Quantitative assignment of reaction directionality in a multicompartmental human metabolic reconstruction.

[1]  Ronan M. T. Fleming,et al.  A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks. , 2011, Journal of theoretical biology.

[2]  Ronan M. T. Fleming,et al.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.

[3]  Ronan M. T. Fleming,et al.  von Bertalanffy 1.0: a COBRA toolbox extension to thermodynamically constrain metabolic models , 2011, Bioinform..

[4]  Vassily Hatzimanikatis,et al.  Thermodynamic calculations for biochemical transport and reaction processes in metabolic networks. , 2010, Biophysical journal.

[5]  Ines Thiele,et al.  Computationally efficient flux variability analysis , 2010, BMC Bioinformatics.

[6]  C. Gille,et al.  HepatoNet1: a comprehensive metabolic reconstruction of the human hepatocyte for the analysis of liver physiology , 2010, Molecular systems biology.

[7]  J. Gasteiger,et al.  IGERS: inferring Gibbs energy changes of biochemical reactions from reaction similarities. , 2010, Biophysical journal.

[8]  Edda Klipp,et al.  Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation , 2010, Bioinform..

[9]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[10]  Christoph Steinbeck,et al.  Chemical Entities of Biological Interest: an update , 2009, Nucleic Acids Res..

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

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

[13]  Jason A. Papin,et al.  Applications of genome-scale metabolic reconstructions , 2009, Molecular systems biology.

[14]  Vassily Hatzimanikatis,et al.  Thermodynamic analysis of biodegradation pathways , 2009, Biotechnology and bioengineering.

[15]  U. Sauer,et al.  13C-based metabolic flux analysis , 2009, Nature Protocols.

[16]  J. Rabinowitz,et al.  Absolute Metabolite Concentrations and Implied Enzyme Active Site Occupancy in Escherichia coli , 2009, Nature chemical biology.

[17]  David S. Wishart,et al.  HMDB: a knowledgebase for the human metabolome , 2008, Nucleic Acids Res..

[18]  Daniel A Beard,et al.  Detailed kinetics and regulation of mammalian NAD-linked isocitrate dehydrogenase. , 2008, Biochimica et biophysica acta.

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

[20]  Adam M. Feist,et al.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.

[21]  Zheng-Tao Wang,et al.  Taxane's Substituents at C3′ Affect Its Regioselective Metabolism: Different in Vitro Metabolism of Cephalomannine and Paclitaxel , 2008, Drug Metabolism and Disposition.

[22]  Nicola Zamboni,et al.  anNET: a tool for network-embedded thermodynamic analysis of quantitative metabolome data , 2008, BMC Bioinformatics.

[23]  U. Sauer,et al.  Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli , 2007, Molecular systems biology.

[24]  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.

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

[26]  Paul F. Cook,et al.  Enzyme Kinetics and Mechanism , 2007 .

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

[28]  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.

[29]  Matthias Heinemann,et al.  Systematic assignment of thermodynamic constraints in metabolic network models , 2006, BMC Bioinformatics.

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

[31]  Bernhard Ø Palsson,et al.  Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints. , 2006, Biophysical journal.

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

[33]  Egon L. Willighagen,et al.  The Blue Obelisk—Interoperability in Chemical Informatics , 2006, J. Chem. Inf. Model..

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

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

[36]  R. L. Brady,et al.  A preliminary account of the properties of recombinant human Glyoxylate reductase (GRHPR), LDHA and LDHB with glyoxylate, and their potential roles in its metabolism. , 2005, Biochimica et biophysica acta.

[37]  R. Alberty Thermodynamics of Biochemical Reactions , 2003 .

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

[39]  O. Ottersen,et al.  Properties and submitochondrial localization of pig and rat renal phosphate-activated glutaminase. , 2000, American journal of physiology. Cell physiology.

[40]  K. Houk,et al.  THERMODYNAMIC AND QUANTUM CHEMICAL STUDY OF THE CONVERSION OF CHORISMATE TO (PYRUVATE + 4-HYDROXYBENZOATE) , 1998 .

[41]  D. Hilvert,et al.  Thermodynamics of the Conversion of Chorismate to Prephenate: Experimental Results and Theoretical Predictions , 1997 .

[42]  R. Alberty Legendre transforms in chemical thermodynamics , 1994 .

[43]  J. Mccammon,et al.  Sulfate Anion in Water: Model Structural, Thermodynamic, and Dynamic Properties , 1994 .

[44]  B. Palsson,et al.  Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates , 1993, Applied and environmental microbiology.

[45]  G. A. Lyles,et al.  The metabolism of aminoacetone to methylglyoxal by semicarbazide-sensitive amine oxidase in human umbilical artery. , 1992, Biochemical pharmacology.

[46]  B. Palsson,et al.  Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism. , 1992, Journal of theoretical biology.

[47]  H. Zollner Regulation of urea synthesis. The effect of ammonia on the N-acetylglutamate content of isolated rat liver cells. , 1981, Biochimica et biophysica acta.

[48]  T. Saheki Regulation of Urea Synthesis , 1979 .

[49]  H. Abelson,et al.  Kinetics of tetrahydrobiopterin synthesis by rabbit brain dihydrofolate reductase. , 1978, The Biochemical journal.

[50]  J. Lopreato,et al.  General system theory : foundations, development, applications , 1970 .

[51]  H. Krebs,et al.  Energy Transformations in Living Matter , 1957 .

[52]  H. Krebs,et al.  A survey of the energy transformations in living matter , 1957 .