Integrated stoichiometric, thermodynamic and kinetic modelling of steady state metabolism.

[1]  Ronan M. T. Fleming,et al.  Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide. , 2010, EcoSal Plus.

[2]  John Ross,et al.  Thermodynamics and Fluctuations Far From Equilibrium , 2008, Entropy.

[3]  B. Palsson,et al.  A protocol for generating a high-quality genome-scale metabolic reconstruction , 2010 .

[4]  Ronan M. T. Fleming,et al.  Quantitative assignment of reaction directionality in constraint-based models of metabolism: application to Escherichia coli. , 2009, Biophysical chemistry.

[5]  Ronan M. T. Fleming,et al.  Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization , 2009, PLoS Comput. Biol..

[6]  Matthew D. Jankowski,et al.  Group contribution method for thermodynamic analysis of complex metabolic networks. , 2008, Biophysical journal.

[7]  D. Broomhead,et al.  Something from nothing − bridging the gap between constraint‐based and kinetic modelling , 2007, The FEBS journal.

[8]  Bernhard O. Palsson,et al.  Estimation of the number of extreme pathways for metabolic networks , 2007, BMC Bioinformatics.

[9]  Wolfgang Wiechert,et al.  The thermodynamic meaning of metabolic exchange fluxes. , 2007, Biophysical journal.

[10]  Adam M. Feist,et al.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information , 2007, Molecular systems biology.

[11]  Andreas Hoppe,et al.  Including metabolite concentrations into flux balance analysis: thermodynamic realizability as a constraint on flux distributions in metabolic networks , 2007, BMC Systems Biology.

[12]  Pei Yee Ho,et al.  Multiple High-Throughput Analyses Monitor the Response of E. coli to Perturbations , 2007, Science.

[13]  Stephen P. Boyd,et al.  A tutorial on geometric programming , 2007, Optimization and Engineering.

[14]  E. Gilles,et al.  Thermodynamically feasible kinetic models of reaction networks. , 2007, Biophysical journal.

[15]  V. Hatzimanikatis,et al.  Thermodynamics-based metabolic flux analysis. , 2007, Biophysical journal.

[16]  Monica L. Mo,et al.  Global reconstruction of the human metabolic network based on genomic and bibliomic data , 2007, Proceedings of the National Academy of Sciences.

[17]  H. Qian,et al.  Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Processes , 2006, PloS one.

[18]  Renate Kania,et al.  Storing and Annotating of Kinetic Data , 2007, Silico Biol..

[19]  S. Panke,et al.  Putative regulatory sites unraveled by network-embedded thermodynamic analysis of metabolome data , 2006, Molecular systems biology.

[20]  Stephan Preibisch,et al.  GeneChip microarrays—signal intensities, RNA concentrations and probe sequences , 2006 .

[21]  Hans Binder,et al.  Thermodynamics of competitive surface adsorption on DNA microarrays , 2006 .

[22]  R. Alberty.  Biochemical thermodynamics: applications of Mathematica. , 2006, Methods of biochemical analysis.

[23]  Matthew D. Jankowski,et al.  Genome-scale thermodynamic analysis of Escherichia coli metabolism. , 2006, Biophysical journal.

[24]  Antoine M. van Oijen,et al.  Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited , 2006, Nature chemical biology.

[25]  Herbert M. Sauro,et al.  Conservation analysis of large biochemical networks , 2006, Bioinform..

[26]  B. Palsson.  Systems Biology: Properties of Reconstructed Networks , 2006 .

[27]  Eric J. Deeds,et al.  A simple physical model for scaling in protein-protein interaction networks. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[28]  H. Qian,et al.  Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium. , 2005, Biophysical chemistry.

[29]  A. Cornish-Bowden,et al.  Enzymes in context: Kinetic characterization of enzymes for systems biology , 2005 .

[30]  B. Palsson,et al.  k-Cone analysis: determining all candidate values for kinetic parameters on a network scale. , 2005, Biophysical journal.

[31]  Andreas Beyer,et al.  Post-transcriptional Expression Regulation in the Yeast Saccharomyces cerevisiae on a Genomic Scale*S , 2004, Molecular & Cellular Proteomics.

[32]  H. Qian,et al.  Thermodynamic constraints for biochemical networks. , 2004, Journal of theoretical biology.

[33]  Markus J. Herrgård,et al.  Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.

[34]  A. Neumaier.  Complete search in continuous global optimization and constraint satisfaction , 2004, Acta Numerica.

[35]  A. Neumaier.  Acta Numerica 2004: Complete search in continuous global optimization and constraint satisfaction , 2004 .

[36]  C. Mathews.  Thermodynamics of biochemical reactions , 2004 .

[37]  R. Mahadevan,et al.  The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.

[38]  Rafael A Irizarry,et al.  Exploration, normalization, and summaries of high density oligonucleotide array probe level data. , 2003, Biostatistics.

[39]  B. Palsson,et al.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.

[40]  H. Qian,et al.  Energy balance for analysis of complex metabolic networks. , 2002, Biophysical journal.

[41]  I. Marison,et al.  Microbial growth by a net heat up-take: a calorimetric and thermodynamic study on acetotrophic methanogenesis by Methanosarcina barkeri. , 2001, Biotechnology and bioengineering.

[42]  B. Palsson,et al.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. , 2000, Journal of theoretical biology.

[43]  D. Avis.  A Revised Implementation of the Reverse Search Vertex Enumeration Algorithm , 2000 .

[44]  G. Ziegler,et al.  Polytopes : combinatorics and computation , 2000 .

[45]  G. Crooks.  Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[46]  A. R. Fresht.  Structure and Mechanism in Protein Science: A Guide to Enzyme Catalysis and Protein Folding , 1999 .

[47]  David Avis,et al.  Computational experience with the reverse search vertex enumeration algorithm , 1998 .

[48]  I. M. Gelʹfand,et al.  Discriminants, Resultants, and Multidimensional Determinants , 1994 .

[49]  B. Palsson,et al.  Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. , 1993, Journal of theoretical biology.

[50]  M. Mavrovouniotis.  Estimation of standard Gibbs energy changes of biotransformations. , 1991, The Journal of biological chemistry.

[51]  E. Schnedler.  The calculation of complex chemical equilibria , 1984 .

[52]  William R. Smith,et al.  Chemical Reaction Equilibrium Analysis: Theory and Algorithms , 1982 .

[53]  A. Cornish-Bowden.  Fundamentals of Enzyme Kinetics , 1979 .

[54]  Anthony Hill,et al.  Free Energy Transduction In Biology , 1977 .

[55]  Alan S. Perelson,et al.  Chemical reaction dynamics part II: Reaction networks , 1974 .

[56]  R. Jackson,et al.  General mass action kinetics , 1972 .