2025
Hernández-Esquivel L, Del Mazo-Monsalvo I, Pacheco-Velázquez SC, Feregrino-Mondragón RD, Robledo-Cadena DX, Sánchez-Thomas R, Jasso-Chávez R, Saavedra E, Marín-Hernández Á (2025) Modeling Krebs cycle from liver, heart and hepatoma mitochondria, supported Complex I as target for specific inhibition of cancer cell proliferation. Frontiers in Oncology 15:1557638
Metabolism
Link
Høyland LE (2025) Disrupting the Balance: Consequences of Sustained Subcellular NAD⁺ Depletion on Cellular Homeostasis. Ph. D. Thesis, The University of Bergen, Norway.
Metabolism
Link
Itatani M, Holló G, Albanese P, Valletti N, Kurunczi S, Horvath R, Rossi F, Lagzi I (2025) Temporal pH waveforms generated in an enzymatic reaction network in batch and cell-sized microcompartments. Cell Reports Physical Science 6:102367
Biochemistry
Metabolism
Link
Kumsuwan S, Tothong C, Limmongkon A, Subsoontorn P (2025) Development and Applications of a Kinetic Model for Resveratrol Production in Escherichia coli Cell Factories. Trends in Sciences 22:9529
Metabolism
Microbiology
Biotechnology
Link
Suarez-Ogando H, Guerra A, Mansilla R, Nieto-Villar JM (2025) Ferroptosis as a Biological Phase Transition III: Ephitelial-Mesenchymal Transition. The Interdisciplinary Journal of Discontinuity, Nonlinearity, and Complexity 14:549–558
Metabolism
Signaling
Link
5 publications
2024
Castaño-Cerezo S, Chamas A, Kulyk H, Treitz C, Bellvert F, Tholey A, Galéote V, Camarasa C, Heux S, Garcia-Alles LF, Millard P, Truan G (2024) Combining systems and synthetic biology for in vivo enzymology. EMBO Journal 43:5169–5185
Synthetic Biology
Metabolism
Laboratory Method
Link
Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) Mathematical kinetic modelling followed by in vitro and in vivo assays reveal the bifunctional rice GTPCHII/DHBPS enzymes and demonstrate the key roles of OsRibA proteins in the vitamin B2 pathway. BMC Plant Biology 24:220
Plant Biology
Metabolism
Link
Faustino M, Lourenço T, Strobbe S, Cao D, Fonseca A, Rocha I, Van Der Straeten D, Oliveira MM (2024) OsTH1 is a key player in thiamin biosynthesis in rice. Scientific Reports 14:13591
Biochemistry
Metabolism
Plant Biology
Link
Fedosov SN, Nexo E, Heegaard CW (2024) Kinetics of Cellular Cobalamin Uptake and Conversion: Comparison of Aquo/Hydroxocobalamin to Cyanocobalamin. Nutrients 16:378
Metabolism
Link
Høyland LE, VanLinden MR, Niere M, Strømland Ø, Sharma S, Dietze J, Tolås I, Lucena E, Bifulco E, Sverkeli LJ, Cimadamore-Werthein C, Ashrafi H, Haukanes KF, van der Hoeven B, Dölle C, Davidsen C, Pettersen IKN, Tronstad KJ, Mjøs SA, Hayat F, Makarov MV, Migaud ME, Heiland I, Ziegler M (2024) Subcellular NAD+ pools are interconnected and buffered by mitochondrial NAD+. Nature Metabolism 6:2319–2337
Metabolism
Biochemistry
Link
Jallet D, Soldan V, Shayan R, Stella A, Ismail N, Zenati R, Cahoreau E, Burlet-Schiltz O, Balor S, Millard P, Heux S (2024) Integrative in vivo analysis of the ethanolamine utilization bacterial microcompartment in Escherichia coli. mSystems 9:e0075024
Metabolism
Microbiology
Link
Khanijou JK, Hee YT, Selvarajoo K (2024) Identifying Key In Silico Knockout for Enhancement of Limonene Yield Through Dynamic Metabolic Modelling. In: Bizzarri M (ed) Systems Biology. Springer US: New York, NY, 3–19.
Biotechnology
Metabolism
Link
Khanijou JK, Hee YT, Scipion CPM, Chen X, Selvarajoo K (2024) Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli. npj Systems Biology and Applications 10:1–14
Biotechnology
Synthetic Biology
Metabolism
Link
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
Phégnon L, Pérochon J, Uttenweiler-Joseph S, Cahoreau E, Millard P, Létisse F (2024) 6-Phosphogluconolactonase is critical for the efficient functioning of the pentose phosphate pathway. FEBS Journal 291:4459–4472
Metabolism
Link
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
Sigg A, Klimacek M, Nidetzky B (2024) Pushing the boundaries of phosphorylase cascade reaction for cellobiose production II: Model-based multiobjective optimization. Biotechnology and Bioengineering 121:566–579
Biotechnology
Metabolism
Link
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
Tseng Y-Y (2024) Comparative mathematical modeling reveals the differential effects of high-fat diet and ketogenic diet on the PI3K-Akt signaling pathway in heart. Nutrition & Metabolism 21:65
Metabolism
Signaling
Link
Uttley M, Horne G, Tsigkinopoulou A, Del Carratore F, Hawari A, Kiezel-Tsugunova M, Kendall AC, Jones J, Messenger D, Bhogal RK, Breitling R, Nicolaou A (2024) An adaptable in silico ensemble model of the arachidonic acid cascade. Molecular Omics 20:453–468
Metabolism
Immunology
Link
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
19 publications
2023
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. EMBO Journal 42:e113079
Metabolism
Microbiology
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
13 publications
2022
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
2021
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, Létisse 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
Microbiology
Link
13 publications
2020
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
Plant Biology
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
Plant Biology
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, Mc Auley 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
2019
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
Plant Biology
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
Parasitology
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
Plant Biology
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
2018
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
2017
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
2016
Altıntaş A, Davidsen K, Garde C, Mortensen UH, Brasen JC, Sams T, Workman CT (2016) High-resolution kinetics and modeling of hydrogen peroxide degradation in live cells. Free Radical Biology and Medicine 101:143–153
Metabolism
Link
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, Mc Auley 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, Mc Auley 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
Plant Biology
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
2015
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
Parasitology
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
2014
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
2013
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 RG, 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
2012
Achcar F, Kerkhoven EJ, The SilicoTryp Consortium, Bakker BM, Barrett MP, Breitling R (2012) Dynamic Modelling under Uncertainty: The Case of Trypanosoma brucei Energy Metabolism. PLOS Computational Biology 8:e1002352
Metabolism
Link
Adamczyk M, Westerhoff HV (2012) Engineering of self-sustaining systems: Substituting the yeast glucose transporter plus hexokinase for the Lactococcus lactis phosphotransferase system in a Lactococcus lactis network in silico. Biotechnology Journal 7:877-883
Metabolism
Microbiology
Link
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
Mc Auley 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
2011
Genc S, Kurnaz IA, Özilgen 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. 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
2010
Costa RS, Machado D, Ferreira EC, Rocha I (2010) Evaluating the integration of proteomic data for the prediction of intracellular fluxes after knockout experiments. IFAC Proceedings Volumes 43:114–119
Computational Method
Metabolism
Link
Costa RS, Machado D, Rocha I, Ferreira EC (2010) Hybrid dynamic modeling of Escherichia coli central metabolic network combining Michaelis-Menten and approximate kinetic equations. BioSystems 100:150–157
Metabolism
Microbiology
Link
Flach EH, Schnell S (2010) Stability of open pathways. Mathematical Biosciences 228:147–152
Theory
Metabolism
Link
Li P, Dada JO, Jameson D, Spasić I, Swainston N, Carroll KM, Dunn WB, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder CL, Wishart J, Broomhead DS, Goble CA, Gaskell SJ, Kell DB, Westerhoff HV, Mendes P, Paton NW (2010) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11:582
Computational Method
Metabolism
Link
Mellor N, Bligh F, Chandler I, Hodgman C (2010) Reduction of Off-Flavor Generation in Soybean Homogenates: A Mathematical Model. Journal of Food Science 75:R131–R138
Metabolism
Biotechnology
Link
Piedrafita G, Montero F, Morán F, Cárdenas ML, Cornish-Bowden A (2010) A Simple Self-Maintaining Metabolic System: Robustness, Autocatalysis, Bistability. PLOS Computational Biology 6:e1000872
Metabolism
Theory
Link
Smallbone K, Simeonidis E, Swainston N, Mendes P (2010) Towards a genome-scale kinetic model of cellular metabolism. BMC Systems Biology 4:6
Genomics
Whole-Cell Models
Metabolism
Link
7 publications
2009
Curien G, Bastien O, Robert-Genthon M, Cornish-Bowden A, Cárdenas ML, Dumas R (2009) Understanding the regulation of aspartate metabolism using a model based on measured kinetic parameters. Molecular Systems Biology 5:271
Metabolism
Plant Biology
Link
Hower V, Mendes P, Torti FM, Laubenbacher R, Akman S, Shulaev V, Torti SV (2009) A general map of iron metabolism and tissue-specific subnetworks. Molecular BioSystems 5:422
Metabolism
Link
Knoke B, Textor S, Gershenzon J, Schuster S (2009) Mathematical modelling of aliphatic glucosinolate chain length distribution in Arabidopsis thaliana leaves. Phytochemistry Reviews 8:39-51
Metabolism
Plant Biology
Link
Liu J, Brazier-Hicks M, Edwards R (2009) A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana. Biophysical Chemistry 143:85–94
Metabolism
Plant Biology
Link
Ma H, Boogerd FC, Goryanin I (2009) Modelling nitrogen assimilation of Escherichia coli at low ammonium concentration. Journal of Biotechnology 144:175–183
Metabolism
Microbiology
Link
Modre-Osprian R, Osprian I, Tilg B, Schreier G, Weinberger KM, Graber A (2009) Dynamic simulations on the mitochondrial fatty acid Beta-oxidation network. BMC Systems Biology 3:2
Metabolism
Link
Pieper I, Wechler K, Katzberg M, Brusch L, Sørensen PG, Mensonides F, Bertau M (2009) Biosimulation of drug metabolism--a yeast based model. European Journal of Pharmaceutical Sciences 36:157–170
Metabolism
Pharmacology
Link
Troncoso-Ponce MA, Kruger NJ, Ratcliffe G, Garcés R, Martínez-Force E (2009) Characterization of glycolytic initial metabolites and enzyme activities in developing sunflower (Helianthus annuus L.) seeds. Phytochemistry 70:1117–1122
Metabolism
Link
Williamson T, Schwartz J-M, Kell DB, Stateva L (2009) Deterministic mathematical models of the cAMP pathway in Saccharomyces cerevisiae. BMC Systems Biology 3:70
Signaling
Metabolism
Link
9 publications
