Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide.
暂无分享,去创建一个
[1] H. Kornberg,et al. Net formation of phosphoenolpyruvate from pyruvate by Escherichia coli. , 1965, Biochimica et biophysica acta.
[2] R. Okinaka,et al. Catabolite Repression and Pyruvate Metabolism in Escherichia coli , 1967, Journal of bacteriology.
[3] D. Fraenkel,et al. Genetic Mapping of Loci for Glucose-6-Phosphate Dehydrogenase, Gluconate-6-Phosphate Dehydrogenase, and Gluconate-6-Phosphate Dehydrase in Escherichia coli , 1968, Journal of bacteriology.
[4] Phosphotransacetylase of Escherichia coli B, activation by pyruvate and inhibition by NADH and certain nucleotides. , 1969, Biochimica et biophysica acta.
[5] D. Fraenkel,et al. Transketolase Mutants of Escherichia coli , 1969, Journal of bacteriology.
[6] W. F. Burke,et al. NADP+-specific isocitrate dehydrogenase of Escherichia coli. II. Subunit structure. , 1974, Biochimica et biophysica acta.
[7] E. Hansen,et al. Two routes for synthesis of phosphoenolpyruvate from C4-dicarboxylic acids in Escherichia coli. , 1974, Biochemical and biophysical research communications.
[8] D. Fraenkel,et al. Sugar Metabolism in Transketolase Mutants of Escherichia coli , 1974, Journal of bacteriology.
[9] R. Cooper,et al. Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles. , 1975, European journal of biochemistry.
[10] J. H. Collins,et al. Reconstitution of the Escherichia coli pyruvate dehydrogenase complex. , 1975, Proceedings of the National Academy of Sciences of the United States of America.
[11] E. Hansen,et al. Isolation of mutants of Escherichia coli lacking NAD- and NADP-linked malic. , 1975, Biochemical and biophysical research communications.
[12] E. Silverstein,et al. Escherichia coli acetate kinase mechanism studied by net initial rate, equilibrium, and independent isotopic exchange kinetics. , 1976, The Journal of biological chemistry.
[13] F. Veronese,et al. Isolation and properties of 6-phosphogluconate dehydrogenase from Escherichia coli. Some comparisons with the thermophilic enzyme from Bacillus stearothermophilus. , 1976, Biochemistry.
[14] W. A. Bridger,et al. Phosphoenolypyruvate synthetase of Escherichia coli: molecular weight, subunit composition, and identification of phosphohistidine in phosphoenzyme intermediate. , 1977, The Journal of biological chemistry.
[15] D. Fraenkel,et al. Pathways of NADPH formation in Escherichia coli. , 1977, The Journal of biological chemistry.
[16] R N Perham,et al. Novel kinetic and structural properties of the class-I D-fructose 1,6-bisphosphate aldolase from Escherichia coli (Crookes' strain). , 1978, The Biochemical journal.
[17] Y. Arita,et al. Studies on regulatory functions of malic enzymes. VI. Purification and molecular properties of NADP-linked malic enzyme from Escherichia coli W. , 1979, Journal of Biochemistry (Tokyo).
[18] S. Rhee,et al. Catalytic cycle of the biosynthetic reaction catalyzed by adenylylated glutamine synthetase from Escherichia coli. , 1982, The Journal of biological chemistry.
[19] R. Cooper,et al. Evidence for two dinstinct pyruvate kinase genes in Escherichia coli K‐12 , 1983 .
[20] F. Daldal,et al. Nucleotide sequence of gene pfkB encoding the minor phosphofructokinase of Escherichia coli K-12. , 1984, Gene.
[21] F. Wittinghofer,et al. Cloning and sequencing of the adenylate kinase gene (adk) of Escherichia coli. , 1985, Nucleic acids research.
[22] G. Branlant,et al. Nucleotide sequence of the Escherichia coli gap gene. Different evolutionary behavior of the NAD+-binding domain and of the catalytic domain of D-glyceraldehyde-3-phosphate dehydrogenase. , 1985, European journal of biochemistry.
[23] E. Meléndez-Hevia,et al. The game of the pentose phosphate cycle. , 1985, Journal of theoretical biology.
[24] L. McAlister-Henn,et al. Isolation and expression of the Escherichia coli gene encoding malate dehydrogenase , 1985, Journal of bacteriology.
[25] P. Owen,et al. The succinate dehydrogenase of Escherichia coli. Immunochemical resolution and biophysical characterization of a 4-subunit enzyme complex. , 1985, The Journal of biological chemistry.
[26] S. Cole,et al. Molecular biology, biochemistry and bioenergetics of fumarate reductase, a complex membrane-bound iron-sulfur flavoenzyme of Escherichia coli. , 1985, Biochimica et biophysica acta.
[27] C. Upton,et al. The subunits of succinyl-coenzyme A synthetase--function and assembly. , 1987, Biochemical Society symposium.
[28] E. Lin,et al. arcA (dye), a global regulatory gene in Escherichia coli mediating repression of enzymes in aerobic pathways. , 1988, Proceedings of the National Academy of Sciences of the United States of America.
[29] J. Guest,et al. Two biochemically distinct classes of fumarase in Escherichia coli. , 1988, Biochimica et biophysica acta.
[30] E. F. Robertson,et al. Escherichia coli isocitrate lyase: properties and comparisons. , 1988, Biochimica et biophysica acta.
[31] D. Clark,et al. The fermentation pathways of Escherichia coli. , 1989, FEMS microbiology reviews.
[32] P. Evans,et al. Crystal structure of unliganded phosphofructokinase from Escherichia coli. , 1989, Journal of molecular biology.
[33] S. Baldwin,et al. Cloning, sequence analysis and over-expression of the gene for the class II fructose 1,6-bisphosphate aldolase of Escherichia coli. , 1989, The Biochemical journal.
[34] J. Guest,et al. Nucleotide sequence of the FNR-regulated fumarase gene (fumB) of Escherichia coli K-12 , 1989, Journal of bacteriology.
[35] T. Atlung,et al. Cloning and characterization of the Escherichia coli phosphoglycerate kinase (pgk) gene. , 1989, Gene.
[36] R. Perham,et al. 2‐Oxo Acid Dehydrogenase Multienzyme Complexes: Domains, Dynamics, and Design a , 1989, Annals of the New York Academy of Sciences.
[37] B. Cain,et al. Proton translocation by the F1F0ATPase of Escherichia coli. Mutagenic analysis of the a subunit. , 1989, The Journal of biological chemistry.
[38] H. Muirhead,et al. Isoenzymes of pyruvate kinase. , 1990, Biochemical Society transactions.
[39] G. Sawers,et al. A radical-chemical route to acetyl-CoA: the anaerobically induced pyruvate formate-lyase system of Escherichia coli. , 1990, FEMS microbiology reviews.
[40] D. K. Willis,et al. Copyright 0 1990 by the Genetics Society of America Physical Analysis of Spontaneous and Mutagen-Induced Mutants of Escherichia coli K-12 Expressing DNA Exonuclease VI11 Activity , 1989 .
[41] Cloning and sequencing of a gene encoding a glutamate and aspartate carrier of Escherichia coli K-12 , 1990, Journal of bacteriology.
[42] C. Prodromou,et al. The aconitase of Escherichia coli: purification of the enzyme and molecular cloning and map location of the gene (acn). , 1991, Journal of general microbiology.
[43] W. Boos,et al. The malX malY operon of Escherichia coli encodes a novel enzyme II of the phosphotransferase system recognizing glucose and maltose and an enzyme abolishing the endogenous induction of the maltose system , 1991, Journal of bacteriology.
[44] G Perrière,et al. Regulation of the acetate operon in Escherichia coli: purification and functional characterization of the IclR repressor. , 1991, The EMBO journal.
[45] J. Knappe,et al. Ultrastructure and pyruvate formate-lyase radical quenching property of the multienzymic AdhE protein of Escherichia coli. , 1992, The Journal of biological chemistry.
[46] Cyclic AMP in prokaryotes. , 1992, Microbiological reviews.
[47] B. Erni,et al. The mannose transporter of Escherichia coli. Structure and function of the IIABMan subunit. , 1993, The Journal of biological chemistry.
[48] B. Palsson,et al. Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors. , 1993, Journal of theoretical biology.
[49] G Sawers,et al. Specific transcriptional requirements for positive regulation of the anaerobically inducible pfl operon by ArcA and FNR , 1993, Molecular microbiology.
[50] S. Teshiba,et al. Identification and characterization of the tktB gene encoding a second transketolase in Escherichia coli K-12 , 1993, Journal of bacteriology.
[51] B. Palsson,et al. Metabolic Capabilities of Escherichia coli II. Optimal Growth Patterns , 1993 .
[52] Jeffrey Green,et al. Regulation of transcription at the ndh promoter of Escherichia coli by FNR and novel factors , 1994, Molecular microbiology.
[53] B. Palsson,et al. Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110 , 1994, Applied and environmental microbiology.
[54] D. Flint,et al. Initial kinetic and mechanistic characterization of Escherichia coli fumarase A. , 1994, Archives of biochemistry and biophysics.
[55] J. Badia,et al. Molecular characterization of Escherichia coli malate synthase G. Differentiation with the malate synthase A isoenzyme. , 1994, European journal of biochemistry.
[56] S. Park,et al. Oxygen, iron, carbon, and superoxide control of the fumarase fumA and fumC genes of Escherichia coli: role of the arcA, fnr, and soxR gene products , 1995, Journal of bacteriology.
[57] L. Wu,et al. A family of homologous substrate-binding proteins with a broad range of substrate specificity and dissimilar biological functions. , 1995, Biochimie.
[58] Transketolase A of Escherichia coli K12. Purification and properties of the enzyme from recombinant strains. , 1995 .
[59] S. Park,et al. Transcriptional regulation of the proton-translocating ATPase (atpIBEFHAGDC) operon of Escherichia coli: control by cell growth rate , 1996, Journal of bacteriology.
[60] S. Grdadolnik,et al. Solution structure of the IIB domain of the glucose transporter of Escherichia coli. , 1996, Biochemistry.
[61] R. Gunsalus,et al. Effect of microaerophilic cell growth conditions on expression of the aerobic (cyoABCDE and cydAB) and anaerobic (narGHJI, frdABCD, and dmsABC) respiratory pathway genes in Escherichia coli , 1996, Journal of bacteriology.
[62] D. Laporte,et al. Regulated expression of a repressor protein: FadR activates iclR , 1996, Journal of bacteriology.
[63] M H Saier,et al. Frur mediates catabolite activation of pyruvate kinase (pykF) gene expression in Escherichia coli , 1996, Journal of bacteriology.
[64] E. Díaz,et al. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12 , 1997, Journal of bacteriology.
[65] C. Tseng. Regulation of fumarase (fumB) gene expression in Escherichia coli in response to oxygen, iron and heme availability: role of the arcA, fur, and hemA gene products. , 1997, FEMS microbiology letters.
[66] S. Park,et al. Aerobic regulation of the sucABCD genes of Escherichia coli, which encode alpha-ketoglutarate dehydrogenase and succinyl coenzyme A synthetase: roles of ArcA, Fnr, and the upstream sdhCDAB promoter , 1997, Journal of bacteriology.
[67] E. Lin,et al. Regulation of expression of the ethanol dehydrogenase gene (adhE) in Escherichia coli by catabolite repressor activator protein Cra , 1997, Journal of bacteriology.
[68] E. Boye,et al. Impaired growth of an Escherichia coli rpe mutant lacking ribulose-5-phosphate epimerase activity. , 1998, Biochimica et biophysica acta.
[69] G. Sawers,et al. A glycyl radical solution: oxygen‐dependent interconversion of pyruvate formate‐lyase , 1998, Molecular microbiology.
[70] A. Fersht. Structure and mechanism in protein science , 1998 .
[71] J. Guest,et al. Transcription and transcript processing in the sdhCDAB-sucABCD operon of Escherichia coli. , 1998, Microbiology.
[72] M. Saier,et al. Multiple mechanisms controlling carbon metabolism in bacteria. , 1998, Biotechnology and bioengineering.
[73] J. Plumbridge. Control of the expression of the manXYZ operon in Escherichia coli: Mlc is a negative regulator of the mannose PTS , 1998, Molecular microbiology.
[74] A. Ashcroft,et al. The dhnA gene of Escherichia coli encodes a class I fructose bisphosphate aldolase. , 1998, The Biochemical journal.
[75] L. Camarena,et al. Transcriptional repression of gdhA in Escherichia coli is mediated by the Nac protein. , 1998, FEMS microbiology letters.
[76] A. Ishihama,et al. FruR-mediated transcriptional activation at the ppsA promoter of Escherichia coli. , 1998, Journal of molecular biology.
[77] Juan Aguilar,et al. Cross-induction of glc and ace Operons ofEscherichia coli Attributable to Pathway Intersection , 1999, The Journal of Biological Chemistry.
[78] D. Rees,et al. Structure of the Escherichia coli fumarate reductase respiratory complex. , 1999, Science.
[79] J. Guest,et al. Inactivation and Regulation of the Aerobic C4-Dicarboxylate Transport (dctA) Gene ofEscherichia coli , 1999, Journal of bacteriology.
[80] S. Tagawa,et al. Electron transfer process in cytochrome bd-type ubiquinol oxidase from Escherichia coli revealed by pulse radiolysis. , 1999, Biochemistry.
[81] M. F. White,et al. The two analogous phosphoglycerate mutases of Escherichia coli , 1999, FEBS letters.
[82] Overexpression of the Escherichia coli nuo-operon and isolation of the overproduced NADH:ubiquinone oxidoreductase (complex I). , 1999, Biochemistry.
[83] T. Inada,et al. Negative regulation of the pts operon by Mlc: mechanism underlying glucose induction in Escherichia coli , 1999, Genes to cells : devoted to molecular & cellular mechanisms.
[84] J. Guest,et al. Identification and Characterization of a Two-Component Sensor-Kinase and Response-Regulator System (DcuS-DcuR) Controlling Gene Expression in Response to C4-Dicarboxylates in Escherichia coli , 1999, Journal of bacteriology.
[85] E. Lin,et al. Regulation of Expression of the adhE Gene, Encoding Ethanol Oxidoreductase in Escherichia coli: Transcription from a Downstream Promoter and Regulation by Fnr and RpoS , 1999, Journal of bacteriology.
[86] B. Palsson,et al. The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[87] S. Kustu,et al. Phosphorylation-Induced Signal Propagation in the Response Regulator NtrC , 2000, Journal of bacteriology.
[88] Amos Bairoch,et al. The ENZYME database in 2000 , 2000, Nucleic Acids Res..
[89] V. Thorsson,et al. Discovery of regulatory interactions through perturbation: inference and experimental design. , 1999, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.
[90] M. Ashburner,et al. Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.
[91] Susumu Goto,et al. KEGG: Kyoto Encyclopedia of Genes and Genomes , 2000, Nucleic Acids Res..
[92] D. Eisenberg,et al. The crystal structure of D-lactate dehydrogenase, a peripheral membrane respiratory enzyme. , 2000, Proceedings of the National Academy of Sciences of the United States of America.
[93] Evelyn Camon,et al. The EMBL Nucleotide Sequence Database , 2000, Nucleic Acids Res..
[94] J. Rydström,et al. Proton translocating nicotinamide nucleotide transhydrogenase from E. coli. Mechanism of action deduced from its structural and catalytic properties. , 2000, Biochimica et biophysica acta.
[95] B. Palsson,et al. In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data , 2001, Nature Biotechnology.
[96] B. Palsson,et al. Regulation of gene expression in flux balance models of metabolism. , 2001, Journal of theoretical biology.
[97] G. Sawers,et al. A novel mechanism controls anaerobic and catabolite regulation of the Escherichia coli tdc operon , 2001, Molecular microbiology.
[98] S. Howitt,et al. Characterization of PitA and PitB fromEscherichia coli , 2001, Journal of bacteriology.
[99] G. Brayer,et al. Comparative analysis of folding and substrate binding sites between regulated hexameric type II citrate synthases and unregulated dimeric type I enzymes. , 2001, Biochemistry.
[100] D. Clark,et al. Regulation of the ldhA gene, encoding the fermentative lactate dehydrogenase of Escherichia coli. , 2001, Microbiology.
[101] B. Luisi,et al. Crystal structure of the Escherichia coli RNA degradosome component enolase. , 2001, Journal of molecular biology.
[102] Lincoln Stein,et al. Genome annotation: from sequence to biology , 2001, Nature Reviews Genetics.
[103] U. Völker,et al. Oxidation of propionate to pyruvate in Escherichia coli. Involvement of methylcitrate dehydratase and aconitase. , 2002, European journal of biochemistry.
[104] Peter D. Karp,et al. Evaluation of computational metabolic-pathway predictions for Helicobacter pylori , 2002, Bioinform..
[105] B. Palsson,et al. Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth , 2002, Nature.
[106] G. Church,et al. Analysis of optimality in natural and perturbed metabolic networks , 2002 .
[107] Y. Kai,et al. Phosphoenolpyruvate carboxylase: three-dimensional structure and molecular mechanisms. , 2003, Archives of biochemistry and biophysics.
[108] A. Burgard,et al. Optknock: A bilevel programming framework for identifying gene knockout strategies for microbial strain optimization , 2003, Biotechnology and bioengineering.
[109] C. Claudel-Renard,et al. Enzyme-specific profiles for genome annotation: PRIAM. , 2003, Nucleic acids research.
[110] S. Iwata,et al. Architecture of Succinate Dehydrogenase and Reactive Oxygen Species Generation , 2003, Science.
[111] R. Mahadevan,et al. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. , 2003, Metabolic engineering.
[112] D. Pe’er,et al. Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data , 2003, Nature Genetics.
[113] Jason A. Papin,et al. Genome-scale microbial in silico models: the constraints-based approach. , 2003, Trends in biotechnology.
[114] H. Mori,et al. Responses of theCentral Metabolism in Escherichia coli to PhosphoglucoseIsomerase and Glucose-6-Phosphate DehydrogenaseKnockouts , 2003, Journal of bacteriology.
[115] R. Alberty. Thermodynamics of Biochemical Reactions , 2003 .
[116] George M. Church,et al. Filling gaps in a metabolic network using expression information , 2004, ISMB/ECCB.
[117] Markus J. Herrgård,et al. Integrating high-throughput and computational data elucidates bacterial networks , 2004, Nature.
[118] A. Barabasi,et al. Global organization of metabolic fluxes in the bacterium Escherichia coli , 2004, Nature.
[119] U. Sauer,et al. The Soluble and Membrane-bound Transhydrogenases UdhA and PntAB Have Divergent Functions in NADPH Metabolism of Escherichia coli* , 2004, Journal of Biological Chemistry.
[120] R. H. Geerse,et al. Cloning and nucleotide sequence of the Escherichia coli K-12 ppsA gene, encoding PEP synthase , 2004, Molecular and General Genetics MGG.
[121] E. Pichersky,et al. Nucleotide sequence of the triose phosphate isomerase gene of Escherichia coli , 2004, Molecular and General Genetics MGG.
[122] D. Court,et al. Identification of the Escherichia coli K-12 ybhE Gene as pgl, Encoding 6-Phosphogluconolactonase , 2004, Journal of bacteriology.
[123] C. Schilling,et al. Flux coupling analysis of genome-scale metabolic network reconstructions. , 2004, Genome research.
[124] L. Prasad,et al. Structure/function studies of phosphoryl transfer by phosphoenolpyruvate carboxykinase. , 2004, Biochimica et biophysica acta.
[125] Kara Dolinski,et al. Saccharomyces Genome Database (SGD) provides tools to identify and analyze sequences from Saccharomyces cerevisiae and related sequences from other organisms , 2004, Nucleic Acids Res..
[126] Markus J. Herrgård,et al. Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model. , 2004, Genome research.
[127] R. Tait,et al. Isolation and characterization of the phosphoglucose isomerase gene from Escherichia coli , 1989, Molecular and General Genetics MGG.
[128] C. Pál,et al. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer , 2005, Nature Genetics.
[129] D. Vitkup,et al. Predicting genes for orphan metabolic activities using phylogenetic profiles , 2006, Genome Biology.
[130] Naryttza N. Diaz,et al. The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.
[131] Peter D. Karp,et al. EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..
[132] Martin J. Lercher,et al. Horizontal gene transfer depends on gene content of the host , 2005, ECCB/JBI.
[133] Jens Nielsen,et al. Evolutionary programming as a platform for in silico metabolic engineering , 2005, BMC Bioinformatics.
[134] Bernhard O Palsson,et al. The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[135] E. Ruppin,et al. Regulatory on/off minimization of metabolic flux changes after genetic perturbations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[136] H. Fromm,et al. Novel Allosteric Activation Site in Escherichia coli Fructose-1,6-bisphosphatase* , 2006, Journal of Biological Chemistry.
[137] B. Palsson,et al. Systems approach to refining genome annotation , 2006, Proceedings of the National Academy of Sciences.
[138] G. Phillips,et al. Crystal structure of ADP/AMP complex of Escherichia coli adenylate kinase , 2005, Proteins.
[139] S. Oliver,et al. Chance and necessity in the evolution of minimal metabolic networks , 2006, Nature.
[140] W. Inwood,et al. A previously undescribed pathway for pyrimidine catabolism. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[141] Peter D. Karp,et al. MetaCyc: a multiorganism database of metabolic pathways and enzymes. , 2004, Nucleic acids research.
[142] J. Rabinowitz,et al. Kinetic flux profiling of nitrogen assimilation in Escherichia coli , 2006, Nature chemical biology.
[143] Bernhard O. Palsson,et al. Matrix Formalism to Describe Functional States of Transcriptional Regulatory Systems , 2006, PLoS Comput. Biol..
[144] John Gould,et al. Toward the automated generation of genome-scale metabolic networks in the SEED , 2007, BMC Bioinformatics.
[145] T. Ideker,et al. Supporting Online Material for A Systems Approach to Mapping DNA Damage Response Pathways , 2006 .
[146] Christian L. Barrett,et al. Systems biology as a foundation for genome-scale synthetic biology. , 2006, Current opinion in biotechnology.
[147] Byung-Kwan Cho,et al. Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA. , 2006, Microbiology.
[148] Bernhard O. Palsson,et al. Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles , 2006, PLoS Comput. Biol..
[149] Tae Hoon Kim,et al. Genome-wide analysis of protein-DNA interactions. , 2006, Annual review of genomics and human genetics.
[150] B. Palsson. Systems Biology: Properties of Reconstructed Networks , 2006 .
[151] Andrew R. Joyce,et al. Experimental and Computational Assessment of Conditionally Essential Genes in Escherichia coli , 2006, Journal of bacteriology.
[152] A. Osterman. A hidden metabolic pathway exposed. , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[153] Inna Dubchak,et al. The integrated microbial genomes (IMG) system , 2005, Nucleic Acids Res..
[154] Monica Riley,et al. Escherichia coli K-12: a cooperatively developed annotation snapshot—2005 , 2006, Nucleic acids research.
[155] Markus J. Herrgård,et al. Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae. , 2006, Genome research.
[156] 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.
[157] Peter D. Karp,et al. Multidimensional annotation of the Escherichia coli K-12 genome , 2007, Nucleic acids research.
[158] J. Collins,et al. Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles , 2007, PLoS biology.
[159] Sanjay Jain,et al. The regulatory network of E. coli metabolism as a Boolean dynamical system exhibits both homeostasis and flexibility of response , 2007 .
[160] Kevin Struhl,et al. Genomic analysis of protein–DNA interactions in bacteria: insights into transcription and chromosome organization , 2007, Molecular microbiology.
[161] Bernhard O. Palsson,et al. Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli , 2007, PLoS Comput. Biol..
[162] Amy K. Schmid,et al. A Predictive Model for Transcriptional Control of Physiology in a Free Living Cell , 2007, Cell.
[163] S. Busby,et al. Transcription factor distribution in Escherichia coli: studies with FNR protein , 2006, Nucleic acids research.
[164] Ian T. Paulsen,et al. TransportDB: a comprehensive database resource for cytoplasmic membrane transport systems and outer membrane channels , 2006, Nucleic Acids Res..
[165] T. Tatusova,et al. Entrez Gene: gene-centered information at NCBI , 2006, Nucleic Acids Res..
[166] Patrick J. Killion,et al. Genetic reconstruction of a functional transcriptional regulatory network , 2007, Nature Genetics.
[167] 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.
[168] S. Lee,et al. Metabolic engineering of Escherichia coli for the production of l-valine based on transcriptome analysis and in silico gene knockout simulation , 2007, Proceedings of the National Academy of Sciences.
[169] Joan L. Slonczewski,et al. pH of the Cytoplasm and Periplasm of Escherichia coli: Rapid Measurement by Green Fluorescent Protein Fluorimetry , 2007, Journal of bacteriology.
[170] Bernhard O. Palsson,et al. Context-Specific Metabolic Networks Are Consistent with Experiments , 2008, PLoS Comput. Biol..
[171] Adam M. Feist,et al. The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli , 2008, Nature Biotechnology.
[172] Akira Ishihama,et al. The Escherichia coli RutR transcription factor binds at targets within genes as well as intergenic regions , 2008, Nucleic acids research.
[173] Bernhard O. Palsson,et al. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory , 2008, BMC Systems Biology.
[174] B. Palsson,et al. Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray. , 2008, Methods in molecular biology.
[175] Christian L. Barrett,et al. Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli , 2008, Proceedings of the National Academy of Sciences.
[176] Byung-Kwan Cho,et al. Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts. , 2008, Genome research.
[177] 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..
[178] Vinay Satish Kumar,et al. GrowMatch: An Automated Method for Reconciling In Silico/In Vivo Growth Predictions , 2009, PLoS Comput. Biol..
[179] Antje Chang,et al. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009 , 2008, Nucleic Acids Res..
[180] Adam M. Feist,et al. Reconstruction of biochemical networks in microorganisms , 2009, Nature Reviews Microbiology.
[181] Bernhard O. Palsson,et al. Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System , 2009, PLoS Comput. Biol..
[182] Erin Beck,et al. The comprehensive microbial resource , 2000, Nucleic Acids Res..
[183] Ronan M. T. Fleming,et al. Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 , 2007, Nature Protocols.