2022
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
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
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 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
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
5 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
Link
Hellgren J (2021) Engineering central carbon metabolism with phosphoketolase pathways in Saccharomyces cerevisiae. PhD 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
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
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
12 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
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
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
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
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
18 publications
2019
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
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
11 publications
2018
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. PhD Thesis, North Carolina State University
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
14 publications
2017
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
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
5 publications
2016
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
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. PhD Thesis, Université Lyon 1-Claude Bernard
Computational Method
Metabolism
Microbiology
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
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
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
17 publications
2015
Castello MA (2015) Lipid Regulation as a Critical Factor in the Development of Alzheimer’s Disease. PhD Thesis, Loma Linda University, Loma Linda, 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 G, 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
Raganatia 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 and Biofuels 8:157
Biotechnology
Metabolism
Link
10 publications
2014
Beauvoit BP, 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
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
Machado D, Rodrigues LR, Rocha I (2014) A kinetic model for curcumin production in Escherichia coli. Biosystems 125:16-21
Synthetic Biology
Metabolism
Link
Marín-Hernández A, 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 A, 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. PhD Thesis, Department of Mathematics and Computer Science, Free University of Berlin.
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
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, Holzhuetter HG, 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
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
15 publications
2013
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
Kerkhoven EJ, Achcar F, Alibu VP, Burchmore RJ, Gilbert IH, Trybilo M, Driessen NN, Gilbert D, 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 FIC, 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
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Penkler GP (2013) A kinetic model of glucose catabolism in Plasmodium falciparum. Ph.D. Thesis, Faculty of Science, University of Stellenbosch, South Africa
Metabolism
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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 AK, 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, Spasic 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
17 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
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 TB (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
11 publications
2010
Li P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL, Simeonidis E, Weichart D, Winder C, 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
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
2 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
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
Link
Liu J, Brazier-Hicks M, Edwards R (2009) A kinetic model for the metabolism of the herbicide safener fenclorim in Arabidopsis thaliana. Biophysical Chemistry 143:85–94
Metabolism
Link
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
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
6 publications
