COPASI

COPASI's Use In Microbiology

2025

0 publication
2024
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
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
Ramsey K, Britt M, Maramba J, Ushijima B, Moller E, Anishkin A, Häse C, Sukharev S (2024) The dynamic hypoosmotic response of Vibrio cholerae relies on the mechanosensitive channel MscS. iScience 27:110001 Signaling Microbiology Link

3 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
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
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
Schuster M, Li C, Smith P, Kuttler C (2023) Parameters, architecture and emergent properties of the Pseudomonas aeruginosa LasI/LasR quorum-sensing circuit. Journal of the Royal Society Interface 20:20220825 Microbiology Signaling Link

4 publications
2022
Anand S, Padmanabhan P, Sahu SS, Mukherjee K (2022) ANN based process optimization for the growth kinetic study of Nostoc ellipsosporum NCIM 2786. IFAC-PapersOnLine 55:423–428 Microbiology Biotechnology Link
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
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
Mokry RL, O’Brien BS, Adelman JW, Rosas S, Schumacher ML, Ebert AD, Terhune SS (2022) Nitric Oxide Attenuates Human Cytomegalovirus Infection yet Disrupts Neural Cell Differentiation and Tissue Organization. Journal of Virology 96:e0012622 Microbiology Immunology Link
Rettenbacher LA, von der Haar T (2022) A quantitative interpretation of oxidative protein folding activity in Escherichia coli. Microbial Cell Factories 21:268 Biochemistry Microbiology 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
Zondervan NA (2022) Patterns in pathogenesis: elucidating bacterial host interaction. Ph.D. Thesis, Wageningen University, The Netherlands. Microbiology Metabolism Link

8 publications
2021
Arya S, Williams A, Reina SV, Knapp CW, Kreft J-U, Hobman JL, Stekel DJ (2021) Towards a general model for predicting minimal metal concentrations co-selecting for antibiotic resistance plasmids. Environmental Pollution 275:116602 Microbiology Biotechnology Environmental Sciences Link
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
Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG (2021) Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif. Journal of Biological Chemistry 297:101175 Macromolecular Biochemistry Microbiology Link
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
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
Virtanen O, Khorobrykh S, Tyystjärvi E (2021) Acclimation of Chlamydomonas reinhardtii to extremely strong light. Photosynthesis Research 147:91–106 Biophysics Microbiology Link

6 publications
2020
Arya S, Todman H, Baker M, Hooton S, Millard A, Kreft J-U, Hobman JL, Stekel DJ (2020) A generalised model for generalised transduction: the importance of co-evolution and stochasticity in phage mediated antimicrobial resistance transfer. FEMS Microbiology Ecology 96:fiaa100 Microbiology Genetics Link
Balasubramanian S, Chandrasekran P, Yesudhas AJR, Ganapathyraman P, Eiteman MA, Subramanian R (2020) In vivo interpretation of model predicted inhibition in acrylate pathway engineered Lactococcus lactis. Biotechnology and Bioengineering 117:3785–3798 Microbiology Metabolism Biotechnology Link
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
Mendes P, Girardi E, Superti-Furga G, Kell DB (2020) Why most transporter mutations that cause antibiotic resistance are to efflux pumps rather than to import transporters. bioRxiv. 2020.01.16.909507 Microbiology Link
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
Zhou Q, Liu Y, Yuan W (2020) Kinetic modeling of butyric acid effects on butanol fermentation by Clostridium saccharoperbutylacetonicum. New Biotechnology 55:118–126 Biotechnology Microbiology Link

9 publications
2019
Chum AP, Shoemaker SR, Fleming PJ, Fleming KG (2019) Plasticity and transient binding are key ingredients of the periplasmic chaperone network. Protein Science 28:1340–1349 Macromolecular Biochemistry Microbiology Link
Kaspar S (2019) The role of promoter architecture in transduction, integration and multiplexing of environmental signals in bacteria. Ph.D. Thesis, University of Heidelberg, Germany Signaling Microbiology Link
Lang SN, Germerodt S, Glock C, Skerka C, Zipfel PF, Schuster S (2019) Molecular crypsis by pathogenic fungi using human factor H. A numerical model. PLoS One 14:e0212187 Immunology Microbiology Link
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
Virtanen O, Valev D, Kruse O, Wobbe L, Tyystjärvi E (2019) Photoinhibition and continuous growth of the wild-type and a high-light tolerant strain of Chlamydomonas reinhardtii. Photosynthetica 57:617–626 Biochemistry Microbiology Link
Zarrella I, Matrella S, Fortunato G, Marchettini N, Proto A, Motta O, Rossi F (2019) Optimization of the anaerobic denitrification process mediated by Bacillus cereus in a batch reactor. Environmental Technology & Innovation 16:100456 Microbiology Environmental Sciences Link

6 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
Buriticá DCC, Mejía BV, Rojas LM, Sáenz L, Yosa J (2018) Análisis determinístico de la red de regulación génica involucrada en la expresión y función del factor de transcripción σ^ 32 en E. coli. Revista Cuarzo 23:7–15 Genetics Microbiology Link
Carpine R, Raganati F, Olivieri G, Hellingwerf KJ, Pollio A, Salatino P, Marzocchella A (2018) Poly-β-hydroxybutyrate (PHB) production by Synechocystis PCC6803 from CO2: Model development. Algal Research 29:49–60 Microbiology Biochemistry Link
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
Parmar JH, Quintana J, Ramírez D, Laubenbacher R, Argüello JM, Mendes P (2018) An important role for periplasmic storage in Pseudomonas aeruginosa copper homeostasis revealed by a combined experimental and computational modeling study. Molecular Microbiology 110:357–369 Microbiology Link
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
Weyder M, Prudhomme M, Bergé M, Polard P, Fichant G (2018) Dynamic modeling of Streptococcus pneumoniae competence provides regulatory mechanistic insights into its tight temporal regulation. Frontiers in Microbiology 9:1637 Microbiology Link
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

10 publications
2017
Barry JK (2017) Mathematical Modelling of the HIV Life Cycle: Identifying Optimal Treatment Strategies. Ph.D. Thesis, Universitätsmedizin der Ernst-Moritz-Arndt-Universität Greifswald, Germany. Microbiology Immunology Link
Baumgart L, Mather W, Hasty J (2017) Synchronized DNA cycling across a bacterial population. Nature Genetics 49:1282–128 Synthetic Biology Microbiology Link
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
Hagen SJ, Son M (2017) Origins of heterogeneity in Streptococcus mutans competence: interpreting an environment-sensitive signaling pathway. Physical Biology 14:015001 Signaling Microbiology Link
Haurat MF, Figueiredo AS, Hoffmann L, Li L, Herr K, Wilson AJ, Beeby M, Schaber J, Albers S-V (2017) ArnS, a kinase involved in starvation-induced archaellum expression. Molecular Microbiology 103:181–194 Microbiology Signaling Link
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
Rodesney CA, Roman B, Dehamani N, Cooley BJ, Katira P, Touhami A, Gordon VD (2017) Mechanosensing of shear by Pseudomonas aeruginosa leads to increased levels of the cyclic-di-GMP signal initiating biofilm development. Proceedings of the National Academy of Sciences USA 114:5906–5911 Microbiology Signaling Link
Wang H, Ray JCJ (2017) Dynamical predictors of an imminent phenotypic switch in bacteria. Physical Biology 14:045007 Microbiology Biochemistry 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

9 publications
2016
Ihekwaba AEC, Mura I, Walshaw J, Peck MW, Barker GC (2016) An Integrative Approach to Computational Modelling of the Gene Regulatory Network Controlling Clostridium botulinum Type A1 Toxin Production. PLoS Computational Biology 12:e1005205 Microbiology 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
Lloréns-Rico V, Cano J, Kamminga T, Gil R, Latorre A, Chen W-H, Bork P, Glass JI, Serrano L, Lluch-Senar M (2016) Bacterial antisense RNAs are mainly the product of transcriptional noise. Science Advances 2:e1501363 Microbiology Genetics Link
Rantasalo A, Czeizler E, Virtanen R, Rousu J, Lähdesmäki H, Penttilä M, Jäntti J, Mojzita D (2016) Synthetic Transcription Amplifier System for Orthogonal Control of Gene Expression in Saccharomyces cerevisiae. PLoS One 11:e0148320 Genetics Microbiology Synthetic Biology Link
Ray JCJ, Wickersheim ML, Jalihal AP, Adeshina YO, Cooper TF, Balázsi G (2016) Cellular Growth Arrest and Persistence from Enzyme Saturation. PLoS Computational Biology 12:e1004825 Microbiology Metabolism Link
Rutkis R, Strazdina I, Balodite E, Lasa Z, Galinina N, Kalnenieks U (2016) The Low Energy-Coupling Respiration in Zymomonas mobilis Accelerates Flux in the Entner-Doudoroff Pathway. PLoS One 11:e0153866 Metabolism Microbiology Link
Salcedo-Sora JE, McAuley MT (2016) A mathematical model of microbial folate biosynthesis and utilisation: implications for antifolate development. Molecular BioSystems 12:923–933 Microbiology Metabolism Biotechnology Link
Seo D, Soeta T, Sakurai H, Sétif P, Sakurai T (2016) Pre-steady-state kinetic studies of redox reactions catalysed by Bacillus subtilis ferredoxin-NADP+ oxidoreductase with NADP+/NADPH and ferredoxin. Biochimica et Biophysica Acta 1857:678–687 Microbiology Enzymology Link
Tyc KM, Herwald SE, Hogan JA, Pierce JV, Klipp E, Kumamoto CA (2016) The game theory of Candida albicans colonization dynamics reveals host status-responsive gene expression. BMC Systems Biology 10:20 Microbiology Immunology Signaling Link

10 publications
2015
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
Ihekwaba AEC, Mura I, Peck MW, Barker GC (2015) The pattern of growth observed for Clostridium botulinum type A1 strain ATCC 19397 is influenced by nutritional status and quorum sensing: a modelling perspective. Pathogens and Disease 73:ftv084 Microbiology Link
Maggi M, Chiarelli LR, Valentini G, Scotti C (2015) Engineering of Helicobacter pylori L-asparaginase: characterization of two functionally distinct groups of mutants. PLoS One 10:e0117025 Microbiology Biotechnology Enzymology Link
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

5 publications
2014
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
Drees B, Reiger M, Jung K, Bischofs IB (2014) A modular view of the diversity of cell-density-encoding schemes in bacterial quorum-sensing systems. Biophysical Journal 107:266-277 Microbiology Link
Fadda A, Ryten M, Droll D, Rojas F, Färber V, Haanstra JR, Merce C, Bakker BM, Matthews KR, Clayton C (2014) Transcriptome-wide analysis of trypanosome mRNA decay reveals complex degradation kinetics and suggests a role for co-transcriptional degradation in determining mRNA levels. Molecular Microbiology 94:307-326 Microbiology Genomics Link
Ihekwaba AEC, Mura I, Barker GC (2014) Computational modelling and analysis of the molecular network regulating sporulation initiation in Bacillus subtilis. BMC Systems Biology 8:119 Microbiology Link
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
Rodriguez Plaza JG, Morales-Nava R, Diener C, Schreiber G, Gonzalez ZD, Lara Ortiz MT, Ortega Blake I, Pantoja O, Volkmer R, Klipp E, Herrmann A, Del Rio G (2014) Cell penetrating peptides and cationic antibacterial peptides: two sides of the same coin. Journal of Biological Chemistry 289:14448–14457 Macromolecular Biochemistry Biophysics Microbiology Link
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
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

8 publications
2013
Altintaş CM (2013) Effects of growth medium conditions on antibiotic production by actinomyces sp. MS Thesis, Dokuz Eylül University, Izmir, Turkey Biotechnology Microbiology Link
Emiola A, Falcarin P, Tocher J, George J (2013) A model for the proteolytic regulation of LpxC in the lipopolysaccharide pathway of Escherichia coli. Computational Biology and Chemistry 47:1–7 Biochemistry Microbiology Link
Rutkis R, Kalnenieks U, Stalidzans E, Fell DA (2013) Kinetic modeling of Zymomonas mobilis Entner-Doudoroff pathway: insights into control and functionality. Microbiology 159:2674-2689 Metabolism Microbiology Link
Saeidi N, Arshath M, Chang MW, Poh CL (2013) Characterization of a quorum sensing device for synthetic biology design: Experimental and modeling validation. Chemical Engineering Science 103:91–99 Synthetic Biology Microbiology Link
Sheng X (2013) Evolutionary and Functional Aspects of Two-Component Signalling Systems. Ph.D. Thesis, Imperial College London, UK. Microbiology 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

6 publications
2012
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
Altintaş CM, Ertas G, Kayali HA (2012) Simulation of Microbial Production of Ramoplanin via Stoichiometric Modeling from Actinoplanes sp. ATCC 33076. New Biotechnology 29:S144–S145 Microbiology Biotechnology Link
Ray JCJ, Igoshin OA (2012) Interplay of Gene Expression Noise and Ultrasensitive Dynamics Affects Bacterial Operon Organization. PLoS Computational Biology 8:e1002672 Microbiology Genetics Link

3 publications
2011
Danis J, Turányi T (2011) Sensitivity analysis of bacterial chemotaxis models. Procedia Computer Science 7:233–234 Signaling Microbiology Link
Hooshangi S, Bentley WE (2011) LsrR quorum sensing “switch” is revealed by a bottom-up approach. PLoS Computational Biology 7:e1002172 Microbiology Signaling Link
Oh E, Lu M, Park C, Park C, Oh HB, Lee SY, Lee J (2011) Dynamic modeling of lactic acid fermentation metabolism with Lactococcus lactis. Journal of Microbiology and Biotechnology 21:162–169 Microbiology Metabolism Link
Shivanandan A (2011) Stochastic modelling and identification of arabinose uptake network in Escherichia coli (PDF Download Available). MS Thesis, Université Joseph Fourier, Grenoble, France. Metabolism Microbiology Link
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

5 publications
2010
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
Tiwari A, Balázsi G, Gennaro ML, Igoshin OA (2010) The interplay of multiple feedback loops with post-translational kinetics results in bistability of mycobacterial stress response. Physical Biology 7:36005 Microbiology Genetics Link

2 publications
2009
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

1 publication
2008
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kırdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB (2008) A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology. Nature Biotechnology 26:1155–1160 Microbiology Computational Method Link

1 publication
2007

0 publication
2006

0 publication
2005

0 publication