COPASI's Use In Metabolism

Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway. BMC Plant Biology 24:220 Plant Biology Metabolism Link
Fedosov SN, Nexo E, Heegaard CW (2024) Kinetics of Cellular Cobalamin Uptake and Conversion: Comparison of Aquo/Hydroxocobalamin to Cyanocobalamin. Nutrients 16:378 Metabolism Link
Khanijou JK, Hee YT, Selvarajoo K (2024) Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling. In: Bizzarri M (ed) Systems Biology. Springer US: New York, NY, 3–19. Biotechnology Metabolism Link
Morgan AE, Salcedo-Sora JE, Mc Auley MT (2024) A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth. BioSystems 235:105088 Metabolism Microbiology Link
Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, Gupta P, Gupta L, Vijayaraghavan P, Sengupta A (2024) Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. Journal of Biomolecular Structure and Dynamics 42:4379–4394 Metabolism Link
Pulsford SB, Outram MA, Förster B, Rhodes T, Williams SJ, Badger MR, Price GD, Jackson CJ, Long BM (2024) Cyanobacterial α-carboxysome carbonic anhydrase is allosterically regulated by the Rubisco substrate RuBP. Science Advances 10:eadk7283 Biochemistry Plant Biology Metabolism Link
Sigg A, Klimacek M, Nidetzky B (2024) Pushing the boundaries of phosphorylase cascade reaction for cellobiose production I: Kinetic model development. Biotechnology and Bioengineering 121:580–592 Biotechnology Metabolism Link
Teshima M, Sutiono S, Döring M, Beer B, Boden M, Schenk G, Sieber V (2024) Development of a Highly Selective NAD+-Dependent Glyceraldehyde Dehydrogenase and its Application in Minimal Cell-Free Enzyme Cascades. ChemSusChem 17:e202301132 Metabolism Enzymology Link
Wei X, Yang X, Hu C, Li Q, Liu Q, Wu Y, Xie L, Ning X, Li F, Cai T, Zhu Z, Zhang Y-HPJ, Zhang Y, Chen X, You C (2024) ATP-free in vitro biotransformation of starch-derived maltodextrin into poly-3-hydroxybutyrate via acetyl-CoA. Nature Communications 15:3267 Metabolism Biotechnology Link
Yabut KCB, Martynova A, Nath A, Zercher BP, Bush MF, Isoherranen N (2024) Drugs Form Ternary Complexes with Human Liver Fatty Acid Binding Protein (FABP1) and FABP1 Binding Alters Drug Metabolism. Molecular Pharmacology 105:395–410 Metabolism Pharmacology Link

10 publications
Bendig T, Ulmer A, Luzia L, Müller S, Sahle S, Bergmann FT, Lösch M, Erdemann F, Zeidan AA, Mendoza SN, Teusink B, Takors R, Kummer U, Figueiredo AS (2023) The pH-dependent lactose metabolism of Lactobacillus delbrueckii subsp. bulgaricus: An integrative view through a mechanistic computational model. Journal of Biotechnology 374:90–100 Metabolism Microbiology Link
Davies C, Morgan AE, Mc Auley MT (2023) Computationally Modelling Cholesterol Metabolism and Atherosclerosis. Biology 12:1133 Metabolism Physiology Link
Decros G, Dussarrat T, Baldet P, Cassan C, Cabasson C, Dieuaide-Noubhani M, Destailleur A, Flandin A, Prigent S, Mori K, Colombié S, Jorly J, Gibon Y, Beauvoit B, Pétriacq P (2023) Enzyme-based kinetic modelling of ASC–GSH cycle during tomato fruit development reveals the importance of reducing power and ROS availability. New Phytologist 240:242–257 Metabolism Plant Biology Link
Espinel Ríos S (2023) Modeling, optimization, and predictive control for metabolic cybergenetics. Ph.D. Thesis, Otto-von-Guericke Universität Magdeburg, Germany Biotechnology Metabolism Link
Huber N, Alcalá-Orozco EA, Rexer T, Reichl U, Klamt S (2023) Model-based optimization of cell-free enzyme cascades exemplified for the production of GDP-fucose. Metabolic Engineering 81:10–25 Biotechnology Metabolism Link
Liska O, Boross G, Rocabert C, Szappanos B, Tengölics R, Papp B (2023) Principles of metabolome conservation in animals. Proceedings of the National Academy of Sciences USA 120:e2302147120 Metabolism Link
Liu Y, Westerhoff HV (2023) ‘Social’ versus ‘asocial’ cells—dynamic competition flux balance analysis. npj Systems Biology and Applications 9:1–13 Metabolism Link
Maheshvare M D, Raha S, König M, Pal D (2023) A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell. Frontiers in Endocrinology 14:1185656 Metabolism Link
Millard P, Gosselin-Monplaisir T, Uttenweiler-Joseph S, Enjalbert B (2023) Acetate is a beneficial nutrient for E. coli at low glycolytic flux. The EMBO journal 42:e113079 Metabolism Microbiology Link
Narad P, Kulshrestha S, Chikara A, Gupta V, Kakrania M, Saxena R, Gupta P, Gupta L, Vijayaraghavan P, Sengupta A (2023) Systems-wide analysis of A. fumigatus using kinetic modeling of metabolic pathways to identify putative drug targets. Journal of Biomolecular Structure and Dynamics doi:10.1080/07391102.2023.2223726 Metabolism Link
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
Olavarria K, Becker MV, Sousa DZ, van Loosdrecht MCM, Wahl SA (2023) Design and thermodynamic analysis of a pathway enabling anaerobic production of poly-3-hydroxybutyrate in Escherichia coli. Synthetic and Systems Biotechnology 8:629–639 Synthetic Biology Microbiology Metabolism Link
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
Szigetvari PD, Patil S, Birkeland E, Kleppe R, Haavik J (2023) The effects of phenylalanine and tyrosine levels on dopamine production in rat PC12 cells. Implications for treatment of phenylketonuria, tyrosinemia type 1 and comorbid neurodevelopmental disorders. Neurochemistry International 171:105629 Metabolism Link

14 publications
Barh A, Sharma K, Bhatt P, Annepu SK, Nath M, Shirur M, Kumari B, Kaundal K, Kamal S, Sharma VP, Gupta S, Sharma A, Gupta M, Dutta U (2022) Identification of Key Regulatory Pathways of Basidiocarp Formation in Pleurotus spp. Using Modeling, Simulation and System Biology Studies. Journal of Fungi 8:1073 Metabolism Microbiology Link
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
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
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
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
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
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
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
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
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
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
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
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
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
Uematsu S, Ohno S, Tanaka KY, Hatano A, Kokaji T, Ito Y, Kubota H, Hironaka K-I, Suzuki Y, Matsumoto M, Nakayama KI, Hirayama A, Soga T, Kuroda S (2022) Multi-omics-based label-free metabolic flux inference reveals obesity-associated dysregulatory mechanisms in liver glucose metabolism. iScience 25:103787 Metabolism Link
Zondervan NA (2022) Patterns in pathogenesis: elucidating bacterial host interaction. Ph.D. Thesis, Wageningen University, The Netherlands. Microbiology Metabolism Link

18 publications
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
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
Hellgren J (2021) Engineering central carbon metabolism with phosphoketolase pathways in Saccharomyces cerevisiae. Ph.D. Thesis, Chalmers University of Technology, Sweden. Metabolism Biotechnology 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
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
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
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
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
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
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
Sigg A, Klimacek M, Nidetzky B (2021) Three-level hybrid modeling for systematic optimization of biocatalytic synthesis: α-glucosyl glycerol production by enzymatic trans-glycosylation from sucrose. Biotechnology and Bioengineering 118:4028–4040 Biotechnology Metabolism Link
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

13 publications
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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

22 publications
Barber AL (2019) Metabolic reprogramming to optimise breast cancer treatment. Ph.D. Thesis, University of Surrey, Guilford, UK. Metabolism Link
Bhatt P, Pal K, Bhandari G, Barh A (2019) Modelling of the methyl halide biodegradation in bacteria and its effect on environmental systems. Pesticide Biochemistry and Physiology 158:88–100 Metabolism Environmental Sciences Link
Bockwoldt M, Houry D, Niere M, Gossmann TI, Reinartz I, Schug A, Ziegler M, Heiland I (2019) Identification of evolutionary and kinetic drivers of NAD-dependent signaling. Proceedings of the National Academy of Sciences USA 116:15957–15966 Signaling Metabolism Link
Chauhan N, Singh S (2019) Integrative Computational Framework for Understanding Metabolic Modulation in Leishmania. Frontiers in Bioengineering and Biotechnology 7:336 Metabolism Parasitology 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
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
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
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
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
Meshram RJ, Goundge MB, Kolte BS, Gacche RN (2019) An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitology International 69:59–70 Metabolism Link
Saavedra E, Encalada R, Vázquez C, Olivos-García A, Michels PAM, Moreno-Sánchez R (2019) Control and regulation of the pyrophosphate-dependent glucose metabolism in Entamoeba histolytica. Molecular and Biochemical Parasitology 229:75–87 Metabolism Link
Sangavai C, Bharathi M, Ganesh SP, Chellapandi P (2019) Kinetic modeling of Stickland reactions-coupled methanogenesis for a methanogenic culture. AMB Express 9:82 Metabolism Microbiology Link
Wheeler LC, Smith SD (2019) Computational Modeling of Anthocyanin Pathway Evolution: Biases, Hotspots, and Trade-offs. Integrative and Comparative Biology 59:585–598 Metabolism Link
Yang X, Yuan Q, Luo H, Li F, Mao Y, Zhao X, Du J, Li P, Ju X, Zheng Y, Chen Y, Liu Y, Jiang H, Yao Y, Ma H, Ma Y (2019) Systematic design and in vitro validation of novel one-carbon assimilation pathways. Metabolic Engineering 56:142–153 Metabolism Synthetic Biology Link

15 publications
Bhardwaj T, Somvanshi P (2018) A computational approach using mathematical modeling to assess the peptidoglycan biosynthesis of Clostridium botulinum ATCC 3502 for potential drug targets. Gene Reports 12:179–186 Metabolism Microbiology Link
Costa RS, Vinga S (2018) Assessing Escherichia coli metabolism models and simulation approaches in phenotype predictions: Validation against experimental data. Biotechnology Progress 34:1344–1354 Metabolism Link
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
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
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
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
Orrico F, Möller MN, Cassina A, Denicola A, Thomson L (2018) Kinetic and stoichiometric constraints determine the pathway of H2O2 consumption by red blood cells. Free Radical Biology and Medicine 121:231–239 Metabolism Link
Rosas Lemus M, Roussarie E, Hammad N, Mougeolle A, Ransac S, Issa R, Mazat J-P, Uribe-Carvajal S, Rigoulet M, Devin A (2018) The role of glycolysis-derived hexose phosphates in the induction of the Crabtree effect. Journal of Biological Chemistry 293:12843–12854 Metabolism Link
Šalagovič J (2018) Computational analysis and model integration of biorhythmic systems. Masters Thesis, Masaryk University, Faculty of Informatics, Czech Republic Metabolism Microbiology Computational Method Link
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
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

15 publications
Ghosh D, De RK (2017) In Silico Modeling of Crabtree Effect. Endocrine, Metabolic & Immune Disorders Drug Targets 17:182–188 Metabolism 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
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
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
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
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
Zhang Y, Kouril T, Snoep JL, Siebers B, Barberis M, Westerhoff HV (2017) The peculiar glycolytic pathway in hyperthermophylic archaea: understanding its whims by experimentation in silico. International Journal of Molecular Sciences 18:876 Metabolism Microbiology Enzymology Link

7 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
Boross G, Papp B (2016) No evidence that protein noise-induced epigenetic epistasis constrains gene expression evolution. Molecular Biology and Evolution 34:380–390 Metabolism Genetics Link
Costa RS, Vinga S (2016) Control analysis of the impact of allosteric regulation mechanism in a Escherichia coli kinetic model: Application to serine production. Biochemical Engineering Journal 110:59–70 Metabolism Link
Espejo Mojica ÁJ (2016) Producción, purificación y caracterización de tres hexosaminidasas lisosomales recombinantes en pichia pastoris. Ph.D. Thesis, Pontificia Universidad Javeriana, Bogotá, Colombia Enzymology Metabolism Link
Gerber S, Fröhlich M, Lichtenberg-Fraté H, Shabala S, Shabala L, Klipp E (2016) A Thermodynamic Model of Monovalent Cation Homeostasis in the Yeast Saccharomyces cerevisiae. PLoS Computational Biology 12:e1004703 Metabolism Physiology Link
Julien-Laferrière A (2016) Models and algorithms applied to metabolism: From revealing the responses to perturbations towards the design of microbial consortia. Ph.D. Thesis, Université Lyon 1-Claude Bernard, France Computational Method Metabolism Microbiology Link
Jablonsky J, Papacek S, Hagemann M (2016) Different strategies of metabolic regulation in cyanobacteria: from transcriptional to biochemical control. Scientific Reports 6:33024 Microbiology Metabolism Link
Lima AP, Baixinho V, Machado D, Rocha I (2016) A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli. IFAC-PapersOnLine 49:270–276 Metabolism Link
Marín-Hernández Á, Rodríguez-Zavala JS, Del Mazo-Monsalvo I, Rodríguez-Enríquez S, Moreno-Sánchez R, Saavedra E (2016) Inhibition of Non-flux-Controlling Enzymes Deters Cancer Glycolysis by Accumulation of Regulatory Metabolites of Controlling Steps. Frontiers in Physiology 7:412 Metabolism Link
Morgan AE, Mooney KM, Wilkinson SJ, Pickles NA, McAuley MT (2016) Mathematically modelling the dynamics of cholesterol metabolism and ageing. BioSystems 145:19–32 Metabolism Link
Orlenko A, Hermansen RA, Liberles DA (2016) Flux control in glycolysis varies across the tree of life. Journal of Molecular Evolution 82:146–161 Metabolism Link
Orlenko A, Teufel AI, Chi PB, Liberles DA (2016) Selection on metabolic pathway function in the presence of mutation-selection-drift balance leads to rate-limiting steps that are not evolutionarily stable. Biology Direct 11:31 Genetics Metabolism Link
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G (2016) Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Computational Biology 12:e1004825 Microbiology Metabolism Link
Rutkis R, Strazdina I, Balodite E, Lasa Z, Galinina N, Kalnenieks U (2016) The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway. PLoS One 11:e0153866 Metabolism Microbiology Link
Salcedo-Sora JE, McAuley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link
Shepelyuk TO, Panteleev MA, Sveshnikova AN (2016) Computational modeling of quiescent platelet energy metabolism in the context of whole-body glucose turnover. Mathematical Modelling of Natural Phenomena 11:91–101 Metabolism Physiology Link
Thiaville JJ, Frelin O, García-Salinas C, Harrison K, Hasnain G, Horenstein NA, de la Garza RID, Henry CS, Hanson AD, de Crécy-Lagard V (2016) Experimental and Metabolic Modeling Evidence for a Folate-Cleaving Side-Activity of Ketopantoate Hydroxymethyltransferase (PanB). Frontiers in Microbiology 7:431 Metabolism Link
Tomalin LE, Day AM, Underwood ZE, Smith GR, Dalle Pezze P, Rallis C, Patel W, Dickinson BC, Bähler J, Brewer TF, Chang CJ-L, Shanley DP, Veal EA (2016) Increasing extracellular H2O2 produces a bi-phasic response in intracellular H2O2, with peroxiredoxin hyperoxidation only triggered once the cellular H2O2-buffering capacity is overwhelmed. Free Radical Biology and Medicine 95:333–348 Metabolism Link
Valero E, Macià H, Ildefonso M, Hernández J-A, González-Sánchez M-I, García-Carmona F (2016) Modeling the ascorbate-glutathione cycle in chloroplasts under light/dark conditions. BMC Systems Biology 10:11 Metabolism Physiology Link
van Eunen K, Volker-Touw CM, Gerding A, Bleeker A, Wolters JC, van Rijt WJ, Martines A-CM, Niezen-Koning KE, Heiner RM, Permentier H, Groen AK, Reijngoud D-J, Derks TGJ, Bakker BM (2016) Living on the edge: substrate competition explains loss of robustness in mitochondrial fatty-acid oxidation disorders. BMC Biology 14:107 Metabolism Link
Woller A, Duez H, Staels B, Lefranc M (2016) A mathematical model of the liver circadian clock linking feeding and fasting cycles to clock function. Cell Reports 17:1087–1097 Metabolism Physiology Signaling Link

21 publications
Castello MA (2015) Lipid Regulation as a Critical Factor in the Development of Alzheimer’s Disease. Ph.D. Thesis, Loma Linda University, California, USA. Metabolism Link
Emiola A, George J, Andrews SS (2015) A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli. PLoS One 10:e0121216 Metabolism Microbiology Link
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
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
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
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
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
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
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

10 publications
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
Beauvoit B, Colombié S, Monier A, Andrieu M-H, Biais B, Bénard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat J-P, Gibon Y (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant Cell 26:3224-42 Metabolism Plant Biology Link
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
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
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
Machado D, Rodrigues L, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. BioSystems 125:16-21 Synthetic Biology Metabolism 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
Pandey V (2014) Metabolic modeling of different degrees of steatohepatitis in mice. Ph.D. Thesis, Department of Mathematics and Computer Science, Free University of Berlin, Germany. Metabolism Link
Pandey V, Sultan M, Kashofer K, Ralser M, Amstislavskiy V, Starmann J, Osprian I, Grimm C, Hache H, Yaspo M-L, Sültmann H, Trauner M, Denk M, Zatloukal K, Lehrach H, Wierling C (2014) Comparative Analysis and Modeling of the Severity of Steatohepatitis in DDC-Treated Mouse Strains. PLoS One 9:e111006. Metabolism Link
Peterson JR, Labhsetwar P, Ellermeier JR, Kohler PR, Jain A, Ha T, Metcalf WW, Luthey-Schulten Z (2014) Towards a computational model of a methane producing archaeum. Archaea 2014:898453 Metabolism Microbiology Whole-Cell Models Link
Rabbani N, Xue M, Thornalley PJ (2014) Activity, regulation, copy number and function in the glyoxalase system. Biochemical Society Transactions 42:419–424 Metabolism Link
Ryll A, Bucher J, Bonin A, Bongard S, Gonçalves E, Saez-Rodriguez J, Niklas J, Klamt S (2014) A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. BioSystems 124:26–38 Metabolism Signaling Genetics Link
Saller S, Kunz L, Berg D, Berg U, Lara H, Urra J, Hecht S, Pavlik R, Thaler CJ, Mayerhofer A (2014) Dopamine in human follicular fluid is associated with cellular uptake and metabolism-dependent generation of reactive oxygen species in granulosa cells: implications for physiology and pathology. Human Reproduction 29:555-67 Physiology Metabolism Link
Schleicher J, Guthke R, Dahmen U, Dirsch O, Holzhütter H-G, Schuster S (2014) A theoretical study of lipid accumulation in the liver—Implications for nonalcoholic fatty liver disease. Biochimica et Biophysica Acta 1841:62–69 Metabolism Link
Sugiura M, Azami C, Koyama K, Rutherford AW, Rappaport F, Boussac A (2014) Modification of the pheophytin redox potential in Thermosynechococcus elongatus Photosystem II with PsbA3 as D1. Biochimica et Biophysica Acta 1837:139–148 Metabolism Microbiology Biophysics Link
Talemi SR, Jacobson T, Garla V, Navarrete C, Wagner A, Tamás MJ, Schaber J (2014) Mathematical modelling of arsenic transport, distribution and detoxification processes in yeast. Molecular Microbiology 92:1343–1356 Toxicology Metabolism Link
Yang X, Zhang Y, Zheng Y, Ma H (2014) Development and analysis of a kinetic model for Escherichia coli threonine biosynthesis. Chinese Journal of Biotechnology 30:18-29. Metabolism Microbiology Link
Zikmanis P, Kampenusa I (2014) Relationship between Metabolic Fluxes and Sequence-Derived Properties of Enzymes. International Scholarly Research Notices 2014:817102 Metabolism Link

21 publications
Challenger JD (2013) The stochastic dynamics of biochemical systems. Ph.D. Thesis, University of Manchester, UK Computational Method Metabolism Link
Galazka M, Hay JO (2013) In silico metabolic control analysis of Brassica napus seeds based on dynamic kinetic modeling. A Compilation of Internship Reports. In (Stegman M, Morris M. and Blackburn N, eds.) A Compilation of Internship Reports. Brookhaven National Laboratory, Office of Educational Programs. pp. 75–80 Metabolism Link
Geenen S, du Preez FB, Snoep JL, Foster AJ, Sarda S, Kenna JG, Wilson ID, Westerhoff HV (2013) Glutathione metabolism modeling: a mechanism for liver drug-robustness and a new biomarker strategy. Biochimica et Biophysica Acta 1830:4943- 59 Toxicology Metabolism Link
Kampenusa I, Zikmanis P (2013) Relationships between metabolic fluxes and enzyme amino acid composition. Central European Journal of Biology 8:107–120 Metabolism Link
Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybilo M, Driessen NN, Gilbert DR, Breitling R, Bakker BM, Barrett MP (2013) Handling Uncertainty in Dynamic Models: The Pentose Phosphate Pathway in Trypanosoma brucei. PLoS Computational Biology 9:e1003371. Metabolism Link
Leroux AE, Haanstra JR, Bakker BM, Krauth-Siegel RL (2013) Dissecting the catalytic mechanism of Trypanosoma brucei trypanothione synthetase by kinetic analysis and computational modeling. Journal of Biological Chemistry 288:23751-23764 Metabolism Link
Levering J, Kummer U, Becker K, Sahle S (2013) Glycolytic oscillations in a model of a lactic acid bacterium metabolism. Biophysical Chemistry 172:53-60 Metabolism Link
Mensonides F, Bakker BM, Cremazy F, Messiha HL, Mendes P, Boogerd FC, Westerhoff HV (2013) A new regulatory principle for in vivo biochemistry: pleiotropic low affinity regulation by the adenine nucleotides illustrated for the glycolytic enzymes of Saccharomyces cerevisiae. FEBS Letters 587:2860-7 Metabolism Link
Miah F, Koliwer-Brandl H, Rejzek M, Field RA, Kalscheuer R, Bornemann S (2013) Flux through trehalose synthase flows from trehalose to the alpha anomer of maltose in mycobacteria. Chemical Biology 20:487-493 Metabolism Link
Mitchell S, Mendes P (2013) A Computational Model of Liver Iron Metabolism. PLoS Computational Biology 9:e1003299 Metabolism Link
Nägele T, Weckwerth W (2013) A workflow for mathematical modeling of subcellular metabolic pathways in leaf metabolism of Arabidopsis thaliana. Frontiers in Plant Science 4:541 Metabolism Plant Biology Link
Penkler GP (2013) A kinetic model of glucose catabolism in Plasmodium falciparum. Ph.D. Thesis, Faculty of Science, University of Stellenbosch, South Africa Metabolism Link
Phelix CF, LeBaron R, Roberson DJ, Villareal G, Perry G (2013) Flux and metabolite pathway mapping in the aging and Alzheimer’s disease hippocampus. Alzheimer’s & Dementia 9:P346–P347 Metabolism Link
Rutkis R, Kalnenieks U, Stalidzans E, Fell DA (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology 159:2674-2689 Metabolism Microbiology Link
Schäuble S, Stavrum A-K, Puntervoll P, Schuster S, Heiland I (2013) Effect of substrate competition in kinetic models of metabolic networks. FEBS Letters 587:2818-2824 Metabolism Link
Shemirani MI (2013) Construction of metabolic pathway of catecholamine from tyrosine in human fibroblast cell. Degree Project Thesis in Medicine, School of Medicine and Health Science, Orerbo University, Sweden Metabolism Link
Singh VK, Ghosh I (2013) Methylerythritol phosphate pathway to isoprenoids: kinetic modeling and in silico enzyme inhibitions in Plasmodium falciparum. FEBS Letters 587:2806-2817 Metabolism Link
Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JEG, Paton NW, Westerhoff HV, Kell DB, Mendes P (2013) A model of yeast glycolysis based on a consistent kinetic characterization of all its enzymes. FEBS Letters 587:2832-41 Metabolism Link
Stavrum A-K, Heiland I, Schuster S, Puntervoll P, Ziegler M (2013) Model of tryptophan metabolism, readily scalable using tissue-specific gene expression data. Journal of Biological Chemistry 288:34555-34566 Metabolism Link
Veith N, Feldman-Salit A, Cojocaru V, Henrich S, Kummer U, Wade RC (2013) Organism-Adapted Specificity of the Allosteric Regulation of Pyruvate Kinase in Lactic Acid Bacteria. PLoS Computational Biology 9:e1003159 Metabolism Microbiology Link
Verma M, Zakhartsev M, Reuss M, Westerhoff HV (2013) “Domino” systems biology and the “A” of ATP. Biochimica et Biophysica Acta 1827:19–29 Metabolism Link
Wilcock P (2013) A systems biology approach for investigating oral squamous cell carcinoma (OSCC). Ph.D. Thesis, University of Manchester, UK Metabolism Biochemistry Link

22 publications
Achcar F, Kerkhoven EJ, The SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R (2012) Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLoS Computational Biology 8:e1002352 Metabolism Link
Adamczyk M, Westerhoff HV (2012) Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal 7:877-883 Metabolism Microbiology Link
Adiamah DA, Schwartz J-M (2012) Construction of a Genome-Scale Kinetic Model of Mycobacterium Tuberculosis Using Generic Rate Equations. Metabolites 2:382-397 Metabolism Whole-Cell Models Link
Davies O, Mendes P, Smallbone K, Malys N (2012) Characterisation of multiple substrate-specific (d)ITP/(d)XTPase and modelling of deaminated purine nucleotide metabolism. BMB reports 45:259-264 Enzymology Metabolism Link
Jozefczuk J, Kashofer K, Ummanni R, Henjes F, Rehman S, Geenen S, Wruck W, Regenbrecht C, Daskalaki A, Wierling C, Turano P, Bertini I, Korf U, Zatloukal K, Westerhoff HV, Lehrach H, Adjaye J (2012) A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells. Frontiers in Physiology 3:339 Metabolism Link
Kleessen S, Nikoloski Z (2012) Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations. BMC Systems Biology 6:16 Computational Method Plant Biology Metabolism Link
Kloster A, Olsen LF (2012) Oscillations in glycolysis in Saccharomyces cerevisiae: the role of autocatalysis and intracellular ATPase activity. Biophysical Chemistry 165–166:39–47 Metabolism Link
Levering J, Musters MWJM, Bekker M, Bellomo D, Fiedler T, de Vos WM, Hugenholtz J, Kreikemeyer B, Kummer U, Teusink B (2012) Role of phosphate in the central metabolism of two lactic acid bacteria - a comparative systems biology approach: Modelling glycolysis of lactic acid bacteria. FEBS Journal 279:1274-1290 Metabolism Link
McAuley MT, Wilkinson DJ, Jones JJ, Kirkwood TBL (2012) A whole-body mathematical model of cholesterol metabolism and its age-associated dysregulation. BMC Systems Biology 6:130 Metabolism Physiology Link
Olin-Sandoval V, González-Chávez Z, Berzunza-Cruz M, Martínez I, Jasso-Chávez R, Becker I, Espinoza B, Moreno-Sánchez R, Saavedra E (2012) Drug target validation of the trypanothione pathway enzymes through metabolic modelling: Kinetic modelling of trypanothione metabolism. FEBS Journal 279:1811-1833 Metabolism Link
Palai T, Mitra S, Bhattacharya PK (2012) Kinetics and design relation for enzymatic conversion of lactose into galacto-oligosaccharides using commercial grade β-galactosidase. Journal of Bioscience and Bioengineering 114:418-423 Metabolism Link
Reyes-Palomares A, Montañez R, Sánchez-Jiménez F, Medina MÁ (2012) A combined model of hepatic polyamine and sulfur amino acid metabolism to analyze S-adenosyl methionine availability. Amino Acids 42:597–610 Metabolism Link
Singh VK, Das K, Seshadri K (2012) Kinetic Modelling of GlmU Reactions - Prioritization of Reaction for Therapeutic Application. PLoS One 7:e43969 Metabolism Link

13 publications
Genc S, Kurnaz IA, Ozilgen M (2011) Astrocyte-neuron lactate shuttle may boost more ATP supply to the neuron under hypoxic conditions-in silico study supported by in vitro expression data. BMC Systems Biology 5:162 Cell Biology Metabolism Link
Jablonsky J, Bauwe H, Wolkenhauer O (2011) Modeling the Calvin-Benson cycle. BMC Systems Biology 5:185 Metabolism Plant Biology Link
Kleppe R, Martinez A, Døskeland SO, Haavik J (2011) The 14-3-3 proteins in regulation of cellular metabolism. Seminars in Cell & Developmental Biology 22:713–719 Signaling Metabolism Link
Kolodkin AN (2011) Emergence of design. Ph.D. Thesis, Vrije Universiteit Amsterdam, The Netherlands. Theory Metabolism Link
Mozga I, Stalidzans E (2011) Convergence dynamics of biochemical models to the global optimum. Paper presented at the 2011 E-Health and Bioengineering Conference (EHB). IEEE: Iaşi, Romania, 1–4 Computational Method Metabolism Link
Oh E, Lu M, Park C, Park C, Oh HB, Lee SY, Lee J (2011) Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis. Journal of Microbiology and Biotechnology 21:162–169 Microbiology Metabolism Link
Shivanandan A (2011) Stochastic modelling and identification of arabinose uptake network in Escherichia coli (PDF Download Available). MS Thesis, Université Joseph Fourier, Grenoble, France. Metabolism Microbiology Link
Sorokina O, Corellou F, Dauvillée D, Sorokin A, Goryanin I, Ball S, Bouget F-Y, Millar AJ (2011) Microarray data can predict diurnal changes of starch content in the picoalga Ostreococcus. BMC Systems Biology 5:36 Metabolism Link
Tsaloglou M-N, Attard GS, Dymond MK (2011) The effect of lipids on the enzymatic activity of 6-phosphofructo-1-kinase from B. stearothermophilus. Chemistry and Physics of Lipids 164:713–721 Enzymology Metabolism Microbiology Link

9 publications