Qualitative simulation of the carbon starvation response in Escherichia coli.

[1]  Robert L. Perlman,et al.  Purification of and Properties of the Cyclic Adenosine 3',5'-Monophosphate Receptor Protein which Mediates Cyclic Adenosine 3',5'-Monophosphate-dependent Gene Transcription in Escherichia coli , 1971 .

[2]  G. Yagil,et al.  On the relation between effector concentration and the rate of induced enzyme synthesis. , 1971, Biophysical journal.

[3]  Action sélective du charbon pour éliminer la vitamine B12 de ses combinaisons avec le facteur intrinsèque et d'autres protéines de transport , 1972 .

[4]  L. Glass,et al.  The logical analysis of continuous, non-linear biochemical control networks. , 1973, Journal of theoretical biology.

[5]  J. Hesse,et al.  Adenosine 3':5'-cyclic monophosphate as mediator of catabolite repression in Escherichia coli. , 1975, Proceedings of the National Academy of Sciences of the United States of America.

[6]  S. Kumar.  Properties of adenyl cyclase and cyclic adenosine 3',5'-monophosphate receptor protein-deficient mutants of Escherichia coli , 1976, Journal of bacteriology.

[7]  C. Benham.  Elastic model of supercoiling. , 1977, Proceedings of the National Academy of Sciences of the United States of America.

[8]  A. Fersht.  Enzyme structure and mechanism , 1977 .

[9]  Effect of carbon sources on the rates of cyclic AMP synthesis, excretion, and degradation, and the ability to produce beta-galactosidase in Escherichia coli. , 1979, Canadian journal of biochemistry.

[10]  C. Benham,et al.  Torsional stress and local denaturation in supercoiled DNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[11]  V. Bankaitis,et al.  Regulation of adenylate cyclase synthesis in Escherichia coli: studies with cya-lac operon and protein fusion strains , 1982, Journal of bacteriology.

[12]  Cloning and promoter analysis of the Escherichia coli adenylate cyclase gene. , 1983, Nucleic acids research.

[13]  A. Danchin,et al.  Regulation of adenylate cyclase synthesis in Escherichia coli: nucleotide sequence of the control region. , 1983, The EMBO journal.

[14]  H. Aiba,et al.  Autoregulation of the Escherichia coli crp gene: CRP is a transcriptional repressor for its own gene , 1983, Cell.

[15]  Purification and characterization of adenylate cyclase from Escherichia coli K12. , 1983, The Journal of biological chemistry.

[16]  M. Gellert,et al.  Regulation of the genes for E. coli DNA gyrase: Homeostatic control of DNA supercoiling , 1983, Cell.

[17]  M. Gellert,et al.  DNA sequence and transcription of the region upstream of the E. coli gyrB gene. , 1984, Nucleic acids research.

[18]  S. Gottesman.  Bacterial regulation: global regulatory networks. , 1984, Annual review of genetics.

[19]  Irwin A. Rose,et al.  Enzyme structure and mechanism (2nd edn): by Alan Fersht, W. H. Freeman & Co., 1985. £14.95 pbk, £28.95 hbk (xxi + 475 pages) ISBN 0 7167 1615 1 , 1985 .

[20]  R. Utsumi,et al.  Negative regulation of adenylate cyclase gene (cya) expression by cyclic AMP-cyclic AMP receptor protein in Escherichia coli: studies with cya-lac protein and operon fusion plasmids , 1985, Journal of bacteriology.

[21]  H. Aiba.  Transcription of the Escherichia coli adenylate cyclase gene is negatively regulated by cAMP-cAMP receptor protein. , 1985, The Journal of biological chemistry.

[22]  H. Aiba,et al.  Evidence for negative control of cya transcription by cAMP and cAMP receptor protein in intact Escherichia coli cells. , 1985, The Journal of biological chemistry.

[23]  K. Okamoto,et al.  Mechanism for the autogenous control of the crp operon: transcriptional inhibition by a divergent RNA transcript. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[24]  M. Gellert,et al.  Fusions of the Escherichia coli gyrA and gyrB control regions to the galactokinase gene are inducible by coumermycin treatment , 1987, Journal of bacteriology.

[25]  M. Gellert,et al.  Modulation of transcription by DNA supercoiling: a deletion analysis of the Escherichia coli gyrA and gyrB promoters. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[26]  J. Gralla,et al.  Changes in the linking number of supercoiled DNA accompany growth transitions in Escherichia coli , 1987, Journal of bacteriology.

[27]  Y. Tse‐Dinh,et al.  Multiple promoters for transcription of the Escherichia coli DNA topoisomerase I gene and their regulation by DNA supercoiling. , 1988, Journal of molecular biology.

[28]  Aleksej F. Filippov,et al.  Differential Equations with Discontinuous Righthand Sides , 1988, Mathematics and Its Applications.

[29]  K. Okamoto,et al.  Evidence in vivo for autogenous control of the cyclic AMP receptor protein gene (crp) in Escherichia coli by divergent RNA , 1988, Journal of bacteriology.

[30]  A. Gunasekera,et al.  Consensus DNA site for the Escherichia coli catabolite gene activator protein (CAP): CAP exhibits a 450-fold higher affinity for the consensus DNA site than for the E. coli lac DNA site. , 1989, Nucleic acids research.

[31]  El Houssine Snoussi.  Qualitative dynamics of piecewise-linear differential equations: a discrete mapping approach , 1989 .

[32]  K. Drlica,et al.  Bacterial topoisomerases and the control of DNA supercoiling. , 1990, Trends in genetics : TIG.

[33]  H. Aiba,et al.  Molecular mechanism of negative autoregulation of Escherichia coli crp gene. , 1991, Nucleic acids research.

[34]  Stuart A. Kauffman,et al.  The origins of order , 1993 .

[35]  Shouchuan Hu.  Differential equations with discontinuous right-hand sides☆ , 1991 .

[36]  R. J. Reece,et al.  DNA gyrase: structure and function. , 1991, Critical reviews in biochemistry and molecular biology.

[37]  R Kahmann,et al.  The E.coli fis promoter is subject to stringent control and autoregulation. , 1992, The EMBO journal.

[38]  M. Ptashne.  A genetic switch : phage λ and higher organisms , 1992 .

[39]  C. Ball,et al.  Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli , 1992, Journal of bacteriology.

[40]  L. Bosch,et al.  FIS-dependent trans activation of stable RNA operons of Escherichia coli under various growth conditions , 1992, Journal of bacteriology.

[41]  H. Aiba,et al.  A new aspect of transcriptional control of the Escherichia coli crp gene: positive autoregulation , 1992, Molecular microbiology.

[42]  R. Kolter,et al.  The stationary phase of the bacterial life cycle. , 1993, Annual review of microbiology.

[43]  H. Aiba,et al.  A lowered concentration of cAMP receptor protein caused by glucose is an important determinant for catabolite repression in Escherichia coli , 1993, Molecular microbiology.

[44]  F. Blattner,et al.  Global regulation of gene expression in Escherichia coli , 1993, Journal of bacteriology.

[45]  J. Joung,et al.  Synergistic activation of transcription by Escherichia coli cAMP receptor protein. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[46]  T. Inada,et al.  Mechanism of the down‐regulation of cAMP receptor protein by glucose in Escherichia coli: role of autoregulation of the crp gene. , 1994, The EMBO journal.

[47]  T. Mestl,et al.  A mathematical framework for describing and analysing gene regulatory networks. , 1995, Journal of theoretical biology.

[48]  D. Thieffry,et al.  Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state , 1995 .

[49]  R. Gourse,et al.  The transcriptional activator protein FIS: DNA interactions and cooperative interactions with RNA polymerase at the Escherichia coli rrnB P1 promoter. , 1995, Journal of molecular biology.

[50]  S. Busby,et al.  The CAP Modulon , 1996 .

[51]  H. Bremer,et al.  Effects of Fis on ribosome synthesis and activity and on rRNA promoter activities in Escherichia coli. , 1996, Journal of molecular biology.

[52]  F. Neidhardt,et al.  Phosphoenolpyruvate:carbohydrate phosphotransferase systems , 1996 .

[53]  R. Kahmann,et al.  FIS is a regulator of metabolism in Escherichia coli , 1996, Molecular microbiology.

[54]  R. Heinrich,et al.  The Regulation of Cellular Systems , 1996, Springer US.

[55]  T. Inada,et al.  Down regulation of cAMP production by cAMP receptor protein in Escherichia coli: an assessment of the contributions of transcriptional and posttranscriptional control of adenylate cyclase , 1996, Molecular and General Genetics MGG.

[56]  A. S. Lynch,et al.  Regulation of Gene Expression in Escherichia coli , 1996, Springer US.

[57]  K. A. Walker,et al.  Deletion analysis of the fis promoter region in Escherichia coli: antagonistic effects of integration host factor and Fis , 1997, Journal of bacteriology.

[58]  A. Ishihama,et al.  Adaptation of gene expression in stationary phase bacteria. , 1997, Current opinion in genetics & development.

[59]  Y. Tse‐Dinh,et al.  Regulation of Escherichia coli topA gene transcription: involvement of a sigmaS-dependent promoter. , 1997, Journal of molecular biology.

[60]  R. Planta.  Regulation of ribosome synthesis in yeast , 1997, Yeast.

[61]  A. Arkin,et al.  Simulation of prokaryotic genetic circuits. , 1998, Annual review of biophysics and biomolecular structure.

[62]  Thomas Mestl,et al.  A methodological basis for description and analysis of systems with complex switch-like interactions , 1998, Journal of mathematical biology.

[63]  P. Postma,et al.  CRP down-regulates adenylate cyclase activity by reducing the level of phosphorylated IIAGlc, the glucose-specific phosphotransferase protein, in Escherichia coli , 1998, Molecular and General Genetics MGG.

[64]  R. Gourse,et al.  Activation of Escherichia coli rRNA Transcription by FIS during a Growth Cycle , 1998, Journal of bacteriology.

[65]  R Kahmann,et al.  Regulation of crp transcription by oscillation between distinct nucleoprotein complexes , 1998, The EMBO journal.

[66]  A. Travers,et al.  A DNA architectural protein couples cellular physiology and DNA topology in Escherichia coli , 1999, Molecular microbiology.

[67]  S. Ueda,et al.  Growth Phase-Dependent Variation in Protein Composition of the Escherichia coli Nucleoid , 1999, Journal of bacteriology.

[68]  K. A. Walker,et al.  Functional Determinants of the Escherichia coli fis Promoter: Roles of −35, −10, and Transcription Initiation Regions in the Response to Stringent Control and Growth Phase-Dependent Regulation , 1999, Journal of bacteriology.

[69]  H. Westerhoff,et al.  Extensive regulation compromises the extent to which DNA gyrase controls DNA supercoiling and growth rate of Escherichia coli. , 1999, European journal of biochemistry.

[70]  H. Bremer.  Modulation of Chemical Composition and Other Parameters of the Cell by Growth Rate , 1999 .

[71]  J. Hopfield,et al.  From molecular to modular cell biology , 1999, Nature.

[72]  H. Westerhoff,et al.  Understanding Glucose Transport by the Bacterial Phosphoenolpyruvate:Glycose Phosphotransferase System on the Basis of Kinetic Measurements in Vitro * , 2000, The Journal of Biological Chemistry.

[73]  A. Sonenshein,et al.  Control of sporulation initiation in Bacillus subtilis. , 2000, Current opinion in microbiology.

[74]  S. Altuvia,et al.  Escherichia coli response to hydrogen peroxide: a role for DNA supercoiling, Topoisomerase I and Fis , 2000, Molecular microbiology.

[75]  A. Travers,et al.  The expression of the Escherichia coli fis gene is strongly dependent on the superhelical density of DNA , 2000, Molecular microbiology.

[76]  G. Church,et al.  RNA expression analysis using a 30 base pair resolution Escherichia coli genome array , 2000, Nature Biotechnology.

[77]  Z Yang,et al.  Monte Carlo implementation of supercoiled double-stranded DNA. , 1999, Biophysical journal.

[78]  E. Gilles,et al.  The organization of metabolic reaction networks. II. Signal processing in hierarchical structured functional units. , 2001, Metabolic engineering.

[79]  K. Kohn.  Molecular interaction maps as information organizers and simulation guides. , 2001, Chaos.

[80]  J G Harman,et al.  Allosteric regulation of the cAMP receptor protein. , 2001, Biochimica et biophysica acta.

[81]  S. Aiyar,et al.  Contributions of UP Elements and the Transcription Factor FIS to Expression from the Seven rrn P1 Promoters inEscherichia coli , 2001, Journal of bacteriology.

[82]  A. Travers,et al.  DNA supercoiling and transcription in Escherichia coli: The FIS connection. , 2001, Biochimie.

[83]  E D Gilles,et al.  Modeling of inducer exclusion and catabolite repression based on a PTS-dependent sucrose and non-PTS-dependent glycerol transport systems in Escherichia coli K-12 and its experimental verification. , 2001, Journal of biotechnology.

[84]  E. Gilles,et al.  The organization of metabolic reaction networks. III. Application for diauxic growth on glucose and lactose. , 2001, Metabolic engineering.

[85]  R. Hengge-aronis,et al.  Signal Transduction and Regulatory Mechanisms Involved in Control of the σS (RpoS) Subunit of RNA Polymerase , 2002, Microbiology and Molecular Biology Reviews.

[86]  U. Alon,et al.  Negative autoregulation speeds the response times of transcription networks. , 2002, Journal of molecular biology.

[87]  G. W. Hatfield,et al.  DNA topology-mediated control of global gene expression in Escherichia coli. , 2002, Annual review of genetics.

[88]  Mark Rochman,et al.  Transcriptional regulation of fis operon involves a module of multiple coupled promoters , 2002, The EMBO journal.

[89]  J. Gouzé,et al.  A class of piecewise linear differential equations arising in biological models , 2002 .

[90]  S. Shen-Orr,et al.  Network motifs in the transcriptional regulation network of Escherichia coli , 2002, Nature Genetics.

[91]  A. Danchin,et al.  The regulation of Enzyme IIA(Glc) expression controls adenylate cyclase activity in Escherichia coli. , 2002, Microbiology.

[92]  A. Khodursky,et al.  Adaptation to famine: A family of stationary-phase genes revealed by microarray analysis , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[93]  Dong-Eun Chang,et al.  Gene expression profiling of Escherichia coli growth transitions: an expanded stringent response model , 2002, Molecular microbiology.

[94]  M. Ehrenberg,et al.  Kinetic properties of rrn promoters in Escherichia coli. , 2002, Biochimie.

[95]  Hidde de Jong,et al.  Modeling and simulation of genetic regulatory systems: a literature review. , 2002, Journal of computational biology : a journal of computational molecular cell biology.

[96]  Peter D. Karp,et al.  The EcoCyc Database , 2002, Nucleic Acids Res..

[97]  Mark S. Thomas,et al.  Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. , 2002, Journal of molecular biology.

[98]  Peter Ruhdal Jensen,et al.  DNA supercoiling in Escherichia coli is under tight and subtle homeostatic control, involving gene-expression and metabolic regulation of both topoisomerase I and DNA gyrase. , 2002, European journal of biochemistry.

[99]  Katherine C. Chen,et al.  Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. , 2003, Current opinion in cell biology.

[100]  J. Collado-Vides,et al.  Identifying global regulators in transcriptional regulatory networks in bacteria. , 2003, Current opinion in microbiology.

[101]  J. Blom,et al.  Why the phosphotransferase system of Escherichia coli escapes diffusion limitation. , 2003, Biophysical journal.

[102]  R. Gourse,et al.  Regulation of the Escherichia coli rrnB P2 Promoter , 2003, Journal of bacteriology.

[103]  R. Gourse,et al.  Control of rRNA expression in Escherichia coli. , 2003, Current opinion in microbiology.

[104]  Reid C. Johnson,et al.  Fis Stabilizes the Interaction between RNA Polymerase and the Ribosomal Promoter rrnB P1, Leading to Transcriptional Activation* , 2003, Journal of Biological Chemistry.

[105]  S. Teichmann,et al.  Evolution of transcription factors and the gene regulatory network in Escherichia coli. , 2003, Nucleic acids research.

[106]  Hidde de Jong,et al.  Genetic Network Analyzer: qualitative simulation of genetic regulatory networks , 2003, Bioinform..

[107]  Mukund Thattai,et al.  Metabolic switching in the sugar phosphotransferase system of Escherichia coli. , 2003, Biophysical journal.

[108]  Thomas Egli,et al.  Molecular components of physiological stress responses in Escherichia coli. , 2004, Advances in biochemical engineering/biotechnology.

[109]  Javier Arsuaga,et al.  Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli , 2004, Genome Biology.

[110]  A. Ullmann,et al.  Multiple regulation of the activity of adenylate cyclase in Escherichia coli , 2004, Molecular and General Genetics MGG.

[111]  Milton H. Saier,et al.  Transcriptome Analysis of Crp-Dependent Catabolite Control of Gene Expression in Escherichia coli , 2004, Journal of bacteriology.

[112]  Stephen Busby,et al.  Regulation at complex bacterial promoters: how bacteria use different promoter organizations to produce different regulatory outcomes. , 2004, Current opinion in microbiology.

[113]  D. Swigon,et al.  Catabolite activator protein: DNA binding and transcription activation. , 2004, Current opinion in structural biology.

[114]  E. Gilles,et al.  Time hierarchies in the Escherichia coli carbohydrate uptake and metabolism. , 2004, Bio Systems.

[115]  R. Gourse,et al.  Unique roles of the rrn P2 rRNA promoters in Escherichia coli , 2004, Molecular microbiology.

[116]  H. D. Jong,et al.  Qualitative simulation of genetic regulatory networks using piecewise-linear models , 2004, Bulletin of mathematical biology.

[117]  Martin Fussenegger,et al.  Modeling the Quorum Sensing Regulatory Network of Human‐Pathogenic Pseudomonas aeruginosa , 2004, Biotechnology progress.

[118]  R. Gourse,et al.  rRNA transcription in Escherichia coli. , 2004, Annual review of genetics.

[119]  M. Ehrenberg,et al.  Control of rRNA Synthesis in Escherichia coli: a Systems Biology Approach , 2004, Microbiology and Molecular Biology Reviews.

[120]  Meranda D Bradley,et al.  Growth Phase-Dependent Regulation and Stringent Control of fis Are Conserved Processes in Enteric Bacteria and Involve a Single Promoter (fis P) in Escherichia coli , 2004, Journal of bacteriology.

[121]  A. Danchin,et al.  The cya locus of escherichia coli K12: Organization and gene products , 2004, Molecular and General Genetics MGG.

[122]  Julio Collado-Vides,et al.  RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12 , 2004, Nucleic Acids Res..

[123]  H. D. Jong,et al.  Qualitative simulation of the initiation of sporulation in Bacillus subtilis , 2004, Bulletin of mathematical biology.

[124]  Radu Mateescu,et al.  Validation of qualitative models of genetic regulatory networks by model checking: analysis of the nutritional stress response in Escherichia coli , 2005, ISMB.

[125]  Peter D. Karp,et al.  EcoCyc: a comprehensive database resource for Escherichia coli , 2004, Nucleic Acids Res..

[126]  G. Casari,et al.  From molecular networks to qualitative cell behavior , 2005, FEBS letters.

[127]  H. D. Jong,et al.  Piecewise-linear Models of Genetic Regulatory Networks: Equilibria and their Stability , 2006, Journal of mathematical biology.

[128]  Vipul Periwal,et al.  Qualitative Approaches to the Analysis of Genetic Regulatory Networks , 2006 .

[129]  Vipul Periwal,et al.  System Modeling in Cellular Biology: From Concepts to Nuts and Bolts , 2006 .