COPASI's Use In Research

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
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
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
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
Collins S, Linnolahti M (2023) Ionization of Cp2ZrMe2 and Lewis Bases by Methylaluminoxane: Computational Insights. ChemPhysChem 24:e202200759 Chemistry 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
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
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
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
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
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
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
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
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
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
Olsen LF (2023) Complex dynamics in an unexplored simple model of the peroxidase–oxidase reaction. Chaos 33:023102 Biochemistry Enzymology 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
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, Suwanmajo T, Krishnan J (2023) Network regulation meets substrate modification chemistry. Journal of the Royal Society Interface 20:20220510 Signaling 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
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
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
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
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

32 publications
Abraha BW, Marchisio MA (2022) NOT Gates Based on Protein Degradation as a Case Study for a New Modular Modeling via SBML Level 3—Comp Package. Frontiers in Bioengineering and Biotechnology 10:845240 Synthetic Biology Link
Akbulut D, Özkar S (2022) A review of the catalytic conversion of glycerol to lactic acid in the presence of aqueous base. RSC Advances 12:18864–18883 Chemistry Link
Altus K (2022) Synthesis and characterisation of platinum(II) methyl complexes and their reactivity towards carbon-hydrogen (C-H) and carbon-halogen bonds (C-X). Ph.D. Thesis, University of British Columbia, Vancouver, Canada. Chemistry Link
Anand S, Padmanabhan P, Sahu SS, Mukherjee K (2022) ANN based process optimization for the growth kinetic study of Nostoc ellipsosporum NCIM 2786. IFAC-PapersOnLine 55:423–428 Microbiology Biotechnology Link
Angelini AAR, Gache SAM, Lurdes Sabeckis M, Melian NA, Flecha FLG (2022) On the role of citrate in 12-molybdophosphoric-acid methods for quantification of phosphate in the presence of ATP. New Journal of Chemistry 46:12401–12409 Chemistry Biochemistry Link
Azevedo LG (2022) Priorização em larga-escala de proteínas-alvo para o desenvolvimento de novos compostos antileishmaniais através de integração de dados multi-ômicos e imuno-informática. MS Thesis, Fundação Oswaldo Cruz, Salvador, Brazil. Parasitology Link
Baggett DW, Nath A (2022) Structure–Activity Relationships of Novel Tau Ligands: Passive Fibril Binders and Active Aggregation Inhibitors. ACS Chemical Biology 17:701–708 Macromolecular Biochemistry Link
Bauerstätter P (2022) Compartment Modeling of Overweight in Toddler Age: Modeling and Simulating a Diets Effect with COPASI. SNE Simulation Notes Europe 32:221–224 Physiology Computational Method Link
Bell M (2022) Mechanochemical modeling of structural plasticity in synapses. Ph.D. Thesis, University of California San Diego, USA. Signaling Link
Bergman D, Marazzi L, Chowkwale M, Maheshvare M D, Bidanta S, Mapder T, Li J (2022) PhysiPKPD: A pharmacokinetics and pharmacodynamics module for PhysiCell. Gigabyte 2022:1–11 Computational Method Pharmacology Link
Berzins K, Muiznieks R, Baumanis MR, Strazdina I, Shvirksts K, Prikule S, Galvanauskas V, Pleissner D, Pentjuss A, Grube M, Kalnenieks U, Stalidzans E (2022) Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential by Crypthecodinium cohnii from Glycerol, Glucose and Ethanol. Marine Drugs 20:115 Metabolism Microbiology Biotechnology Environmental Sciences Link
Boldova AE, Korobkin JD, Nechipurenko YD, Sveshnikova AN (2022) Theoretical Explanation for the Rarity of Antibody-Dependent Enhancement of Infection (ADE) in COVID-19. International Journal of Molecular Sciences 23:11364 Immunology Link
Boonekamp FJ, Knibbe E, Vieira-Lara MA, Wijsman M, Luttik MAH, van Eunen K, Ridder M den, Bron R, Almonacid Suarez AM, van Rijn P, Wolters JC, Pabst M, Daran J-M, Bakker BM, Daran-Lapujade P (2022) Full humanization of the glycolytic pathway in Saccharomyces cerevisiae. Cell Reports 39:111010 Metabolism Link
Borg Y, Alsford S, Pavlika V, Zaikin A, Nesbeth DN (2022) Synthetic biology tools for engineering Goodwin oscillation in Trypanosoma brucei brucei. Heliyon 8:e08891 Synthetic Biology Link
Bourdon-García RD, Ágreda J, Burgos-Salcedo J, Hochberg D, Ribó JM, Bargueño P, Salamanca AE (2022) Stoichiometric network analysis in reaction networks yielding spontaneous mirror symmetry breaking in a prebiotic atmosphere. Physical Chemistry Chemical Physics 24:20788–20802 Biochemistry Chemistry Link
Burger GA, Nesenberend DN, Lems CM, Hille SC, Beltman JB (2022) Bidirectional crosstalk between epithelial-mesenchymal plasticity and IFNγ-induced PD-L1 expression promotes tumour progression. Royal Society Open Science 9:220186 Signaling Link
Chatzinikolaou PN, Margaritelis NV, Chatzinikolaou AN, Paschalis V, Theodorou AA, Vrabas IS, Kyparos A, Nikolaidis MG (2022) Oxygen Transport: A Redox O2dyssey. In: Cobley JN and Davison GW (eds) Oxidative Eustress in Exercise Physiology. CRC Press Metabolism Link
Chedere A, Mishra M, Kulkarni O, Sriraman S, Chandra N (2022) Personalized quantitative models of NAD metabolism in hepatocellular carcinoma identify a subgroup with poor prognosis. Frontiers in Oncology 12:954512 Metabolism Physiology Link
Daas JCJ, Förster J, Pahle J (2022) Dynamic publication media with the COPASI R Connector (CoRC). Mathematical Biosciences 348:108822 Computational Method Link
Das A, Mandal SC, Pathak B (2022) Mechanistic exploration of CO2 conversion to dimethoxymethane (DMM) using transition metal (Co, Ru) catalysts: an energy span model. Physical Chemistry Chemical Physics 24:8387–8397 Chemistry Link
de la Sovera V, Martínez S, Umpiérrez D, Vila MA, Gonzalez D, Seoane G, Veiga N, Carrera I (2022) Synthesis of Azido-Dienediols by Enzymatic Dioxygenation of Benzylazides: An Experimental and Theoretical Study. European Journal of Organic Chemistry 2022:e202101156 Chemistry Enzymology Link
Deem MC, Derasp JS, Malig TC, Legard K, Berlinguette CP, Hein JE (2022) Ring walking as a regioselectivity control element in Pd-catalyzed C-N cross-coupling. Nature Communications 13:2869 Chemistry Link
Dotsenko OI (2022) The whole-cell kinetic metabolic model of the pH regulation mechanisms in human erythrocytes. Regulatory Mechanisms in Biosystems 13:272–280 Metabolism Whole-Cell Models Link
Erdem C, Mutsuddy A, Bensman EM, Dodd WB, Saint-Antoine MM, Bouhaddou M, Blake RC, Gross SM, Heiser LM, Feltus FA, Birtwistle MR (2022) A scalable, open-source implementation of a large-scale mechanistic model for single cell proliferation and death signaling. Nature Communications 13:3555 Computational Method Signaling Link
Esposito M, Picchiami L (2022) A Comparative Study of AI Search Methods for Personalised Cancer Therapy Synthesis in COPASI. In: Bandini S, Gasparini F, Mascardi V, Palmonari M and Vizzari G (eds) AIxIA 2021 – Advances in Artificial Intelligence. Lecture Notes in Computer Science 13196:638–654 Pharmacology Physiology Computational Method Link
Faraj SE, Valsecchi WM, Ferreira-Gomes MS, Centeno M, Saint Martin EM, Fedosova NU, Rossi JPFC, Montes MR, Rossi RC (2022) Measurements of Na+-occluded intermediates during the catalytic cycle of the Na+/K+-ATPase provide novel insights into the mechanism of Na+ transport. Journal of Biological Chemistry 299:102811 Biochemistry Biophysics Link
Ferrari Gianlupi J, Mapder T, Sego TJ, Sluka JP, Quinney SK, Craig M, Stratford RE, Glazier JA (2022) Multiscale Model of Antiviral Timing, Potency, and Heterogeneity Effects on an Epithelial Tissue Patch Infected by SARS-CoV-2. Viruses 14:605 Epidemiology Pharmacology Link
Franco R, Serrano-Marín J (2022) Robustness of the Krebs Cycle under Physiological Conditions and in Cancer: New Clues for Evaluating Metabolism-Modifying Drug Therapies. Biomedicines 10:1199 Metabolism Link
Fueyo-González F, McGinty M, Ningoo M, Anderson L, Cantarelli C, Andrea Angeletti null, Demir M, Llaudó I, Purroy C, Marjanovic N, Heja D, Sealfon SC, Heeger PS, Cravedi P, Fribourg M (2022) Interferon-β acts directly on T cells to prolong allograft survival by enhancing regulatory T cell induction through Foxp3 acetylation. Immunity 55:459-474.e7 Immunology Link
Gallas JAC, Olsen LF (2022) Complexity in subnetworks of a peroxidase-oxidase reaction model. Chaos 32:063122 Biochemistry Enzymology Link
Garay-Ruiz D, Bo C (2022) Chemical reaction network knowledge graphs: the OntoRXN ontology. Journal of Cheminformatics 14:29 Software Computational Method Link
Greenyer H (2022) Evaluation of network inference algorithms and their effects on network analysis for the study of small metabolomic data sets. MS Thesis, University of Victoria, Canada. Computational Method Metabolism Link
Großeholz R, Wanke F, Rohr L, Glöckner N, Rausch L, Scholl S, Scacchi E, Spazierer A-J, Shabala L, Shabala S, Schumacher K, Kummer U, Harter K (2022) Computational modeling and quantitative physiology reveal central parameters for brassinosteroid-regulated early cell physiological processes linked to elongation growth of the Arabidopsis root. eLife 11:e73031 Signaling Physiology Plant Biology Link
Guimera AM, Clark P, Wordsworth J, Anugula S, Rasmussen LJ, Shanley DP (2022) Systems modelling predicts chronic inflammation and genomic instability prevent effective mitochondrial regulation during biological ageing. Experimental Gerontology 166:111889 Signaling Link
Gulhane P, Nimsarkar P, Kharat K, Singh S (2022) Deciphering miR-520c-3p as a probable target for immunometabolism in non-small cell lung cancer using systems biology approach. Oncotarget 13:725–746 Genetics Link
Hamsath A, Lederberg OL, Cui Q, Shieh M, Lam Y, Brummett BJ, Xu S, Robinson JR, Xian M (2022) Intramolecular tetrazine-acryloyl cycloaddition: chemistry and applications. Chemical Science 13:10336–10341 Chemistry Link
He Y, Li K, Wang J, Xu L, Yan J, Yang M, Yan Y (2022) A novel strategy for biodiesel production by combination of liquid lipase, deep eutectic solvent and ultrasonic-assistance in scaled-up reactor: Optimization and kinetics. Journal of Cleaner Production 372:133740 Enzymology Biotechnology Link
Holman SDL, Wills AG, Fazakerley NJ, Poole DL, Coe DM, Berlouis LA, Reid M (2022) Electrochemical Synthesis of Isoxazolines: Method and Mechanism. Chemistry 28:e202103728 Chemistry Link
Huang Q, Lee GY, Li J, Wang C, Zhao RL, Deng Z, Houk KN, Zhao Y-L (2022) Origin of iodine preferential attack at sulfur in phosphorothioate and subsequent P-O or P-S bond dissociation. Proceedings of the National Academy of Sciences USA 119:e2119032119 Chemistry Link
Irgen-Gioro S, Yoshida SR, Walling V, Chong S (2022) Fixation can change the appearance of phase separation in living cells. eLife 11:e79903 Cell Biology Biophysics Link
Jad A-C, Ricardo C-M, Rodrigo M-R (2022) mi-RNA129-1 and mi-RNA24-2 as regulators of over-expressed genes in lung typical carcinoid tumors: Potential targets for molecular therapy. Proceedings of the 2022 IEEE 4th International Conference on BioInspired Processing (BIP), 1–8 Genetics Link
Jin Q, Wu Q, Shapiro BM, McKernan SE (2022) Limited Mechanistic Link Between the Monod Equation and Methanogen Growth: a Perspective from Metabolic Modeling. Microbiology Spectrum 10:e0225921 Microbiology Metabolism Link
Juarez A, Vega IA, Mayorga LS, Guevara SR, Arribére MA (2022) An Arsenic-76 radiotracer to study the routes of assimilation, hemolymph distribution, and tissue inventories in the bioindicator organism Pomacea canaliculata. Science of the Total Environment 815:152760 Environmental Sciences Link
Kathan M, Crespi S, Thiel NO, Stares DL, Morsa D, de Boer J, Pacella G, van den Enk T, Kobauri P, Portale G, Schalley CA, Feringa BL (2022) A light-fuelled nanoratchet shifts a coupled chemical equilibrium. Nature Nanotechnology 17:159–165 Chemistry Biotechnology Macromolecular Biochemistry Link
Knox HL, Sinner EK, Townsend CA, Boal AK, Booker SJ (2022) Structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis. Nature 602:343–348 Biochemistry Enzymology Link
Kouka T, Akase S, Sogabe I, Jin C, Karlsson NG, Aoki-Kinoshita KF (2022) Computational Modeling of O-Linked Glycan Biosynthesis in CHO Cells. Molecules 27:1766 Metabolism Link
Kumar S (2022) Compact, Causal and Multivariate Functional Statistics in Model-Free Discrete Pattern Discovery. Ph.D. Thesis, New Mexico State University, USA. Computational Method Link
Kumar A, Nimsarkar P, Singh S (2022) Systems pharmacology aiding benzimidazole scaffold as potential lead compounds against leishmaniasis for functional therapeutics. Life Sciences 308:120960 Pharmacology Link
Kurlovics J, Zake DM, Zaharenko L, Berzins K, Klovins J, Stalidzans E (2022) Metformin Transport Rates Between Plasma and Red Blood Cells in Humans. Clinical Pharmacokinetics 61:133–142 Pharmacology Link
Kurokhtina AA, Larina EV, Lagoda NA, Schmidt AF (2022) The Role of Catalyst Formation–Deactivation Processes and Evidence for a Nonlinear Mechanism in the Mizoroki–Heck Reaction with Aryl Chlorides. Kinetics and Catalysis 63:543–554 Chemistry Link
Lee JY, Styczynski MP (2022) Diverse classes of constraints enable broader applicability of a linear programming-based dynamic metabolic modeling framework. Scientific Reports 12:762 Computational Method Metabolism Link
Li G-Q, Huo Z-Y, Wu Q-Y, Chen Z, Wu Y-H, Lu Y, Hu H-Y (2022) Photolysis of free chlorine and production of reactive radicals in the UV/chlorine system using polychromatic spectrum LEDs as UV sources. Chemosphere 286:131828 Chemistry Link
Li M, Liao R-Z (2022) Water Oxidation Catalyzed by a Bioinspired Tetranuclear Manganese Complex: Mechanistic Study and Prediction. ChemSusChem 15:e202200187 Chemistry Link
Li Y, Cheng H (2022) Autocatalytic effect of in situ formed (hydro)quinone intermediates in Fenton and photo-Fenton degradation of non-phenolic aromatic pollutants and chemical kinetic modeling. Chemical Engineering Journal 449:137812 Chemistry Link
Liu Y, Wang W, Zeng A-P (2022) Biosynthesizing structurally diverse diols via a general route combining oxidative and reductive formations of OH-groups. Nature Communications 13:1595 Biotechnology Synthetic Biology Link
Lo-Thong-Viramoutou O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2022) Non-linearity of Metabolic Pathways Critically Influences the Choice of Machine Learning Model. Frontiers in Artificial Intelligence 5:744755 Computational Method Link
Lucido A, Basallo O, Sorribas A, Marin-Sanguino A, Vilaprinyo E, Alves R (2022) A mathematical model for strigolactone biosynthesis in plants. Frontiers in Plant Science 13:979162 Metabolism Plant Biology Link
Lueckheide MJ, Ertem MZ, Michon MA, Chmielniak P, Robinson JR (2022) Peroxide-Selective Reduction of O2 at Redox-Inactive Rare-Earth(III) Triflates Generates an Ambiphilic Peroxide. Journal of the American Chemical Society 144:17295–17306 Chemistry Link
MacKeown H, von Gunten U, Criquet J (2022) Iodide sources in the aquatic environment and its fate during oxidative water treatment - A critical review. Water Research 217:118417 Chemistry Environmental Sciences Link
Maestri S, Merelli E, Pettini M (2022) Agent-based models for detecting the driving forces of biomolecular interactions. Scientific Reports 12:1878 Computational Method Metabolism Link
Maier BD, Aguilera LU, Sahle S, Mutz P, Kalra P, Dächert C, Bartenschlager R, Binder M, Kummer U (2022) Stochastic dynamics of Type-I interferon responses. PLoS Computational Biology 18:e1010623 Immunology Signaling Link
Marazzi L, Shah M, Balakrishnan S, Patil A, Vera-Licona P (2022) NETISCE: a network-based tool for cell fate reprogramming. npj Systems Biology and Applications 8:21 Computational Method Link
Mattila H, Tyystjärvi E (2022) Light-induced damage to photosystem II at a very low temperature (195 K) depends on singlet oxygen. Physiologia Plantarum 174:e13824 Plant Biology Biochemistry Link
Mayer RJ, Hampel N, Ofial AR, Mayr H (2022) Resolving the Mechanistic Complexity in Triarylborane-Induced Conjugate Additions. ACS Catalysis 12:15298–15309 Chemistry Link
Mayr S, Zipse H (2022) Annelated Pyridine Bases for the Selective Acylation of 1,2-Diols. European Journal of Organic Chemistry 2022:e202101521 Chemistry Link
McDaniel T, Smith NE, Cueny ES, Landis CR (2022) Dual-Chain Polymerization at an Early Transition-Metal Single-Site Catalyst. ACS Catalysis 12:10680–10689 Chemistry Link
Mirabella CFM, Aragay G, Ballester P (2022) Influence of the solvent in the self-assembly and binding properties of [1 + 1] tetra-imine bis-calix[4]pyrrole cages. Chemical Science 14:186–195 Chemistry Link
Mokry RL, O’Brien BS, Adelman JW, Rosas S, Schumacher ML, Ebert AD, Terhune SS (2022) Nitric Oxide Attenuates Human Cytomegalovirus Infection yet Disrupts Neural Cell Differentiation and Tissue Organization. Journal of Virology 96:e0012622 Microbiology Immunology Link
Momma TY, Ottaviani JI (2022) There is no direct competition between arginase and nitric oxide synthase for the common substrate l-arginine. Nitric Oxide: Biology and Chemistry 129:16–24 Metabolism Link
Nelson TF, Baumgartner R, Jaggi M, Bernasconi SM, Battagliarin G, Sinkel C, Künkel A, Kohler H-PE, McNeill K, Sander M (2022) Biodegradation of poly(butylene succinate) in soil laboratory incubations assessed by stable carbon isotope labelling. Nature Communications 13:5691 Link
Német N, Miele Y, Shuszter G, Tóth EL, Maróti JE, Szabó PJ, Rossi F, Lagzi I (2022) Inhibition of the urea-urease reaction by the components of the zeolite imidazole frameworks-8 and the formation of urease-zinc-imidazole hybrid compound. Reaction Kinetics, Mechanisms and Catalysis 135:15–28 Chemistry Link
Nieto F, Garrido F, Dinamarca S, Cebrian I, Mayorga LS (2022) Kinetics of antigen cross-presentation assessed experimentally and by a model of the complete endomembrane system. Cellular Immunology 382:104636 Immunology Link
Orrico F, Lopez AC, Saliwonczyk D, Acosta C, Rodriguez-Grecco I, Mouro-Chanteloup I, Ostuni MA, Denicola A, Thomson L, Möller MN (2022) The permeability of human red blood cell membranes to hydrogen peroxide is independent of aquaporins. Journal of Biological Chemistry 298:101503 Biophysics Biochemistry Link
Pallu J, Rabin C, Hui P, Moreira TS, Creste G, Calvet C, Limoges B, Mavré F, Branca M (2022) Exponential amplification by redox cross-catalysis and unmasking of doubly protected molecular probes. Chemical Science 13:2764–2777 Chemistry Link
Pérez-Saavedra B, Velasco-Rubio Á, Rivera-Chao E, Varela JA, Saá C, Fañanás-Mastral M (2022) Catalytic Lewis Base Additive Enables Selective Copper-Catalyzed Borylative α-C-H Allylation of Alicyclic Amines. Journal of the American Chemical Society 144:16206–16216 Chemistry Link
Pini F, Francés-Soriano L, Peruffo N, Barbon A, Hildebrandt N, Natile MM (2022) Spatial and Temporal Resolution of Luminescence Quenching in Small Upconversion Nanocrystals. ACS Applied Materials & Interfaces 14:11883–11894 Chemistry Link
Poucet T, Beauvoit B, González-Moro MB, Cabasson C, Pétriacq P, Flandin A, Gibon Y, Marino D, Dieuaide-Noubhani M (2022) Impaired cell growth under ammonium stress explained by modeling the energy cost of vacuole expansion in tomato leaves. The Plant Journal 112:1014–1028 Physiology Plant Biology Link
Ranallo S, Sorrentino D, Delibato E, Ercolani G, Plaxco KW, Ricci F (2022) Protein-Protein Communication Mediated by an Antibody-Responsive DNA Nanodevice. Angewandte Chemie 61:e202115680 Laboratory Method Link
Range J, Halupczok C, Lohmann J, Swainston N, Kettner C, Bergmann FT, Weidemann A, Wittig U, Schnell S, Pleiss J (2022) EnzymeML-a data exchange format for biocatalysis and enzymology. FEBS Journal 289:5864–5874 Enzymology Computational Method Link
Rietmeyer L (2022) Étude fonctionnelle et structurale des transférases de la famille Fem de Staphylococcus aureus. Ph.D. Thesis, Sorbonne Université, Paris, France Enzymology Link
Rivas FJ (2022) Monopersulfate in water treatment: Kinetics. Journal of Hazardous Materials 430:128383 Chemistry Link
Sader S, Miliordos E (2022) Being negative can be positive: metal oxide anions promise more selective methane to methanol conversion. Physical Chemistry Chemical Physics 24:21583–21587 Chemistry Link
Santos JPG, Pajo K, Trpevski D, Stepaniuk A, Eriksson O, Nair AG, Keller D, Hellgren Kotaleski J, Kramer A (2022) A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Neuroinformatics 20:241–259 Computational Method Link
Sarang K (2022) Atmospheric Secondary Organic Aerosol: Kinetic and Chemical Studies of in-Cloud Reactions of Selected Plant Volatiles. Ph.D. Thesis, Institute of Physical Chemistry of the Polish Academy of Sciences, Warsaw, Poland. Chemistry Environmental Sciences Link
Schälte Y, Klinger E, Alamoudi E, Hasenauer J (2022) pyABC: Efficient and robust easy-to-use approximate Bayesian computation. Journal of Open Source Software 7:4304 Software Link
Schmallegger M, Grützmacher H, Gescheidt G (2022) Bis(acyl)phosphine Oxides as Stoichiometric Photo-Reductants for Copper Nanoparticle Synthesis: Efficiency and Kinetics. ChemPhotoChem 6:e202200155 Chemistry Link
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Sharma S, Hsieh Y-C, Dietze J, Bockwoldt M, Strømland Ø, Ziegler M, Heiland I (2022) Early Evolutionary Selection of NAD Biosynthesis Pathway in Bacteria. Metabolites 12:569 Metabolism Microbiology Link
Shelton MG, Kerns KA, Castora FJ, Coleman RA (2022) Incorporating Mitochondrial Gene Expression Changes Within a Testable Mathematical Model for Alzheimer’s Disease: Stress Response Modulation Predicts Potential Therapeutic Targets. Journal of Alzheimer’s Disease 90:109–117 Signaling Metabolism Link
Sinner EK, Townsend CA (2022) Purification and characterization of sequential cobalamin-dependent radical SAM methylases ThnK and TokK in carbapenem β-lactam antibiotic biosynthesis. Methods in Enzymology 669:29–44 Enzymology Link
Sotnikov DV, Barshevskaya LV, Bartosh AV, Zherdev AV, Dzantiev BB (2022) Double Competitive Immunodetection of Small Analyte: Realization for Highly Sensitive Lateral Flow Immunoassay of Chloramphenicol. Biosensors 12:343 Laboratory Method Link
Sumi T, Harada K (2022) Immune response to SARS-CoV-2 in severe disease and long COVID-19. iScience 25:104723 Immunology Link
Sun Y, Zhou P, Zhang P, Meng S, Zhou C, Liu Y, Zhang H, Xiong Z, Duan X, Lai B (2022) New insight into carbon materials enhanced Fenton oxidation: A strategy for green iron(III)/iron(II) cycles. Chemical Engineering Journal 450:138423 Chemistry Link
Tamosiunaite N, Logie LC, Neale SE, Singh K, Davies DL, Macgregor SA (2022) Experimental and Computational Studies on the Acetate-Assisted C–H Activation of N-Aryl Imidazolium Salts at Rhodium and Iridium: A Chloride Additive Changes the Selectivity of C–H Activation. Journal of Organic Chemistry 87:1445–1456 Chemistry Link
Tokarev A, Mozokhina A, Volpert V (2022) Competition of SARS-CoV-2 Variants in Cell Culture and Tissue: Wins the Fastest Viral Autowave. Vaccines 10:995 Immunology Link
Toyoda R, Hoang NV, Moghaddam KG, Crespi S, Pooler DRS, Faraji S, Pshenichnikov MS, Feringa BL (2022) Synergistic interplay between photoisomerization and photoluminescence in a light-driven rotary molecular motor. Nature Communications 13:5765 Biophysics Link
Trošanová Z, Louša P, Kozeleková A, Brom T, Gašparik N, Tungli J, Weisová V, Župa E, Žoldák G, Hritz J (2022) Quantitation of Human 14-3-3ζ Dimerization and the Effect of Phosphorylation on Dimer-monomer Equilibria. Journal of Molecular Biology 434:167479 Signaling Macromolecular Biochemistry Link
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Ulrich EC, Drennan CL (2022) The Atypical Cobalamin-Dependent S-Adenosyl-l-Methionine Nonradical Methylase TsrM and Its Radical Counterparts. Journal of the American Chemical Society 144:5673–5684 Biochemistry Link
Valverde MB, Rodríguez RM (2022) miRNA networks regulating gene expression in response to tension or compression forces in the cells of the periodontal ligament. 2022 IEEE 4th International Conference on BioInspired Processing (BIP), Cartago, Costa Rica: 1–6 Genetics Link
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107 publications
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
Friedhoff VN, Antunes G, Falcke M, Simões de Souza FM (2021) Stochastic reaction-diffusion modeling of calcium dynamics in 3D dendritic spines of Purkinje cells. Biophysical Journal 120:2112–2123 Signaling Link
Frolova AY, Pakhomov AA, Martynov VI (2021) Physicochemical Properties of Photoconvertible Fluorescent Protein from Montastraea cavernosa. Russian Journal of Bioorganic Chemistry 47:244–251 Chemistry Link
Gallas JAC, Hauser MJB, Olsen LF (2021) Complexity of a peroxidase-oxidase reaction model. Physical Chemistry Chemical Physics 23:1943–1955 Enzymology Link
Genovese D, Baschieri A, Vona D, Baboi RE, Mollica F, Prodi L, Amorati R, Zaccheroni N (2021) Nitroxides as Building Blocks for Nanoantioxidants. ACS Applied Materials & Interfaces 13:31996–32004 Chemistry Materials Science Link
Guhe V, Soni B, Ingale P, Singh S (2021) Autophagy proteins and its homeostasis in cellular environment. Advances in Protein Chemistry and Structural Biology 123:73–93 Cell Biology Signaling Link
Gupta A, Mendes P (2021) ShinyCOPASI: a web-based exploratory interface for COPASI models. arXiv:2110.03796. Software Link
Guo Y, Baschieri A, Mollica F, Valgimigli L, Cedrowski J, Litwinienko G, Amorati R (2021) Hydrogen Atom Transfer from HOO. to ortho-Quinones Explains the Antioxidant Activity of Polydopamine. Angewandte Chemie International Edition 60:15220–15224 Chemistry Link
Guzman-Luna V, Fuchs AM, Allen AJ, Staikos A, Cavagnero S (2021) An intrinsically disordered nascent protein interacts with specific regions of the ribosomal surface near the exit tunnel. Communications Biology 4:1236 Macromolecular Biochemistry Link
Haque MA, Morozova K, Lawrence N, Ferrentino G, Scampicchio M (2021) Radical Scavenging Activity of Antioxidants by Cyclic Voltammetry. Electroanalysis 33:23–28 Chemistry Biophysics Link
Hellgren J (2021) Engineering central carbon metabolism with phosphoketolase pathways in Saccharomyces cerevisiae. Ph.D. Thesis, Chalmers University of Technology, Sweden. Metabolism Biotechnology Link
Héron JDJ (2021) C-H Activation and CuAAC Reactions with 1,8-Naphthyridine Based Dicopper Complexes from a Computational Perspective. Ph.D. Thesis, University of Oslo, Norway. Chemistry Link
Hetmanski JHR, Jones MC, Chunara F, Schwartz J-M, Caswell PT (2021) Combinatorial mathematical modelling approaches to interrogate rear retraction dynamics in 3D cell migration. PLoS Computational Biology 17:e1008213 Cell Biology Signaling Link
Holzheu P, Großeholz R, Kummer U (2021) Impact of explicit area scaling on kinetic models involving multiple compartments. BMC Bioinformatics 22:21 Theory Link
Huysmans GHM, Ciftci D, Wang X, Blanchard SC, Boudker O (2021) The high-energy transition state of the glutamate transporter homologue GltPh. EMBO Journal 40:e105415 Enzymology Link
Ibáňez Gaspar V, Catozzi S, Ternet C, Luthert PJ, Kiel C (2021) Analysis of Ras-effector interaction competition in large intestine and colorectal cancer context. Small GTPases 12:209–225 Signaling Link
Kalkman ED, Hartwig JF (2021) Direct Observation of Diastereomeric α-C-Bound Enolates during Enantioselective α-Arylations: Synthesis, Characterization, and Reactivity of Arylpalladium Fluorooxindole Complexes. Journal of the American Chemical Society 143:11741–11750 Chemistry Link
King J, Mihaila SM, Ahmed S, Truckenmüller R, Giselbrecht S, Masereeuw R, Carlier A (2021) The Influence of OAT1 Density and Functionality on Indoxyl Sulfate Transport in the Human Proximal Tubule: An Integrated Computational and In Vitro Study. Toxins 13:674 Toxicology Physiology Link
Kleineberg C (2021) Bottom-up assembly of a light-driven ATP regeneration module in lipid, polymer and hybrid vesicles. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany. Synthetic Biology Biochemistry Link
Klimacek M, Zhong C, Nidetzky B (2021) Kinetic modeling of phosphorylase-catalyzed iterative β-1,4-glycosylation for degree of polymerization-controlled synthesis of soluble cello-oligosaccharides. Biotechnology for Biofuels and Bioproducts 14:134 Biotechnology Enzymology Link
Koch D, Alexandrovich A, Funk F, Kho AL, Schmitt JP, Gautel M (2021) Molecular noise filtering in the β-adrenergic signaling network by phospholamban pentamers. Cell Reports 36:109448 Signaling Link
Korobkin JD, Balabin FA, Yakovenko SA, Simonenko EY, Sveshnikova AN (2021) Occurrence of Calcium Oscillations in Human Spermatozoa Is Based on Spatial Signaling Enzymes Distribution. International Journal of Molecular Sciences 22:8018 Signaling Link
Koshy-Chenthittayil S, Dimitrova E, Jenkins EW, Dean BC (2021) A computational framework for finding parameter sets associated with chaotic dynamics. In Silico Biology 14:41–51 Computational Method Link
Lakhova TN, Kazantsev FV, Lashin SA, Matushkin YG (2021) The finding and researching algorithm for potentially oscillating enzymatic systems. Vavilov Journal of Genetics and Breeding 25:318–330 Computational Method Metabolism Link
Leopold M, Siebert M, Siegle AF, Trapp O (2021) Reaction Network Analysis of the Ruthenium-Catalyzed Reduction of Carbon Dioxide to Dimethoxymethane. ChemCatChem 13:2807–2814 Chemistry Link
Li Y, Cheng H (2021) Chemical kinetic modeling of organic pollutant degradation in Fenton and solar photo-Fenton processes. Journal of the Taiwan Institute of Chemical Engineers 123:175–184 Chemistry Environmental Sciences Link
Lin Q, Fu Y, Liu P, Diao T (2021) Monovalent Nickel-Mediated Radical Formation: A Concerted Halogen-Atom Dissociation Pathway Determined by Electroanalytical Studies. Journal of the American Chemical Society 143:14196–14206 Chemistry Link
Liu S, Boudjelel M, Schrock RR, Conley MP, Tsay C (2021) Interconversion of Molybdenum or Tungsten d2 Styrene Complexes with d0 1-Phenethylidene Analogues. Journal of the American Chemical Society 143:17209–17218 Chemistry Link
Long BM, Förster B, Pulsford SB, Price GD, Badger MR (2021) Rubisco proton production can drive the elevation of CO2 within condensates and carboxysomes. Proceedings of the National Academy of Sciences USA 118:e2014406118 Metabolism Biophysics Plant Biology Link
Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG (2021) Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. Journal of Biological Chemistry 297:101175 Macromolecular Biochemistry Microbiology Link
Marchisio MA (2021) Modular Modeling of Genetic Circuits in SBML Level 3. Methods in Molecular Biology 2189:45–63 Synthethic Biology Computational Method Link
Matsuura R, Karunananda MK, Liu M, Nguyen N, Blackmond DG, Engle KM (2021) Mechanistic Studies of Pd(II)-Catalyzed E/Z Isomerization of Unactivated Alkenes: Evidence for a Monometallic Nucleopalladation Pathway. ACS Catalysis 11:4239–4246 Chemistry Link
Mazat J-P, Devin A, Yoboue E, Ransac S (2021) A Theoretical Model of Mitochondrial ATP Synthase Deficiencies. The Role of Mitochondrial Carriers. Processes 9:1424 Metabolism Link
McBane GC (2021) SIR (Susceptible–Infectious–Removed) Model of Epidemiology as an Extended Example for Chemical Kinetics Students. Journal of Chemical Education 98:2906–2911 Education Epidemiology Link
Meftah Y, Boumedjane Y, Fleurat-Lessard P, Delbecq F, Michel C (2021) Enantioselective reduction of prochiral ketones promoted by amino amide ruthenium complexes: A DFT study. Journal of Organometallic Chemistry 939:121765 Chemistry Link
Millard P, Enjalbert B, Uttenweiler-Joseph S, Portais J-C, Letisse F (2021) Control and regulation of acetate overflow in Escherichia coli. eLife 10:e63661 Metabolism Microbiology Link
Mısırlı G, Yang B, James K, Wipat A (2021) Virtual Parts Repository 2: Model-Driven Design of Genetic Regulatory Circuits. ACS Synthetic Biology 10:3304–3315 Computational Method Synthetic Biology Link
Mohapatra SR, Sadik A, Sharma S, Poschet G, Gegner HM, Lanz TV, Lucarelli P, Klingmüller U, Platten M, Heiland I, Opitz CA (2021) Hypoxia Routes Tryptophan Homeostasis Towards Increased Tryptamine Production. Frontiers in Immunology 12:590532 Metabolism Physiology Link
Monti M, Guiducci G, Paone A, Rinaldo S, Giardina G, Liberati FR, Cutruzzolá F, Tartaglia GG (2021) Modelling of SHMT1 riboregulation predicts dynamic changes of serine and glycine levels across cellular compartments. Computational and Structural Biotechnology Journal 19:3034–3041 Macromolecular Biochemistry Link
Novichkov AI, Hanopolskyi AI, Miao X, Shimon LJW, Diskin-Posner Y, Semenov SN (2021) Autocatalytic and oscillatory reaction networks that form guanidines and products of their cyclization. Nature Communications 12:2994 Biochemistry Link
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
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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
Vaginay A, Boukhobza T, Smaïl-Tabbone M (2021) From quantitative SBML models to boolean networks. CNA 2021 - 10th International Conference on Complex Networks and their Applications, Nov 2021, Madrid, Spain. Computational Method Link
Valletti N, Budroni MA, Lagzi I, Marchettini N, Sanchez-Dominguez M, Rossi F (2021) Interfacial Mass Transfer in Trichloroethylene/Surfactants/ Water Systems: Implications for Remediation Strategies. Reactions 2:312–322 Chemistry Environmental Sciences Link
Vasilev GA, Filkova AA, Sveshnikova AN (2021) Study of Reversible Platelet Aggregation Model by Nonlinear Dynamics. Mathematics 9:759 Immunology Link
Virtanen O, Khorobrykh S, Tyystjärvi E (2021) Acclimation of Chlamydomonas reinhardtii to extremely strong light. Photosynthesis Research 147:91–106 Biophysics Microbiology Link
Wang JY, Choi K, Zuend SJ, Borate K, Shinde H, Goetz R, Hartwig JF (2021) Cross-Coupling between Hydrazine and Aryl Halides with Hydroxide Base at Low Loadings of Palladium by Rate-Determining Deprotonation of Bound Hydrazine. Angewandte Chemie International Edition 60:399–408 Chemistry Link
Whitehead CB, Handwerk DR, Shipman PD, Li Y, Frenkel AI, Ingham B, Kirby NM, Finke RG (2021) Nanoparticle Formation Kinetics, Mechanisms, and Accurate Rate Constants: Examination of a Second-Generation Ir(0)n Particle Formation System by Five Monitoring Methods Plus Initial Mechanism-Enabled Population Balance Modeling. Journal of Physical Chemistry 125:13449–13476 Chemistry Link
Yahya G, Pérez AP, Mendoza MB, Parisi E, Moreno DF, Artés MH, Gallego C, Aldea M (2021) Stress granules display bistable dynamics modulated by Cdk. Journal of Cell Biology 220:jcb202005102 Cell Biology Signaling Link
Yamada TG, Ii K, König M, Feierabend M, Dräger A, Funahashi A (2021) SBMLWebApp: Web-Based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models. Processes 9:1830 Software Link
Yang Y, Filipovic D, Bhattacharya S (2021) A Negative Feedback Loop and Transcription Factor Cooperation Regulate Zonal Gene Induction by 2, 3, 7, 8-Tetrachlorodibenzo-p-Dioxin in the Mouse Liver. Hepatology Communications 6:750-764 Signaling Physiology Toxicology Link
Yeom J-S, Georgouli K, Blake R, Navid A (2021) Towards dynamic simulation of a whole cell model. In: Proceedings of the 12th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics, August 1–4, 2021, Gainesville, FL, USA, pp. 1–10. DOI:10.1145/3459930.3471161 Computational Method Link
Yin Q, Xu Z, Lian T, Musaev DG, Hill CL, Geletii YV (2021) Tafel Slope Analyses for Homogeneous Catalytic Reactions. Catalysts 11:87 Chemistry Link
Younas SL, Streuff J (2021) Kinetic Analysis Uncovers Hidden Autocatalysis and Inhibition Pathways in Titanium(III)-Catalyzed Ketone-Nitrile Couplings. ACS Catalysis 11:11451–11458 Chemistry Link
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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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Zhu N, Hu X, Fang Z, Guo K (2021) Chemoselective Polymerizations. Progress in Polymer Science 117:101397 Chemistry Link
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118 publications
Abudukelimu A, Barberis M, Redegeld FA, Sahin N, Sharma RP, Westerhoff HV (2020) Complex Stability and an Irrevertible Transition Reverted by Peptide and Fibroblasts in a Dynamic Model of Innate Immunity. Frontiers in Immunology 10:3091 Immunology Signaling Link
Ajjolli Nagaraja A, Charton P, Cadet XF, Fontaine N, Delsaut M, Wiltschi B, Voit A, Offmann B, Damour C, Grondin-Perez B, Cadet F (2020) A Machine Learning Approach for Efficient Selection of Enzyme Concentrations and Its Application for Flux Optimization. Catalysts 10:291 Computational Method Metabolism Link
Alexander JR, Packard MH, Hildebrandt AM, Ott AA, Topczewski JJ (2020) Divergent Mechanisms of the Banert Cascade with Propargyl Azides. Journal of Organic Chemistry 85:3174–3181 Chemistry Link
Artús Suàrez L, Jayarathne U, Balcells D, Bernskoetter WH, Hazari N, Jaraíz M, Nova A (2020) Rational selection of co-catalysts for the deaminative hydrogenation of amides. Chemical Science 11:2225–2230 Chemistry Link
Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft J-U, Hobman JL, Stekel DJ (2020) A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology 96:fiaa100 Microbiology Genetics Link
Balasubramanian S, Chandrasekran P, Yesudhas AJR, Ganapathyraman P, Eiteman MA, Subramanian R (2020) In vivo interpretation of model predicted inhibition in acrylate pathway engineered Lactococcus lactis. Biotechnology and Bioengineering 117:3785–3798 Microbiology Metabolism Biotechnology Link
Balzer CJ, James ML, Narvaez-Ortiz HY, Helgeson LA, Sirotkin V, Nolen BJ (2020) Synergy between Wsp1 and Dip1 may initiate assembly of endocytic actin networks. eLife 9:e60419 Cell Biology Macromolecular Biochemistry Link
Barrett TM (2020) Thioamides and proteolysis: Examining the effects and applications of a single-atom substitution. Ph.D. Thesis, University of Pennsylvania, USA. Biochemistry Link
Bartoli V, Meaker GA, di Bernardo M, Gorochowski TE (2020) Tunable genetic devices through simultaneous control of transcription and translation. Nature Communications 11:2095 Synthetic Biology Link
Benchoam D, Semelak JA, Cuevasanta E, Mastrogiovanni M, Grassano JS, Ferrer-Sueta G, Zeida A, Trujillo M, Möller MN, Estrin DA, Alvarez B (2020) Acidity and nucleophilic reactivity of glutathione persulfide. Journal of Biological Chemistry 295:15466–15481 Biochemistry Link
Benedek Z, Papp M, Oláh J, Szilvási T (2020) Demonstrating the Direct Relationship between Hydrogen Evolution Reaction and Catalyst Deactivation in Synthetic Fe Nitrogenases. ACS Catalysis 10:12555–12568 Biochemistry Link
Bora N, Jha AN (2020) In silico Metabolic Pathway Analysis Identifying Target Against Leishmaniasis - A Kinetic Modeling Approach. Frontiers in Genetics 11:179 Parasitology Metabolism Link
Bourouina A, Oswald A, Lido V, Dong L, Rataboul F, Djakovitch L, de Bellefon C, Meille V (2020) Kinetic Study of the Herrmann–Beller Palladacycle-Catalyzed Suzuki–Miyaura Coupling of 4-Iodoacetophenone and Phenylboronic Acid. Catalysts 10:989 Chemistry Link
Bragança CE, Kraut DA (2020) Mode of targeting to the proteasome determines GFP fate. Journal of Biological Chemistry 295:15892–15901 Biochemistry Link
Cabré A, Rafael S, Sciortino G, Ujaque G, Verdaguer X, Lledós A, Riera A (2020) Catalytic Regioselective Isomerization of 2,2-Disubstituted Oxetanes to Homoallylic Alcohols. Angewandte Chemie International Edition 59:7521–7527 Chemistry Link
Carlson-Stevermer J, Das A, Abdeen AA, Fiflis D, Grindel BI, Saxena S, Akcan T, Alam T, Kletzien H, Kohlenberg L, Goedland M, Dombroe MJ, Saha K (2020) Design of efficacious somatic cell genome editing strategies for recessive and polygenic diseases. Nature Communications 11:6277 Laboratory Method Genetics Link
Chauhan N, Singh S (2020) Multiscale Process Modelling in Translational Systems Biology of Leishmania major: A Holistic view. Scientific Reports 10:785 Metabolism Parasitology Link
Cho D-J, Függer M, Hopper C, Kushwaha M, Nowak T, Soubeyran Q (2020) Distributed Computation with Continual Population Growth. In: Attiya H (ed) 34th International Symposium on Distributed Computing (DISC 2020). Dagstuhl, Germany: Schloss Dagstuhl–Leibniz-Zentrum für Informatik, 7:1-7:17. Theory Link
Clark TJ, Guo L, Morgan J, Schwender J (2020) Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models. Annual Review of Plant Biology 71:303–326 Metabolism Plant Biology Link
Ćorović M, Milivojević A, Simović M, Banjanac K, Pjanović R, Bezbradica D (2020) Enzymatically derived oil-based L-ascorbyl esters: Synthesis, antioxidant properties and controlled release from cosmetic formulations. Sustainable Chemistry and Pharmacy 15:100231 Biotechnology Link
Dalle Pezze P, Karanasios E, Kandia V, Manifava M, Walker SA, Le Novère NG, Ktistakis NT (2020) ATG13 dynamics in nonselective autophagy and mitophagy: insights from live imaging studies and mathematical modeling. Autophagy 17:1131-1141 Cell Biology Link
Desoeuvres A, Trombettoni G, Radulescu O (2020) Interval Constraint Satisfaction and Optimization for Biological Homeostasis and Multistationarity. In: Abate A, Petrov T and Wolf V (eds.) Computational Methods in Systems Biology. Springer International Publishing, 79–101 Computational Method Link
Dhasmana A, Uniyal S, Anukriti, Kashyap VK, Somvanshi P, Gupta M, Bhardwaj U, Jaggi M, Yallapu MM, Haque S, Chauhan SC (2020) Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin. Scientific Reports 10:12045 Signaling Link
Dooley III CJ, Burtea A, Mitilian C, Dao WT, Qu B, Salzameda NT, Rychnovsky SD (2020) Using the Competing Enantioselective Conversion Method to Assign the Absolute Configuration of Cyclic Amines with Bode’s Acylation Reagents. Journal of Organic Chemistry 85:10750–10759 Chemistry Link
Dromms RA, Lee JY, Styczynski MP (2020) LK-DFBA: a linear programming-based modeling strategy for capturing dynamics and metabolite-dependent regulation in metabolism. BMC Bioinformatics 21:93 Computational Method Metabolism Link
Eastwood JB, Hammarback LA, McRobie MT, Clark IP, Towrie M, Fairlamb IJS, Lynam JM (2020) Time-resolved infra-red spectroscopy reveals competitive water and dinitrogen coordination to a manganese(I) carbonyl complex. Dalton Transactions 49:5463–5470 Chemistry Link
Erlendsson S, Teilum K (2020) Binding Revisited-Avidity in Cellular Function and Signaling. Frontiers in Molecular Biosciences 7:615565 Signaling Theory Link
Ferrall-Fairbanks MC, Kieslich CA, Platt MO (2020) Reassessing enzyme kinetics: Considering protease-as-substrate interactions in proteolytic networks. Proceedings of the National Academy of Sciences USA 117:3307–3318 Enzymology Link
Finke RG, Watzky MA, Whitehead CB (2020) Response to “Particle Size Is a Primary Determinant for Sigmoidal Kinetics of Nanoparticle Formation: A ‘Disproof’ of the Finke–Watzky (F-W) Nanoparticle Nucleation and Growth Mechanism”. Chemistry of Materials 32:3657–3672 Chemistry Materials Science Link
Firczuk H, Teahan J, Mendes P, McCarthy JEG (2020) Multisite rate control analysis identifies ribosomal scanning as the sole high-capacity/low-flux-control step in mRNA translation. FEBS Journal 287:925940 Macromolecular Biochemistry Link
Foth PJ, Malig TC, Yu H, Bolduc TG, Hein JE, Sammis GM (2020) Halide-Accelerated Acyl Fluoride Formation Using Sulfuryl Fluoride. Organic Letters 22:6682–6686 Chemistry Link
Fournié M, Truan G (2020) Multiplicity of carotene patterns derives from competition between phytoene desaturase diversification and biological environments. Scientific Reports 10:21106 Biochemistry Metabolism Link
Fribourg M (2020) A case for the reuse and adaptation of mechanistic computational models to study transplant immunology. American Journal of Transplantation 20:355–361 Immunology Link
Frühwirt P, Kregar A, Törring JT, Katrašnik T, Gescheidt G (2020) Holistic approach to chemical degradation of Nafion membranes in fuel cells: modelling and predictions. Physical Chemistry Chemical Physics 22:5647–5666 Chemistry Link
Fuchino K, Kalnenieks U, Rutkis R, Grube M, Bruheim P (2020) Metabolic Profiling of Glucose-Fed Metabolically Active Resting Zymomonas mobilis Strains. Metabolites 10:E81 Metabolism Microbiology Biotechnology Link
Gallego AM, Peñas de Frutos MN, Marcos-Ayuso G, Martin-Alvarez JM, Martínez-Ilarduya JM, Espinet P (2020) Experimental study of speciation and mechanistic implications when using chelating ligands in aryl-alkynyl Stille coupling. Dalton Transactions 49:11336–11345 Chemistry Link
Garde R, Ewald J, Kovács ÁT, Schuster S (2020) Modelling population dynamics in a unicellular social organism community using a minimal model and evolutionary game theory. Open Biology 10:200206 Microbiology Metabolism Ecology Link
Garde R, Ibrahim B, Schuster S (2020) Extending the minimal model of metabolic oscillations in Bacillus subtilis biofilms. Scientific Reports 10:5579 Microbiology Metabolism Link
Garde R, Ibrahim B, Kovács ÁT, Schuster S (2020) Differential equation-based minimal model describing metabolic oscillations in Bacillus subtilis biofilms. Royal Society Open Science 7:190810 Microbiology Metabolism Link
Garzon Dasgupta AK, Martyanov AA, Filkova AA, Panteleev MA, Sveshnikova AN (2020) Development of a Simple Kinetic Mathematical Model of Aggregation of Particles or Clustering of Receptors. Life 10:E97 Biophysics Link
Ghorbani S, Szigetvari PD, Haavik J, Kleppe R (2020) Serine 19 phosphorylation and 14-3-3 binding regulate phosphorylation and dephosphorylation of tyrosine hydroxylase on serine 31 and serine 40. Journal of Neurochemistry 152:29–47 Signaling Link
Glont M, Arankalle C, Tiwari K, Nguyen TVN, Hermjakob H, Malik-Sheriff RS (2020) BioModels Parameters: a treasure trove of parameter values from published systems biology models. Bioinformatics 36:4649–4654 Computational Method Link
Greiss F, Daube SS, Noireaux V, Bar-Ziv R (2020) From deterministic to fuzzy decision-making in artificial cells. Nature Communications 11:5648 Synthetic Biology Genetics Link
Gutterød ES, Pulumati SH, Kaur G, Lazzarini A, Solemsli BG, Gunnæs AE, Ahoba-Sam C, Kalyva ME, Sannes JA, Svelle S, Skúlason E, Nova A, Olsbye U (2020) Influence of Defects and H2O on the Hydrogenation of CO2 to Methanol over Pt Nanoparticles in UiO-67 Metal-Organic Framework. Journal of the American Chemical Society 142:17105–17118 Chemistry Link
Handwerk DR, Shipman PD, Özkar S, Finke RG (2020) Dust Effects on Ir(0)n Nanoparticle Formation Nucleation and Growth Kinetics and Particle Size-Distributions: Analysis by and Insights from Mechanism-Enabled Population Balance Modeling. Langmuir 36:1496–1506 Chemistry Materials Science Link
Hellgren J, Godina A, Nielsen J, Siewers V (2020) Promiscuous phosphoketolase and metabolic rewiring enables novel non-oxidative glycolysis in yeast for high-yield production of acetyl-CoA derived products. Metabolic Engineering 62:150–160 Metabolism Link
Herrmann HA, Schwartz J-M, Johnson GN (2020) From empirical to theoretical models of light response curves - linking photosynthetic and metabolic acclimation. Photosynthesis Research 145:5–14 Metabolism Link
Hinze T (2020) Coping with dynamical reaction system topologies using deterministic P modules: a case study of photosynthesis. Journal of Membrane Computing 2:281–289 Computational Method Link
Horváth D, Taricska N, Keszei E, Stráner P, Farkas V, Tóth GK, Perczel A (2020) Compactness of Protein Folds Alters Disulfide-Bond Reducibility by Three Orders of Magnitude: A Comprehensive Kinetic Case Study on the Reduction of Differently Sized Tryptophan Cage Model Proteins. ChemBioChem 21:681–695 Biochemistry Link
Howell RSM, Klemm C, Thorpe PH, Csikász-Nagy A (2020) Unifying the mechanism of mitotic exit control in a spatiotemporal logical model. PLoS Biology 18:e3000917 Cell Biology Link
Iwasaki T, Takiguchi R, Hiraiwa T, Yamada TG, Yamazaki K, Hiroi NF, Funahashi A (2020) Neural Differentiation Dynamics Controlled by Multiple Feedback Loops in a Comprehensive Molecular Interaction Network. Processes 8:166 Signaling Link
Jones SM, Heppner DE, Vu K, Kosman DJ, Solomon EI (2020) Rapid Decay of the Native Intermediate in the Metallooxidase Fet3p Enables Controlled FeII Oxidation for Efficient Metabolism. Journal of the American Chemical Society 142:10087–10101 Chemistry Link
Karakhim SO, Zhuk PF, Kosterin SO (2020) Kinetics simulation of transmembrane transport of ions and molecules through a semipermeable membrane. Journal of Bioenergetics and Biomembranes 52:47–60 Biophysics Link
Karlstaedt A, Khanna R, Thangam M, Taegtmeyer H (2020) Glucose 6-Phosphate Accumulates via Phosphoglucose Isomerase Inhibition in Heart Muscle. Circulation Research 126:60–74 Metabolism Link
Khaliq W, Großmann P, Neugebauer S, Kleyman A, Domizi R, Calcinaro S, Brealey D, Gräler M, Kiehntopf M, Schäuble S, Singer M, Panagiotou G, Bauer M (2020) Lipid metabolic signatures deviate in sepsis survivors compared to non-survivors. Computational and Structural Biotechnology Journal 18:3678–3691 Metabolism Link
Khurshid G, Abbassi AZ, Khalid MF, Gondal MN, Naqvi TA, Shah MM, Chaudhary SU, Ahmad R (2020) A cyanobacterial photorespiratory bypass model to enhance photosynthesis by rerouting photorespiratory pathway in C3 plants. Scientific Reports 10:20879 Metabolism Link
Kolodkin AN, Sharma RP, Colangelo AM, Ignatenko A, Martorana F, Jennen D, Briedé JJ, Brady NR, Barberis M, Mondeel TDGA, Papa M, Kumar V, Peters B, Skupin A, Alberghina L, Balling R, Westerhoff HV (2020) ROS networks: designs, aging, Parkinson’s disease and precision therapies. npj Systems Biology and Applications 6:34 Biochemistry Link
Leuba SI, Yaesoubi R, Antillon M, Cohen T, Zimmer C (2020) Tracking and predicting U.S. influenza activity with a real-time surveillance network. PLoS Computational Biology 16:e1008180 Epidemiology Link
Li L, Lai M, Cole S, Le Novère N, Edelstein SJ (2020) Neurogranin stimulates Ca2+/calmodulin-dependent kinase II by suppressing calcineurin activity at specific calcium spike frequencies. PLoS Computational Biology 16:e1006991 Signaling Link
Lo-Thong O, Charton P, Cadet XF, Grondin-Perez B, Saavedra E, Damour C, Cadet F (2020) Identification of flux checkpoints in a metabolic pathway through white-box, grey-box and black-box modeling approaches. Scientific Reports 10:13446 Metabolism Link
Malig TC, Tan Y, Wisniewski SR, Higman CS, Carrasquillo-Flores R, Ortiz A, Purdum GE, Kolotuchin S, Hein JE (2020) Development of a telescoped synthesis of 4-(1H)-cyanoimidazole core accelerated by orthogonal reaction monitoring. Reaction Chemistry & Engineering 5:1421–1428 Chemistry Laboratory Method Link
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Computational Method Link
Maquilón C, Limburg B, Laserna V, Garay-Ruiz D, González-Fabra J, Bo C, Martínez Belmonte M, Escudero-Adán EC, Kleij AW (2020) Effect of an Al(III) Complex on the Regio- and Stereoisomeric Formation of Bicyclic Organic Carbonates. Organometallics 39:1642–1651 Chemistry Link
Marín-Hernández Á, Gallardo-Pérez JC, Reyes-García MA, Sosa-Garrocho M, Macías-Silva M, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2020) Kinetic modeling of glucose central metabolism in hepatocytes and hepatoma cells. Biochimica et Biophysica Acta 1864:129687 Metabolism Link
Martin DJ, Wise CF, Pegis ML, Mayer JM (2020) Developing Scaling Relationships for Molecular Electrocatalysis through Studies of Fe-Porphyrin-Catalyzed O2 Reduction. Accounts of Chemical Research 53:1056–1065 Chemistry Link
Martyanov AA, Balabin FA, Dunster JL, Panteleev MA, Gibbins JM, Sveshnikova AN (2020) Control of Platelet CLEC-2-Mediated Activation by Receptor Clustering and Tyrosine Kinase Signaling. Biophysical Journal 118:2641–2655 Immunology Signaling Link
Martyanov AA, Morozova DS, Sorokina MA, Filkova AA, Fedorova DV, Uzueva SS, Suntsova EV, Novichkova GA, Zharkov PA, Panteleev MA, Sveshnikova AN (2020) Heterogeneity of Integrin αIIbβ3 Function in Pediatric Immune Thrombocytopenia Revealed by Continuous Flow Cytometry Analysis. International Journal of Molecular Sciences 21:3035 Immunology Link
Mayorga L, Samartino CG, Flores G, Masuelli S, Sánchez MV, Sánchez CG, Mayorga LS (2020) COVID-19 lockdown: if, when and how. medRxiv, 2020.06.20.20136325 Epidemiology Link
Mazet F, Tindall MJ, Gibbins JM, Fry MJ (2020) A model of the PI cycle reveals the regulating roles of lipid-binding proteins and pitfalls of using mosaic biological data. Scientific Reports 10:13244 Signaling Link
Mendes P, Girardi E, Superti-Furga G, Kell DB (2020) Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters. bioRxiv. 2020.01.16.909507 Microbiology Link
Merk LN, Shur AS, Pandey A, Murray RM, Green LN (2020) Engineering Logical Inflammation Sensing Circuit for Gut Modulation. bioRxiv 2020.11.10.377085 Immunology Link
Meyer K, Morales-Navarrete H, Seifert S, Wilsch-Braeuninger M, Dahmen U, Tanaka EM, Brusch L, Kalaidzidis Y, Zerial M (2020) Bile canaliculi remodeling activates YAP via the actin cytoskeleton during liver regeneration. Molecular Systems Biology 16:e8985 Signaling Cell Biology Link
Mochão H, Barahona P, Costa RS (2020) KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling. Database 2020:baaa093 Computational Method Link
Mokry RL, Schumacher ML, Hogg N, Terhune SS (2020) Nitric Oxide Circumvents Virus-Mediated Metabolic Regulation during Human Cytomegalovirus Infection. mBio 11:e02630-20 Immunology Link
Mondeel TDGA, Ivanov O, Westerhoff HV, Liebermeister W, Barberis M (2020) Clb3-centered regulations are recurrent across distinct parameter regions in minimal autonomous cell cycle oscillator designs. npj Systems Biology and Applications 6:8 Cell Biology Link
Morgan AE, McAuley MT (2020) Cholesterol Homeostasis: An In Silico Investigation into How Aging Disrupts Its Key Hepatic Regulatory Mechanisms. Biology 9:E314 Metabolism Link
Noga MJ, Büke F, van den Broek NJF, Imholz NCE, Scherer N, Yang F, Bokinsky G (2020) Posttranslational Control of PlsB Is Sufficient To Coordinate Membrane Synthesis with Growth in Escherichia coli. mBio 11:e02703-19 Microbiology Metabolism Link
Padayachee L, Rohwer JM, Pillay CS (2020) The thioredoxin redox potential and redox charge are surrogate measures for flux in the thioredoxin system. Archives of Biochemistry and Biophysics 680:108231 Biochemistry Metabolism Link
Pakhomov AA, Frolova AY, Tabakmakher VM, Chugunov AO, Efremov RG, Martynov VI (2020) Impact of external amino acids on fluorescent protein chromophore biosynthesis revealed by molecular dynamics and mutagenesis studies. Journal of Photochemistry and Photobiology B: Biology 206:111853 Biophysics Link
Panigrahi A, Whitaker D, Vitorica-Yrezabal IJ, Larrosa I (2020) Ag/Pd Cocatalyzed Direct Arylation of Fluoroarene Derivatives with Aryl Bromides. ACS Catalysis 10:2100–2107 Chemistry Link
Pappalardo F, Russo G, Pennisi M, Parasiliti Palumbo GA, Sgroi G, Motta S, Maimone D (2020) The Potential of Computational Modeling to Predict Disease Course and Treatment Response in Patients with Relapsing Multiple Sclerosis. Cells 9:586 Immunology Link
Peñas de Frutos MN (2020) Combining modern tools in the study of physical properties, reaction processes and mechanisms. Ph.D. Thesis, Universidad de Valladolid, Spain Chemistry Link
Potter ME, Armstrong L-M, Carravetta M, Mezza TM, Raja R (2020) Designing Multi-Dopant Species in Microporous Architectures to Probe Reaction Pathways in Solid-Acid Catalysis. Frontiers in Chemistry 8:171 Chemistry Link
Rana P (2020) Mathematical models of cellular signaling and supramolecular self-assembly. Ph.D. Thesis, Virginia Commonwealth University, USA. Signaling Macromolecular Biochemistry Link
Ribó JM, Hochberg D (2020) Spontaneous mirror symmetry breaking: an entropy production survey of the racemate instability and the emergence of stable scalemic stationary states. Physical Chemistry Chemical Physics 22:14013–14025 Chemistry Theory Link
Sanders JN, Jun H, Yu RA, Gleason JL, Houk KN (2020) Mechanism of an Organocatalytic Cope Rearrangement Involving Iminium Intermediates: Elucidating the Role of Catalyst Ring Size. Journal of the American Chemical Society 142:16877–16886 Chemistry Link
Schluschaß B (2020) N2 Splitting and Functionalization in the Coordination Sphere of Tungsten. Ph.D. Thesis, Georg-August University Göttingen, Germany. Chemistry Link
Schmallegger M, Barbon A, Bortolus M, Chemelli A, Bilkis I, Gescheidt G, Weiner L (2020) Systematic Quantification of Electron Transfer in a Bare Phospholipid Membrane Using Nitroxide-Labeled Stearic Acids: Distance Dependence, Kinetics, and Activation Parameters. Langmuir 36:10429–10437 Biophysics Biochemistry Link
Septian A, Shin WS (2020) Slow-release persulfate candle-assisted electrochemical oxidation of 2-methylnaphthalene: Effects of chloride, sulfate, and bicarbonate. Journal of Hazardous Materials 400:123196 Chemistry Link
Shelton M, Castora FJ, Kerns KA, Coleman RA (2020) Modeling the effects of respirasome supercomplex formation on AD progression by incorporation of mitochondrial gene expression data. Alzheimer’s & Dementia 16:e046371 Metabolism Link
Solís RR, Rivas FJ, Chávez AM, Dionysiou DD (2020) Peroxymonosulfate/solar radiation process for the removal of aqueous microcontaminants. Kinetic modeling, influence of variables and matrix constituents. Journal of Hazardous Materials 400:123118 Chemistry Link
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111 publications
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Broto Vispe JM (2019) Adding new functionality to COPASI, a software for simulation of biological circuits in systems biology. Bachelors Thesis, Universitat de Lleida, Spain. Computational Method Link
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Cababie LA, Incicco JJ, González-Lebrero RM, Roman EA, Gebhard LG, Gamarnik AV, Kaufman SB (2019) Thermodynamic study of the effect of ions on the interaction between dengue virus NS3 helicase and single stranded RNA. Scientific Reports 9:10569 Biophysics Macromolecular Biochemistry Link
Carbonell P, Faulon J-L, Breitling R (2019) Efficient learning in metabolic pathway designs through optimal assembling. IFAC-PapersOnLine 52:7–12 Synthetic Biology Link
Chauhan N, Singh S (2019) Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania. Frontiers in Bioengineering and Biotechnology 7:336 Metabolism Parasitology Link
Chum AP, Shoemaker SR, Fleming PJ, Fleming KG (2019) Plasticity and transient binding are key ingredients of the periplasmic chaperone network. Protein Science 28:1340–1349 Macromolecular Biochemistry Microbiology Link
Diccianni JB, Katigbak J, Hu C, Diao T (2019) Mechanistic Characterization of (Xantphos)Ni(I)-Mediated Alkyl Bromide Activation: Oxidative Addition, Electron Transfer, or Halogen-Atom Abstraction. Journal of the American Chemical Society 141:1788–1796 Chemistry Link
Dietz M, Johnson A, Martínez-Martínez AJ, Weller AS (2019) The [Rh(Xantphos)]+ catalyzed hydroboration of diphenylacetylene using trimethylamine-borane. Inorganica Chimica Acta 491:9–13 Chemistry Link
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Escala DM, Muñuzuri AP (2019) Interface Fingering Instability Triggered by a Density-Coupled Oscillatory Chemical Reaction via Precipitation. Langmuir 35:13769–13781 Chemistry Link
Faraj SE, Centeno M, Rossi RC, Montes MR (2019) A kinetic comparison between E2P and the E2P-like state induced by a beryllium fluoride complex in the Na,K-ATPase. Interactions with Rb. Biochimica Et Biophysica Acta. Biomembranes 1861:355–365 Enzymology Link
Faraj SE, Noguera ME, Delfino JM, Santos J (2019) Global Implications of Local Unfolding Phenomena, Probed by Cysteine Reactivity in Human Frataxin. Scientific Reports 9:1–12 Biochemistry Link
Fecteau KM, Gould IR, Glein CR, Williams LB, Hartnett HE, Shock EL (2019) Production of Carboxylic Acids from Aldehydes under Hydrothermal Conditions: A Kinetics Study of Benzaldehyde. ACS Earth and Space Chemistry 3:170–191 Chemistry Link
Fedorova GF, Lapina VA, Menshov VA, Naumov VV, Trofimov AV, Tsaplev YB, Vasil’ev RF, Yablonskaya OI (2019) Updating the Chemiluminescence Oxygen-Aftereffect Method for Determining the Rate Constant of the Peroxy-Radical Self-Reaction: Oxidation of Cyclohexene. Photochemistry and Photobiology 95:780–786 Chemistry Link
Feldman-Salit A, Veith N, Wirtz M, Hell R, Kummer U (2019) Distribution of control in the sulfur assimilation in Arabidopsis thaliana depends on environmental conditions. New Phytologist 222:1392–1404 Metabolism Link
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González-Chávez Z, Vázquez C, Mejia-Tlachi M, Márquez-Dueñas C, Manning-Cela R, Encalada R, Rodríguez-Enríquez S, Michels PAM, Moreno-Sánchez R, Saavedra E (2019) Gamma-glutamylcysteine synthetase and tryparedoxin 1 exert high control on the antioxidant system in Trypanosoma cruzi contributing to drug resistance and infectivity. Redox Biology 26:101231 Metabolism Link
Green K-A, Hoover JM (2019) Intermediacy of Copper(I) under Oxidative Conditions in the Aerobic Copper-Catalyzed Decarboxylative Thiolation of Benzoic Acids. ACS Catalysis 10:1769–1782 Chemistry Link
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Hochberg D, Ribó JM (2019) Entropic Analysis of Mirror Symmetry Breaking in Chiral Hypercycles. Life 9:28 Biochemistry Link
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Houston MT, Gutierrez JB (2019) The FRiND Model: A Mathematical Model for Representing Macrophage Plasticity in Muscular Dystrophy Pathogenesis. Bulletin of Mathematical Biology 81:3976–3997 Immunology Link
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Jahagirdar S, Suarez-Diez M, Saccenti E (2019) Simulation and Reconstruction of Metabolite-Metabolite Association Networks Using a Metabolic Dynamic Model and Correlation Based Algorithms. Journal of Proteome Research 18:1099–1113 Computational Method Metabolism Link
Jaime JC, Mesa-Álvarez MD, Martin RR, Betancourt-Mar JA, Cocho G, Mansilla R, Nieto-Villar JM (2019) Chronotherapy of cancer: periodic perturbations in vascular growth and metastasis. Biological Rhythm Research 50:495–504 Physiology Link
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Kennedy CR, Zhong H, Macaulay RL, Chirik PJ (2019) Regio- and Diastereoselective Iron-Catalyzed [4+4]-Cycloaddition of 1,3-Dienes. Journal of the American Chemical Society 141:8557–8573 Chemistry Link
Knight-Schrijver V (2019) Towards systems pharmacology models of druggable targets and disease mechanisms. Thesis, University of Cambridge, UK Pharmacology Physiology Signaling Link
Koeman M, Engel J, Jansen J, Buydens L (2019) Critical comparison of methods for fault diagnosis in metabolomics data. Scientific Reports 9:1123 Metabolism Computational Method Link
Krahmer J, Goralogia GS, Kubota A, Zardilis A, Johnson RS, Song YH, MacCoss MJ, Le Bihan T, Halliday KJ, Imaizumi T, Millar AJ (2019) Time-resolved interaction proteomics of the GIGANTEA protein under diurnal cycles in Arabidopsis. FEBS Letters 593:319–338 Physiology Link
Kumar A, Chauhan N, Singh S (2019) Understanding the Cross-Talk of Redox Metabolism and Fe-S Cluster Biogenesis in Leishmania Through Systems Biology Approach. Frontiers in Cellular and Infection Microbiology 9:15 Metabolism Link
Kuoka T, Akase S, Karlsson NG, Aoki-Kinoshita KF (2019) 252. In-silico simulation of o-linked glycan biosynthesis in cho cells. Glycoconjugate Journal 36:267–397 (Glyco25, XXV International Symposium on Glycoconjugates) Metabolism Link
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Lang SN, Germerodt S, Glock C, Skerka C, Zipfel PF, Schuster S (2019) Molecular crypsis by pathogenic fungi using human factor H. A numerical model. PLoS One 14:e0212187 Immunology Microbiology Link
Lebar T, Verbič A, Ljubetič A, Jerala R (2019) Polarized displacement by transcription activator-like effectors for regulatory circuits. Nature Chemical Biology 15:80–87 Synthetic Biology Genetics Link
Leischner T, Suarez LA, Spannenberg A, Junge K, Nova A, Beller M (2019) Highly selective hydrogenation of amides catalysed by a molybdenum pincer complex: scope and mechanism. Chemical Science 10:10566–10576 Chemistry Link
Lombardo SD, Presti M, Mangano K, Petralia MC, Basile MS, Libra M, Candido S, Fagone P, Mazzon E, Nicoletti F, Bramanti A (2019) Prediction of PD-L1 Expression in Neuroblastoma via Computational Modeling. Brain Sciences 9:E221 Signaling Link
Macikova L, Sinica V, Kadkova A, Villette S, Ciaccafava A, Faherty J, Lecomte S, Alves ID, Vlachova V (2019) Putative interaction site for membrane phospholipids controls activation of TRPA1 channel at physiological membrane potentials. FEBS Journal 286:3664–3683 Signaling Biochemistry Link
Madec M (2019) Systemes heterogenes : outils CAO et applications a la biologie. Habilitation Thesis, Universite de Strasbourg, France. Computational Method Link
Malik-Sheriff RS, Glont M, Nguyen TVN, Tiwari K, Roberts MG, Xavier A, Vu MT, Men J, Maire M, Kananathan S, Fairbanks EL, Meyer JP, Arankalle C, Varusai TM, Knight-Schrijver V, Li L, Dueñas-Roca C, Dass G, Keating SM, Park YM, Buso N, Rodriguez N, Hucka M, Hermjakob H (2020) BioModels—15 years of sharing computational models in life science. Nucleic Acids Research 48:D407–D415 Software Computational Method Link
Mandal M, Luke AM, Dereli B, Elwell CE, Reineke TM, Tolman WB, Cramer CJ (2019) Computational Prediction and Experimental Verification of ε-Caprolactone Ring-Opening Polymerization Activity by an Aluminum Complex of an Indolide/Schiff-Base Ligand. ACS Catalysis 9:885–889 Chemistry Link
Mandal SC, Rawat KS, Nandi S, Pathak B (2019) Theoretical insights into CO 2 hydrogenation to methanol by a Mn–PNP complex. Catalysis Science & Technology 9:1867–1878 Chemistry Link
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Meyer-Almes F-J (2019) Determination of the binding mechanism of histone deacetylase inhibitors. Chemical Biology & Drug Design 93:1214–1250 Enzymology Link
Miller DSJ, Schmierer B, Hill CS (2019) TGF-β family ligands exhibit distinct signalling dynamics that are driven by receptor localisation. Journal of Cell Science 132:jcs234039 Signaling Link
Mitchell S, Hoffmann A (2019) Substrate complex competition is a regulatory motif that allows NFκB RelA to license but not amplify NFκB RelB. Proceedings of the National Academy of Sciences USA 116:10592–10597 Signaling Link
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138 publications
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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
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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
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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
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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
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Wei D, Sadek O, Dorcet V, Roisnel T, Darcel C, Gras E, Clot E, Sortais J-B (2018) Selective mono N-methylation of anilines with methanol catalyzed by rhenium complexes: An experimental and theoretical study. Journal of Catalysis 366:300–309 Chemistry Link
Wei Y, Mayoral-Delgado I, Stewart NA, Dymond MK (2018) Macromolecular crowding and membrane binding proteins: the case of phospholipase A1. Chemistry and Physics of Lipids 218:91–102 Biochemistry Biophysics Link
Welsh CM, Fullard N, Proctor CJ, Martinez-Guimera A, Isfort RJ, Bascom CC, Tasseff R, Przyborski SA, Shanley DP (2018) PyCoTools: A Python Toolbox for COPASI. Bioinformatics 34:3702–3710 Computational Method Software Link
Weyder M, Prudhomme M, Bergé M, Polard P, Fichant G (2018) Dynamic modeling of Streptococcus pneumoniae competence provides regulatory mechanistic insights into its tight temporal regulation. Frontiers in Microbiology 9:1637 Microbiology Link
Wiebe HA (2018) Mechanistic applications of volume profiles for chemical and biochemical processes. Ph.D. Thesis, Simon Fraser University, Canada Chemistry Link
Winter F, Bludszuweit-Philipp C, Wolkenhauer O (2018) Mathematical analysis of the influence of brain metabolism on the BOLD signal in Alzheimer’s disease. Journal of Cerebral Blood Flow & Metabolism 38:304–316 Physiology Metabolism Biophysics Link
Woller A, Gonze D (2018) Modeling clock-related metabolic syndrome due to conflicting light and food cues. Scientific Reports 8:13641 Physiology Metabolism Link
Woo SS, Kim J, Sarpeshkar R (2018) A Digitally Programmable Cytomorphic Chip for Simulation of Arbitrary Biochemical Reaction Networks. IEEE Transactions on Biomedical Circuits and Systems 12:360–378 Computational Method Link
Ximing L (2018) Insights into Delivery of Somatic Calcium Signals to the Nucleus During LTP Revealed by Computational Modeling. Ph.D. Thesis, Ohio University, USA Signaling Biochemistry Link
Xu H, Curtis TY, Powers SJ, Raffan S, Gao R, Huang J, Heiner M, Gilbert DR, Halford NG (2018) Genomic, biochemical and modelling analyses of asparagine synthetases from wheat. Frontiers in Plant Science 8:2237 Biochemistry Plant Biology Link
Yeom K-H, Mitchell S, Linares AJ, Zheng S, Lin C-H, Wang X-J, Hoffmann A, Black DL (2018) Polypyrimidine tract-binding protein blocks miRNA-124 biogenesis to enforce its neuronal-specific expression in the mouse. Proceedings of the National Academy of Sciences USA 115:E11061–E11070 Genetics Biochemistry Link
Yu Y, Rebek Jr J (2018) Reactions of Folded Molecules in Water. Accounts of Chemical Research 51:3031–3040 Chemistry Link
Zhou Q (2018) Kinetic Modeling of Inhibitor Effects on Butanol Synthesis by Clostridium saccharoperbutylacetonicum. Ph.D. Thesis, North Carolina State University, USA Metabolism Microbiology Link
Zhou Q, Liu Y, Yuan W (2018) Kinetic modeling of lactic acid and acetic acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. Fuel 226:181–189 Metabolism Microbiology Biotechnology Link
Zhou Q, Zheng H, Yuan W (2018) Modeling Butanol Synthesis in Xylose by Clostridium saccharoperbutylacetonicum. BioResources 13:7270–7280 Metabolism Microbiology Link
Zimmer C, Leuba SI, Cohen T, Yaesoubi R (2018) Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Statistical Methods in Medical Research 28:3591-3608 Epidemiology Link

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