':6',2''-terpyridine)ruthenium (ii) complexes and their N-alkylated derivatives in catalytic light-driven water oxidation. RSC Advances 3:20647-20654 Chemistry Link
Maccari G, Mori M, Rodríguez-Salarichs J, Fang W, Díaz JF, Botta M (2013) Free Energy Profile and Kinetics Studies of Paclitaxel Internalization from the Outer to the Inner Wall of Microtubules. Journal of Chemical Theory and Computation 9:698-706 Cell Biology Macromolecular Biochemistry Pharmacology Link
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (2013) Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits. BMC Systems Biology 7:42 Computational Method Link
Mednis M, Vigants A (2013) Automatic comparison of metabolites names: impact of criteria thresholds. Biosystems and Information Technology 2:1-5 Computational Method Link
Mei Y, Carbo A, Hontecillas R, Bassaganya-Riera J (2013) ENISI SDE: a novel web-based stochastic modeling tool for computational biology. 2013 Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pp. 392-397 Computational Method Software Link
Mei Y, Hontecillas R, Zhang X, Carbo A, Bassaganya-Riera J (2013) Neural network models for classifying immune cell subsets. 2013 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) 18-21 Dec. 2013, pp.5-11 Computational Method Link
Mensonides F, Bakker BM, Cremazy F, Messiha HL, Mendes P, Boogerd FC, Westerhoff HV (2013) A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters 587:2860-7 Metabolism Link
Miah F, Koliwer-Brandl H, Rejzek M, Field RA, Kalscheuer R, Bornemann S (2013) Flux through trehalose synthase flows from trehalose to the alpha anomer of maltose in mycobacteria. Chemical Biology 20:487-493 Metabolism Link
Mitchell S, Mendes P (2013) A Computational Model of Liver Iron Metabolism. PLoS Computational Biology 9:e1003299 Metabolism Link
Mozga I (2013) Determinition of best set of adjustable parameters with full search and limited search methods. Biosystems and Information Technology 2:11–14 Computational Method Link
Nim TH, White JK, Tucker-Kellogg L (2013) SPEDRE: a web server for estimating rate parameters for cell signaling dynamics in data-rich environments. Nucleic Acids Research 41:W187-191 Software Link
Nobile MS , Besozzi D, Cazzaniga P, Mauri G, Pescini D (2013) cupSODA: a CUDA-powered simulator of mass-action kinetics. Parallel Computing Technologies Proceedings of the 12th International Conference, PaCT 2013, St. Petersburg, pp.344-357 Computational Method Link
Nägele T, Weckwerth W (2013) A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Frontiers in Plant Science 4:541 Metabolism Plant Biology Link
Palai T, Bhattacharya PK (2013) Kinetics of lactose conversion to galacto-oligosaccharides by beta-galactosidase immobilized on PVDF membrane. Journal of Bioscience and Bioengineering 115:668-673 Enzymology Link
Palaniappan SK (2013) Probabilistic verification and analysis of biopathway dynamics. Ph.D. Thesis School of Computing, National University of Singapore Computational Method Link
Penkler GP (2013) A kinetic model of glucose catabolism in Plasmodium falciparum. Ph.D. Thesis, Faculty of Science, University of Stellenbosch, South Africa Metabolism Link
Phelix CF, LeBaron R, Roberson DJ, Villareal G, Perry G (2013) Flux and metabolite pathway mapping in the aging and Alzheimer’s disease hippocampus. Alzheimer’s & Dementia 9:P346–P347 Metabolism Link
Phelix CF, Villareal G, LeBaron RG, Roberson DJ (2013) Molecular neural model recreates electrophysiology: Transcriptome-To-Physiome™ NeurobioSimulations using COPASI® software. Proceedings of the 2013 6th International IEEE/EMBS Conference on Neural Engineering (NER). San Diego, CA, 178–181 Physiology Link
Philipson CW, Bassaganya-Riera J, Hontecillas R (2013) Animal models of enteroaggregative Escherichia coli infection. Gut Microbes 4:281-291 Immunology Link
Proctor CJ, Boche D, Gray DA, Nicoll JAR (2013) Investigating Interventions in Alzheimer's Disease with Computer Simulation Models. PLoS One 8:e73631 Macromolecular Biochemistry Link
Pun D, Diao T, Stahl SS (2013) Aerobic dehydrogenation of cyclohexanone to phenol catalyzed by Pd (TFA) 2/2-dimethylaminopyridine: Evidence for the role of Pd nanoparticles. Journal of the American Chemical Society 135:8213–8221 Chemistry Link
Qi Y-F, Huang Y-X, Wang H-Y, Zhang Y, Bao Y-L, Sun L-G, Wu Y, Yu C-L, Song Z-B, Zheng L-H, Sun Y, Wang G-N, Li Y-X (2013) Elucidating the crosstalk mechanism between IFN-gamma and IL-6 via mathematical modelling. BMC Bioinformatics 14:41 Signaling Link
Ravichandran S, Rao KVS, Jain S (2013) Bistability in a model of early B cell receptor activation and its role in tonic signaling and system tunability. Molecular BioSystems 9:2498-2511 Signaling Link
Reeves BD, Hilmer JK, Mellmann L, Hartzheim M, Poffenberger K, Johnson K, Joshi N, Singel DJ, Grieco PA (2013) Selective trapping of SNO-BSA and GSNO by benzenesulfinic acid sodium salt: mechanistic study of thiosulfonate formation and feasibility as a protein S-nitrosothiol detection strategy. Tetrahedron Letters 54:5707-10 Chemistry Link
Roberts E, Stone JE, Luthey-Schulten Z (2013) Lattice microbes: High-performance stochastic simulation method for the reaction-diffusion master equation. Journal of Computational Chemistry 34:245-255 Computational Method Link
Rutkis R, Kalnenieks U, Stalidzans E, Fell DA (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology 159:2674-2689 Metabolism Microbiology Link
Saeidi N, Arshath M, Chang MW, Poh CL (2013) Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation. Chemical Engineering Science 103:91–99 Synthetic Biology Microbiology Link
Sahaboglu A, Paquet-Durand O, Dietter J, Dengler K, Bernhard-Kurz S, Ekström PAR, Hitzmann B, Ueffing M, Paquet-Durand F (2013) Retinitis pigmentosa: rapid neurodegeneration is governed by slow cell death mechanisms. Cell Death & Disease 4:e488 Cell Biology Signaling Link
Sarma U, Gade PM, Saha B (2013) A mathematical model for dynamics of CD40 clustering. Systems and Synthetic Biology 7:197-208 Macromolecular Biochemistry Link
Schäuble S, Stavrum A-K, Puntervoll P, Schuster S, Heiland I (2013) Effect of substrate competition in kinetic models of metabolic networks. FEBS Letters 587:2818-2824 Metabolism Link
Scheller S, Goenrich M, Thauer RK, Jaun B (2013) Methyl-coenzyme M reductase from methanogenic archaea: isotope effects on label exchange and ethane formation with the homologous substrate ethyl-coenzyme M. Journal of the American Chemical Society 135:14985-14995 Chemistry Enzymology Link
Schokker D, Bannink A, Smits MA, Rebel JMJ (2013) A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue. Journal of Theoretical Biology 330:75–87 Immunology Link
Sharma V (2013) Language design for computational modeling, simulation, and visualization. Proceedings of the 2013 Winter Simulation Conference: Simulation: Making Decisions in a Complex World. Washington, D.C.: IEEE Press, 3934–3935 Computational Method Link
Sharma V, Compagnoni A (2013) Computational and mathematical models of the JAK-STAT signal transduction pathway. Proceedings of the 2013 Summer Computer Simulation Conference 15 Computational Method Signaling Link
Sharp GC (2013) Comprehensive data analysis to study parturition. Ph.D. Thesis, University of Edinburgh, UK. Signaling Link
Sharp GC, Ma H, Saunders PTK, Norman JE (2013) A Computational Model of Lipopolysaccharide-Induced Nuclear Factor Kappa B Activation: A Key Signalling Pathway in Infection-Induced Preterm Labour. PLoS One 8:e70180 Signaling Link
Shemirani MI (2013) Construction of metabolic pathway of catecholamine from tyrosine in human fibroblast cell. Degree Project Thesis in Medicine, School of Medicine and Health Science, Orerbo University, Sweden Metabolism Link
Sheng X (2013) Evolutionary and Functional Aspects of Two-Component Signalling Systems. Ph.D. Thesis, Imperial College London, UK. Microbiology Link
Singh VK, Ghosh I (2013) Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Letters 587:2806-2817 Metabolism Link
Skvortsov A, Gray P (2013) A simple model for assessment of anti-toxin antibodies. BioMed Research International 2013:230906 Laboratory Method Link
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Letters 587:2832-41 Metabolism Link
Smith GR, Shanley DP (2013) Computational modelling of the regulation of Insulin signalling by oxidative stress. BMC Systems Biology 7:41 Signaling Link
Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W (2013) Systematic construction of kinetic models from genome-scale metabolic networks. PLoS One 8:e79195 Computational Method Whole-Cell Models Link
Stavrum A-K, Heiland I, Schuster S, Puntervoll P, Ziegler M (2013) Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. Journal of Biological Chemistry 288:34555-34566 Metabolism Link
Sundin S, Dahlgren B, Roth O, Jonsson M (2013) H2O2 and radiation induced dissolution of UO2 and SIMFUEL in deficient aqueous solution. Journal of Nuclear Materials 443:291-297 Chemistry Link
Sütterlin T, Kolb C, Dickhaus H, Jäger D, Grabe N (2013) Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI. Bioinformatics 29:223-9 Software Link
Tapinos A, Mendes P (2013) A Method for Comparing Multivariate Time Series with Different Dimensions. PLoS One 8:e54201 Computational Method Theory Link
Toney MD (2013) Common enzymological experiments allow free energy profile determination. Biochemistry 52:5952-5965 Enzymology Link
van't Erve TJ (2013) Discoveries on the storage of red blood cells and the exposure of cells in culture to xenobiotics. D.Phil. Thesis, The University of Iowa, USA Toxicology Link
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013) Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria. PLoS Computational Biology 9:e1003159 Metabolism Microbiology Link
Verma M, Zakhartsev M, Reuss M, Westerhoff HV (2013) “Domino” systems biology and the “A” of ATP. Biochimica et Biophysica Acta 1827:19–29 Metabolism Link
Viladomiu M, Hontecillas R, Yuan L, Lu P, Bassaganya-Riera J (2013) Nutritional protective mechanisms against gut inflammation. Journal of Nutritional Biochemistry 24:929-939 Immunology Link
Wang H-Y, Huang Y-X, Qi Y-F, Zhang Y, Bao Y-L, Sun L-G, Zheng L-H, Zhang Y-W, Ma Z-Q, Li Y-X (2013) Mathematical models for the Notch and Wnt signaling pathways and the crosstalk between them during somitogenesis. Theoretical Biology & Medical Modelling 10:27 Signaling Link
Wilcock P (2013) A systems biology approach for investigating oral squamous cell carcinoma (OSCC). Ph.D. Thesis, University of Manchester, UK Metabolism Biochemistry Link

91 publications
2012
Achcar F, Kerkhoven EJ, The SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R (2012) Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLoS Computational Biology 8:e1002352 Metabolism Link
Adamczyk M, Westerhoff HV (2012) Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal 7:877-883 Metabolism Microbiology Link
Adams RR, Tsorman N, Stratford K, Akman OE, Gilmore S, Juty N, Le Novère N, Millar AJ, Millar AJ (2012) The Input Signal Step Function (ISSF), a standard method to encode input signals in SBML models with software support, applied to circadian clock models. Journal of Biological Rhythms 27:328–332 Computational Method Link
Adiamah DA, Schwartz J-M (2012) Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations. Metabolites 2:382-397 Metabolism Whole-Cell Models Link
Altintaş CM, Ertas G, Kayali HA (2012) Simulation of Microbial Production of Ramoplanin via Stoichiometric Modeling from Actinoplanes sp. ATCC 33076. New Biotechnology 29:S144–S145 Microbiology Biotechnology Link
Betney R, de Silva E, Mertens C, Knox Y, Krishnan J, Stansfield I (2012) Regulation of release factor expression using a translational negative feedback loop: A systems analysis. RNA 18:2320-2334 Signaling Link
Biswas S, Huang Z, Choliy Y, Wang DY, Brookhart M, Krogh-Jespersen K, Goldman AS (2012) Olefin Isomerization by Iridium Pincer Catalysts. Experimental Evidence for an η 3 -Allyl Pathway and an Unconventional Mechanism Predicted by DFT Calculations. Journal of the American Chemical Society 134:13276-13295 Chemistry Link
Bodenstein C, Heiland I, Schuster S (2012) Temperature compensation and entrainment in circadian rhythms. Physical Biology 9:036011 Theory Link
Bortolussi L, Policriti A (2012) Studying cancer-cell populations by programmable models of networks. Network Modeling Analysis in Health Informatics and Bioinformatics 1:117-133 Cell Biology Link
Burés J, Armstrong A, Blackmond DG (2012) Curtin-Hammett Paradigm for Stereocontrol in Organocatalysis by Diarylprolinol Ether Catalysts. Journal of the American Chemical Society 134:6741-6750 Chemistry Link
Challenger JD, McKane AJ, Pahle J (2012) Multi-compartment linear noise approximation. Journal of Statistical Mechanics: Theory and Experiment 2012:P11010 Computational Method Link
Chang J-Y, Chantrathammachart P, Monroe DM, Key NS (2012) Studies on the mechanism of action of the aptamer BAX499, an Inhibitor of tissue factor pathway inhibitor. Thrombosis Research 130:e151-e157 Macromolecular Biochemistry Link
Chua HE, Bhowmick SS, Tucker-Kellogg L, Forbes Dewey C (2012) STEROID: in silico heuristic target combination identification for disease-related signaling networks. Proceedings of the 2012 ACM Conference on Bioinformatics, Computational Biology and Biomedicine BCB'12 pp. 4-11 Computational Method Link
Criquet J, Allard S, Salhi E, Joll CA, Heitz A, von Gunten U (2012) Iodate and Iodo-Trihalomethane Formation during Chlorination of Iodide-Containing Waters: Role of Bromide. Environmental Science & Technology 46:7350-7357 Chemistry Environmental Sciences Link
Cristovao M, Sisamakis E, Hingorani MM, Marx AD, Jung CP, Rothwell PJ, Seidel CAM, Friedhoff P (2012) Single-molecule multiparameter fluorescence spectroscopy reveals directional MutS binding to mismatched bases in DNA. Nucleic Acids Research 40:5448-5464 Genomics Link
Czeizler E, Mizera A, Czeizler E, Back R-J, Eriksson JE, Petre I (2012) Quantitative Analysis of the Self-Assembly Strategies of Intermediate Filaments from Tetrameric Vimentin. IEEE/ACM Transactions on Computational Biology and Bioinformatics 9:885-898 Cell Biology Link
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Dalle Pezze P, Sonntag AG, Thien A, Prentzell MT, Godel M, Fischer S, Neumann-Haefelin E, Huber TB, Baumeister R, Shanley DP, Thedieck K (2012) A Dynamic Network Model of mTOR Signaling Reveals TSC-Independent mTORC2 Regulation. Science Signaling 5:ra25-ra25 Signaling Link
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Ding K, Miranda MO, Moscato-Goodpaster B, Ajellal N, Breyfogle LE, Hermes ED, Schaller CP, Roe SE, Cramer CJ, Hillmyer MA, Tolman WB (2012) Roles of Monomer Binding and Alkoxide Nucleophilicity in Aluminum-Catalyzed Polymerization of ε-Caprolactone. Macromolecules 45:5387-5396 Chemistry Link
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Hamberg A, Maurer S, Hult K (2012) Rational engineering of Candida antarctica lipase B for selective monoacylation of diols. Chemical Communications 48:10013 Biochemistry Link
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Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B (2012) Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach: Modelling glycolysis of lactic acid bacteria. FEBS Journal 279:1274-1290 Metabolism Link
Li Y, Wang M, Carra C, Cucinotta FA (2012) Modularized Smad-regulated TGFβ signaling pathway. Mathematical Biosciences 240:187-200 Signaling Link
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Maiwald T (2012) Computational Analysis of The Interferon Alpha Signalling Using a Systems Biology Modelling Approach Pathway. Ph.D. Thesis, Heidelberg University, Germany. Signaling Link
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Mazemondet O, John M, Leye S, Rolfs A, Uhrmacher AM (2012) Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS One 7:e42792 Signaling Link
McAuley MT, Wilkinson DJ, Jones JJ, Kirkwood TBL (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link
Micheau J-C, Coudret C, Cruz J-M, Buhse T (2012) Amplification of enantiomeric excess, mirror-image symmetry breaking and kinetic proofreading in Soai reaction models with different oligomeric orders. Physical Chemistry Chemical Physics 14:13239 Chemistry Link
Monge ME, Rosenorn T, Favez O, Muller M, Adler G, Abo Riziq A, Rudich Y, Herrmann H, George C, D’Anna B (2012) Alternative pathway for atmospheric particles growth. Proceedings of the National Academy of Sciences USA 109:6840-6844 Chemistry Link
Moscato BM, Zhu B, Landis CR (2012) Mechanistic Investigations into the Behavior of a Labeled Zirconocene Polymerization Catalyst. Organometallics 31:2097-2107 Chemistry Link
Muntean N, Thuy LB, Kály-Kullai K, Wittmann M, Noszticzius Z, Onel L, Furrow SD (2012) Measurement of Hypoiodous Acid Concentration by a Novel Type Iodide Selective Electrode and a New Method To Prepare HOI. Monitoring HOI Levels in the Briggs-Rauscher Oscillatory Reaction. Journal of Physical Chemistry 116:6630-6642 Chemistry Link
Olin-Sandoval V, González-Chávez Z, Berzunza-Cruz M, Martínez I, Jasso-Chávez R, Becker I, Espinoza B, Moreno-Sánchez R, Saavedra E (2012) Drug target validation of the trypanothione pathway enzymes through metabolic modelling: Kinetic modelling of trypanothione metabolism. FEBS Journal 279:1811-1833 Metabolism Link
Pahle J, Challenger JD, Mendes P, McKane AJ (2012) Biochemical fluctuations, optimisation and the linear noise approximation. BMC Systems Biology 6:86 Computational Method Software Link
Palai T, Mitra S, Bhattacharya PK (2012) Kinetics and design relation for enzymatic conversion of lactose into galacto-oligosaccharides using commercial grade β-galactosidase. Journal of Bioscience and Bioengineering 114:418-423 Metabolism Link
Phelix CF, Rahimi O, Colom L, Perry G, Ginsberg S (2012) Transcriptome-to-reactome biosimulation: Basal forebrain cholinergic neuron neurotrophin signaling. Alzheimer’s & Dementia 8:P467–P468 Signaling Link
Phelix CF, Villareal G, Perez-Cordova M, Hernandez S, Perry G, Colom L (2012) P3-395: Reanimating basal forebrain cholinergic neurons in electrophysiology biosimulations using COPASI software. Alzheimer’s & Dementia 8:P593–P594 Physiology Biophysics Link
Pinna F, Sahle S, Beuke K, Bissinger M, Tuncay S, D’Alessandro LA, Gauges R, Raue A, Timmer J, Klingmüller U, Schirmacher P, Kummer U, Breuhahn K (2012) A Systems Biology Study on NFκB Signaling in Primary Mouse Hepatocytes. Frontiers in Physiology 3:466 Signaling Link
Piras V, Hayashi K, Tomita M, Selvarajoo K (2012) Investigation of stochasticity in TRAIL signaling cancer model. Proceedings of the 2012 ICME International Conference on Complex Medical Engineering (CME) 609-614. Signaling Link
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Ray JCJ, Igoshin OA (2012) Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLoS Computational Biology 8:e1002672 Microbiology Genetics Link
Reyes-Palomares A, Montañez R, Sánchez-Jiménez F, Medina MÁ (2012) A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability. Amino Acids 42:597–610 Metabolism Link
Salvado B, Vilaprinyo E, Karathia H, Sorribas A, Alves R (2012) Two Component Systems: Physiological Effect of a Third Component. PLoS One 7:e31095 Signaling Link
Sarma U, Ghosh I (2012) Different designs of kinase-phosphatase interactions and phosphatase sequestration shapes the robustness and signal flow in the MAPK cascade. BMC Systems Biology 6:82 Signaling Link
Sarma U, Ghosh I (2012) Oscillations in MAPK cascade triggered by two distinct designs of coupled positive and negative feedback loops. BMC Research Notes 5:287 Signaling Link
Sarma U, Sareen A, Maiti M, Kamat V, Sudan R, Pahari S, Srivastava N, Roy S, Sinha S, Ghosh I, Chande AG, Mukhopadhyaya R, Saha B (2012) Modeling and Experimental Analyses Reveals Signaling Plasticity in a Bi-Modular Assembly of CD40 Receptor Activated Kinases. PLoS One 7:e39898 Signaling Link
Schaber J (2012) Easy parameter identifiability analysis with COPASI. BioSystems 110:183-185 Computational Method Link
Schaber J, Baltanas R, Bush A, Klipp E, Colman-Lerner A (2012) Modelling reveals novel roles of two parallel signalling pathways and homeostatic feedbacks in yeast. Molecular Systems Biology 8:622 Signaling Link
Schimek C, Vlaic S, Wöstemeyer J, Werner S, Schuster S, Schroeter A (2012) Model of the synthesis of trisporic acid in Mucorales showing bistability. IET Systems Biology 6:207-214 Signaling Link
Singh VK, Das K, Seshadri K (2012) Kinetic Modelling of GlmU Reactions - Prioritization of Reaction for Therapeutic Application. PLoS One 7:e43969 Metabolism Link
Stalidzans E, Kostromins A, Sulins J (2012) Two stage optimization of biochemical pathways using parallel runs of global stochastic optimization methods. 13th IEEE International Symposium on Computational Intelligence and Informatics (CINTI 2012), IEEE, 365–369 Computational Method Link
Stefan MI, Marshall DP, Le Novère N (2012) Structural Analysis and Stochastic Modelling Suggest a Mechanism for Calmodulin Trapping by CaMKII. PLoS One 7:e29406 Enzymology Link
Steinacher A, Leyser O, Clayton RH (2012) A computational model of auxin and pH dynamics in a single plant cell. Journal of Theoretical Biology 296:84-94 Cell Biology Link
Sulins J, Mednis M (2012) Automatic termination of parallel optimization runs of stochastic global optimization methods in consensus or stagnation cases. Biosystems and Information Technology 1:1-5 Software Computational Method Link
Surovtsova I, Simus N, Hübner K, Sahle S, Kummer U (2012) Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics. BMC Systems Biology 6:14 Software Computational Method Link
Tagore S, De RK (2012) SAGPAR: Structural Grammar-based automated pathway reconstruction. Interdisciplinary Sciences: Computational Life Sciences 4:116-127 Software Computational Method Link
Tiedemann MT, Heinrichs DE, Stillman MJ (2012) Multiprotein Heme Shuttle Pathway in Staphylococcus aureus : Iron-Regulated Surface Determinant Cog-Wheel Kinetics. Journal of the American Chemical Society 134:16578-16585 Signaling Link
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Usuyama M, Ushida C, Shingai R (2012) A model of the intracellular response of an olfactory neuron in Caenorhabditis elegans to odor stimulation. PLoS One 7:e42907 Signaling Link
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85 publications
2011
Baez M, Wilson CA, Babul J (2011) Folding kinetic pathway of phosphofructokinase-2 from Escherichia coli: a homodimeric enzyme with a complex domain organization. FEBS Letters 585:2158–2164 Macromolecular Biochemistry Link
Bairy S, Wong CF (2011) Influence of kinetics of drug binding on EGFR signaling: A comparative study of three EGFR signaling pathway models. Proteins: Structure, Function, and Bioinformatics 79:2491–2504 Signaling Link
Baker SM, Poskar CH, Junker BH (2011) Unscented Kalman filter with parameter identifiability analysis for the estimation of multiple parameters in kinetic models. EURASIP Journal on Bioinformatics & Systems Biology 2011:7 Computational Method Link
Bandaru P, Bansal M, Nemenman I (2011) Mass Conservation and Inference of Metabolic Networks from High-Throughput Mass Spectrometry Data. Journal of Computational Biology 18:147-154 Laboratory Method Computational Method Link
Berestovsky N (2011) On the modeling of signaling networks with petri nets. MS Thesis, Rice University, Houston, Texas, USA. Computational Method Link
Casas A, Ramos MJ, Pérez Á (2011) Kinetics of chemical interesterification of sunflower oil with methyl acetate for biodiesel and triacetin production. Chemical Engineering Journal 171:1324–1332 Biotechnology Chemistry Link
Chandran D (2011) TinkerCell: Computer-Aided Design for Synthetic Biology. Ph.D. Thesis, University of Washington, Seattle, USA. Software Synthetic Biology Link
Checkley S (2011) Engineering Tuneable Gene Circuits in Yeast. Ph.D. Thesis, University of Manchester, UK. Synthetic Biology Link
Chen X (2011) Glutathione suppresses the autoxidation of 2’,5’-dihydroxy-4-chlorobiphenyl. MS Thesis, University of Iowa, USA. Toxicology Link
Criquet J, Karpel Vel Leitner N (2011) Electron beam irradiation of aqueous solution of persulfate ions. Chemical Engineering Journal 169:258–262 Chemistry Link
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234 Signaling Microbiology Link
DasGupta B, Vera-Licona P, Sontag E (2011) Reverse engineering of molecular networks from a common combinatorial approach. In Algorithms in Computational Molecular Biology: Techniques, Approaches and Applications, M. Elloumi and A. Zomaya (editors). John Wiley & Sons, Inc. Computational Method Link
Diao T, Stahl SS (2011) Synthesis of Cyclic Enones via Direct Palladium-Catalyzed Aerobic Dehydrogenation of Ketones. Journal of the American Chemical Society 133:14566–9 Chemistry Link
Fabrini R, Bocedi A, Dawood KF, Turella P, Stella L, Parker MW, Pedersen JZ, Federici G, Antonini G, Ricci G (2011) The extended catalysis of glutathione transferase. FEBS Letters 585:341–345 Enzymology Link
Fedosov SN, Xu X (2011) Enzymatic synthesis of biodiesel from fatty acids. Kinetics of the reaction measured by fluorescent response of Nile Red. Biochemical Engineering Journal 56:172–183 Biotechnology Link
Gauges R (2011) Standards and Tools for Model Exchange and Analysis in Systems Biology. Ph.D. Thesis, Heidelberg University, Germany Software Computational Method Link
Genc S, Kurnaz IA, Ozilgen M (2011) Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions-in silico study supported by in vitro expression data. BMC Systems Biology 5:162 Cell Biology Metabolism Link
Gerber S (2011) In silico modeling of cation homeostasis in Saccharomyces cerevisiae. Ph.D. Thesis, Humboldt-University of Berlin, Germany. Physiology Link
Hein JE, Armstrong A, Blackmond DG (2011) Kinetic profiling of prolinate-catalyzed α-amination of aldehydes. Organic Letters 13:4300–4303 Chemistry Link
Hill MP, Freer LH, Vang MC, Carroll EC, Larsen DS (2011) Multiphoton Manipulations of Enzymatic Photoactivity in Aspartate Aminotransferase. Journal of Physical Chemistry 115:4474–4483 Enzymology Link
Hinze T, Schumann M, Bodenstein C, Heiland I, Schuster S (2011) Biochemical Frequency Control by Synchronisation of Coupled Repressilators: An In Silico Study of Modules for Circadian Clock Systems. Computational Intelligence and Neuroscience 2011:1–9 Theory Link
Hoffman-Sommer M, Supady A, Klipp E (2011) Cell-to-Cell Communication Circuits: Quantitative Analysis of Synthetic Logic Gates. Frontiers in Physiology 3:287–287 Synthetic Biology Link
Hooshangi S, Bentley WE (2011) LsrR quorum sensing “switch” is revealed by a bottom-up approach. PLoS Computational Biology 7:e1002172 Microbiology Signaling Link
Iwasaki H, Takeuchi O, Teraguchi S, Matsushita K, Uehata T, Kuniyoshi K, Satoh T, Saitoh T, Matsushita M, Standley DM, Akira S (2011) The IkB kinase complex regulates the stability of cytokine-encoding mRNA induced by TLR-IL-1R by controlling degradation of regnase-1. Nature Immunology 12:1167-75 Immunology Signaling Link
Izawa Y, Pun D, Stahl SS (2011) Palladium-Catalyzed Aerobic Dehydrogenation of Substituted Cyclohexanones to Phenols. Science 333:209-213 Chemistry Link
Jablonsky J, Bauwe H, Wolkenhauer O (2011) Modeling the Calvin-Benson cycle. BMC Systems Biology 5:185 Metabolism Plant Biology Link
Johnson KRD, Hayes PG (2011) Kinetic and Mechanistic Investigation of Metallacycle Ring Opening in an Ortho-Metalated Lutetium Aryl Complex. Organometallics 30:58–67 Chemistry Link
Keitz BK, Grubbs RH (2011) Probing the origin of degenerate metathesis selectivity via characterization and dynamics of ruthenacyclobutanes containing variable NHCs. Journal of the American Chemical Society 133:16277-16284 Chemistry Link
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology 22:713–719 Signaling Metabolism Link
Klotz C, Ziegler T, Figueiredo AS, Rausch S, Hepworth MR, Obsivac N, Sers C, Lang R, Hammerstein P, Lucius R, Hartmann S (2011) A Helminth Immunomodulator Exploits Host Signaling Events to Regulate Cytokine Production in Macrophages. PLoS Pathogens 7:e1001248 Immunology Link
Koh G, Hsu D, Thiagarajan PS (2011) Component-based construction of bio-pathway models: The parameter estimation problem. Theoretical Computer Science 412:2840–2853 Computational Method Link
Koh G, Lee D-Y (2011) Mathematical modeling and sensitivity analysis of the integrated TNFα-mediated apoptotic pathway for identifying key regulators. Computers in Biology and Medicine 41:512–528 Signaling Link
Kolodkin AN (2011) Emergence of design. Ph.D. Thesis, Vrije Universiteit Amsterdam, The Netherlands. Theory Metabolism Link
Lauro FM, DeMaere MZ, Yau S, Brown MV, Ng C, Wilkins D, Raftery MJ, Gibson JAE, Andrews-Pfannkoch C, Lewis M, Hoffman JM, Thomas T, Cavicchioli R (2011) An integrative study of a meromictic lake ecosystem in Antarctica. ISME Journal 5:879-95 Ecology Link
Le Roux J, Gallard H, Croué J-P (2011) Chloramination of nitrogenous contaminants (pharmaceuticals and pesticides): NDMA and halogenated DBPs formation. Water Research 45:3164–3174 Environmental Sciences Chemistry Link
Lee MV, Topper SE, Hubler SL, Hose J, Wenger CD, Coon JJ, Gasch AP (2011) A dynamic model of proteome changes reveals new roles for transcript alteration in yeast. Molecular Systems Biology 7:514 Genomics Link
Li Y, Cucinotta FA (2011) Modeling non-homologous end joining. Journal of Theoretical Biology 283:122–135 Genetics Theory Macromolecular Biochemistry Link
Liu B, Hsu D, Thiagarajan PS (2011) Probabilistic approximations of ODEs based bio-pathway dynamics. Theoretical Computer Science 412:2188–2206 Theory Link
Liu B, Zhang J, Tan PY, Hsu D, Blom AM, Leong B, Sethi S, Ho B, Ding JL, Thiagarajan PS (2011) A computational and experimental study of the regulatory mechanisms of the complement system. PLoS Computational Biology 7:e1001059 Immunology Signaling Link
Marchisio MA, Stelling J (2011) Automatic Design of Digital Synthetic Gene Circuits. PLoS Computational Biology 7:e1001083 Synthetic Biology Link
Matuszak Z (2011) Photodynamic therapy of melanoma. Monte Carlo modeling of light transport in human pigmented skin. Bio Algorithms Med Syst. 7:85–93 Biophysics Link
Mauch S, Stalzer M (2011) Efficient formulations for exact stochastic simulation of chemical systems. IEEE/ACM Transactions on Computational Biology and Bioinformatics 8:27-35 Computational Method Link
Mozga I, Stalidzans E (2011) Convergence dynamics of biochemical models to the global optimum. Paper presented at the 2011 E-Health and Bioengineering Conference (EHB). IEEE: Iaşi, Romania, 1–4 Computational Method Metabolism Link
Oh E, Lu M, Park C, Park C, Oh HB, Lee SY, Lee J (2011) Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis. Journal of Microbiology and Biotechnology 21:162–169 Microbiology Metabolism Link
Proctor CJ, Lorimer IAJ (2011) Modelling the role of the Hsp70/Hsp90 system in the maintenance of protein homeostasis. PLoS One 6:e22038 Macromolecular Biochemistry Link
Qian L, Winfree E (2011) A simple DNA gate motif for synthesizing large-scale circuits. Journal of the Royal Society Interface 8:1281-97 Synthetic Biology Link
Qian L, Winfree E (2011) Scaling up digital circuit computation with DNA strand displacement cascades. Science 332:1196–1201 Synthetic Biology Link
Rodriguez F, Bustos MA, Zanetti MN, Ruete MC, Mayorga LS, Tomes CN (2011) alpha-SNAP prevents docking of the acrosome during sperm exocytosis because it sequesters monomeric syntaxin. PLoS One 6:e21925 Cell Biology Macromolecular Biochemistry Link
Schaber J, Flöttmann M, Li J, Tiger C-F, Hohmann S, Klipp E (2011) Automated ensemble modeling with modelMaGe: analyzing feedback mechanisms in the Sho1 branch of the HOG pathway. PLoS One 6:e14791 Signaling Computational Method Software Link
Schweizer N (2011) Calcium signaling in fish cells. Ph.D. Thesis, University of Heidelberg, Germany. Signaling Link
Schweizer N, Kummer U, Hercht H, Braunbeck T (2011) Amplitude-encoded calcium oscillations in fish cells. Biophysical Chemistry 159:294–302 Signaling Link
Shivanandan A (2011) Stochastic modelling and identification of arabinose uptake network in Escherichia coli (PDF Download Available). MS Thesis, Université Joseph Fourier, Grenoble, France. Metabolism Microbiology Link
Sorokina O, Corellou F, Dauvillée D, Sorokin A, Goryanin I, Ball S, Bouget F-Y, Millar AJ (2011) Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC Systems Biology 5:36 Metabolism Link
Tsaloglou M-N, Attard GS, Dymond MK (2011) The effect of lipids on the enzymatic activity of 6-phosphofructo-1-kinase from B. stearothermophilus. Chemistry and Physics of Lipids 164:713–721 Enzymology Metabolism Microbiology Link
Waltemath D, Adams RR, Beard DA, Bergmann FT, Bhalla US, Britten R, Chelliah V, Cooling MT, Cooper J, Crampin EJ, Garny A, Hoops S, Hucka M, Hunter P, Klipp E, Laibe C, Miller AK, Moraru II, Nickerson DP, Nielsen P, Nikolski M, Sahle S, Sauro HM, Schmidt H, Snoep JL, Tolle D, Wolkenhauer O, Le Novère N (2011) Minimum Information About a Simulation Experiment (MIASE). PLoS Computational Biology 7:e1001122 Computational Method Link
Wendelsdorf K (2011) Models of the Mucosal Inflammatory and Regulatory Immune Pathways: The Role of Host Response in Microbial Persistence and Pathogenesis. Ph.D. Thesis, Virginia Tech, USA. Immunology Link
Yang J (2011) Midazolam as a Probe Drug to Study Cytochrome P450 3A Allosterism. Ph.D. Thesis, University of Washington, Seattle, USA. Enzymology Pharmacology Link
Yao G, Tan C, West M, Nevins JR, You L (2011) Origin of bistability underlying mammalian cell cycle entry. Molecular Systems Biology 7:485 Cell Biology Link

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

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

43 publications
2008
Ciocchetta F, Hillston J, Kos M, Tollervey D (2008) Modelling co-transcriptional cleavage in the synthesis of yeast pre-rRNA. Theoretical Computer Science 408:41–54 Macromolecular Biochemistry Link
Colby DA, Bergman RG, Ellman JA (2008) Synthesis of dihydropyridines and pyridines from imines and alkynes via C- H activation. Journal of the American Chemical Society 130:3645–3651 Chemistry Link
Colvin RA, Bush AI, Volitakis I, Fontaine CP, Thomas D, Kikuchi K, Holmes WR (2008) Insights into Zn2+ homeostasis in neurons from experimental and modeling studies. American Journal of Physiology 294:C726-C742 Physiology Link
Del Conte-Zerial P, Brusch L, Rink JC, Collinet C, Kalaidzidis Y, Zerial M, Deutsch A (2008) Membrane identity and GTPase cascades regulated by toggle and cut-out switches. Molecular Systems Biology 4:206 Signaling Link
Díaz Cuervo H (2008) Analysis of the role of Cdc14/Flp1 in checkpoint response to genotoxic stress in “Schizosaccharomyces pombe.” Ph.D. Thesis, Universidad de Salamanca, Spain. Signaling Link
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kırdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26:1155–1160 Microbiology Computational Method Link
Jordão L, Bleck CKE, Mayorga LS, Griffiths G, Anes E (2008) On the killing of mycobacteria by macrophages. Cellular Microbiology 10:529-48 Immunology Link
Jungmann R, Renner S, Simmel FC (2008) From DNA nanotechnology to synthetic biology. HFSP Journal 2:99-109 Synthetic Biology Link
Koh G, Hsu D, Thiagarajan PS (2008) Composition of signaling pathway models and its application to parameter estimation. ACM International Conference on Computational Biology (RECOMB) Poster Book, Singapore Link
Kühn C, Pe℡enz E, Nordlander B, Schaber J, Hohmann S, Klipp E (2008) Exploring the Impact of Osmoadaptation on Glycolysis Using Time-Varying Response-Coefficients. Genome Informatics 20:77–90 Metabolism Link
Kühnel M, Mayorga LS, Dandekar T, Thakar J, Schwarz R, Anes E, Griffiths G, Reich J (2008) Modelling phagosomal lipid networks that regulate actin assembly. BMC Systems Biology 2:107 Metabolism Macromolecular Biochemistry Link
Lagzdina L, Mozga I, Stalidzans E (2008) Algorithm for bioethanol yield optimisation in Saccharomyces cerevisiae glycolysis using “COPASI.” Paper presented at the International Scientific Conference: Applied Information and Communication Technologies, , Jelgava (Latvia), 10-12 Apr 2008. Latvia University of Agriculture. Biotechnology Link
Long J, Roth M (2008) Synthetic microarray data generation with RANGE and NEMO. Bioinformatics 24:132–134 Computational Method Genomics Link
Marchisio MA (2008) How to design synthetic gene circuits with composable parts and pools in the ProMoT framework. CiteSeer Preprint Synthetic Biology Link
Marchisio MA, Stelling J (2008) Computational design of synthetic gene circuits with composable parts. Bioinformatics 24:1903-10. Synthetic Biology Link
Pahle J (2008) Stochastic simulation and analysis of biochemical networks. Ph.D. Thesis, Humboldt-Universität zu Berlin, Germany Computational Method Link
Roy S, Werner-Washburne M, Lane T (2008) A system for generating transcription regulatory networks with combinatorial control of transcription. Bioinformatics 24:1318-1320 Software Link
Sahle S, Mendes P, Hoops S, Kummer U (2008) A new strategy for assessing sensitivities in biochemical models. Philosophical Transactions of the Royal Society A 366:3619-3631 Computational Method Link
Schmierer B, Tournier AL, Bates PA, Hill CS (2008) Mathematical modeling identifies Smad nucleocytoplasmic shuttling as a dynamic signal-interpreting system. Proceedings of the National Academy of Sciences USA 105:6608-13 Cell Biology Signaling Link
Stefan MI, Edelstein SJ, Le Novère N (2008) An allosteric model of calmodulin explains differential activation of PP2B and CaMKII. Proceedings of the National Academy of Sciences USA 105:10768-73 Physiology Signaling Macromolecular Biochemistry Link
Wilkinson SJ, Benson N, Kell DB (2008) Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Molecular BioSystems 4:74–97 Computational Method Link
Zotova N (2008) Kinetic and Mechanistic Investigation of Asymmetric Organocatalytic Reactions. Ph.D. Thesis, Imperial College London, UK Chemistry Link

22 publications
2007
Camacho D, Vera-Licona P, Mendes P, Laubenbacher R (2007) Comparison of reverse-engineering methods using an in silico network. Annals of the New York Academy of Sciences 1115:73-89. Computational Method Link
Ellman JA, Colby DA, Bergman R (2007) Synthesis of Dihydropyridines and Pyridines from Imines and Alkynes via CH Activation. Technical Report, Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, California, USA. Chemistry Link
Kelly MP, Isiegas C, Cheung YF, Tokarczyk J, Yang X, Esposito MF, Rapoport DA, Fabian SA, Siegel SJ, Wand G, Houslay MD, Kanes SJ, Abel T (2007) Constitutive activation of Galphas within forebrain neurons causes deficits in sensorimotor gating because of PKA-dependent decreases in cAMP. Neuropsychopharmacology 32:577-88 Pharmacology Signaling Link
Klipp E, Liebermeister W, Helbig A, Kowald A, Schaber J (2007) Systems biology standards - The community speaks. Nature Biotechnology 25:390-1 Computational Method Link
Kummer U, Zobeley J, Brasen JC, Fahmy R, Kindzelskii AL, Petty AR, Clark AJ, Petty HR (2007) Elevated Glucose Concentrations Promote Receptor-Independent Activation of Adherent Human Neutrophils: An Experimental and Computational Approach. Biophysical Journal 92:2597-2607 Immunology Link
Mandel JJ, Fuß H, Palfreyman NM, Dubitzky W (2007) Modeling biochemical transformation processes and information processing with Narrator. BMC Bioinformatics 8:103 Computational Method Software Link
Rippe K, Schrader A, Riede P, Strohner R, Lehmann E,Längst G (2007) DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes. Proceedings of the National Academy of Sciences USA 104:15635-40 Macromolecular Biochemistry Cell Biology Link
Ralser M, Wamelink MM, Kowald A, Gerisch B, Heeren G, Struys EA, Klipp E, Jakobs C, Breitenbach M, Lehrach H, Krobitsch S (2007) Dynamic rerouting of the carbohydrate flux is key to counteracting oxidative stress. Journal of Biology 6:10 Metabolism Link
Uys L, Botha FC, Hofmeyr J-HS, Rohwer JM (2007) Kinetic model of sucrose accumulation in maturing sugarcane culm tissue. Phytochemistry 68:2375-92 Metabolism Link
Xie Z (2007) Modelling genetic regulatory networks: A new model for circadian rhythms in Drosophila and investigation of genetic noise in a viral infection process. Ph.D. Thesis. Lincoln University, New Zealand Cell Biology Link

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

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

1 publication