Team:INSA-Lyon/Project/References
From 2010.igem.org
Line 35: | Line 35: | ||
<h3>References</h3> | <h3>References</h3> | ||
+ | |||
+ | |||
+ | <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd"> | ||
+ | |||
+ | <html lang="en"> | ||
+ | |||
+ | <head> | ||
+ | |||
+ | <title>JabRef References output</title> | ||
+ | |||
+ | <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> | ||
+ | |||
+ | <style type="text/css"> | ||
+ | |||
+ | body { font-size: 12px; font-family: Arial, sans-serif; } | ||
+ | |||
+ | dt { margin-top: 1em; font-weight: bold; } | ||
+ | |||
+ | </style> | ||
+ | |||
+ | </head> | ||
+ | |||
+ | <body> | ||
+ | |||
+ | <dl> | ||
+ | |||
+ | <dt><em>article</em><a name="Adhya1989"> (Adhya1989)</a></dt> | ||
+ | <dd>Adhya, S.</dd> | ||
+ | <dd>Multipartite genetic control elements: communication by DNA loop.</dd> | ||
+ | <dd><em>Annu Rev Genet,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892., </em><b>1989</b><i>, 23</i>, 227-250</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Aguilera2008"> (Aguilera2008)</a></dt> | ||
+ | <dd>Aguilera, L.; Campos, E.; Giménez, R.; Badía, J.; Aguilar, J. & Baldoma, L.</dd> | ||
+ | <dd>Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Departament de Bioquímica i Biología Molecular, Facultat de Farmacia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain., </em><b>2008</b><i>, 190</i>, 2997-3005</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Alberti1993"> (Alberti1993)</a></dt> | ||
+ | <dd>Alberti, S.; Oehler, S.; von Wilcken-Bergmann, B. & Müller-Hill, B.</dd> | ||
+ | <dd>Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><em>Institut für Genetik, Universität zu Köln, FRG., </em><b>1993</b><i>, 12</i>, 3227-3236</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Allen2006"> (Allen2006)</a></dt> | ||
+ | <dd>Allen, T. E.; Price, N. D.; Joyce, A. R. & Palsson, B. Ø.</dd> | ||
+ | <dd>Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><em>Department of Bioengineering, University of California San Diego, La Jolla, California, USA., </em><b>2006</b><i>, 2</i>, e2</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Alon2007"> (Alon2007)</a></dt> | ||
+ | <dd>Alon, U.</dd> | ||
+ | <dd>Network motifs: theory and experimental approaches.</dd> | ||
+ | <dd><em>Nat Rev Genet,</em></dd> | ||
+ | <dd><b>2007</b><i>, 8</i>, 450-461</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Alon2006"> (Alon2006)</a></dt> | ||
+ | <dd>Alon, U.</dd> | ||
+ | <dd>An Introduction to Systems Biology</dd> | ||
+ | <dd><em>Chapman & Hall/CRC, </em><b>2006</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Altan-Bonnet2003"> (Altan-Bonnet2003)</a></dt> | ||
+ | <dd>Altan-Bonnet, G.; Libchaber, A. & Krichevsky, O.</dd> | ||
+ | <dd>Bubble dynamics in double-stranded DNA.</dd> | ||
+ | <dd><em>Phys Rev Lett,</em></dd> | ||
+ | <dd><em>Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA., </em><b>2003</b><i>, 90</i>, 138101</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Amouyal2005"> (Amouyal2005)</a></dt> | ||
+ | <dd>Amouyal, M.</dd> | ||
+ | <dd>Gene regulation at-a-distance in E. coli: new insights.</dd> | ||
+ | <dd><em>C R Biol,</em></dd> | ||
+ | <dd><b>2005</b><i>, 328</i>, 1-9</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Amouyal1989"> (Amouyal1989)</a></dt> | ||
+ | <dd>Amouyal, M.; Mortensen, L.; Buc, H. & Hammer, K.</dd> | ||
+ | <dd>Single and double loop formation when deoR repressor binds to its natural operator sites.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><em>Unité de Physicochimie des Macromolécules Biologiques, URA1149 du CNRS, Institut Pasteur, Paris, France., </em><b>1989</b><i>, 58</i>, 545-551</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ansel2008"> (Ansel2008)</a></dt> | ||
+ | <dd>Ansel, J.; Bottin, H.; Rodriguez-Beltran, C.; Damon, C.; Nagarajan, M.; Fehrmann, S.; François, J. & Yvert, G.</dd> | ||
+ | <dd>Cell-to-cell stochastic variation in gene expression is a complex genetic trait.</dd> | ||
+ | <dd><em>PLoS Genet,</em></dd> | ||
+ | <dd><em>Université de Lyon, Lyon, France., </em><b>2008</b><i>, 4</i>, e1000049</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Atkinson2003"> (Atkinson2003)</a></dt> | ||
+ | <dd>Atkinson, M. R.; Savageau, M. A.; Myers, J. T. & Ninfa, A. J.</dd> | ||
+ | <dd>Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><b>2003</b><i>, 113</i>, 597-607</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Atlung1997"> (Atlung1997)</a></dt> | ||
+ | <dd>Atlung, T. & Ingmer, H.</dd> | ||
+ | <dd>H-NS: a modulator of environmentally regulated gene expression.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Department of Chemistry and Life Sciences, Roskilde University, Denmark. atlung@virgil.ruc.dk, </em><b>1997</b><i>, 24</i>, 7-17</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bachellier1999"> (Bachellier1999)</a></dt> | ||
+ | <dd>Bachellier, S.; Clément, J. M. & Hofnung, M.</dd> | ||
+ | <dd>Short palindromic repetitive DNA elements in enterobacteria: a survey.</dd> | ||
+ | <dd><em>Res Microbiol,</em></dd> | ||
+ | <dd><em>Programmation moléculaire et toxicologie génétique, département des biotechnologies, CNRS URA 1444, Institut Pasteur, Paris, France. bachelli@pasteur.fr, </em><b>1999</b><i>, 150</i>, 627-639</dd> | ||
+ | |||
+ | <dt><em>mastersthesis</em><a name="Baglio2008"> (Baglio2008)</a></dt> | ||
+ | <dd>Baglio, J.</dd> | ||
+ | <dd>Dynamique du biopolymére ADN en suivi de particule unique :simulations et expériences dans le cadre du s mécanisme de transposition.</dd> | ||
+ | <dd><em>ENS, </em><b>2008</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bahloul2001"> (Bahloul2001)</a></dt> | ||
+ | <dd>Bahloul, A.; Boubrik, F. & Rouviere-Yaniv, J.</dd> | ||
+ | <dd>Roles of Escherichia coli histone-like protein HU in DNA replication: HU-beta suppresses the thermosensitivity of dnaA46ts.</dd> | ||
+ | <dd><em>Biochimie,</em></dd> | ||
+ | <dd><em>Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, 75005, Paris, France., </em><b>2001</b><i>, 83</i>, 219-229</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Barkai2000"> (Barkai2000)</a></dt> | ||
+ | <dd>Barkai, N. & Leibler, S.</dd> | ||
+ | <dd>Circadian clocks limited by noise.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2000</b><i>, 403</i>, 267-268</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Becskei2000"> (Becskei2000)</a></dt> | ||
+ | <dd>Becskei, A. & Serrano, L.</dd> | ||
+ | <dd>Engineering stability in gene networks by autoregulation.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2000</b><i>, 405</i>, 590-593</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Behar2007"> (Behar2007)</a></dt> | ||
+ | <dd>Behar, M.; Dohlman, H. G. & Elston, T. C.</dd> | ||
+ | <dd>Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2007</b><i>, 104</i>, 16146-16151</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Berg1981"> (Berg1981)</a></dt> | ||
+ | <dd>Berg, O. G.; Winter, R. B. & von Hippel, P. H.</dd> | ||
+ | <dd>Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.</dd> | ||
+ | <dd><em>Biochemistry,</em></dd> | ||
+ | <dd><b>1981</b><i>, 20</i>, 6929-6948</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bergstrom1998"> (Bergstrom1998)</a></dt> | ||
+ | <dd>Bergstrom, L. C.; Qin, L.; Harlocker, S. L.; Egger, L. A. & Inouye, M.</dd> | ||
+ | <dd>Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli.</dd> | ||
+ | <dd><em>Genes Cells,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA. inouye@rwja.umdnj.edu, </em><b>1998</b><i>, 3</i>, 777-788</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bhalla1999"> (Bhalla1999)</a></dt> | ||
+ | <dd>Bhalla, U. S. & Iyengar, R.</dd> | ||
+ | <dd>Emergent properties of networks of biological signaling pathways.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>1999</b><i>, 283</i>, 381-387</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Blanco1986"> (Blanco1986)</a></dt> | ||
+ | <dd>Blanco, C.; Ritzenthaler, P. & Mata-Gilsinger, M.</dd> | ||
+ | <dd>Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression.</dd> | ||
+ | <dd><em>Genetics,</em></dd> | ||
+ | <dd><b>1986</b><i>, 112</i>, 173-182</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Blot2002"> (Blot2002)</a></dt> | ||
+ | <dd>Blot, N.; Berrier, C.; Hugouvieux-Cotte-Pattat, N.; Ghazi, A. & Condemine, G.</dd> | ||
+ | <dd>The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Unité de Microbiologie et Génétique, Composante INSA, UMR-CNRS 5122, INSA, Bâtiment Louis Pasteur, 11 Avenue Jean Capelle, 69621 Villeurbanne Cedex, France., </em><b>2002</b><i>, 277</i>, 7936-7944</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bondarenko2003"> (Bondarenko2003)</a></dt> | ||
+ | <dd>Bondarenko, V. A.; Liu, Y. V.; Jiang, Y. I. & Studitsky, V. M.</dd> | ||
+ | <dd>Communication over a large distance: enhancers and insulators.</dd> | ||
+ | <dd><em>Biochem Cell Biol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA., </em><b>2003</b><i>, 81</i>, 241-251</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Brunetti2001"> (Brunetti2001)</a></dt> | ||
+ | <dd>Brunetti, R.; Prosseda, G.; Beghetto, E.; Colonna, B. & Micheli, G.</dd> | ||
+ | <dd>The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains.</dd> | ||
+ | <dd><em>Biochimie,</em></dd> | ||
+ | <dd><em>Centro Acidi Nucleici C.N.R., Università La Sapienza, P. le A. Moro 5, Rome 00185, Italy., </em><b>2001</b><i>, 83</i>, 873-882</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Buchler2003"> (Buchler2003)</a></dt> | ||
+ | <dd>Buchler, N. E.; Gerland, U. & Hwa, T.</dd> | ||
+ | <dd>On schemes of combinatorial transcription logic.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA., </em><b>2003</b><i>, 100</i>, 5136-5141</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Bundschuh2003"> (Bundschuh2003)</a></dt> | ||
+ | <dd>Bundschuh, R.; Hayot, F. & Jayaprakash, C.</dd> | ||
+ | <dd>The role of dimerization in noise reduction of simple genetic networks.</dd> | ||
+ | <dd><em>J Theor Biol,</em></dd> | ||
+ | <dd><b>2003</b><i>, 220</i>, 261-269</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Carew1972"> (Carew1972)</a></dt> | ||
+ | <dd>Carew, T. J.; Pinsker, H. M. & Kandel, E. R.</dd> | ||
+ | <dd>Long-Term Habituation of a Defensive Withdrawal Reflex in Aplysia.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>1972</b><i>, 175</i>, 451-454</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Carlo2006"> (Carlo2006)</a></dt> | ||
+ | <dd>Carlo, S. D.; Chen, B.; Hoover, T. R.; Kondrashkina, E.; Nogales, E. & Nixon, B. T.</dd> | ||
+ | <dd>The structural basis for regulated assembly and function of the transcriptional activator NtrC.</dd> | ||
+ | <dd><em>Genes Dev,</em></dd> | ||
+ | <dd><em>Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA., </em><b>2006</b><i>, 20</i>, 1485-1495</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Carpentier2005"> (Carpentier2005)</a></dt> | ||
+ | <dd>Carpentier, A.; Torrésani, B.; Grossmann, A. & Hénaut, A.</dd> | ||
+ | <dd>Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data.</dd> | ||
+ | <dd><em>BMC Genomics,</em></dd> | ||
+ | <dd><em>Laboratoire Génome et Informatique, CNRS UMR 8116, Tour Evry2, 523 Place des Terrasses, 91034 Evry Cedex, France. carpentier@genopole.cnrs.fr, </em><b>2005</b><i>, 6</i>, 84</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Castillo1998"> (Castillo1998)</a></dt> | ||
+ | <dd>Castillo, A.; Nasser, W.; Condemine, G. & Reverchon, S.</dd> | ||
+ | <dd>The PecT repressor interacts with regulatory regions of pectate lyase genes in Erwinia chrysanthemi.</dd> | ||
+ | <dd><em>Biochim Biophys Acta,</em></dd> | ||
+ | <dd><b>1998</b><i>, 1442</i>, 148-160</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Charlier1992"> (Charlier1992)</a></dt> | ||
+ | <dd>Charlier, D.; Roovers, M.; Vliet, F. V.; Boyen, A.; Cunin, R.; Nakamura, Y.; Glansdorff, N. & Piérard, A.</dd> | ||
+ | <dd>Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Research Institute of the CERIA-COOVI, Brussels, Belgium., </em><b>1992</b><i>, 226</i>, 367-386</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Chen2010"> (Chen2010)</a></dt> | ||
+ | <dd>Chen, Y.; Milstein, J. N. & Meiners, J.</dd> | ||
+ | <dd>Femtonewton entropic forces can control the formation of protein-mediated DNA loops.</dd> | ||
+ | <dd><em>Phys Rev Lett,</em></dd> | ||
+ | <dd><em>Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA., </em><b>2010</b><i>, 104</i>, 048301</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Cherry2000"> (Cherry2000)</a></dt> | ||
+ | <dd>Cherry, J. L. & Adler, F. R.</dd> | ||
+ | <dd>How to make a biological switch.</dd> | ||
+ | <dd><em>J Theor Biol,</em></dd> | ||
+ | <dd><em>Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA. cherry@biology.utah.edu, </em><b>2000</b><i>, 203</i>, 117-133</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Chiam2007"> (Chiam2007)</a></dt> | ||
+ | <dd>Chiam, K. & Rajagopal, G.</dd> | ||
+ | <dd>Oscillations in intracellular signaling cascades.</dd> | ||
+ | <dd><em>Phys Rev E Stat Nonlin Soft Matter Phys,</em></dd> | ||
+ | <dd><b>2007</b><i>, 75</i>, 061901</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ciliberti2007"> (Ciliberti2007)</a></dt> | ||
+ | <dd>Ciliberti, S.; Martin, O. C. & Wagner, A.</dd> | ||
+ | <dd>Innovation and robustness in complex regulatory gene networks.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2007</b><i>, 104</i>, 13591-13596</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ciliberto2005"> (Ciliberto2005)</a></dt> | ||
+ | <dd>Ciliberto, A.; Novak, B. & Tyson, J. J.</dd> | ||
+ | <dd>Steady states and oscillations in the p53/Mdm2 network.</dd> | ||
+ | <dd><em>Cell Cycle,</em></dd> | ||
+ | <dd><b>2005</b><i>, 4</i>, 488-493</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Condemine1992"> (Condemine1992)</a></dt> | ||
+ | <dd>Condemine, G.; Dorel, C.; Hugouvieux-Cotte-Pattat, N. & Robert-Baudouy, J.</dd> | ||
+ | <dd>Some of the out genes involved in the secretion of pectate lyases in Erwinia chrysanthemi are regulated by kdgR.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Laboratoire de Génetique Moléculaire des Microorganismes, URA CNRS 1486, INSA Bâtiment 406, Villeurbanne, France., </em><b>1992</b><i>, 6</i>, 3199-3211</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Cook2002"> (Cook2002)</a></dt> | ||
+ | <dd>Cook, P. R.</dd> | ||
+ | <dd>Predicting three-dimensional genome structure from transcriptional activity.</dd> | ||
+ | <dd><em>Nat Genet,</em></dd> | ||
+ | <dd><em>Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. peter.cook@path.ox.ac.uk, </em><b>2002</b><i>, 32</i>, 347-352</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Cox2006"> (Cox2006)</a></dt> | ||
+ | <dd>Cox, C. D.; McCollum, J. M.; Austin, D. W.; Allen, M. S.; Dar, R. D. & Simpson, M. L.</dd> | ||
+ | <dd>Frequency domain analysis of noise in simple gene circuits.</dd> | ||
+ | <dd><em>Chaos,</em></dd> | ||
+ | <dd><b>2006</b><i>, 16</i>, 026102</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Frederic2002"> (Frederic2002)</a></dt> | ||
+ | <dd>Dardel, F. & Képès, F.</dd> | ||
+ | <dd>de l'Ecole Polytechnique, L. E. <i>(ed.)</i></dd> | ||
+ | <dd>Bioinformatique Génomique et post-génomique</dd> | ||
+ | <dd><b>2002</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dekker2008"> (Dekker2008)</a></dt> | ||
+ | <dd>Dekker, J.</dd> | ||
+ | <dd>Gene regulation in the third dimension.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>2008</b><i>, 319</i>, 1793-1794</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dekker2002"> (Dekker2002)</a></dt> | ||
+ | <dd>Dekker, J.; Rippe, K.; Dekker, M. & Kleckner, N.</dd> | ||
+ | <dd>Capturing chromosome conformation.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><em>Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. jdekker@fas.harvard.edu, </em><b>2002</b><i>, 295</i>, 1306-1311</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Delord2007"> (Delord2007)</a></dt> | ||
+ | <dd>Delord, B.; Berry, H.; Guigon, E. & Genet, S.</dd> | ||
+ | <dd>A new principle for information storage in an enzymatic pathway model.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 3</i>, e124</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dolmetsch1998"> (Dolmetsch1998)</a></dt> | ||
+ | <dd>Dolmetsch, R. E.; Xu, K. & Lewis, R. S.</dd> | ||
+ | <dd>Calcium oscillations increase the efficiency and specificity of gene expression.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>1998</b><i>, 392</i>, 933-936</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dostie2007"> (Dostie2007)</a></dt> | ||
+ | <dd>Dostie, J.; Zhan, Y. & Dekker, J.</dd> | ||
+ | <dd>Chromosome conformation capture carbon copy technology.</dd> | ||
+ | <dd><em>Curr Protoc Mol Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, Chapter 21</i>, Unit 21.14</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dunlap2004"> (Dunlap2004)</a></dt> | ||
+ | <dd>Dunlap, J. C. & Loros, J. J.</dd> | ||
+ | <dd>The neurospora circadian system.</dd> | ||
+ | <dd><em>J Biol Rhythms,</em></dd> | ||
+ | <dd><b>2004</b><i>, 19</i>, 414-424</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dunn1984"> (Dunn1984)</a></dt> | ||
+ | <dd>Dunn, T. M.; Hahn, S.; Ogden, S. & Schleif, R. F.</dd> | ||
+ | <dd>An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>1984</b><i>, 81</i>, 5017-5020</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dupont1992"> (Dupont1992)</a></dt> | ||
+ | <dd>Dupont, G. & Goldbeter, A.</dd> | ||
+ | <dd>Protein phosphorylation driven by intracellular calcium oscillations: a kinetic analysis.</dd> | ||
+ | <dd><em>Biophys Chem,</em></dd> | ||
+ | <dd><b>1992</b><i>, 42</i>, 257-270</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dupont2003"> (Dupont2003)</a></dt> | ||
+ | <dd>Dupont, G.; Houart, G. & Koninck, P. D.</dd> | ||
+ | <dd>Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations: a simple model.</dd> | ||
+ | <dd><em>Cell Calcium,</em></dd> | ||
+ | <dd><b>2003</b><i>, 34</i>, 485-497</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Dworkin1998"> (Dworkin1998)</a></dt> | ||
+ | <dd>Dworkin, J.; Ninfa, A. J. & Model, P.</dd> | ||
+ | <dd>A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein.</dd> | ||
+ | <dd><em>Genes Dev,</em></dd> | ||
+ | <dd><em>Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA. dworkin@biosun.harvard.edu, </em><b>1998</b><i>, 12</i>, 894-900</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Elowitz2000"> (Elowitz2000)</a></dt> | ||
+ | <dd>Elowitz, M. & Leibler, S.</dd> | ||
+ | <dd>A synthetic oscillatory network of transcriptionnal regulators.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2000</b><i>, 403</i>, 335-338</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Espeli1997"> (Espeli1997)</a></dt> | ||
+ | <dd>Espéli, O. & Boccard, F.</dd> | ||
+ | <dd>In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Laboratoire de Chimie Bactérienne, UPR 9043, Institut de Biologie Structurale et Microbiologie du CNRS, Marseille, France., </em><b>1997</b><i>, 26</i>, 767-777</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Espeli2001"> (Espeli2001)</a></dt> | ||
+ | <dd>Espéli, O.; Moulin, L. & Boccard, F.</dd> | ||
+ | <dd>Transcription attenuation associated with bacterial repetitive extragenic BIME elements.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Centre de Génétique Moléculaire du CNRS, Centre National de la Recherche Scientifique, Gif-sur-Yvette Cedex, F-91198, France., </em><b>2001</b><i>, 314</i>, 375-386</dd> | ||
+ | |||
+ | <dt><em>phdthesis</em><a name="Francois2005"> (Francois2005)</a></dt> | ||
+ | <dd>François, P.</dd> | ||
+ | <dd>Réseaux génétiques conception, modélisation et dynamique</dd> | ||
+ | <dd><em>Ecole Normale Supérieure, </em><b>2005</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Francois2005a"> (Francois2005a)</a></dt> | ||
+ | <dd>François, P. & Hakim, V.</dd> | ||
+ | <dd>Core genetic module: the mixed feedback loop.</dd> | ||
+ | <dd><em>Phys Rev E Stat Nonlin Soft Matter Phys,</em></dd> | ||
+ | <dd><b>2005</b><i>, 72</i>, 031908</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Francois2004"> (Francois2004)</a></dt> | ||
+ | <dd>François, P. & Hakim, V.</dd> | ||
+ | <dd>Design of genetic networks with specified functions by evolution in silico.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8550, Ecole Normale Supérieure, 24, Rue Lhomond, 75231 Paris, France., </em><b>2004</b><i>, 101</i>, 580-585</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gama-Castro2008"> (Gama-Castro2008)</a></dt> | ||
+ | <dd>Gama-Castro, S.; Jiménez-Jacinto, V.; Peralta-Gil, M.; Santos-Zavaleta, A.; Peñaloza-Spinola, M. I.; Contreras-Moreira, B.; Segura-Salazar, J.; Muñiz-Rascado, L.; Martínez-Flores, I.; Salgado, H.; Bonavides-Martínez, C.; Abreu-Goodger, C.; Rodríguez-Penagos, C.; Miranda-Ríos, J.; Morett, E.; Merino, E.; Huerta, A. M.; Treviño-Quintanilla, L. & Collado-Vides, J.</dd> | ||
+ | <dd>RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>Program of Computational Genomics, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico., </em><b>2008</b><i>, 36</i>, D120-D124</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gardner2000"> (Gardner2000)</a></dt> | ||
+ | <dd>Gardner, T. S.; Cantor, C. R. & Collins, J. J.</dd> | ||
+ | <dd>Construction of a genetic toggle switch in Escherichia coli.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2000</b><i>, 403</i>, 339-342</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Geanacopoulos1997"> (Geanacopoulos1997)</a></dt> | ||
+ | <dd>Geanacopoulos, M. & Adhya, S.</dd> | ||
+ | <dd>Functional characterization of roles of GalR and GalS as regulators of the gal regulon.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA., </em><b>1997</b><i>, 179</i>, 228-234</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gene-Wei2009"> (Gene-Wei2009)</a></dt> | ||
+ | <dd>Gene-Wei Li, Otto G. Berg, J. E.</dd> | ||
+ | <dd>Effects of macromolecular crowding and DNA looping on gene regulation kinetics.</dd> | ||
+ | <dd><em>Nature Physics,</em></dd> | ||
+ | <dd><b>2009</b><i>, 5, no. 4</i>, 294-297</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Geva-Zatorsky2006"> (Geva-Zatorsky2006)</a></dt> | ||
+ | <dd>Geva-Zatorsky, N.; Rosenfeld, N.; Itzkovitz, S.; Milo, R.; Sigal, A.; Dekel, E.; Yarnitzky, T.; Liron, Y.; Polak, P.; Lahav, G. & Alon, U.</dd> | ||
+ | <dd>Oscillations and variability in the p53 system.</dd> | ||
+ | <dd><em>Mol Syst Biol,</em></dd> | ||
+ | <dd><b>2006</b><i>, 2</i>, 2006.0033</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Guillespie1977"> (Guillespie1977)</a></dt> | ||
+ | <dd>Gillespie, D.</dd> | ||
+ | <dd>Exact stochastic simulation of coupled chemical reactions</dd> | ||
+ | <dd><em>J. Phys. Chem.,</em></dd> | ||
+ | <dd><b>1977</b><i>, 81</i>, 2340-2361</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Glass1973"> (Glass1973)</a></dt> | ||
+ | <dd>Glass, L. & Kauffman, S.</dd> | ||
+ | <dd>The logical analysis of continuous, non-linear biochemical control networks.</dd> | ||
+ | <dd><em>J Theor Bio,</em></dd> | ||
+ | <dd><b>1973</b><i>, 39</i>, 103-129</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Goldbeter1996"> (Goldbeter1996)</a></dt> | ||
+ | <dd>Goldbeter, A.</dd> | ||
+ | <dd>Cambridge <i>(ed.)</i></dd> | ||
+ | <dd>Biochemical Oscillations and Cellular Rhythms: The molecular bases of periodic and chaotic behaviour.</dd> | ||
+ | <dd><em>Cambridge University Press, </em><b>1996</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Goldbeter1990"> (Goldbeter1990)</a></dt> | ||
+ | <dd>Goldbeter, A.; Dupont, G. & Berridge, M. J.</dd> | ||
+ | <dd>Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>1990</b><i>, 87</i>, 1461-1465</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Goldbeter1981"> (Goldbeter1981)</a></dt> | ||
+ | <dd>Goldbeter, A. & Koshland, D. E.</dd> | ||
+ | <dd>An amplified sensitivity arising from covalent modification in biological systems.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>1981</b><i>, 78</i>, 6840-6844</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gomez-Uribe2007"> (Gomez-Uribe2007)</a></dt> | ||
+ | <dd>Gomez-Uribe, C.; Verghese, G. C. & Mirny, L. A.</dd> | ||
+ | <dd>Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 3</i>, e246</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gonze2002"> (Gonze2002)</a></dt> | ||
+ | <dd>Gonze, D.; Halloy, J. & Goldbeter, A.</dd> | ||
+ | <dd>Robustness of circadian rhythms with respect to molecular noise.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2002</b><i>, 99</i>, 673-678</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Goodwin1965"> (Goodwin1965)</a></dt> | ||
+ | <dd>Goodwin, B. C.</dd> | ||
+ | <dd>Oscillatory behavior in enzymatic control processes.</dd> | ||
+ | <dd><em>Adv Enzyme Regul,</em></dd> | ||
+ | <dd><b>1965</b><i>, 3</i>, 425-438</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Goss2002"> (Goss2002)</a></dt> | ||
+ | <dd>Goss, T. J.; Janes, B. K. & Bender, R. A.</dd> | ||
+ | <dd>Repression of glutamate dehydrogenase formation in Klebsiella aerogenes requires two binding sites for the nitrogen assimilation control protein, NAC.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109-1048, USA., </em><b>2002</b><i>, 184</i>, 6966-6975</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gouze2002"> (Gouze2002)</a></dt> | ||
+ | <dd>Gouzé, J. & Sari, T.</dd> | ||
+ | <dd>A class of piecewise linear differential equations arising in biological models</dd> | ||
+ | <dd><em>Dyn. Syst.,</em></dd> | ||
+ | <dd><b>2002</b><i>, 17</i>, 299-316.</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Gowers2005"> (Gowers2005)</a></dt> | ||
+ | <dd>Gowers, D. M.; Wilson, G. G. & Halford, S. E.</dd> | ||
+ | <dd>Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom., </em><b>2005</b><i>, 102</i>, 15883-15888</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Grainger2005"> (Grainger2005)</a></dt> | ||
+ | <dd>Grainger, D. C.; Hurd, D.; Harrison, M.; Holdstock, J. & Busby, S. J. W.</dd> | ||
+ | <dd>Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom. d.grainger@bham.ac.uk, </em><b>2005</b><i>, 102</i>, 17693-17698</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Griffith1986"> (Griffith1986)</a></dt> | ||
+ | <dd>Griffith, J.; Hochschild, A. & Ptashne, M.</dd> | ||
+ | <dd>DNA loops induced by cooperative binding of lambda repressor.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>1986</b><i>, 322</i>, 750-752</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Guantes2006"> (Guantes2006)</a></dt> | ||
+ | <dd>Guantes, R. & Poyatos, J. F.</dd> | ||
+ | <dd>Dynamical principles of two-component genetic oscillators.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2006</b><i>, 2</i>, e30</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Guelzim2002"> (Guelzim2002)</a></dt> | ||
+ | <dd>Guelzim, N.; Bottani, S.; Bourgine, P. & Képès, F.</dd> | ||
+ | <dd>Topological and causal structure of the yeast transcriptional regulatory network.</dd> | ||
+ | <dd><em>Nat Genet,</em></dd> | ||
+ | <dd><em>ATelier de Génomique Cognitive, Centre National de la Recherche Scientifique ESA 8071, genopole(R), 523 Terrasses de l'Agora, 91000 Evry, France., </em><b>2002</b><i>, 31</i>, 60-63</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Haber1988"> (Haber1988)</a></dt> | ||
+ | <dd>Haber, R. & Adhya, S.</dd> | ||
+ | <dd>Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892., </em><b>1988</b><i>, 85</i>, 9683-9687</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hanke2003"> (Hanke2003)</a></dt> | ||
+ | <dd>Hanke, A. & Metzler, R.</dd> | ||
+ | <dd>Entropy loss in long-distance DNA looping.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><em>Institute for Theoretical Physics, University of Stuttgart, Stuttgart, Germany., </em><b>2003</b><i>, 85</i>, 167-173</dd> | ||
+ | |||
+ | <dt><em>techreport</em><a name="Hayot2006"> (Hayot2006)</a></dt> | ||
+ | <dd>Hayot, F. & Jayaprakash, C.</dd> | ||
+ | <dd>A tutorial on cellular stochasticity and Gillespie’s algorithm.</dd> | ||
+ | <dd><em>Department of Neurology, Mount Sinai School of Medicine, New York, Department of Physics, The Ohio State University, Columbus, </em><b>2006</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="He1994"> (He1994)</a></dt> | ||
+ | <dd>He, B. & Zalkin, H.</dd> | ||
+ | <dd>Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907., </em><b>1994</b><i>, 176</i>, 1009-1013</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Heinrich2002"> (Heinrich2002)</a></dt> | ||
+ | <dd>Heinrich, R.; Neel, B. G. & Rapoport, T. A.</dd> | ||
+ | <dd>Mathematical models of protein kinase signal transduction.</dd> | ||
+ | <dd><em>Mol Cell,</em></dd> | ||
+ | <dd><b>2002</b><i>, 9</i>, 957-970</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Henning2007"> (Henning2007)</a></dt> | ||
+ | <dd>Henning, J.; Koczan, D.; Glass, A.; Karopka, T.; Pahnke, J.; Rolfs, A.; Benecke, R. & Gimsa, U.</dd> | ||
+ | <dd>Deep brain stimulation in a rat model modulates TH, CaMKIIa and Homer1 gene expression.</dd> | ||
+ | <dd><em>Eur J Neurosci,</em></dd> | ||
+ | <dd><b>2007</b><i>, 25</i>, 239-250</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hersen2008"> (Hersen2008)</a></dt> | ||
+ | <dd>Hersen, P.; McClean, M. N.; Mahadevan, L. & Ramanathan, S.</dd> | ||
+ | <dd>Signal processing by the HOG MAP kinase pathway.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2008</b><i>, 105</i>, 7165-7170</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Horowitz1984"> (Horowitz1984)</a></dt> | ||
+ | <dd>Horowitz, D. S. & Wang, J. C.</dd> | ||
+ | <dd>Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>1984</b><i>, 173</i>, 75-91</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Huang1996"> (Huang1996)</a></dt> | ||
+ | <dd>Huang, C. Y. & Ferrell, J. E.</dd> | ||
+ | <dd>Ultrasensitivity in the mitogen-activated protein kinase cascade.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>1996</b><i>, 93</i>, 10078-10083</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Huang1994"> (Huang1994)</a></dt> | ||
+ | <dd>Huang, K. J.; Schieberl, J. L. & Igo, M. M.</dd> | ||
+ | <dd>A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Section of Microbiology, University of California, Davis 95616., </em><b>1994</b><i>, 176</i>, 1309-1315</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hugouvieux-Cotte-Pattat1996"> (Hugouvieux-Cotte-Pattat1996)</a></dt> | ||
+ | <dd>Hugouvieux-Cotte-Pattat, N.; Condemine, G.; Nasser, W. & Reverchon, S.</dd> | ||
+ | <dd>Regulation of pectinolysis in Erwinia chrysanthemi.</dd> | ||
+ | <dd><em>Annu Rev Microbiol,</em></dd> | ||
+ | <dd><em>Laboratoire de Génétique Moléculaire des Microorganismes, UMR-CNRS 5577, Villeurbanne, France., </em><b>1996</b><i>, 50</i>, 213-257</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hugouvieux-Cotte-Pattat1992"> (Hugouvieux-Cotte-Pattat1992)</a></dt> | ||
+ | <dd>Hugouvieux-Cotte-Pattat, N.; Dominguez, H. & Robert-Baudouy, J.</dd> | ||
+ | <dd>Environmental conditions affect transcription of the pectinase genes of Erwinia chrysanthemi 3937.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Laboratoire de Génétique Moléculaire des Microorganismes, URA-CNRS, Institut National des Sciences Appliquées batiment 406, Villeurbanne, France., </em><b>1992</b><i>, 174</i>, 7807-7818</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hugouvieux-Cotte-Pattat1994"> (Hugouvieux-Cotte-Pattat1994)</a></dt> | ||
+ | <dd>Hugouvieux-Cotte-Pattat, N.; Nasser, W. & Robert-Baudouy, J.</dd> | ||
+ | <dd>Molecular characterization of the Erwinia chrysanthemi kdgK gene involved in pectin degradation.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Laboratoire de Généteique Moléculaire des Microorganismes, CNRS URA-1486, INSA de Lyon, Villeurbanne, France., </em><b>1994</b><i>, 176</i>, 2386-2392</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Hutcheon2000"> (Hutcheon2000)</a></dt> | ||
+ | <dd>Hutcheon, B. & Yarom, Y.</dd> | ||
+ | <dd>Resonance, oscillation and the intrinsic frequency preferences of neurons.</dd> | ||
+ | <dd><em>Trends Neurosci,</em></dd> | ||
+ | <dd><b>2000</b><i>, 23</i>, 216-222</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Izhikevich2006"> (Izhikevich2006)</a></dt> | ||
+ | <dd>Izhikevich, E. M.</dd> | ||
+ | <dd>Bursting</dd> | ||
+ | <dd><em>Scholarpedia,</em></dd> | ||
+ | <dd><b>2006</b><i>, 1(3):1300</i></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="JACOB1961"> (JACOB1961)</a></dt> | ||
+ | <dd>JACOB, F. & MONOD, J.</dd> | ||
+ | <dd>Genetic regulatory mechanisms in the synthesis of proteins.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>1961</b><i>, 3</i>, 318-356</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Jeong2004"> (Jeong2004)</a></dt> | ||
+ | <dd>Jeong, K. S.; Ahn, J. & Khodursky, A. B.</dd> | ||
+ | <dd>Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.</dd> | ||
+ | <dd><em>Genome Biol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA. jeong009@umn.edu, </em><b>2004</b><i>, 5</i>, R86</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Jun2006"> (Jun2006)</a></dt> | ||
+ | <dd>Jun, S. & Mulder, B.</dd> | ||
+ | <dd>Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Stichting voor Fundamenteel Onderzoek der Materie (FOM) Institute for Atomic and Molecular Physics (AMOLF), Kruislaan 407, 1098 SJ, Amsterdam, The Netherlands. jun@amolf.nl, </em><b>2006</b><i>, 103</i>, 12388-12393</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kahramanoglou2006"> (Kahramanoglou2006)</a></dt> | ||
+ | <dd>Kahramanoglou, C.; Webster, C. L.; El-Robh, M. S.; Belyaeva, T. A. & Busby, S. J. W.</dd> | ||
+ | <dd>Mutational analysis of the Escherichia coli melR gene suggests a two-state concerted model to explain transcriptional activation and repression in the melibiose operon.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom., </em><b>2006</b><i>, 188</i>, 3199-3207</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kandel2004"> (Kandel2004)</a></dt> | ||
+ | <dd>Kandel, E. R.</dd> | ||
+ | <dd>The molecular biology of memory storage: a dialog between genes and synapses.</dd> | ||
+ | <dd><em>Biosci Rep,</em></dd> | ||
+ | <dd><b>2004</b><i>, 24</i>, 475-522</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kania1977"> (Kania1977)</a></dt> | ||
+ | <dd>Kania, J. & Müller-Hill, B.</dd> | ||
+ | <dd>Construction, isolation and implications of repressor-galactosidase - beta-galactosidase hybrid molecules.</dd> | ||
+ | <dd><em>Eur J Biochem,</em></dd> | ||
+ | <dd><b>1977</b><i>, 79</i>, 381-386</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Karimova1998"> (Karimova1998)</a></dt> | ||
+ | <dd>Karimova, G.; Pidoux, J.; Ullmann, A. & Ladant, D.</dd> | ||
+ | <dd>A bacterial two-hybrid system based on a reconstituted signal transduction pathway.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Unité de Biochimie Cellulaire (Centre National de la Recherche Scientifique, Unité de Recherche Associée 1129), Institut Pasteur, 75724 Paris Cedex 15, France., </em><b>1998</b><i>, 95</i>, 5752-5756</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kashtan2007"> (Kashtan2007)</a></dt> | ||
+ | <dd>Kashtan, N.; Noor, E. & Alon, U.</dd> | ||
+ | <dd>Varying environments can speed up evolution.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2007</b><i>, 104</i>, 13711-13716</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kepler2001"> (Kepler2001)</a></dt> | ||
+ | <dd>Kepler, T. B. & Elston, T. C.</dd> | ||
+ | <dd>Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><em>Santa Fe Institute, Santa Fe, New Mexico 87501, USA. kepler@santafe.edu, </em><b>2001</b><i>, 81</i>, 3116-3136</dd> | ||
+ | |||
+ | <dt><em>unpublished</em><a name="Kepseu"> (Kepseu)</a></dt> | ||
+ | <dd>Kepseu W.D., W. P. & J-A, S.</dd> | ||
+ | <dd>Dynamics of the transition to pathogenicity in Erwinia chrysanthemi</dd> | ||
+ | <dd></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kholodenko2000"> (Kholodenko2000)</a></dt> | ||
+ | <dd>Kholodenko, B. N.</dd> | ||
+ | <dd>Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.</dd> | ||
+ | <dd><em>Eur J Biochem,</em></dd> | ||
+ | <dd><b>2000</b><i>, 267</i>, 1583-1588</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Koninck1998"> (Koninck1998)</a></dt> | ||
+ | <dd>Koninck, P. D. & Schulman, H.</dd> | ||
+ | <dd>Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>1998</b><i>, 279</i>, 227-230</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kornacker1998"> (Kornacker1998)</a></dt> | ||
+ | <dd>Kornacker, M. G.; Remsburg, B. & Menzel, R.</dd> | ||
+ | <dd>Gene activation by the AraC protein can be inhibited by DNA looping between AraC and a LexA repressor that interacts with AraC: possible applications as a two-hybrid system.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Department of Macromolecular Structure, Bristol-Myers Squibb Pharmaceutical Research Institute, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA. KornackM@BMS.com, </em><b>1998</b><i>, 30</i>, 615-624</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kramer2005"> (Kramer2005)</a></dt> | ||
+ | <dd>Kramer, B. P. & Fussenegger, M.</dd> | ||
+ | <dd>Hysteresis in a synthetic mammalian gene network.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2005</b><i>, 102</i>, 9517-9522</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Krin2003"> (Krin2003)</a></dt> | ||
+ | <dd>Krin, E.; Laurent-Winter, C.; Bertin, P. N.; Danchin, A. & Kolb, A.</dd> | ||
+ | <dd>Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France. ekrin@pasteur.fr, </em><b>2003</b><i>, 185</i>, 3139-3146</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kussell2005"> (Kussell2005)</a></dt> | ||
+ | <dd>Kussell, E. & Leibler, S.</dd> | ||
+ | <dd>Phenotypic diversity, population growth, and information in fluctuating environments.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><em>Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021-6399, USA. kussele@rockefeller.edu, </em><b>2005</b><i>, 309</i>, 2075-2078</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kepes2005"> (Kepes2005)</a></dt> | ||
+ | <dd>Képès, F.</dd> | ||
+ | <dd>[Epigenetics as an aspect of post-genomics]</dd> | ||
+ | <dd><em>Med Sci (Paris),</em></dd> | ||
+ | <dd><em>Programme d'Epigénomique, Genopole, ATelier de Génomique Cognitive, CNRS UMR 8071/Genopole, 93, rue Henri-Rochefort, 91000 Evry, France. Francois.Kepes@genopole.cnrs.fr, </em><b>2005</b><i>, 21</i>, 371-376</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kepes2004"> (Kepes2004)</a></dt> | ||
+ | <dd>Képès, F.</dd> | ||
+ | <dd>Periodic transcriptional organization of the E.coli genome.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>2004</b><i>, 340</i>, 957-964</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Kepes2003"> (Kepes2003)</a></dt> | ||
+ | <dd>Képès, F.</dd> | ||
+ | <dd>Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>2003</b><i>, 329</i>, 859-865</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Francois2003"> (Francois2003)</a></dt> | ||
+ | <dd>Képès, F. & Vaillant, C.</dd> | ||
+ | <dd>Transcription-Based Solenoidal Model of Chromosomes</dd> | ||
+ | <dd><em>Complexus,</em></dd> | ||
+ | <dd><b>2003</b><i>, 1-No 4</i>, 171-180</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Laat2007"> (Laat2007)</a></dt> | ||
+ | <dd>de Laat, W.</dd> | ||
+ | <dd>Long-range DNA contacts: romance in the nucleus?</dd> | ||
+ | <dd><em>Curr Opin Cell Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 19</i>, 317-320</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Laat2003"> (Laat2003)</a></dt> | ||
+ | <dd>de Laat, W. & Grosveld, F.</dd> | ||
+ | <dd>Spatial organization of gene expression: the active chromatin hub.</dd> | ||
+ | <dd><em>Chromosome Res,</em></dd> | ||
+ | <dd><b>2003</b><i>, 11</i>, 447-459</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Larson1992"> (Larson1992)</a></dt> | ||
+ | <dd>Larson, T. J.; Cantwell, J. S. & van Loo-Bhattacharya, A. T.</dd> | ||
+ | <dd>Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., </em><b>1992</b><i>, 267</i>, 6114-6121</dd> | ||
+ | |||
+ | <dt><em>phdthesis</em><a name="LAUTIER2007"> (LAUTIER2007)</a></dt> | ||
+ | <dd>LAUTIER, T.</dd> | ||
+ | <dd>Rôle de la protéine associée au nucléoïde Fis dans le contrôle de la virulence chez la bactérie phytopathogène Erwinia chrysanthemi.</dd> | ||
+ | <dd><em>L’Institut National des Sciences Appliquées de Lyon, </em><b>2007</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lee1993"> (Lee1993)</a></dt> | ||
+ | <dd>Lee, H. S.; Ishihama, A. & Kustu, S.</dd> | ||
+ | <dd>The C terminus of the alpha subunit of RNA polymerase is not essential for transcriptional activation of sigma 54 holoenzyme.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Plant Pathology, University of California, Berkeley 94720., </em><b>1993</b><i>, 175</i>, 2479-2482</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lercher2006"> (Lercher2006)</a></dt> | ||
+ | <dd>Lercher, M. J. & Hurst, L. D.</dd> | ||
+ | <dd>Co-expressed yeast genes cluster over a long range but are not regularly spaced.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. m.j.lercher@bath.ac.uk, </em><b>2006</b><i>, 359</i>, 825-831</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lewis2003"> (Lewis2003)</a></dt> | ||
+ | <dd>Lewis, J.</dd> | ||
+ | <dd>Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator.</dd> | ||
+ | <dd><em>Curr Biol,</em></dd> | ||
+ | <dd><b>2003</b><i>, 13</i>, 1398-1408</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Li2008a"> (Li2008a)</a></dt> | ||
+ | <dd>Li, D. & Li, C.</dd> | ||
+ | <dd>Noise-induced dynamics in the mixed-feedback-loop network motif.</dd> | ||
+ | <dd><em>Phys Rev E Stat Nonlin Soft Matter Phys,</em></dd> | ||
+ | <dd><em>Centre for Nonlinear and Complex Systems, School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu 610054, People's Republic of China., </em><b>2008</b><i>, 77</i>, 011903</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Li2009"> (Li2009)</a></dt> | ||
+ | <dd>Li, G.; G.Berg, O. & Elf, J.</dd> | ||
+ | <dd>Effects of macromolecular crowding and DNA looping on gene regulation kinetics</dd> | ||
+ | <dd><em>Nature Physics,</em></dd> | ||
+ | <dd><b>2009</b><i>, 5 No 4</i>, 237-308</dd> | ||
+ | |||
+ | <dt><em>unpublished</em><a name="Li2008"> (Li2008)</a></dt> | ||
+ | <dd>Li, G.; G.Berg, O. & Elf, J.</dd> | ||
+ | <dd>Targe location by DNA-Binding Proteins: Effects of Roadblocks and DNA looping</dd> | ||
+ | <dd><b>2008</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Li1990"> (Li1990)</a></dt> | ||
+ | <dd>Li, Y. & Goldbeter, A.</dd> | ||
+ | <dd>Frequency encoding of pulsatile signals of cAMP based on receptor desensitization in Dictyostelium cells.</dd> | ||
+ | <dd><em>J Theor Biol,</em></dd> | ||
+ | <dd><b>1990</b><i>, 146</i>, 355-367</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Li1989"> (Li1989)</a></dt> | ||
+ | <dd>Li, Y. & Goldbeter, A.</dd> | ||
+ | <dd>Frequency specificity in intercellular communication. Influence of patterns of periodic signaling on target cell responsiveness.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><b>1989</b><i>, 55</i>, 125-145</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lia2003"> (Lia2003)</a></dt> | ||
+ | <dd>Lia, G.; Bensimon, D.; Croquette, V.; Allemand, J.; Dunlap, D.; Lewis, D. E. A.; Adhya, S. & Finzi, L.</dd> | ||
+ | <dd>Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Biology, University of Milan, 20133 Milan, Italy., </em><b>2003</b><i>, 100</i>, 11373-11377</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lipan2008"> (Lipan2008)</a></dt> | ||
+ | <dd>Lipan, O.</dd> | ||
+ | <dd>Systems biology. Enlightening Rhythms.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>2008</b><i>, 319</i>, 417-418</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lipan2005"> (Lipan2005)</a></dt> | ||
+ | <dd>Lipan, O. & Wong, W. H.</dd> | ||
+ | <dd>The use of oscillatory signals in the study of genetic networks.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2005</b><i>, 102</i>, 7063-7068</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Little1999"> (Little1999)</a></dt> | ||
+ | <dd>Little, J. W.; Shepley, D. P. & Wert, D. W.</dd> | ||
+ | <dd>Robustness of a gene regulatory circuit.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><em>Departments of Biochemistry, University of Arizona, Tucson, AZ 85721, USA. jlittle@u.arizona.edu, </em><b>1999</b><i>, 18</i>, 4299-4307</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lobell1991"> (Lobell1991)</a></dt> | ||
+ | <dd>Lobell, R. B. & Schleif, R. F.</dd> | ||
+ | <dd>AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Brandeis University, Waltham, MA 02254., </em><b>1991</b><i>, 218</i>, 45-54</dd> | ||
+ | |||
+ | <dt><em>unpublished</em><a name="Locasale"> (Locasale)</a></dt> | ||
+ | <dd>Locasale, J. W.</dd> | ||
+ | <dd>Signal duration and the time scale dependence of signal integration in biochemical pathways.</dd> | ||
+ | <dd><b>2008</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Loinger2007"> (Loinger2007)</a></dt> | ||
+ | <dd>Loinger, A.; Lipshtat, A.; Balaban, N. Q. & Biham, O.</dd> | ||
+ | <dd>Stochastic simulations of genetic switch systems.</dd> | ||
+ | <dd><em>Phys Rev E Stat Nonlin Soft Matter Phys,</em></dd> | ||
+ | <dd><b>2007</b><i>, 75</i>, 021904</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lomvardas2006"> (Lomvardas2006)</a></dt> | ||
+ | <dd>Lomvardas, S.; Barnea, G.; Pisapia, D. J.; Mendelsohn, M.; Kirkland, J. & Axel, R.</dd> | ||
+ | <dd>Interchromosomal interactions and olfactory receptor choice.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA., </em><b>2006</b><i>, 126</i>, 403-413</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lu1999"> (Lu1999)</a></dt> | ||
+ | <dd>Lu, C. D. & Abdelal, A. T.</dd> | ||
+ | <dd>Role of ArgR in activation of the ast operon, encoding enzymes of the arginine succinyltransferase pathway in Salmonella typhimurium.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Biology, Georgia State University, Atlanta, Georgia, USA., </em><b>1999</b><i>, 181</i>, 1934-1938</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Lyubchenko1997"> (Lyubchenko1997)</a></dt> | ||
+ | <dd>Lyubchenko, Y. L.; Shlyakhtenko, L. S.; Aki, T. & Adhya, S.</dd> | ||
+ | <dd>Atomic force microscopic demonstration of DNA looping by GalR and HU.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>Department of Microbiology, Arizona State University, Tempe 85287-2701, USA., </em><b>1997</b><i>, 25</i>, 873-876</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mackey1977"> (Mackey1977)</a></dt> | ||
+ | <dd>Mackey, M. C. & Glass, L.</dd> | ||
+ | <dd>Oscillation and chaos in physiological control systems.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>1977</b><i>, 197</i>, 287-289</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Majumdar1984"> (Majumdar1984)</a></dt> | ||
+ | <dd>Majumdar, A. & Adhya, S.</dd> | ||
+ | <dd>Demonstration of two operator elements in gal: in vitro repressor binding studies.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>1984</b><i>, 81</i>, 6100-6104</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mandal1990"> (Mandal1990)</a></dt> | ||
+ | <dd>Mandal, N.; Su, W.; Haber, R.; Adhya, S. & Echols, H.</dd> | ||
+ | <dd>DNA looping in cellular repression of transcription of the galactose operon.</dd> | ||
+ | <dd><em>Genes Dev,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892., </em><b>1990</b><i>, 4</i>, 410-418</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mangan2006"> (Mangan2006)</a></dt> | ||
+ | <dd>Mangan, S.; Itzkovitz, S.; Zaslaver, A. & Alon, U.</dd> | ||
+ | <dd>The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>2006</b><i>, 356</i>, 1073-1081</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Marenduzzo2007"> (Marenduzzo2007)</a></dt> | ||
+ | <dd>Marenduzzo, D.; Faro-Trindade, I. & Cook, P. R.</dd> | ||
+ | <dd>What are the molecular ties that maintain genomic loops?</dd> | ||
+ | <dd><em>Trends Genet,</em></dd> | ||
+ | <dd><em>School of Physics, University of Edinburgh, Mayfield Road, Edinburgh, UK., </em><b>2007</b><i>, 23</i>, 126-133</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Marenduzzo2006"> (Marenduzzo2006)</a></dt> | ||
+ | <dd>Marenduzzo, D.; Micheletti, C. & Cook, P. R.</dd> | ||
+ | <dd>Entropy-driven genome organization.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><em>Mathematics Institute, University of Warwick, Coventry, United Kingdom., </em><b>2006</b><i>, 90</i>, 3712-3721</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Marhl2006"> (Marhl2006)</a></dt> | ||
+ | <dd>Marhl, M.; Perc, M. & Schuster, S.</dd> | ||
+ | <dd>A minimal model for decoding of time-limited Ca2+ oscillations.</dd> | ||
+ | <dd><em>Biophys Chem,</em></dd> | ||
+ | <dd><b>2006</b><i>, 120</i>, 161-167</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Marhl2005"> (Marhl2005)</a></dt> | ||
+ | <dd>Marhl, M.; Perc, M. & Schuster, S.</dd> | ||
+ | <dd>Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations.</dd> | ||
+ | <dd><em>FEBS Lett,</em></dd> | ||
+ | <dd><b>2005</b><i>, 579</i>, 5461-5465</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Martinez-Antonio2003"> (Martinez-Antonio2003)</a></dt> | ||
+ | <dd>Martínez-Antonio, A. & Collado-Vides, J.</dd> | ||
+ | <dd>Identifying global regulators in transcriptional regulatory networks in bacteria.</dd> | ||
+ | <dd><em>Curr Opin Microbiol,</em></dd> | ||
+ | <dd><em>Program of Computational Genomics, CIFN, Universidad Nacional Autónoma de México A. P. 565-A Cuernavaca, 62100, Morelos, Mexico. agustino@cifn.unam.mx, </em><b>2003</b><i>, 6</i>, 482-489</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Matthews1992"> (Matthews1992)</a></dt> | ||
+ | <dd>Matthews, K. S.</dd> | ||
+ | <dd>DNA looping.</dd> | ||
+ | <dd><em>Microbiol Rev,</em></dd> | ||
+ | <dd><em> Cell Biology, Rice University, Houston, Texas 77251., </em><b>1992</b><i>, 56</i>, 123-136</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mazurie2005"> (Mazurie2005)</a></dt> | ||
+ | <dd>Mazurie, A.; Bottani, S. & Vergassola, M.</dd> | ||
+ | <dd>An evolutionary and functional assessment of regulatory network motifs.</dd> | ||
+ | <dd><em>Genome Biol,</em></dd> | ||
+ | <dd><b>2005</b><i>, 6</i>, R35</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="McClean2007"> (McClean2007)</a></dt> | ||
+ | <dd>McClean, M. N.; Mody, A.; Broach, J. R. & Ramanathan, S.</dd> | ||
+ | <dd>Cross-talk and decision making in MAP kinase pathways.</dd> | ||
+ | <dd><em>Nat Genet,</em></dd> | ||
+ | <dd><b>2007</b><i>, 39</i>, 409-414</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mercier2008"> (Mercier2008)</a></dt> | ||
+ | <dd>Mercier, R.; Petit, M.; Schbath, S.; Robin, S.; Karoui, M. E.; Boccard, F. & Espéli, O.</dd> | ||
+ | <dd>The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><em>Centre de Génétique Moléculaire du CNRS, 91198 Gif-sur-Yvette, France., </em><b>2008</b><i>, 135</i>, 475-485</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mettetal2008"> (Mettetal2008)</a></dt> | ||
+ | <dd>Mettetal, J. T.; Muzzey, D.; Gómez-Uribe, C. & van Oudenaarden, A.</dd> | ||
+ | <dd>The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>2008</b><i>, 319</i>, 482-484</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Moore1983"> (Moore1983)</a></dt> | ||
+ | <dd>Moore, C. L.; Klevan, L.; Wang, J. C. & Griffith, J. D.</dd> | ||
+ | <dd>Gyrase . DNA complexes visualized as looped structures by electron microscopy.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><b>1983</b><i>, 258</i>, 4612-4617</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Moran1968"> (Moran1968)</a></dt> | ||
+ | <dd>Moran, F.; Nasuno, S. & Starr, M. P.</dd> | ||
+ | <dd>Extracellular and intracellular polygllacturonic acid trans-eliminases of Erwinia carotovora.</dd> | ||
+ | <dd><em>Arch Biochem Biophys,</em></dd> | ||
+ | <dd><b>1968</b><i>, 123</i>, 298-306</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Morelli2009"> (Morelli2009)</a></dt> | ||
+ | <dd>Morelli, M. J.; Wolde, P. R. T. & Allen, R. J.</dd> | ||
+ | <dd>DNA looping provides stability and robustness to the bacteriophage lambda switch.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>FOM Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands., </em><b>2009</b><i>, 106</i>, 8101-8106</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Murray1989"> (Murray1989)</a></dt> | ||
+ | <dd>Murray, J.</dd> | ||
+ | <dd>Mathematical Biology</dd> | ||
+ | <dd><em>Springer, </em><b>1989</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mueller-Hill2006"> (Mueller-Hill2006)</a></dt> | ||
+ | <dd>Müller-Hill, B.</dd> | ||
+ | <dd>What is life? The paradigm of DNA and protein cooperation at high local concentrations.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><b>2006</b><i>, 60</i>, 253-255</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Mueller-Hill1998"> (Mueller-Hill1998)</a></dt> | ||
+ | <dd>Müller-Hill, B.</dd> | ||
+ | <dd>The function of auxiliary operators.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><b>1998</b><i>, 29</i>, 13-18</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Mueller-Hill1996"> (Mueller-Hill1996)</a></dt> | ||
+ | <dd>Müller-Hill, B.</dd> | ||
+ | <dd>de Gruyter, W. <i>(ed.)</i></dd> | ||
+ | <dd>The lac Operon: a short history of a genetic paradigm</dd> | ||
+ | <dd><b>1996</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Nakashima1991"> (Nakashima1991)</a></dt> | ||
+ | <dd>Nakashima, K.; Kanamaru, K.; Aiba, H. & Mizuno, T.</dd> | ||
+ | <dd>Signal transduction and osmoregulation in Escherichia coli. A novel type of mutation in the phosphorylation domain of the activator protein, OmpR, results in a defect in its phosphorylation-dependent DNA binding.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Laboratory of Microbiology, School of Agriculture, Nagoya University, Japan., </em><b>1991</b><i>, 266</i>, 10775-10780</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Nasser2007"> (Nasser2007)</a></dt> | ||
+ | <dd>Nasser, W. & Reverchon, S.</dd> | ||
+ | <dd>New insights into the regulatory mechanisms of the LuxR family of quorum sensing regulators.</dd> | ||
+ | <dd><em>Anal Bioanal Chem,</em></dd> | ||
+ | <dd><em>Unité de Microbiologie et Génétique, UMR CNRS-INSA-Université Lyon 1 5122, Domaine Scientifique de la Doua, 10 rue R. Dubois, bât A. Lwoff, 69622, Villeurbanne Cedex, France. William.nasser@insa-lyon.fr, </em><b>2007</b><i>, 387</i>, 381-390</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Novick1957"> (Novick1957)</a></dt> | ||
+ | <dd>Novick, A. & Weiner, M.</dd> | ||
+ | <dd>ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>DEPARTMENT OF MICROBIOLOGY AND COMMITTEE ON BIOPHYSICS, UNIVERSITY OF CHICAGO., </em><b>1957</b><i>, 43</i>, 553-566</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Novak2008"> (Novak2008)</a></dt> | ||
+ | <dd>Novák, B. & Tyson, J. J.</dd> | ||
+ | <dd>Design principles of biochemical oscillators.</dd> | ||
+ | <dd><em>Nat Rev Mol Cell Biol,</em></dd> | ||
+ | <dd><b>2008</b><i>, 9</i>, 981-991</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Oehler1994"> (Oehler1994)</a></dt> | ||
+ | <dd>Oehler, S.; Amouyal, M.; Kolkhof, P.; von Wilcken-Bergmann, B. & Müller-Hill, B.</dd> | ||
+ | <dd>Quality and position of the three lac operators of E. coli define efficiency of repression.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><b>1994</b><i>, 13</i>, 3348-3355</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Oehler1990"> (Oehler1990)</a></dt> | ||
+ | <dd>Oehler, S.; Eismann, E. R.; Krämer, H. & Müller-Hill, B.</dd> | ||
+ | <dd>The three operators of the lac operon cooperate in repression.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><b>1990</b><i>, 9</i>, 973-979</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ohlsson2007"> (Ohlsson2007)</a></dt> | ||
+ | <dd>Ohlsson, R. & Göndör, A.</dd> | ||
+ | <dd>The 4C technique: the 'Rosetta stone' for genome biology in 3D?</dd> | ||
+ | <dd><em>Curr Opin Cell Biol,</em></dd> | ||
+ | <dd><em> Genetics, Norbyvägen 18A, Evolution Biology Centre, Uppsala University, S-752 36 Uppsala, Sweden. rolf.ohlsson@ebc.uu.se, </em><b>2007</b><i>, 19</i>, 321-325</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ozbudak2004"> (Ozbudak2004)</a></dt> | ||
+ | <dd>Ozbudak, E. M.; Thattai, M.; Lim, H. N.; Shraiman, B. I. & Oudenaarden, A. V.</dd> | ||
+ | <dd>Multistability in the lactose utilization network of Escherichia coli.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2004</b><i>, 427</i>, 737-740</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Pal2008"> (Pal2008)</a></dt> | ||
+ | <dd>Pal, R.; Basu, D. & Banerjee, M.</dd> | ||
+ | <dd>Modelling of phytoplankton allelopathy with Monod-Haldane-type functional response-A mathematical study.</dd> | ||
+ | <dd><em>Biosystems,</em></dd> | ||
+ | <dd><b>2008</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Peekhaus1998"> (Peekhaus1998)</a></dt> | ||
+ | <dd>Peekhaus, N. & Conway, T.</dd> | ||
+ | <dd>Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Microbiology, The Ohio State University, Columbus 43210-1292, USA. peekhaus.1@osu.edu, </em><b>1998</b><i>, 180</i>, 1777-1785</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Perlmutter2006"> (Perlmutter2006)</a></dt> | ||
+ | <dd>Perlmutter, J. S. & Mink, J. W.</dd> | ||
+ | <dd>Deep brain stimulation.</dd> | ||
+ | <dd><em>Annu Rev Neurosci,</em></dd> | ||
+ | <dd><b>2006</b><i>, 29</i>, 229-257</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Phillips1989"> (Phillips1989)</a></dt> | ||
+ | <dd>Phillips, S. E.; Manfield, I.; Parsons, I.; Davidson, B. E.; Rafferty, J. B.; Somers, W. S.; Margarita, D.; Cohen, G. N.; Saint-Girons, I. & Stockley, P. G.</dd> | ||
+ | <dd>Cooperative tandem binding of met repressor of Escherichia coli.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><em>Astbury Department of Biophysics, University of Leeds, UK., </em><b>1989</b><i>, 341</i>, 711-715</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Plumbridge1995"> (Plumbridge1995)</a></dt> | ||
+ | <dd>Plumbridge, J.</dd> | ||
+ | <dd>Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-chimique (URA1139), Paris, France., </em><b>1995</b><i>, 14</i>, 3958-3965</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Plumbridge1998"> (Plumbridge1998)</a></dt> | ||
+ | <dd>Plumbridge, J. & Kolb, A.</dd> | ||
+ | <dd>DNA bending and expression of the divergent nagE-B operons.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-chimique (UPR9073), 13 rue P. et M. Curie, 75005 Paris, France. plumbridge@ibpc.fr, </em><b>1998</b><i>, 26</i>, 1254-1260</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Plumbridge1993"> (Plumbridge1993)</a></dt> | ||
+ | <dd>Plumbridge, J. & Kolb, A.</dd> | ||
+ | <dd>DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-chimique (URA1139), Paris, France., </em><b>1993</b><i>, 10</i>, 973-981</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Plumbridge1991"> (Plumbridge1991)</a></dt> | ||
+ | <dd>Plumbridge, J. & Kolb, A.</dd> | ||
+ | <dd>CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-chimique, URA1139, Paris, France., </em><b>1991</b><i>, 217</i>, 661-679</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Plumbridge2004"> (Plumbridge2004)</a></dt> | ||
+ | <dd>Plumbridge, J. & Pellegrini, O.</dd> | ||
+ | <dd>Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-Chimique (CNRS UPR9073), 13, rue Pierre et Marie Curie, 75005 Paris, France. Jackie.Plumbridge@ibpc.fr, </em><b>2004</b><i>, 52</i>, 437-449</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Porco1997"> (Porco1997)</a></dt> | ||
+ | <dd>Porco, A.; Peekhaus, N.; Bausch, C.; Tong, S.; Isturiz, T. & Conway, T.</dd> | ||
+ | <dd>Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>School of Biological Sciences, University of Nebraska-Lincoln, 68588-0118, USA., </em><b>1997</b><i>, 179</i>, 1584-1590</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Pouget2006"> (Pouget2006)</a></dt> | ||
+ | <dd>Pouget, N.; Turlan, C.; Destainville, N.; Salomé, L. & Chandler, M.</dd> | ||
+ | <dd>IS911 transpososome assembly as analysed by tethered particle motion.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>Laboratoire de Microbiologie et Génétique Moléculaire, UMR CNRS 5100, 118 route de Narbonne, 31062 Toulouse cedex, France., </em><b>2006</b><i>, 34</i>, 4313-4323</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Pruess2006"> (Pruess2006)</a></dt> | ||
+ | <dd>Prüss, B. M.; Besemann, C.; Denton, A. & Wolfe, A. J.</dd> | ||
+ | <dd>A complex transcription network controls the early stages of biofilm development by Escherichia coli.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Veterinary and Microbiological Sciences, North Dakota State University, 1523 Centennial Blvd., Fargo, ND 58105, USA. Birgit.Pruess@ndsu.edu, </em><b>2006</b><i>, 188</i>, 3731-3739</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Qaidi2008"> (Qaidi2008)</a></dt> | ||
+ | <dd>Qaidi, S. E. & Plumbridge, J.</dd> | ||
+ | <dd>Switching control of expression of ptsG from the Mlc regulon to the NagC regulon.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Institut de Biologie Physico-Chimique, UPR9073-CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France., </em><b>2008</b><i>, 190</i>, 4677-4686</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Qiao2007"> (Qiao2007)</a></dt> | ||
+ | <dd>Qiao, L.; Nachbar, R. B.; Kevrekidis, I. G. & Shvartsman, S. Y.</dd> | ||
+ | <dd>Bistability and oscillations in the huang-ferrell model of MAPK signaling.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 3</i>, e184</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rampersaud1994"> (Rampersaud1994)</a></dt> | ||
+ | <dd>Rampersaud, A.; Harlocker, S. L. & Inouye, M.</dd> | ||
+ | <dd>The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Department of Pathology, Ohio State University, Columbus 43210., </em><b>1994</b><i>, 269</i>, 12559-12566</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rao2002"> (Rao2002)</a></dt> | ||
+ | <dd>Rao, C. V.; Wolf, D. M. & Arkin, A. P.</dd> | ||
+ | <dd>Control, exploitation and tolerance of intracellular noise.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><em>Department of Bioengineering, University of California, Berkeley, California 94720, USA. c_rao@lbl.gov, </em><b>2002</b><i>, 420</i>, 231-237</dd> | ||
+ | |||
+ | <dt><em>phdthesis</em><a name="Ray1999"> (Ray1999)</a></dt> | ||
+ | <dd>Ray, W. K.</dd> | ||
+ | <dd>Characterization of AgaR and YihW, Members of the DeoR Family of Transcriptional Regulators, and GlpE, a Rhodanese Belonging to the GlpR Regulon, Also a Member of the DeoR Family</dd> | ||
+ | <dd><em>Faculty of the Virginia Polytechnic Institute and State, </em><b>1999</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Reitzer1986"> (Reitzer1986)</a></dt> | ||
+ | <dd>Reitzer, L. J. & Magasanik, B.</dd> | ||
+ | <dd>Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><b>1986</b><i>, 45</i>, 785-792</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Resibois1984"> (Resibois1984)</a></dt> | ||
+ | <dd>Resibois, A.; Colet, M.; Faelen, M.; Schoonejans, E. & Toussaint, A.</dd> | ||
+ | <dd>phiEC2, a new generalized transducing phage of Erwinia chrysanthemi.</dd> | ||
+ | <dd><em>Virology,</em></dd> | ||
+ | <dd><em>Laboratoire d'Histolvie, Faculté de Médecine, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium., </em><b>1984</b><i>, 137</i>, 102-112</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Reverchon1991"> (Reverchon1991)</a></dt> | ||
+ | <dd>Reverchon, S.; Nasser, W. & Robert-Baudouy, J.</dd> | ||
+ | <dd>Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Laboratoire de Génétique Moléculaire des Microorganismes, Institut National des Sciences Appliquées, Villeurbanne, France., </em><b>1991</b><i>, 5</i>, 2203-2216</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rice1996"> (Rice1996)</a></dt> | ||
+ | <dd>Rice, P. A.; Yang, S.; Mizuuchi, K. & Nash, H. A.</dd> | ||
+ | <dd>Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA., </em><b>1996</b><i>, 87</i>, 1295-1306</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rodionov2004"> (Rodionov2004)</a></dt> | ||
+ | <dd>Rodionov, D. A.; Gelfand, M. S. & Hugouvieux-Cotte-Pattat, N.</dd> | ||
+ | <dd>Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.</dd> | ||
+ | <dd><em>Microbiology,</em></dd> | ||
+ | <dd><em>State Scientific Centre GosNIIGenetika, Moscow, 117545, Russia. rodionov@genetika.ru, </em><b>2004</b><i>, 150</i>, 3571-3590</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Roeder1985"> (Roeder1985)</a></dt> | ||
+ | <dd>Roeder, D. L. & Collmer, A.</dd> | ||
+ | <dd>Marker-exchange mutagenesis of a pectate lyase isozyme gene in Erwinia chrysanthemi.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><b>1985</b><i>, 164</i>, 51-56</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rosario2005"> (Rosario2005)</a></dt> | ||
+ | <dd>Rosario, C. J. & Bender, R. A.</dd> | ||
+ | <dd>Importance of tetramer formation by the nitrogen assimilation control protein for strong repression of glutamate dehydrogenase formation in Klebsiella pneumoniae.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Molecular Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048, USA., </em><b>2005</b><i>, 187</i>, 8291-8299</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rosenfeld2002"> (Rosenfeld2002)</a></dt> | ||
+ | <dd>Rosenfeld, N.; Elowitz, M. B. & Alon, U.</dd> | ||
+ | <dd>Negative autoregulation speeds the response times of transcription networks.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel., </em><b>2002</b><i>, 323</i>, 785-793</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rosenfeld2006"> (Rosenfeld2006)</a></dt> | ||
+ | <dd>Rosenfeld, N.; Perkins, T. J.; Alon, U.; Elowitz, M. B. & Swain, P. S.</dd> | ||
+ | <dd>A fluctuation method to quantify in vivo fluorescence data.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><b>2006</b><i>, 91</i>, 759-766</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rosenfeld2005"> (Rosenfeld2005)</a></dt> | ||
+ | <dd>Rosenfeld, N.; Young, J. W.; Alon, U.; Swain, P. S. & Elowitz, M. B.</dd> | ||
+ | <dd>Gene regulation at the single-cell level.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>2005</b><i>, 307</i>, 1962-1965</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Rouanet2004"> (Rouanet2004)</a></dt> | ||
+ | <dd>Rouanet, C.; Reverchon, S.; Rodionov, D. A. & Nasser, W.</dd> | ||
+ | <dd>Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><b>2004</b><i>, 279</i>, 30158-30167</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Saiz2008"> (Saiz2008)</a></dt> | ||
+ | <dd>Saiz, L. & Vilar, J. M. G.</dd> | ||
+ | <dd>Ab initio thermodynamic modeling of distal multisite transcription regulation.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><b>2008</b><i>, 36</i>, 726-731</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Saiz2006"> (Saiz2006)</a></dt> | ||
+ | <dd>Saiz, L. & Vilar, J. M. G.</dd> | ||
+ | <dd>DNA looping: the consequences and its control.</dd> | ||
+ | <dd><em>Curr Opin Struct Biol,</em></dd> | ||
+ | <dd><b>2006</b><i>, 16</i>, 344-350</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Samarasinghe2008"> (Samarasinghe2008)</a></dt> | ||
+ | <dd>Samarasinghe, S.; El-Robh, M. S.; Grainger, D. C.; Zhang, W.; Soultanas, P. & Busby, S. J. W.</dd> | ||
+ | <dd>Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK., </em><b>2008</b><i>, 36</i>, 2667-2676</dd> | ||
+ | |||
+ | <dt><em>book</em><a name="Sambrook1989"> (Sambrook1989)</a></dt> | ||
+ | <dd>Sambrook J, Fritsch E. F, M. T.</dd> | ||
+ | <dd>Harbor, C. S. <i>(ed.)</i></dd> | ||
+ | <dd>Molecular cloning: a laboratory manual</dd> | ||
+ | <dd><em>Cold Spring Harbor Laboratory, </em><b>1989</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Samson2005"> (Samson2005)</a></dt> | ||
+ | <dd>Samson, R.; Legendre, J. B.; Christen, R.; Saux, M. F.; Achouak, W. & Gardan, L.</dd> | ||
+ | <dd>Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.</dd> | ||
+ | <dd><em>Int J Syst Evol Microbiol,</em></dd> | ||
+ | <dd><em>UMR de Pathologie Végétale INRA INH Université, BP 57, 42 rue G. Morel, 49071 Beaucouzé, France. samson@angers.inra.fr, </em><b>2005</b><i>, 55</i>, 1415-1427</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Savageau1974"> (Savageau1974)</a></dt> | ||
+ | <dd>Savageau, M. A.</dd> | ||
+ | <dd>Comparison of classical and autogenous systems of regulation in inducible operons.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>1974</b><i>, 252</i>, 546-549</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Schafer1991"> (Schafer1991)</a></dt> | ||
+ | <dd>Schafer, D. A.; Gelles, J.; Sheetz, M. P. & Landick, R.</dd> | ||
+ | <dd>Transcription by single molecules of RNA polymerase observed by light microscopy.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><em>Department of Cell Biology, Washington University, St. Louis, Missouri 63130., </em><b>1991</b><i>, 352</i>, 444-448</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Schleif1992"> (Schleif1992)</a></dt> | ||
+ | <dd>Schleif, R.</dd> | ||
+ | <dd>DNA LOOPING</dd> | ||
+ | <dd><em>Annu. Rev. Biochem.,</em></dd> | ||
+ | <dd><b>1992</b><i>, 61</i>, 199-223</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Schleif1992a"> (Schleif1992a)</a></dt> | ||
+ | <dd>Schleif, R.</dd> | ||
+ | <dd>DNA looping.</dd> | ||
+ | <dd><em>Annu Rev Biochem,</em></dd> | ||
+ | <dd><em>Biology Department, Johns Hopkins University, Baltimore, Maryland 21218., </em><b>1992</b><i>, 61</i>, 199-223</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Schultz1991"> (Schultz1991)</a></dt> | ||
+ | <dd>Schultz, S. C.; Shields, G. C. & Steitz, T. A.</dd> | ||
+ | <dd>Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><em>Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511., </em><b>1991</b><i>, 253</i>, 1001-1007</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Segel1986"> (Segel1986)</a></dt> | ||
+ | <dd>Segel, L. A.; Goldbeter, A.; Devreotes, P. N. & Knox, B. E.</dd> | ||
+ | <dd>A mechanism for exact sensory adaptation based on receptor modification.</dd> | ||
+ | <dd><em>J Theor Biol,</em></dd> | ||
+ | <dd><b>1986</b><i>, 120</i>, 151-179</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Semsey2002"> (Semsey2002)</a></dt> | ||
+ | <dd>Semsey, S.; Geanacopoulos, M.; Lewis, D. E. A. & Adhya, S.</dd> | ||
+ | <dd>Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><em>Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute/ National Institutes of Health, Bethesda, MD 20892-4264, USA., </em><b>2002</b><i>, 21</i>, 4349-4356</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Sepulchre2007"> (Sepulchre2007)</a></dt> | ||
+ | <dd>Sepulchre, J.; Reverchon, S. & Nasser, W.</dd> | ||
+ | <dd>Modeling the onset of virulence in a pectinolytic bacterium.</dd> | ||
+ | <dd><em>J Theor Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 244</i>, 239-257</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Sequencing2005"> (Sequencing2005)</a></dt> | ||
+ | <dd>Sequencing, C. & Consortium, A.</dd> | ||
+ | <dd>Initial sequence of the chimpanzee genome and comparison with the human genome.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2005</b><i>, 437</i>, 69-87</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Shadel1992"> (Shadel1992)</a></dt> | ||
+ | <dd>Shadel, G. S. & Baldwin, T. O.</dd> | ||
+ | <dd>Identification of a distantly located regulatory element in the luxD gene required for negative autoregulation of the Vibrio fischeri luxR gene.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>M University, College Station 77843., </em><b>1992</b><i>, 267</i>, 7690-7695</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Shankaran2007a"> (Shankaran2007a)</a></dt> | ||
+ | <dd>Shankaran, H.; Resat, H. & Wiley, H. S.</dd> | ||
+ | <dd>Cell surface receptors for signal transduction and ligand transport: a design principles study.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 3</i>, e101</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Shankaran2007"> (Shankaran2007)</a></dt> | ||
+ | <dd>Shankaran, H.; Wiley, H. S. & Resat, H.</dd> | ||
+ | <dd>Receptor downregulation and desensitization enhance the information processing ability of signalling receptors.</dd> | ||
+ | <dd><em>BMC Syst Biol,</em></dd> | ||
+ | <dd><b>2007</b><i>, 1</i>, 48</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Shin1995"> (Shin1995)</a></dt> | ||
+ | <dd>Shin, S. & Park, C.</dd> | ||
+ | <dd>Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yusong-Ku, Taejon., </em><b>1995</b><i>, 177</i>, 4696-4702</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Smolen2007"> (Smolen2007)</a></dt> | ||
+ | <dd>Smolen, P.</dd> | ||
+ | <dd>A model of late long-term potentiation simulates aspects of memory maintenance.</dd> | ||
+ | <dd><em>PLoS ONE,</em></dd> | ||
+ | <dd><b>2007</b><i>, 2</i>, e445</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Smolen2006"> (Smolen2006)</a></dt> | ||
+ | <dd>Smolen, P.; Baxter, D. A. & Byrne, J. H.</dd> | ||
+ | <dd>A model of the roles of essential kinases in the induction and expression of late long-term potentiation.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><b>2006</b><i>, 90</i>, 2760-2775</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Smolen1998"> (Smolen1998)</a></dt> | ||
+ | <dd>Smolen, P.; Baxter, D. A. & Byrne, J. H.</dd> | ||
+ | <dd>Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems.</dd> | ||
+ | <dd><em>Am J Physiol,</em></dd> | ||
+ | <dd><b>1998</b><i>, 274</i>, C531-C542</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Sohanpal2004"> (Sohanpal2004)</a></dt> | ||
+ | <dd>Sohanpal, B. K.; El-Labany, S.; Lahooti, M.; Plumbridge, J. A. & Blomfield, I. C.</dd> | ||
+ | <dd>Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom., </em><b>2004</b><i>, 101</i>, 16322-16327</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Song2007"> (Song2007)</a></dt> | ||
+ | <dd>Song, H.; Smolen, P.; Av-Ron, E.; Baxter, D. A. & Byrne, J. H.</dd> | ||
+ | <dd>Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><b>2007</b><i>, 92</i>, 3407-3424</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Soule2003"> (Soule2003)</a></dt> | ||
+ | <dd>Soulé, C.</dd> | ||
+ | <dd>Graphic requirements for multistationarity</dd> | ||
+ | <dd><em>Complexus,</em></dd> | ||
+ | <dd><b>2003</b><i>, 1</i>, 123-133</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Stauffer1998"> (Stauffer1998)</a></dt> | ||
+ | <dd>Stauffer, L. T. & Stauffer, G. V.</dd> | ||
+ | <dd>Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli.</dd> | ||
+ | <dd><em>Microbiology,</em></dd> | ||
+ | <dd><em>Department of Microbiology, University of Iowa, Iowa City 52242, USA., </em><b>1998</b><i>, 144 ( Pt 5)</i>, 1417-1422</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Stauffer1998a"> (Stauffer1998a)</a></dt> | ||
+ | <dd>Stauffer, L. T. & Stauffer, G. V.</dd> | ||
+ | <dd>Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli.</dd> | ||
+ | <dd><em>Microbiology,</em></dd> | ||
+ | <dd><em>Department of Microbiology, University of Iowa, Iowa City 52242, USA. george-stauffer@uiowa.edu, </em><b>1998</b><i>, 144 ( Pt 10)</i>, 2865-2872</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Su1990"> (Su1990)</a></dt> | ||
+ | <dd>Su, W.; Porter, S.; Kustu, S. & Echols, H.</dd> | ||
+ | <dd>DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Molecular and Cell Biology, University of California, Berkeley 94720., </em><b>1990</b><i>, 87</i>, 5504-5508</dd> | ||
+ | |||
+ | <dt><em>unpublished</em><a name="Sumedha"> (Sumedha)</a></dt> | ||
+ | <dd>Sumedha & Weigt, M.</dd> | ||
+ | <dd>Agglomeration of DNA-looping proteins</dd> | ||
+ | <dd><b>2008</b></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Sumedha2008"> (Sumedha2008)</a></dt> | ||
+ | <dd>Sumedha & Weigt, M.</dd> | ||
+ | <dd>A thermodynamic model for the agglomeration of DNA-looping proteins</dd> | ||
+ | <dd><em>Journal of Statistical Mechanics: Theory and Experiment,</em></dd> | ||
+ | <dd><b>2008</b><i>, 11</i>, 11005</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Swinger2004"> (Swinger2004)</a></dt> | ||
+ | <dd>Swinger, K. K. & Rice, P. A.</dd> | ||
+ | <dd>IHF and HU: flexible architects of bent DNA.</dd> | ||
+ | <dd><em>Curr Opin Struct Biol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA., </em><b>2004</b><i>, 14</i>, 28-35</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Thomas1980"> (Thomas1980)</a></dt> | ||
+ | <dd>Thomas, R.</dd> | ||
+ | <dd>[The biological role of positive and negative feedback loops]</dd> | ||
+ | <dd><em>Bull Mem Acad R Med Belg,</em></dd> | ||
+ | <dd><b>1980</b><i>, 135</i>, 664-673</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Towles2009"> (Towles2009)</a></dt> | ||
+ | <dd>Towles, K. B.; Beausang, J. F.; Garcia, H. G.; Phillips, R. & Nelson, P. C.</dd> | ||
+ | <dd>First-principles calculation of DNA looping in tethered particle experiments.</dd> | ||
+ | <dd><em>Phys Biol,</em></dd> | ||
+ | <dd><em>Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA., </em><b>2009</b><i>, 6</i>, 25001</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Travers2001"> (Travers2001)</a></dt> | ||
+ | <dd>Travers, A.; Schneider, R. & Muskhelishvili, G.</dd> | ||
+ | <dd>DNA supercoiling and transcription in Escherichia coli: The FIS connection.</dd> | ||
+ | <dd><em>Biochimie,</em></dd> | ||
+ | <dd><em>MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. aat@mrc-lmb.cam.ac.uk, </em><b>2001</b><i>, 83</i>, 213-217</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Tuskan2006"> (Tuskan2006)</a></dt> | ||
+ | <dd>Tuskan, G. A.; Difazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev, I.; Hellsten, U.; Putnam, N.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R. R.; Bhalerao, R. P.; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Carlson, J.; Chalot, M.; Chapman, J.; Chen, G.; Cooper, D.; Coutinho, P. M.; Couturier, J.; Covert, S.; Cronk, Q.; Cunningham, R.; Davis, J.; Degroeve, S.; Déjardin, A.; Depamphilis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehlting, J.; Ellis, B.; Gendler, K.; Goodstein, D.; Gribskov, M.; Grimwood, J.; Groover, A.; Gunter, L.; Hamberger, B.; Heinze, B.; Helariutta, Y.; Henrissat, B.; Holligan, D.; Holt, R.; Huang, W.; Islam-Faridi, N.; Jones, S.; Jones-Rhoades, M.; Jorgensen, R.; Joshi, C.; Kangasjärvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leplé, J.; Locascio, P.; Lou, Y.; Lucas, S.; Martin, F.; Montanini, B.; Napoli, C.; Nelson, D. R.; Nelson, C.; Nieminen, K.; Nilsson, O.; Pereda, V.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouzé, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui, A.; Sterky, F.; Terry, A.; Tsai, C.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra, M.; Sandberg, G.; de Peer, Y. V. & Rokhsar, D.</dd> | ||
+ | <dd>The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><em>Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. gtk@ornl.gov, </em><b>2006</b><i>, 313</i>, 1596-1604</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Tyson2002"> (Tyson2002)</a></dt> | ||
+ | <dd>Tyson, J. J.; Csikasz-Nagy, A. & Novak, B.</dd> | ||
+ | <dd>The dynamics of cell cycle regulation.</dd> | ||
+ | <dd><em>Bioessays,</em></dd> | ||
+ | <dd><b>2002</b><i>, 24</i>, 1095-1109</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Valens2004"> (Valens2004)</a></dt> | ||
+ | <dd>Valens, M.; Penaud, S.; Rossignol, M.; Cornet, F. & Boccard, F.</dd> | ||
+ | <dd>Macrodomain organization of the Escherichia coli chromosome.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><em>Centre de Génétique Moléculaire du CNRS, Avenue de la Terrasse, Gif-sur-Yvette, France., </em><b>2004</b><i>, 23</i>, 4330-4341</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Valentin-Hansen1986"> (Valentin-Hansen1986)</a></dt> | ||
+ | <dd>Valentin-Hansen, P.; Albrechtsen, B. & Larsen, J. E. L.</dd> | ||
+ | <dd>DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor.</dd> | ||
+ | <dd><em>EMBO J,</em></dd> | ||
+ | <dd><b>1986</b><i>, 5</i>, 2015-2021</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Ventura2008"> (Ventura2008)</a></dt> | ||
+ | <dd>Ventura, A. C.; Sepulchre, J. & Merajver, S. D.</dd> | ||
+ | <dd>A hidden feedback in signaling cascades is revealed.</dd> | ||
+ | <dd><em>PLoS Comput Biol,</em></dd> | ||
+ | <dd><b>2008</b><i>, 4</i>, e1000041</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Vilar2002"> (Vilar2002)</a></dt> | ||
+ | <dd>Vilar, J. M. G.; Kueh, H. Y.; Barkai, N. & Leibler, S.</dd> | ||
+ | <dd>Mechanisms of noise-resistance in genetic oscillators.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><b>2002</b><i>, 99</i>, 5988-5992</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Vilar2003"> (Vilar2003)</a></dt> | ||
+ | <dd>Vilar, J. M. G. & Leibler, S.</dd> | ||
+ | <dd>DNA looping and physical constraints on transcription regulation.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><b>2003</b><i>, 331</i>, 981-989</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Vilar2005"> (Vilar2005)</a></dt> | ||
+ | <dd>Vilar, J. M. G. & Saiz, L.</dd> | ||
+ | <dd>DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.</dd> | ||
+ | <dd><em>Curr Opin Genet Dev,</em></dd> | ||
+ | <dd><em>Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA. vilar@cbio.mskcc.org, </em><b>2005</b><i>, 15</i>, 136-144</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Wang1996"> (Wang1996)</a></dt> | ||
+ | <dd>Wang, J. H. & Kelly, P. T.</dd> | ||
+ | <dd>The balance between postsynaptic Ca(2+)-dependent protein kinase and phosphatase activities controlling synaptic strength.</dd> | ||
+ | <dd><em>Learn Mem,</em></dd> | ||
+ | <dd><b>1996</b><i>, 3</i>, 170-181</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Wang2007"> (Wang2007)</a></dt> | ||
+ | <dd>Wang, Z.; Hou, Z.; Xin, H. & Zhang, Z.</dd> | ||
+ | <dd>Engineered internal noise stochastic resonator in gene network: a model study.</dd> | ||
+ | <dd><em>Biophys Chem,</em></dd> | ||
+ | <dd><em>Teda Bio-X Research Center, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 29, The 13th Avenue of Teda, Tianjin, PR China, 300457., </em><b>2007</b><i>, 125</i>, 281-285</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Wedel1990"> (Wedel1990)</a></dt> | ||
+ | <dd>Wedel, A.; Weiss, D. S.; Popham, D.; Dröge, P. & Kustu, S.</dd> | ||
+ | <dd>A bacterial enhancer functions to tether a transcriptional activator near a promoter.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><em>Department of Plant Pathology, University of California, Berkeley 94720., </em><b>1990</b><i>, 248</i>, 486-490</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Weissenborn1992"> (Weissenborn1992)</a></dt> | ||
+ | <dd>Weissenborn, D. L.; Wittekindt, N. & Larson, T. J.</dd> | ||
+ | <dd>Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., </em><b>1992</b><i>, 267</i>, 6122-6131</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Weissenborn1992a"> (Weissenborn1992a)</a></dt> | ||
+ | <dd>Weissenborn, D. L.; Wittekindt, N. & Larson, T. J.</dd> | ||
+ | <dd>Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12.</dd> | ||
+ | <dd><em>J Biol Chem,</em></dd> | ||
+ | <dd><em>Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., </em><b>1992</b><i>, 267</i>, 6122-6131</dd> | ||
+ | |||
+ | <dt><em>misc</em><a name="Wikipedia"> (Wikipedia)</a></dt> | ||
+ | <dd>Wikipedia</dd> | ||
+ | <dd>Microscope à force atomique</dd> | ||
+ | <dd></dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Winder1998"> (Winder1998)</a></dt> | ||
+ | <dd>Winder, D. G.; Mansuy, I. M.; Osman, M.; Moallem, T. M. & Kandel, E. R.</dd> | ||
+ | <dd>Genetic and pharmacological evidence for a novel, intermediate phase of long-term potentiation suppressed by calcineurin.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><b>1998</b><i>, 92</i>, 25-37</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Wolf2003"> (Wolf2003)</a></dt> | ||
+ | <dd>Wolf, D. M. & Arkin, A. P.</dd> | ||
+ | <dd>Motifs, modules and games in bacteria.</dd> | ||
+ | <dd><em>Curr Opin Microbiol,</em></dd> | ||
+ | <dd><b>2003</b><i>, 6</i>, 125-134</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Xiong2003"> (Xiong2003)</a></dt> | ||
+ | <dd>Xiong, W. & Ferrell, J. E.</dd> | ||
+ | <dd>A positive-feedback-based bistable 'memory module' that governs a cell fate decision.</dd> | ||
+ | <dd><em>Nature,</em></dd> | ||
+ | <dd><b>2003</b><i>, 426</i>, 460-465</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yamamoto2003"> (Yamamoto2003)</a></dt> | ||
+ | <dd>Yamamoto, K. & Ishihama, A.</dd> | ||
+ | <dd>Two different modes of transcription repression of the Escherichia coli acetate operon by IclR.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8504, Japan., </em><b>2003</b><i>, 47</i>, 183-194</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yang1997"> (Yang1997)</a></dt> | ||
+ | <dd>Yang, B.; Gerhardt, S. G. & Larson, T. J.</dd> | ||
+ | <dd>Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12.</dd> | ||
+ | <dd><em>Mol Microbiol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA., </em><b>1997</b><i>, 24</i>, 511-521</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yang1996"> (Yang1996)</a></dt> | ||
+ | <dd>Yang, B. & Larson, T. J.</dd> | ||
+ | <dd>Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12.</dd> | ||
+ | <dd><em>J Bacteriol,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA., </em><b>1996</b><i>, 178</i>, 7090-7098</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yang1988"> (Yang1988)</a></dt> | ||
+ | <dd>Yang, Y. & Ames, G. F.</dd> | ||
+ | <dd>DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.</dd> | ||
+ | <dd><em>Proc Natl Acad Sci U S A,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, University of California, Berkeley 94720., </em><b>1988</b><i>, 85</i>, 8850-8854</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yao2006"> (Yao2006)</a></dt> | ||
+ | <dd>Yao, Y.; Martinez-Yamout, M. A.; Dickerson, T. J.; Brogan, A. P.; Wright, P. E. & Dyson, H. J.</dd> | ||
+ | <dd>Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones.</dd> | ||
+ | <dd><em>J Mol Biol,</em></dd> | ||
+ | <dd><em>Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA., </em><b>2006</b><i>, 355</i>, 262-273</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yin1994"> (Yin1994)</a></dt> | ||
+ | <dd>Yin, H.; Landick, R. & Gelles, J.</dd> | ||
+ | <dd>Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule.</dd> | ||
+ | <dd><em>Biophys J,</em></dd> | ||
+ | <dd><em>Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254., </em><b>1994</b><i>, 67</i>, 2468-2478</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yin1995"> (Yin1995)</a></dt> | ||
+ | <dd>Yin, J. C.; Vecchio, M. D.; Zhou, H. & Tully, T.</dd> | ||
+ | <dd>CREB as a memory modulator: induced expression of a dCREB2 activator isoform enhances long-term memory in Drosophila.</dd> | ||
+ | <dd><em>Cell,</em></dd> | ||
+ | <dd><b>1995</b><i>, 81</i>, 107-115</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Yu2006"> (Yu2006)</a></dt> | ||
+ | <dd>Yu, J.; Xiao, J.; Ren, X.; Lao, K. & Xie, X. S.</dd> | ||
+ | <dd>Probing gene expression in live cells, one protein molecule at a time.</dd> | ||
+ | <dd><em>Science,</em></dd> | ||
+ | <dd><b>2006</b><i>, 311</i>, 1600-1603</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Zhang2006"> (Zhang2006)</a></dt> | ||
+ | <dd>Zhang, Y.; McEwen, A. E.; Crothers, D. M. & Levene, S. D.</dd> | ||
+ | <dd>Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.</dd> | ||
+ | <dd><em>PLoS One,</em></dd> | ||
+ | <dd><em>Department of Chemistry, Yale University, New Haven, Connecticut, United States of America. ylzhang@lbl.gov, </em><b>2006</b><i>, 1</i>, e136</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Zhu2007"> (Zhu2007)</a></dt> | ||
+ | <dd>Zhu, C.; Zheng, Y. & Jia, Y.</dd> | ||
+ | <dd>A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations.</dd> | ||
+ | <dd><em>Biophys Chem,</em></dd> | ||
+ | <dd><b>2007</b><i>, 129</i>, 49-55</dd> | ||
+ | |||
+ | <dt><em>article</em><a name="Zurla2009"> (Zurla2009)</a></dt> | ||
+ | <dd>Zurla, C.; Manzo, C.; Dunlap, D.; Lewis, D. E. A.; Adhya, S. & Finzi, L.</dd> | ||
+ | <dd>Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor.</dd> | ||
+ | <dd><em>Nucleic Acids Res,</em></dd> | ||
+ | <dd><em>Physics Department, Emory University, Atlanta, GA 30322, USA., </em><b>2009</b><i>, 37</i>, 2789-2795</dd> | ||
+ | |||
+ | </dl> | ||
+ | |||
+ | </body> | ||
+ | |||
+ | </html> | ||
+ | |||
+ | |||
<br><p style="text-indent: 30px; text-align:justify;">"Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications." Grage K., Jahns A. C., Parlane N., Palanisamy R., Rasiah I. A., Atwood J. A. and Rehm B. H. A. 2009. Biomacromolecules 10, 660-669. | <br><p style="text-indent: 30px; text-align:justify;">"Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications." Grage K., Jahns A. C., Parlane N., Palanisamy R., Rasiah I. A., Atwood J. A. and Rehm B. H. A. 2009. Biomacromolecules 10, 660-669. | ||
<br><br> | <br><br> |
Revision as of 17:14, 26 October 2010
References
- article (Adhya1989)
- Adhya, S.
- Multipartite genetic control elements: communication by DNA loop.
- Annu Rev Genet,
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892., 1989, 23, 227-250
- article (Aguilera2008)
- Aguilera, L.; Campos, E.; Giménez, R.; Badía, J.; Aguilar, J. & Baldoma, L.
- Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.
- J Bacteriol,
- Departament de Bioquímica i Biología Molecular, Facultat de Farmacia, Universitat de Barcelona, Av. Diagonal 643, E-08028 Barcelona, Spain., 2008, 190, 2997-3005
- article (Alberti1993)
- Alberti, S.; Oehler, S.; von Wilcken-Bergmann, B. & Müller-Hill, B.
- Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle.
- EMBO J,
- Institut für Genetik, Universität zu Köln, FRG., 1993, 12, 3227-3236
- article (Allen2006)
- Allen, T. E.; Price, N. D.; Joyce, A. R. & Palsson, B. Ø.
- Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
- PLoS Comput Biol,
- Department of Bioengineering, University of California San Diego, La Jolla, California, USA., 2006, 2, e2
- article (Alon2007)
- Alon, U.
- Network motifs: theory and experimental approaches.
- Nat Rev Genet,
- 2007, 8, 450-461
- book (Alon2006)
- Alon, U.
- An Introduction to Systems Biology
- Chapman & Hall/CRC, 2006
- article (Altan-Bonnet2003)
- Altan-Bonnet, G.; Libchaber, A. & Krichevsky, O.
- Bubble dynamics in double-stranded DNA.
- Phys Rev Lett,
- Center for Studies in Physics and Biology, The Rockefeller University, New York, New York 10021, USA., 2003, 90, 138101
- article (Amouyal2005)
- Amouyal, M.
- Gene regulation at-a-distance in E. coli: new insights.
- C R Biol,
- 2005, 328, 1-9
- article (Amouyal1989)
- Amouyal, M.; Mortensen, L.; Buc, H. & Hammer, K.
- Single and double loop formation when deoR repressor binds to its natural operator sites.
- Cell,
- Unité de Physicochimie des Macromolécules Biologiques, URA1149 du CNRS, Institut Pasteur, Paris, France., 1989, 58, 545-551
- article (Ansel2008)
- Ansel, J.; Bottin, H.; Rodriguez-Beltran, C.; Damon, C.; Nagarajan, M.; Fehrmann, S.; François, J. & Yvert, G.
- Cell-to-cell stochastic variation in gene expression is a complex genetic trait.
- PLoS Genet,
- Université de Lyon, Lyon, France., 2008, 4, e1000049
- article (Atkinson2003)
- Atkinson, M. R.; Savageau, M. A.; Myers, J. T. & Ninfa, A. J.
- Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.
- Cell,
- 2003, 113, 597-607
- article (Atlung1997)
- Atlung, T. & Ingmer, H.
- H-NS: a modulator of environmentally regulated gene expression.
- Mol Microbiol,
- Department of Chemistry and Life Sciences, Roskilde University, Denmark. atlung@virgil.ruc.dk, 1997, 24, 7-17
- article (Bachellier1999)
- Bachellier, S.; Clément, J. M. & Hofnung, M.
- Short palindromic repetitive DNA elements in enterobacteria: a survey.
- Res Microbiol,
- Programmation moléculaire et toxicologie génétique, département des biotechnologies, CNRS URA 1444, Institut Pasteur, Paris, France. bachelli@pasteur.fr, 1999, 150, 627-639
- mastersthesis (Baglio2008)
- Baglio, J.
- Dynamique du biopolymére ADN en suivi de particule unique :simulations et expériences dans le cadre du s mécanisme de transposition.
- ENS, 2008
- article (Bahloul2001)
- Bahloul, A.; Boubrik, F. & Rouviere-Yaniv, J.
- Roles of Escherichia coli histone-like protein HU in DNA replication: HU-beta suppresses the thermosensitivity of dnaA46ts.
- Biochimie,
- Laboratoire de Physiologie Bactérienne, CNRS, UPR 9073, Institut de Biologie Physico-Chimique, 13, rue Pierre-et-Marie-Curie, 75005, Paris, France., 2001, 83, 219-229
- article (Barkai2000)
- Barkai, N. & Leibler, S.
- Circadian clocks limited by noise.
- Nature,
- 2000, 403, 267-268
- article (Becskei2000)
- Becskei, A. & Serrano, L.
- Engineering stability in gene networks by autoregulation.
- Nature,
- 2000, 405, 590-593
- article (Behar2007)
- Behar, M.; Dohlman, H. G. & Elston, T. C.
- Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks.
- Proc Natl Acad Sci U S A,
- 2007, 104, 16146-16151
- article (Berg1981)
- Berg, O. G.; Winter, R. B. & von Hippel, P. H.
- Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.
- Biochemistry,
- 1981, 20, 6929-6948
- article (Bergstrom1998)
- Bergstrom, L. C.; Qin, L.; Harlocker, S. L.; Egger, L. A. & Inouye, M.
- Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli.
- Genes Cells,
- Department of Biochemistry, Robert Wood Johnson Medical School, Piscataway, NJ 08854, USA. inouye@rwja.umdnj.edu, 1998, 3, 777-788
- article (Bhalla1999)
- Bhalla, U. S. & Iyengar, R.
- Emergent properties of networks of biological signaling pathways.
- Science,
- 1999, 283, 381-387
- article (Blanco1986)
- Blanco, C.; Ritzenthaler, P. & Mata-Gilsinger, M.
- Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression.
- Genetics,
- 1986, 112, 173-182
- article (Blot2002)
- Blot, N.; Berrier, C.; Hugouvieux-Cotte-Pattat, N.; Ghazi, A. & Condemine, G.
- The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family.
- J Biol Chem,
- Unité de Microbiologie et Génétique, Composante INSA, UMR-CNRS 5122, INSA, Bâtiment Louis Pasteur, 11 Avenue Jean Capelle, 69621 Villeurbanne Cedex, France., 2002, 277, 7936-7944
- article (Bondarenko2003)
- Bondarenko, V. A.; Liu, Y. V.; Jiang, Y. I. & Studitsky, V. M.
- Communication over a large distance: enhancers and insulators.
- Biochem Cell Biol,
- Department of Biochemistry and Molecular Biology, Wayne State University School of Medicine, Detroit, MI 48201, USA., 2003, 81, 241-251
- article (Brunetti2001)
- Brunetti, R.; Prosseda, G.; Beghetto, E.; Colonna, B. & Micheli, G.
- The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains.
- Biochimie,
- Centro Acidi Nucleici C.N.R., Università La Sapienza, P. le A. Moro 5, Rome 00185, Italy., 2001, 83, 873-882
- article (Buchler2003)
- Buchler, N. E.; Gerland, U. & Hwa, T.
- On schemes of combinatorial transcription logic.
- Proc Natl Acad Sci U S A,
- Department of Physics and Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, CA 92093-0319, USA., 2003, 100, 5136-5141
- article (Bundschuh2003)
- Bundschuh, R.; Hayot, F. & Jayaprakash, C.
- The role of dimerization in noise reduction of simple genetic networks.
- J Theor Biol,
- 2003, 220, 261-269
- article (Carew1972)
- Carew, T. J.; Pinsker, H. M. & Kandel, E. R.
- Long-Term Habituation of a Defensive Withdrawal Reflex in Aplysia.
- Science,
- 1972, 175, 451-454
- article (Carlo2006)
- Carlo, S. D.; Chen, B.; Hoover, T. R.; Kondrashkina, E.; Nogales, E. & Nixon, B. T.
- The structural basis for regulated assembly and function of the transcriptional activator NtrC.
- Genes Dev,
- Howard Hughes Medical Institute, Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, California 94720, USA., 2006, 20, 1485-1495
- article (Carpentier2005)
- Carpentier, A.; Torrésani, B.; Grossmann, A. & Hénaut, A.
- Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data.
- BMC Genomics,
- Laboratoire Génome et Informatique, CNRS UMR 8116, Tour Evry2, 523 Place des Terrasses, 91034 Evry Cedex, France. carpentier@genopole.cnrs.fr, 2005, 6, 84
- article (Castillo1998)
- Castillo, A.; Nasser, W.; Condemine, G. & Reverchon, S.
- The PecT repressor interacts with regulatory regions of pectate lyase genes in Erwinia chrysanthemi.
- Biochim Biophys Acta,
- 1998, 1442, 148-160
- article (Charlier1992)
- Charlier, D.; Roovers, M.; Vliet, F. V.; Boyen, A.; Cunin, R.; Nakamura, Y.; Glansdorff, N. & Piérard, A.
- Arginine regulon of Escherichia coli K-12. A study of repressor-operator interactions and of in vitro binding affinities versus in vivo repression.
- J Mol Biol,
- Research Institute of the CERIA-COOVI, Brussels, Belgium., 1992, 226, 367-386
- article (Chen2010)
- Chen, Y.; Milstein, J. N. & Meiners, J.
- Femtonewton entropic forces can control the formation of protein-mediated DNA loops.
- Phys Rev Lett,
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA., 2010, 104, 048301
- article (Cherry2000)
- Cherry, J. L. & Adler, F. R.
- How to make a biological switch.
- J Theor Biol,
- Department of Biology, University of Utah, Salt Lake City, UT, 84112, USA. cherry@biology.utah.edu, 2000, 203, 117-133
- article (Chiam2007)
- Chiam, K. & Rajagopal, G.
- Oscillations in intracellular signaling cascades.
- Phys Rev E Stat Nonlin Soft Matter Phys,
- 2007, 75, 061901
- article (Ciliberti2007)
- Ciliberti, S.; Martin, O. C. & Wagner, A.
- Innovation and robustness in complex regulatory gene networks.
- Proc Natl Acad Sci U S A,
- 2007, 104, 13591-13596
- article (Ciliberto2005)
- Ciliberto, A.; Novak, B. & Tyson, J. J.
- Steady states and oscillations in the p53/Mdm2 network.
- Cell Cycle,
- 2005, 4, 488-493
- article (Condemine1992)
- Condemine, G.; Dorel, C.; Hugouvieux-Cotte-Pattat, N. & Robert-Baudouy, J.
- Some of the out genes involved in the secretion of pectate lyases in Erwinia chrysanthemi are regulated by kdgR.
- Mol Microbiol,
- Laboratoire de Génetique Moléculaire des Microorganismes, URA CNRS 1486, INSA Bâtiment 406, Villeurbanne, France., 1992, 6, 3199-3211
- article (Cook2002)
- Cook, P. R.
- Predicting three-dimensional genome structure from transcriptional activity.
- Nat Genet,
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK. peter.cook@path.ox.ac.uk, 2002, 32, 347-352
- article (Cox2006)
- Cox, C. D.; McCollum, J. M.; Austin, D. W.; Allen, M. S.; Dar, R. D. & Simpson, M. L.
- Frequency domain analysis of noise in simple gene circuits.
- Chaos,
- 2006, 16, 026102
- book (Frederic2002)
- Dardel, F. & Képès, F.
- de l'Ecole Polytechnique, L. E. (ed.)
- Bioinformatique Génomique et post-génomique
- 2002
- article (Dekker2008)
- Dekker, J.
- Gene regulation in the third dimension.
- Science,
- 2008, 319, 1793-1794
- article (Dekker2002)
- Dekker, J.; Rippe, K.; Dekker, M. & Kleckner, N.
- Capturing chromosome conformation.
- Science,
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. jdekker@fas.harvard.edu, 2002, 295, 1306-1311
- article (Delord2007)
- Delord, B.; Berry, H.; Guigon, E. & Genet, S.
- A new principle for information storage in an enzymatic pathway model.
- PLoS Comput Biol,
- 2007, 3, e124
- article (Dolmetsch1998)
- Dolmetsch, R. E.; Xu, K. & Lewis, R. S.
- Calcium oscillations increase the efficiency and specificity of gene expression.
- Nature,
- 1998, 392, 933-936
- article (Dostie2007)
- Dostie, J.; Zhan, Y. & Dekker, J.
- Chromosome conformation capture carbon copy technology.
- Curr Protoc Mol Biol,
- 2007, Chapter 21, Unit 21.14
- article (Dunlap2004)
- Dunlap, J. C. & Loros, J. J.
- The neurospora circadian system.
- J Biol Rhythms,
- 2004, 19, 414-424
- article (Dunn1984)
- Dunn, T. M.; Hahn, S.; Ogden, S. & Schleif, R. F.
- An operator at -280 base pairs that is required for repression of araBAD operon promoter: addition of DNA helical turns between the operator and promoter cyclically hinders repression.
- Proc Natl Acad Sci U S A,
- 1984, 81, 5017-5020
- article (Dupont1992)
- Dupont, G. & Goldbeter, A.
- Protein phosphorylation driven by intracellular calcium oscillations: a kinetic analysis.
- Biophys Chem,
- 1992, 42, 257-270
- article (Dupont2003)
- Dupont, G.; Houart, G. & Koninck, P. D.
- Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations: a simple model.
- Cell Calcium,
- 2003, 34, 485-497
- article (Dworkin1998)
- Dworkin, J.; Ninfa, A. J. & Model, P.
- A protein-induced DNA bend increases the specificity of a prokaryotic enhancer-binding protein.
- Genes Dev,
- Laboratory of Genetics, The Rockefeller University, New York, New York 10021, USA. dworkin@biosun.harvard.edu, 1998, 12, 894-900
- article (Elowitz2000)
- Elowitz, M. & Leibler, S.
- A synthetic oscillatory network of transcriptionnal regulators.
- Nature,
- 2000, 403, 335-338
- article (Espeli1997)
- Espéli, O. & Boccard, F.
- In vivo cleavage of Escherichia coli BIME-2 repeats by DNA gyrase: genetic characterization of the target and identification of the cut site.
- Mol Microbiol,
- Laboratoire de Chimie Bactérienne, UPR 9043, Institut de Biologie Structurale et Microbiologie du CNRS, Marseille, France., 1997, 26, 767-777
- article (Espeli2001)
- Espéli, O.; Moulin, L. & Boccard, F.
- Transcription attenuation associated with bacterial repetitive extragenic BIME elements.
- J Mol Biol,
- Centre de Génétique Moléculaire du CNRS, Centre National de la Recherche Scientifique, Gif-sur-Yvette Cedex, F-91198, France., 2001, 314, 375-386
- phdthesis (Francois2005)
- François, P.
- Réseaux génétiques conception, modélisation et dynamique
- Ecole Normale Supérieure, 2005
- article (Francois2005a)
- François, P. & Hakim, V.
- Core genetic module: the mixed feedback loop.
- Phys Rev E Stat Nonlin Soft Matter Phys,
- 2005, 72, 031908
- article (Francois2004)
- François, P. & Hakim, V.
- Design of genetic networks with specified functions by evolution in silico.
- Proc Natl Acad Sci U S A,
- Laboratoire de Physique Statistique, Centre National de la Recherche Scientifique-Unité Mixte de Recherche 8550, Ecole Normale Supérieure, 24, Rue Lhomond, 75231 Paris, France., 2004, 101, 580-585
- article (Gama-Castro2008)
- Gama-Castro, S.; Jiménez-Jacinto, V.; Peralta-Gil, M.; Santos-Zavaleta, A.; Peñaloza-Spinola, M. I.; Contreras-Moreira, B.; Segura-Salazar, J.; Muñiz-Rascado, L.; Martínez-Flores, I.; Salgado, H.; Bonavides-Martínez, C.; Abreu-Goodger, C.; Rodríguez-Penagos, C.; Miranda-Ríos, J.; Morett, E.; Merino, E.; Huerta, A. M.; Treviño-Quintanilla, L. & Collado-Vides, J.
- RegulonDB (version 6.0): gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and Textpresso navigation.
- Nucleic Acids Res,
- Program of Computational Genomics, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, A.P. 565-A, Cuernavaca, Morelos 62100, Mexico., 2008, 36, D120-D124
- article (Gardner2000)
- Gardner, T. S.; Cantor, C. R. & Collins, J. J.
- Construction of a genetic toggle switch in Escherichia coli.
- Nature,
- 2000, 403, 339-342
- article (Geanacopoulos1997)
- Geanacopoulos, M. & Adhya, S.
- Functional characterization of roles of GalR and GalS as regulators of the gal regulon.
- J Bacteriol,
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-4255, USA., 1997, 179, 228-234
- article (Gene-Wei2009)
- Gene-Wei Li, Otto G. Berg, J. E.
- Effects of macromolecular crowding and DNA looping on gene regulation kinetics.
- Nature Physics,
- 2009, 5, no. 4, 294-297
- article (Geva-Zatorsky2006)
- Geva-Zatorsky, N.; Rosenfeld, N.; Itzkovitz, S.; Milo, R.; Sigal, A.; Dekel, E.; Yarnitzky, T.; Liron, Y.; Polak, P.; Lahav, G. & Alon, U.
- Oscillations and variability in the p53 system.
- Mol Syst Biol,
- 2006, 2, 2006.0033
- article (Guillespie1977)
- Gillespie, D.
- Exact stochastic simulation of coupled chemical reactions
- J. Phys. Chem.,
- 1977, 81, 2340-2361
- article (Glass1973)
- Glass, L. & Kauffman, S.
- The logical analysis of continuous, non-linear biochemical control networks.
- J Theor Bio,
- 1973, 39, 103-129
- book (Goldbeter1996)
- Goldbeter, A.
- Cambridge (ed.)
- Biochemical Oscillations and Cellular Rhythms: The molecular bases of periodic and chaotic behaviour.
- Cambridge University Press, 1996
- article (Goldbeter1990)
- Goldbeter, A.; Dupont, G. & Berridge, M. J.
- Minimal model for signal-induced Ca2+ oscillations and for their frequency encoding through protein phosphorylation.
- Proc Natl Acad Sci U S A,
- 1990, 87, 1461-1465
- article (Goldbeter1981)
- Goldbeter, A. & Koshland, D. E.
- An amplified sensitivity arising from covalent modification in biological systems.
- Proc Natl Acad Sci U S A,
- 1981, 78, 6840-6844
- article (Gomez-Uribe2007)
- Gomez-Uribe, C.; Verghese, G. C. & Mirny, L. A.
- Operating Regimes of Signaling Cycles: Statics, Dynamics, and Noise Filtering.
- PLoS Comput Biol,
- 2007, 3, e246
- article (Gonze2002)
- Gonze, D.; Halloy, J. & Goldbeter, A.
- Robustness of circadian rhythms with respect to molecular noise.
- Proc Natl Acad Sci U S A,
- 2002, 99, 673-678
- article (Goodwin1965)
- Goodwin, B. C.
- Oscillatory behavior in enzymatic control processes.
- Adv Enzyme Regul,
- 1965, 3, 425-438
- article (Goss2002)
- Goss, T. J.; Janes, B. K. & Bender, R. A.
- Repression of glutamate dehydrogenase formation in Klebsiella aerogenes requires two binding sites for the nitrogen assimilation control protein, NAC.
- J Bacteriol,
- Department of Molecular Cellular and Developmental Biology, University of Michigan, Ann Arbor 48109-1048, USA., 2002, 184, 6966-6975
- article (Gouze2002)
- Gouzé, J. & Sari, T.
- A class of piecewise linear differential equations arising in biological models
- Dyn. Syst.,
- 2002, 17, 299-316.
- article (Gowers2005)
- Gowers, D. M.; Wilson, G. G. & Halford, S. E.
- Measurement of the contributions of 1D and 3D pathways to the translocation of a protein along DNA.
- Proc Natl Acad Sci U S A,
- Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol BS8 1TD, United Kingdom., 2005, 102, 15883-15888
- article (Grainger2005)
- Grainger, D. C.; Hurd, D.; Harrison, M.; Holdstock, J. & Busby, S. J. W.
- Studies of the distribution of Escherichia coli cAMP-receptor protein and RNA polymerase along the E. coli chromosome.
- Proc Natl Acad Sci U S A,
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom. d.grainger@bham.ac.uk, 2005, 102, 17693-17698
- article (Griffith1986)
- Griffith, J.; Hochschild, A. & Ptashne, M.
- DNA loops induced by cooperative binding of lambda repressor.
- Nature,
- 1986, 322, 750-752
- article (Guantes2006)
- Guantes, R. & Poyatos, J. F.
- Dynamical principles of two-component genetic oscillators.
- PLoS Comput Biol,
- 2006, 2, e30
- article (Guelzim2002)
- Guelzim, N.; Bottani, S.; Bourgine, P. & Képès, F.
- Topological and causal structure of the yeast transcriptional regulatory network.
- Nat Genet,
- ATelier de Génomique Cognitive, Centre National de la Recherche Scientifique ESA 8071, genopole(R), 523 Terrasses de l'Agora, 91000 Evry, France., 2002, 31, 60-63
- article (Haber1988)
- Haber, R. & Adhya, S.
- Interaction of spatially separated protein-DNA complexes for control of gene expression: operator conversions.
- Proc Natl Acad Sci U S A,
- Laboratory of Molecular Biology, National Cancer Institute, Bethesda, MD 20892., 1988, 85, 9683-9687
- article (Hanke2003)
- Hanke, A. & Metzler, R.
- Entropy loss in long-distance DNA looping.
- Biophys J,
- Institute for Theoretical Physics, University of Stuttgart, Stuttgart, Germany., 2003, 85, 167-173
- techreport (Hayot2006)
- Hayot, F. & Jayaprakash, C.
- A tutorial on cellular stochasticity and Gillespie’s algorithm.
- Department of Neurology, Mount Sinai School of Medicine, New York, Department of Physics, The Ohio State University, Columbus, 2006
- article (He1994)
- He, B. & Zalkin, H.
- Regulation of Escherichia coli purA by purine repressor, one component of a dual control mechanism.
- J Bacteriol,
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907., 1994, 176, 1009-1013
- article (Heinrich2002)
- Heinrich, R.; Neel, B. G. & Rapoport, T. A.
- Mathematical models of protein kinase signal transduction.
- Mol Cell,
- 2002, 9, 957-970
- article (Henning2007)
- Henning, J.; Koczan, D.; Glass, A.; Karopka, T.; Pahnke, J.; Rolfs, A.; Benecke, R. & Gimsa, U.
- Deep brain stimulation in a rat model modulates TH, CaMKIIa and Homer1 gene expression.
- Eur J Neurosci,
- 2007, 25, 239-250
- article (Hersen2008)
- Hersen, P.; McClean, M. N.; Mahadevan, L. & Ramanathan, S.
- Signal processing by the HOG MAP kinase pathway.
- Proc Natl Acad Sci U S A,
- 2008, 105, 7165-7170
- article (Horowitz1984)
- Horowitz, D. S. & Wang, J. C.
- Torsional rigidity of DNA and length dependence of the free energy of DNA supercoiling.
- J Mol Biol,
- 1984, 173, 75-91
- article (Huang1996)
- Huang, C. Y. & Ferrell, J. E.
- Ultrasensitivity in the mitogen-activated protein kinase cascade.
- Proc Natl Acad Sci U S A,
- 1996, 93, 10078-10083
- article (Huang1994)
- Huang, K. J.; Schieberl, J. L. & Igo, M. M.
- A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene.
- J Bacteriol,
- Section of Microbiology, University of California, Davis 95616., 1994, 176, 1309-1315
- article (Hugouvieux-Cotte-Pattat1996)
- Hugouvieux-Cotte-Pattat, N.; Condemine, G.; Nasser, W. & Reverchon, S.
- Regulation of pectinolysis in Erwinia chrysanthemi.
- Annu Rev Microbiol,
- Laboratoire de Génétique Moléculaire des Microorganismes, UMR-CNRS 5577, Villeurbanne, France., 1996, 50, 213-257
- article (Hugouvieux-Cotte-Pattat1992)
- Hugouvieux-Cotte-Pattat, N.; Dominguez, H. & Robert-Baudouy, J.
- Environmental conditions affect transcription of the pectinase genes of Erwinia chrysanthemi 3937.
- J Bacteriol,
- Laboratoire de Génétique Moléculaire des Microorganismes, URA-CNRS, Institut National des Sciences Appliquées batiment 406, Villeurbanne, France., 1992, 174, 7807-7818
- article (Hugouvieux-Cotte-Pattat1994)
- Hugouvieux-Cotte-Pattat, N.; Nasser, W. & Robert-Baudouy, J.
- Molecular characterization of the Erwinia chrysanthemi kdgK gene involved in pectin degradation.
- J Bacteriol,
- Laboratoire de Généteique Moléculaire des Microorganismes, CNRS URA-1486, INSA de Lyon, Villeurbanne, France., 1994, 176, 2386-2392
- article (Hutcheon2000)
- Hutcheon, B. & Yarom, Y.
- Resonance, oscillation and the intrinsic frequency preferences of neurons.
- Trends Neurosci,
- 2000, 23, 216-222
- article (Izhikevich2006)
- Izhikevich, E. M.
- Bursting
- Scholarpedia,
- 2006, 1(3):1300
- article (JACOB1961)
- JACOB, F. & MONOD, J.
- Genetic regulatory mechanisms in the synthesis of proteins.
- J Mol Biol,
- 1961, 3, 318-356
- article (Jeong2004)
- Jeong, K. S.; Ahn, J. & Khodursky, A. B.
- Spatial patterns of transcriptional activity in the chromosome of Escherichia coli.
- Genome Biol,
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, St. Paul, MN 55108, USA. jeong009@umn.edu, 2004, 5, R86
- article (Jun2006)
- Jun, S. & Mulder, B.
- Entropy-driven spatial organization of highly confined polymers: lessons for the bacterial chromosome.
- Proc Natl Acad Sci U S A,
- Stichting voor Fundamenteel Onderzoek der Materie (FOM) Institute for Atomic and Molecular Physics (AMOLF), Kruislaan 407, 1098 SJ, Amsterdam, The Netherlands. jun@amolf.nl, 2006, 103, 12388-12393
- article (Kahramanoglou2006)
- Kahramanoglou, C.; Webster, C. L.; El-Robh, M. S.; Belyaeva, T. A. & Busby, S. J. W.
- Mutational analysis of the Escherichia coli melR gene suggests a two-state concerted model to explain transcriptional activation and repression in the melibiose operon.
- J Bacteriol,
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, United Kingdom., 2006, 188, 3199-3207
- article (Kandel2004)
- Kandel, E. R.
- The molecular biology of memory storage: a dialog between genes and synapses.
- Biosci Rep,
- 2004, 24, 475-522
- article (Kania1977)
- Kania, J. & Müller-Hill, B.
- Construction, isolation and implications of repressor-galactosidase - beta-galactosidase hybrid molecules.
- Eur J Biochem,
- 1977, 79, 381-386
- article (Karimova1998)
- Karimova, G.; Pidoux, J.; Ullmann, A. & Ladant, D.
- A bacterial two-hybrid system based on a reconstituted signal transduction pathway.
- Proc Natl Acad Sci U S A,
- Unité de Biochimie Cellulaire (Centre National de la Recherche Scientifique, Unité de Recherche Associée 1129), Institut Pasteur, 75724 Paris Cedex 15, France., 1998, 95, 5752-5756
- article (Kashtan2007)
- Kashtan, N.; Noor, E. & Alon, U.
- Varying environments can speed up evolution.
- Proc Natl Acad Sci U S A,
- 2007, 104, 13711-13716
- article (Kepler2001)
- Kepler, T. B. & Elston, T. C.
- Stochasticity in transcriptional regulation: origins, consequences, and mathematical representations.
- Biophys J,
- Santa Fe Institute, Santa Fe, New Mexico 87501, USA. kepler@santafe.edu, 2001, 81, 3116-3136
- unpublished (Kepseu)
- Kepseu W.D., W. P. & J-A, S.
- Dynamics of the transition to pathogenicity in Erwinia chrysanthemi
- article (Kholodenko2000)
- Kholodenko, B. N.
- Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.
- Eur J Biochem,
- 2000, 267, 1583-1588
- article (Koninck1998)
- Koninck, P. D. & Schulman, H.
- Sensitivity of CaM kinase II to the frequency of Ca2+ oscillations.
- Science,
- 1998, 279, 227-230
- article (Kornacker1998)
- Kornacker, M. G.; Remsburg, B. & Menzel, R.
- Gene activation by the AraC protein can be inhibited by DNA looping between AraC and a LexA repressor that interacts with AraC: possible applications as a two-hybrid system.
- Mol Microbiol,
- Department of Macromolecular Structure, Bristol-Myers Squibb Pharmaceutical Research Institute, Route 206 and Province Line Road, Princeton, NJ 08543-4000, USA. KornackM@BMS.com, 1998, 30, 615-624
- article (Kramer2005)
- Kramer, B. P. & Fussenegger, M.
- Hysteresis in a synthetic mammalian gene network.
- Proc Natl Acad Sci U S A,
- 2005, 102, 9517-9522
- article (Krin2003)
- Krin, E.; Laurent-Winter, C.; Bertin, P. N.; Danchin, A. & Kolb, A.
- Transcription regulation coupling of the divergent argG and metY promoters in Escherichia coli K-12.
- J Bacteriol,
- Unité de Génétique des Génomes Bactériens, Institut Pasteur, 75724 Paris Cedex 15, France. ekrin@pasteur.fr, 2003, 185, 3139-3146
- article (Kussell2005)
- Kussell, E. & Leibler, S.
- Phenotypic diversity, population growth, and information in fluctuating environments.
- Science,
- Laboratory of Living Matter and Center for Studies in Physics and Biology, Rockefeller University, 1230 York Avenue, Box 34, New York, NY 10021-6399, USA. kussele@rockefeller.edu, 2005, 309, 2075-2078
- article (Kepes2005)
- Képès, F.
- [Epigenetics as an aspect of post-genomics]
- Med Sci (Paris),
- Programme d'Epigénomique, Genopole, ATelier de Génomique Cognitive, CNRS UMR 8071/Genopole, 93, rue Henri-Rochefort, 91000 Evry, France. Francois.Kepes@genopole.cnrs.fr, 2005, 21, 371-376
- article (Kepes2004)
- Képès, F.
- Periodic transcriptional organization of the E.coli genome.
- J Mol Biol,
- 2004, 340, 957-964
- article (Kepes2003)
- Képès, F.
- Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites.
- J Mol Biol,
- 2003, 329, 859-865
- article (Francois2003)
- Képès, F. & Vaillant, C.
- Transcription-Based Solenoidal Model of Chromosomes
- Complexus,
- 2003, 1-No 4, 171-180
- article (Laat2007)
- de Laat, W.
- Long-range DNA contacts: romance in the nucleus?
- Curr Opin Cell Biol,
- 2007, 19, 317-320
- article (Laat2003)
- de Laat, W. & Grosveld, F.
- Spatial organization of gene expression: the active chromatin hub.
- Chromosome Res,
- 2003, 11, 447-459
- article (Larson1992)
- Larson, T. J.; Cantwell, J. S. & van Loo-Bhattacharya, A. T.
- Interaction at a distance between multiple operators controls the adjacent, divergently transcribed glpTQ-glpACB operons of Escherichia coli K-12.
- J Biol Chem,
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., 1992, 267, 6114-6121
- phdthesis (LAUTIER2007)
- LAUTIER, T.
- Rôle de la protéine associée au nucléoïde Fis dans le contrôle de la virulence chez la bactérie phytopathogène Erwinia chrysanthemi.
- L’Institut National des Sciences Appliquées de Lyon, 2007
- article (Lee1993)
- Lee, H. S.; Ishihama, A. & Kustu, S.
- The C terminus of the alpha subunit of RNA polymerase is not essential for transcriptional activation of sigma 54 holoenzyme.
- J Bacteriol,
- Department of Plant Pathology, University of California, Berkeley 94720., 1993, 175, 2479-2482
- article (Lercher2006)
- Lercher, M. J. & Hurst, L. D.
- Co-expressed yeast genes cluster over a long range but are not regularly spaced.
- J Mol Biol,
- Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK. m.j.lercher@bath.ac.uk, 2006, 359, 825-831
- article (Lewis2003)
- Lewis, J.
- Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator.
- Curr Biol,
- 2003, 13, 1398-1408
- article (Li2008a)
- Li, D. & Li, C.
- Noise-induced dynamics in the mixed-feedback-loop network motif.
- Phys Rev E Stat Nonlin Soft Matter Phys,
- Centre for Nonlinear and Complex Systems, School of Electronic Engineering, University of Electronic Science and Technology of China, Chengdu 610054, People's Republic of China., 2008, 77, 011903
- article (Li2009)
- Li, G.; G.Berg, O. & Elf, J.
- Effects of macromolecular crowding and DNA looping on gene regulation kinetics
- Nature Physics,
- 2009, 5 No 4, 237-308
- unpublished (Li2008)
- Li, G.; G.Berg, O. & Elf, J.
- Targe location by DNA-Binding Proteins: Effects of Roadblocks and DNA looping
- 2008
- article (Li1990)
- Li, Y. & Goldbeter, A.
- Frequency encoding of pulsatile signals of cAMP based on receptor desensitization in Dictyostelium cells.
- J Theor Biol,
- 1990, 146, 355-367
- article (Li1989)
- Li, Y. & Goldbeter, A.
- Frequency specificity in intercellular communication. Influence of patterns of periodic signaling on target cell responsiveness.
- Biophys J,
- 1989, 55, 125-145
- article (Lia2003)
- Lia, G.; Bensimon, D.; Croquette, V.; Allemand, J.; Dunlap, D.; Lewis, D. E. A.; Adhya, S. & Finzi, L.
- Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping.
- Proc Natl Acad Sci U S A,
- Department of Biology, University of Milan, 20133 Milan, Italy., 2003, 100, 11373-11377
- article (Lipan2008)
- Lipan, O.
- Systems biology. Enlightening Rhythms.
- Science,
- 2008, 319, 417-418
- article (Lipan2005)
- Lipan, O. & Wong, W. H.
- The use of oscillatory signals in the study of genetic networks.
- Proc Natl Acad Sci U S A,
- 2005, 102, 7063-7068
- article (Little1999)
- Little, J. W.; Shepley, D. P. & Wert, D. W.
- Robustness of a gene regulatory circuit.
- EMBO J,
- Departments of Biochemistry, University of Arizona, Tucson, AZ 85721, USA. jlittle@u.arizona.edu, 1999, 18, 4299-4307
- article (Lobell1991)
- Lobell, R. B. & Schleif, R. F.
- AraC-DNA looping: orientation and distance-dependent loop breaking by the cyclic AMP receptor protein.
- J Mol Biol,
- Department of Biochemistry, Brandeis University, Waltham, MA 02254., 1991, 218, 45-54
- unpublished (Locasale)
- Locasale, J. W.
- Signal duration and the time scale dependence of signal integration in biochemical pathways.
- 2008
- article (Loinger2007)
- Loinger, A.; Lipshtat, A.; Balaban, N. Q. & Biham, O.
- Stochastic simulations of genetic switch systems.
- Phys Rev E Stat Nonlin Soft Matter Phys,
- 2007, 75, 021904
- article (Lomvardas2006)
- Lomvardas, S.; Barnea, G.; Pisapia, D. J.; Mendelsohn, M.; Kirkland, J. & Axel, R.
- Interchromosomal interactions and olfactory receptor choice.
- Cell,
- Department of Biochemistry and Molecular Biophysics and Howard Hughes Medical Institute, College of Physicians and Surgeons, Columbia University, New York, NY 10032, USA., 2006, 126, 403-413
- article (Lu1999)
- Lu, C. D. & Abdelal, A. T.
- Role of ArgR in activation of the ast operon, encoding enzymes of the arginine succinyltransferase pathway in Salmonella typhimurium.
- J Bacteriol,
- Department of Biology, Georgia State University, Atlanta, Georgia, USA., 1999, 181, 1934-1938
- article (Lyubchenko1997)
- Lyubchenko, Y. L.; Shlyakhtenko, L. S.; Aki, T. & Adhya, S.
- Atomic force microscopic demonstration of DNA looping by GalR and HU.
- Nucleic Acids Res,
- Department of Microbiology, Arizona State University, Tempe 85287-2701, USA., 1997, 25, 873-876
- article (Mackey1977)
- Mackey, M. C. & Glass, L.
- Oscillation and chaos in physiological control systems.
- Science,
- 1977, 197, 287-289
- article (Majumdar1984)
- Majumdar, A. & Adhya, S.
- Demonstration of two operator elements in gal: in vitro repressor binding studies.
- Proc Natl Acad Sci U S A,
- 1984, 81, 6100-6104
- article (Mandal1990)
- Mandal, N.; Su, W.; Haber, R.; Adhya, S. & Echols, H.
- DNA looping in cellular repression of transcription of the galactose operon.
- Genes Dev,
- Laboratory of Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892., 1990, 4, 410-418
- article (Mangan2006)
- Mangan, S.; Itzkovitz, S.; Zaslaver, A. & Alon, U.
- The incoherent feed-forward loop accelerates the response-time of the gal system of Escherichia coli.
- J Mol Biol,
- 2006, 356, 1073-1081
- article (Marenduzzo2007)
- Marenduzzo, D.; Faro-Trindade, I. & Cook, P. R.
- What are the molecular ties that maintain genomic loops?
- Trends Genet,
- School of Physics, University of Edinburgh, Mayfield Road, Edinburgh, UK., 2007, 23, 126-133
- article (Marenduzzo2006)
- Marenduzzo, D.; Micheletti, C. & Cook, P. R.
- Entropy-driven genome organization.
- Biophys J,
- Mathematics Institute, University of Warwick, Coventry, United Kingdom., 2006, 90, 3712-3721
- article (Marhl2006)
- Marhl, M.; Perc, M. & Schuster, S.
- A minimal model for decoding of time-limited Ca2+ oscillations.
- Biophys Chem,
- 2006, 120, 161-167
- article (Marhl2005)
- Marhl, M.; Perc, M. & Schuster, S.
- Selective regulation of cellular processes via protein cascades acting as band-pass filters for time-limited oscillations.
- FEBS Lett,
- 2005, 579, 5461-5465
- article (Martinez-Antonio2003)
- Martínez-Antonio, A. & Collado-Vides, J.
- Identifying global regulators in transcriptional regulatory networks in bacteria.
- Curr Opin Microbiol,
- Program of Computational Genomics, CIFN, Universidad Nacional Autónoma de México A. P. 565-A Cuernavaca, 62100, Morelos, Mexico. agustino@cifn.unam.mx, 2003, 6, 482-489
- article (Matthews1992)
- Matthews, K. S.
- DNA looping.
- Microbiol Rev,
- Cell Biology, Rice University, Houston, Texas 77251., 1992, 56, 123-136
- article (Mazurie2005)
- Mazurie, A.; Bottani, S. & Vergassola, M.
- An evolutionary and functional assessment of regulatory network motifs.
- Genome Biol,
- 2005, 6, R35
- article (McClean2007)
- McClean, M. N.; Mody, A.; Broach, J. R. & Ramanathan, S.
- Cross-talk and decision making in MAP kinase pathways.
- Nat Genet,
- 2007, 39, 409-414
- article (Mercier2008)
- Mercier, R.; Petit, M.; Schbath, S.; Robin, S.; Karoui, M. E.; Boccard, F. & Espéli, O.
- The MatP/matS site-specific system organizes the terminus region of the E. coli chromosome into a macrodomain.
- Cell,
- Centre de Génétique Moléculaire du CNRS, 91198 Gif-sur-Yvette, France., 2008, 135, 475-485
- article (Mettetal2008)
- Mettetal, J. T.; Muzzey, D.; Gómez-Uribe, C. & van Oudenaarden, A.
- The frequency dependence of osmo-adaptation in Saccharomyces cerevisiae.
- Science,
- 2008, 319, 482-484
- article (Moore1983)
- Moore, C. L.; Klevan, L.; Wang, J. C. & Griffith, J. D.
- Gyrase . DNA complexes visualized as looped structures by electron microscopy.
- J Biol Chem,
- 1983, 258, 4612-4617
- article (Moran1968)
- Moran, F.; Nasuno, S. & Starr, M. P.
- Extracellular and intracellular polygllacturonic acid trans-eliminases of Erwinia carotovora.
- Arch Biochem Biophys,
- 1968, 123, 298-306
- article (Morelli2009)
- Morelli, M. J.; Wolde, P. R. T. & Allen, R. J.
- DNA looping provides stability and robustness to the bacteriophage lambda switch.
- Proc Natl Acad Sci U S A,
- FOM Institute for Atomic and Molecular Physics, Amsterdam, The Netherlands., 2009, 106, 8101-8106
- book (Murray1989)
- Murray, J.
- Mathematical Biology
- Springer, 1989
- article (Mueller-Hill2006)
- Müller-Hill, B.
- What is life? The paradigm of DNA and protein cooperation at high local concentrations.
- Mol Microbiol,
- 2006, 60, 253-255
- article (Mueller-Hill1998)
- Müller-Hill, B.
- The function of auxiliary operators.
- Mol Microbiol,
- 1998, 29, 13-18
- book (Mueller-Hill1996)
- Müller-Hill, B.
- de Gruyter, W. (ed.)
- The lac Operon: a short history of a genetic paradigm
- 1996
- article (Nakashima1991)
- Nakashima, K.; Kanamaru, K.; Aiba, H. & Mizuno, T.
- Signal transduction and osmoregulation in Escherichia coli. A novel type of mutation in the phosphorylation domain of the activator protein, OmpR, results in a defect in its phosphorylation-dependent DNA binding.
- J Biol Chem,
- Laboratory of Microbiology, School of Agriculture, Nagoya University, Japan., 1991, 266, 10775-10780
- article (Nasser2007)
- Nasser, W. & Reverchon, S.
- New insights into the regulatory mechanisms of the LuxR family of quorum sensing regulators.
- Anal Bioanal Chem,
- Unité de Microbiologie et Génétique, UMR CNRS-INSA-Université Lyon 1 5122, Domaine Scientifique de la Doua, 10 rue R. Dubois, bât A. Lwoff, 69622, Villeurbanne Cedex, France. William.nasser@insa-lyon.fr, 2007, 387, 381-390
- article (Novick1957)
- Novick, A. & Weiner, M.
- ENZYME INDUCTION AS AN ALL-OR-NONE PHENOMENON.
- Proc Natl Acad Sci U S A,
- DEPARTMENT OF MICROBIOLOGY AND COMMITTEE ON BIOPHYSICS, UNIVERSITY OF CHICAGO., 1957, 43, 553-566
- article (Novak2008)
- Novák, B. & Tyson, J. J.
- Design principles of biochemical oscillators.
- Nat Rev Mol Cell Biol,
- 2008, 9, 981-991
- article (Oehler1994)
- Oehler, S.; Amouyal, M.; Kolkhof, P.; von Wilcken-Bergmann, B. & Müller-Hill, B.
- Quality and position of the three lac operators of E. coli define efficiency of repression.
- EMBO J,
- 1994, 13, 3348-3355
- article (Oehler1990)
- Oehler, S.; Eismann, E. R.; Krämer, H. & Müller-Hill, B.
- The three operators of the lac operon cooperate in repression.
- EMBO J,
- 1990, 9, 973-979
- article (Ohlsson2007)
- Ohlsson, R. & Göndör, A.
- The 4C technique: the 'Rosetta stone' for genome biology in 3D?
- Curr Opin Cell Biol,
- Genetics, Norbyvägen 18A, Evolution Biology Centre, Uppsala University, S-752 36 Uppsala, Sweden. rolf.ohlsson@ebc.uu.se, 2007, 19, 321-325
- article (Ozbudak2004)
- Ozbudak, E. M.; Thattai, M.; Lim, H. N.; Shraiman, B. I. & Oudenaarden, A. V.
- Multistability in the lactose utilization network of Escherichia coli.
- Nature,
- 2004, 427, 737-740
- article (Pal2008)
- Pal, R.; Basu, D. & Banerjee, M.
- Modelling of phytoplankton allelopathy with Monod-Haldane-type functional response-A mathematical study.
- Biosystems,
- 2008
- article (Peekhaus1998)
- Peekhaus, N. & Conway, T.
- Positive and negative transcriptional regulation of the Escherichia coli gluconate regulon gene gntT by GntR and the cyclic AMP (cAMP)-cAMP receptor protein complex.
- J Bacteriol,
- Department of Microbiology, The Ohio State University, Columbus 43210-1292, USA. peekhaus.1@osu.edu, 1998, 180, 1777-1785
- article (Perlmutter2006)
- Perlmutter, J. S. & Mink, J. W.
- Deep brain stimulation.
- Annu Rev Neurosci,
- 2006, 29, 229-257
- article (Phillips1989)
- Phillips, S. E.; Manfield, I.; Parsons, I.; Davidson, B. E.; Rafferty, J. B.; Somers, W. S.; Margarita, D.; Cohen, G. N.; Saint-Girons, I. & Stockley, P. G.
- Cooperative tandem binding of met repressor of Escherichia coli.
- Nature,
- Astbury Department of Biophysics, University of Leeds, UK., 1989, 341, 711-715
- article (Plumbridge1995)
- Plumbridge, J.
- Co-ordinated regulation of amino sugar biosynthesis and degradation: the NagC repressor acts as both an activator and a repressor for the transcription of the glmUS operon and requires two separated NagC binding sites.
- EMBO J,
- Institut de Biologie Physico-chimique (URA1139), Paris, France., 1995, 14, 3958-3965
- article (Plumbridge1998)
- Plumbridge, J. & Kolb, A.
- DNA bending and expression of the divergent nagE-B operons.
- Nucleic Acids Res,
- Institut de Biologie Physico-chimique (UPR9073), 13 rue P. et M. Curie, 75005 Paris, France. plumbridge@ibpc.fr, 1998, 26, 1254-1260
- article (Plumbridge1993)
- Plumbridge, J. & Kolb, A.
- DNA loop formation between Nag repressor molecules bound to its two operator sites is necessary for repression of the nag regulon of Escherichia coli in vivo.
- Mol Microbiol,
- Institut de Biologie Physico-chimique (URA1139), Paris, France., 1993, 10, 973-981
- article (Plumbridge1991)
- Plumbridge, J. & Kolb, A.
- CAP and Nag repressor binding to the regulatory regions of the nagE-B and manX genes of Escherichia coli.
- J Mol Biol,
- Institut de Biologie Physico-chimique, URA1139, Paris, France., 1991, 217, 661-679
- article (Plumbridge2004)
- Plumbridge, J. & Pellegrini, O.
- Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP.
- Mol Microbiol,
- Institut de Biologie Physico-Chimique (CNRS UPR9073), 13, rue Pierre et Marie Curie, 75005 Paris, France. Jackie.Plumbridge@ibpc.fr, 2004, 52, 437-449
- article (Porco1997)
- Porco, A.; Peekhaus, N.; Bausch, C.; Tong, S.; Isturiz, T. & Conway, T.
- Molecular genetic characterization of the Escherichia coli gntT gene of GntI, the main system for gluconate metabolism.
- J Bacteriol,
- School of Biological Sciences, University of Nebraska-Lincoln, 68588-0118, USA., 1997, 179, 1584-1590
- article (Pouget2006)
- Pouget, N.; Turlan, C.; Destainville, N.; Salomé, L. & Chandler, M.
- IS911 transpososome assembly as analysed by tethered particle motion.
- Nucleic Acids Res,
- Laboratoire de Microbiologie et Génétique Moléculaire, UMR CNRS 5100, 118 route de Narbonne, 31062 Toulouse cedex, France., 2006, 34, 4313-4323
- article (Pruess2006)
- Prüss, B. M.; Besemann, C.; Denton, A. & Wolfe, A. J.
- A complex transcription network controls the early stages of biofilm development by Escherichia coli.
- J Bacteriol,
- Department of Veterinary and Microbiological Sciences, North Dakota State University, 1523 Centennial Blvd., Fargo, ND 58105, USA. Birgit.Pruess@ndsu.edu, 2006, 188, 3731-3739
- article (Qaidi2008)
- Qaidi, S. E. & Plumbridge, J.
- Switching control of expression of ptsG from the Mlc regulon to the NagC regulon.
- J Bacteriol,
- Institut de Biologie Physico-Chimique, UPR9073-CNRS, 13 rue Pierre et Marie Curie, 75005 Paris, France., 2008, 190, 4677-4686
- article (Qiao2007)
- Qiao, L.; Nachbar, R. B.; Kevrekidis, I. G. & Shvartsman, S. Y.
- Bistability and oscillations in the huang-ferrell model of MAPK signaling.
- PLoS Comput Biol,
- 2007, 3, e184
- article (Rampersaud1994)
- Rampersaud, A.; Harlocker, S. L. & Inouye, M.
- The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation.
- J Biol Chem,
- Department of Pathology, Ohio State University, Columbus 43210., 1994, 269, 12559-12566
- article (Rao2002)
- Rao, C. V.; Wolf, D. M. & Arkin, A. P.
- Control, exploitation and tolerance of intracellular noise.
- Nature,
- Department of Bioengineering, University of California, Berkeley, California 94720, USA. c_rao@lbl.gov, 2002, 420, 231-237
- phdthesis (Ray1999)
- Ray, W. K.
- Characterization of AgaR and YihW, Members of the DeoR Family of Transcriptional Regulators, and GlpE, a Rhodanese Belonging to the GlpR Regulon, Also a Member of the DeoR Family
- Faculty of the Virginia Polytechnic Institute and State, 1999
- article (Reitzer1986)
- Reitzer, L. J. & Magasanik, B.
- Transcription of glnA in E. coli is stimulated by activator bound to sites far from the promoter.
- Cell,
- 1986, 45, 785-792
- article (Resibois1984)
- Resibois, A.; Colet, M.; Faelen, M.; Schoonejans, E. & Toussaint, A.
- phiEC2, a new generalized transducing phage of Erwinia chrysanthemi.
- Virology,
- Laboratoire d'Histolvie, Faculté de Médecine, Faculté des Sciences, Université Libre de Bruxelles, Brussels, Belgium., 1984, 137, 102-112
- article (Reverchon1991)
- Reverchon, S.; Nasser, W. & Robert-Baudouy, J.
- Characterization of kdgR, a gene of Erwinia chrysanthemi that regulates pectin degradation.
- Mol Microbiol,
- Laboratoire de Génétique Moléculaire des Microorganismes, Institut National des Sciences Appliquées, Villeurbanne, France., 1991, 5, 2203-2216
- article (Rice1996)
- Rice, P. A.; Yang, S.; Mizuuchi, K. & Nash, H. A.
- Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn.
- Cell,
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA., 1996, 87, 1295-1306
- article (Rodionov2004)
- Rodionov, D. A.; Gelfand, M. S. & Hugouvieux-Cotte-Pattat, N.
- Comparative genomics of the KdgR regulon in Erwinia chrysanthemi 3937 and other gamma-proteobacteria.
- Microbiology,
- State Scientific Centre GosNIIGenetika, Moscow, 117545, Russia. rodionov@genetika.ru, 2004, 150, 3571-3590
- article (Roeder1985)
- Roeder, D. L. & Collmer, A.
- Marker-exchange mutagenesis of a pectate lyase isozyme gene in Erwinia chrysanthemi.
- J Bacteriol,
- 1985, 164, 51-56
- article (Rosario2005)
- Rosario, C. J. & Bender, R. A.
- Importance of tetramer formation by the nitrogen assimilation control protein for strong repression of glutamate dehydrogenase formation in Klebsiella pneumoniae.
- J Bacteriol,
- Department of Molecular Cellular and Developmental Biology, The University of Michigan, Ann Arbor, MI 48109-1048, USA., 2005, 187, 8291-8299
- article (Rosenfeld2002)
- Rosenfeld, N.; Elowitz, M. B. & Alon, U.
- Negative autoregulation speeds the response times of transcription networks.
- J Mol Biol,
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel., 2002, 323, 785-793
- article (Rosenfeld2006)
- Rosenfeld, N.; Perkins, T. J.; Alon, U.; Elowitz, M. B. & Swain, P. S.
- A fluctuation method to quantify in vivo fluorescence data.
- Biophys J,
- 2006, 91, 759-766
- article (Rosenfeld2005)
- Rosenfeld, N.; Young, J. W.; Alon, U.; Swain, P. S. & Elowitz, M. B.
- Gene regulation at the single-cell level.
- Science,
- 2005, 307, 1962-1965
- article (Rouanet2004)
- Rouanet, C.; Reverchon, S.; Rodionov, D. A. & Nasser, W.
- Definition of a consensus DNA-binding site for PecS, a global regulator of virulence gene expression in Erwinia chrysanthemi and identification of new members of the PecS regulon.
- J Biol Chem,
- 2004, 279, 30158-30167
- article (Saiz2008)
- Saiz, L. & Vilar, J. M. G.
- Ab initio thermodynamic modeling of distal multisite transcription regulation.
- Nucleic Acids Res,
- 2008, 36, 726-731
- article (Saiz2006)
- Saiz, L. & Vilar, J. M. G.
- DNA looping: the consequences and its control.
- Curr Opin Struct Biol,
- 2006, 16, 344-350
- article (Samarasinghe2008)
- Samarasinghe, S.; El-Robh, M. S.; Grainger, D. C.; Zhang, W.; Soultanas, P. & Busby, S. J. W.
- Autoregulation of the Escherichia coli melR promoter: repression involves four molecules of MelR.
- Nucleic Acids Res,
- School of Biosciences, The University of Birmingham, Edgbaston, Birmingham B15 2TT, UK., 2008, 36, 2667-2676
- book (Sambrook1989)
- Sambrook J, Fritsch E. F, M. T.
- Harbor, C. S. (ed.)
- Molecular cloning: a laboratory manual
- Cold Spring Harbor Laboratory, 1989
- article (Samson2005)
- Samson, R.; Legendre, J. B.; Christen, R.; Saux, M. F.; Achouak, W. & Gardan, L.
- Transfer of Pectobacterium chrysanthemi (Burkholder et al. 1953) Brenner et al. 1973 and Brenneria paradisiaca to the genus Dickeya gen. nov. as Dickeya chrysanthemi comb. nov. and Dickeya paradisiaca comb. nov. and delineation of four novel species, Dickeya dadantii sp. nov., Dickeya dianthicola sp. nov., Dickeya dieffenbachiae sp. nov. and Dickeya zeae sp. nov.
- Int J Syst Evol Microbiol,
- UMR de Pathologie Végétale INRA INH Université, BP 57, 42 rue G. Morel, 49071 Beaucouzé, France. samson@angers.inra.fr, 2005, 55, 1415-1427
- article (Savageau1974)
- Savageau, M. A.
- Comparison of classical and autogenous systems of regulation in inducible operons.
- Nature,
- 1974, 252, 546-549
- article (Schafer1991)
- Schafer, D. A.; Gelles, J.; Sheetz, M. P. & Landick, R.
- Transcription by single molecules of RNA polymerase observed by light microscopy.
- Nature,
- Department of Cell Biology, Washington University, St. Louis, Missouri 63130., 1991, 352, 444-448
- article (Schleif1992)
- Schleif, R.
- DNA LOOPING
- Annu. Rev. Biochem.,
- 1992, 61, 199-223
- article (Schleif1992a)
- Schleif, R.
- DNA looping.
- Annu Rev Biochem,
- Biology Department, Johns Hopkins University, Baltimore, Maryland 21218., 1992, 61, 199-223
- article (Schultz1991)
- Schultz, S. C.; Shields, G. C. & Steitz, T. A.
- Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees.
- Science,
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06511., 1991, 253, 1001-1007
- article (Segel1986)
- Segel, L. A.; Goldbeter, A.; Devreotes, P. N. & Knox, B. E.
- A mechanism for exact sensory adaptation based on receptor modification.
- J Theor Biol,
- 1986, 120, 151-179
- article (Semsey2002)
- Semsey, S.; Geanacopoulos, M.; Lewis, D. E. A. & Adhya, S.
- Operator-bound GalR dimers close DNA loops by direct interaction: tetramerization and inducer binding.
- EMBO J,
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute/ National Institutes of Health, Bethesda, MD 20892-4264, USA., 2002, 21, 4349-4356
- article (Sepulchre2007)
- Sepulchre, J.; Reverchon, S. & Nasser, W.
- Modeling the onset of virulence in a pectinolytic bacterium.
- J Theor Biol,
- 2007, 244, 239-257
- article (Sequencing2005)
- Sequencing, C. & Consortium, A.
- Initial sequence of the chimpanzee genome and comparison with the human genome.
- Nature,
- 2005, 437, 69-87
- article (Shadel1992)
- Shadel, G. S. & Baldwin, T. O.
- Identification of a distantly located regulatory element in the luxD gene required for negative autoregulation of the Vibrio fischeri luxR gene.
- J Biol Chem,
- M University, College Station 77843., 1992, 267, 7690-7695
- article (Shankaran2007a)
- Shankaran, H.; Resat, H. & Wiley, H. S.
- Cell surface receptors for signal transduction and ligand transport: a design principles study.
- PLoS Comput Biol,
- 2007, 3, e101
- article (Shankaran2007)
- Shankaran, H.; Wiley, H. S. & Resat, H.
- Receptor downregulation and desensitization enhance the information processing ability of signalling receptors.
- BMC Syst Biol,
- 2007, 1, 48
- article (Shin1995)
- Shin, S. & Park, C.
- Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR.
- J Bacteriol,
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Yusong-Ku, Taejon., 1995, 177, 4696-4702
- article (Smolen2007)
- Smolen, P.
- A model of late long-term potentiation simulates aspects of memory maintenance.
- PLoS ONE,
- 2007, 2, e445
- article (Smolen2006)
- Smolen, P.; Baxter, D. A. & Byrne, J. H.
- A model of the roles of essential kinases in the induction and expression of late long-term potentiation.
- Biophys J,
- 2006, 90, 2760-2775
- article (Smolen1998)
- Smolen, P.; Baxter, D. A. & Byrne, J. H.
- Frequency selectivity, multistability, and oscillations emerge from models of genetic regulatory systems.
- Am J Physiol,
- 1998, 274, C531-C542
- article (Sohanpal2004)
- Sohanpal, B. K.; El-Labany, S.; Lahooti, M.; Plumbridge, J. A. & Blomfield, I. C.
- Integrated regulatory responses of fimB to N-acetylneuraminic (sialic) acid and GlcNAc in Escherichia coli K-12.
- Proc Natl Acad Sci U S A,
- Department of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, United Kingdom., 2004, 101, 16322-16327
- article (Song2007)
- Song, H.; Smolen, P.; Av-Ron, E.; Baxter, D. A. & Byrne, J. H.
- Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins.
- Biophys J,
- 2007, 92, 3407-3424
- article (Soule2003)
- Soulé, C.
- Graphic requirements for multistationarity
- Complexus,
- 2003, 1, 123-133
- article (Stauffer1998)
- Stauffer, L. T. & Stauffer, G. V.
- Spacing and orientation requirements of GcvA-binding sites 3 and 2 and the Lrp-binding region for gcvT::lacZ expression in Escherichia coli.
- Microbiology,
- Department of Microbiology, University of Iowa, Iowa City 52242, USA., 1998, 144 ( Pt 5), 1417-1422
- article (Stauffer1998a)
- Stauffer, L. T. & Stauffer, G. V.
- Roles for GcvA-binding sites 3 and 2 and the Lrp-binding region in gcvT::lacZ expression in Escherichia coli.
- Microbiology,
- Department of Microbiology, University of Iowa, Iowa City 52242, USA. george-stauffer@uiowa.edu, 1998, 144 ( Pt 10), 2865-2872
- article (Su1990)
- Su, W.; Porter, S.; Kustu, S. & Echols, H.
- DNA-looping and enhancer activity: association between DNA-bound NtrC activator and RNA polymerase at the bacterial glnA promoter.
- Proc Natl Acad Sci U S A,
- Department of Molecular and Cell Biology, University of California, Berkeley 94720., 1990, 87, 5504-5508
- unpublished (Sumedha)
- Sumedha & Weigt, M.
- Agglomeration of DNA-looping proteins
- 2008
- article (Sumedha2008)
- Sumedha & Weigt, M.
- A thermodynamic model for the agglomeration of DNA-looping proteins
- Journal of Statistical Mechanics: Theory and Experiment,
- 2008, 11, 11005
- article (Swinger2004)
- Swinger, K. K. & Rice, P. A.
- IHF and HU: flexible architects of bent DNA.
- Curr Opin Struct Biol,
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA., 2004, 14, 28-35
- article (Thomas1980)
- Thomas, R.
- [The biological role of positive and negative feedback loops]
- Bull Mem Acad R Med Belg,
- 1980, 135, 664-673
- article (Towles2009)
- Towles, K. B.; Beausang, J. F.; Garcia, H. G.; Phillips, R. & Nelson, P. C.
- First-principles calculation of DNA looping in tethered particle experiments.
- Phys Biol,
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA., 2009, 6, 25001
- article (Travers2001)
- Travers, A.; Schneider, R. & Muskhelishvili, G.
- DNA supercoiling and transcription in Escherichia coli: The FIS connection.
- Biochimie,
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK. aat@mrc-lmb.cam.ac.uk, 2001, 83, 213-217
- article (Tuskan2006)
- Tuskan, G. A.; Difazio, S.; Jansson, S.; Bohlmann, J.; Grigoriev, I.; Hellsten, U.; Putnam, N.; Ralph, S.; Rombauts, S.; Salamov, A.; Schein, J.; Sterck, L.; Aerts, A.; Bhalerao, R. R.; Bhalerao, R. P.; Blaudez, D.; Boerjan, W.; Brun, A.; Brunner, A.; Busov, V.; Campbell, M.; Carlson, J.; Chalot, M.; Chapman, J.; Chen, G.; Cooper, D.; Coutinho, P. M.; Couturier, J.; Covert, S.; Cronk, Q.; Cunningham, R.; Davis, J.; Degroeve, S.; Déjardin, A.; Depamphilis, C.; Detter, J.; Dirks, B.; Dubchak, I.; Duplessis, S.; Ehlting, J.; Ellis, B.; Gendler, K.; Goodstein, D.; Gribskov, M.; Grimwood, J.; Groover, A.; Gunter, L.; Hamberger, B.; Heinze, B.; Helariutta, Y.; Henrissat, B.; Holligan, D.; Holt, R.; Huang, W.; Islam-Faridi, N.; Jones, S.; Jones-Rhoades, M.; Jorgensen, R.; Joshi, C.; Kangasjärvi, J.; Karlsson, J.; Kelleher, C.; Kirkpatrick, R.; Kirst, M.; Kohler, A.; Kalluri, U.; Larimer, F.; Leebens-Mack, J.; Leplé, J.; Locascio, P.; Lou, Y.; Lucas, S.; Martin, F.; Montanini, B.; Napoli, C.; Nelson, D. R.; Nelson, C.; Nieminen, K.; Nilsson, O.; Pereda, V.; Peter, G.; Philippe, R.; Pilate, G.; Poliakov, A.; Razumovskaya, J.; Richardson, P.; Rinaldi, C.; Ritland, K.; Rouzé, P.; Ryaboy, D.; Schmutz, J.; Schrader, J.; Segerman, B.; Shin, H.; Siddiqui, A.; Sterky, F.; Terry, A.; Tsai, C.; Uberbacher, E.; Unneberg, P.; Vahala, J.; Wall, K.; Wessler, S.; Yang, G.; Yin, T.; Douglas, C.; Marra, M.; Sandberg, G.; de Peer, Y. V. & Rokhsar, D.
- The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
- Science,
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA. gtk@ornl.gov, 2006, 313, 1596-1604
- article (Tyson2002)
- Tyson, J. J.; Csikasz-Nagy, A. & Novak, B.
- The dynamics of cell cycle regulation.
- Bioessays,
- 2002, 24, 1095-1109
- article (Valens2004)
- Valens, M.; Penaud, S.; Rossignol, M.; Cornet, F. & Boccard, F.
- Macrodomain organization of the Escherichia coli chromosome.
- EMBO J,
- Centre de Génétique Moléculaire du CNRS, Avenue de la Terrasse, Gif-sur-Yvette, France., 2004, 23, 4330-4341
- article (Valentin-Hansen1986)
- Valentin-Hansen, P.; Albrechtsen, B. & Larsen, J. E. L.
- DNA-protein recognition: demonstration of three genetically separated operator elements that are required for repression of the Escherichia coli deoCABD promoters by the DeoR repressor.
- EMBO J,
- 1986, 5, 2015-2021
- article (Ventura2008)
- Ventura, A. C.; Sepulchre, J. & Merajver, S. D.
- A hidden feedback in signaling cascades is revealed.
- PLoS Comput Biol,
- 2008, 4, e1000041
- article (Vilar2002)
- Vilar, J. M. G.; Kueh, H. Y.; Barkai, N. & Leibler, S.
- Mechanisms of noise-resistance in genetic oscillators.
- Proc Natl Acad Sci U S A,
- 2002, 99, 5988-5992
- article (Vilar2003)
- Vilar, J. M. G. & Leibler, S.
- DNA looping and physical constraints on transcription regulation.
- J Mol Biol,
- 2003, 331, 981-989
- article (Vilar2005)
- Vilar, J. M. G. & Saiz, L.
- DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.
- Curr Opin Genet Dev,
- Computational Biology Center, Memorial Sloan-Kettering Cancer Center, 307 East 63rd Street, New York, NY 10021, USA. vilar@cbio.mskcc.org, 2005, 15, 136-144
- article (Wang1996)
- Wang, J. H. & Kelly, P. T.
- The balance between postsynaptic Ca(2+)-dependent protein kinase and phosphatase activities controlling synaptic strength.
- Learn Mem,
- 1996, 3, 170-181
- article (Wang2007)
- Wang, Z.; Hou, Z.; Xin, H. & Zhang, Z.
- Engineered internal noise stochastic resonator in gene network: a model study.
- Biophys Chem,
- Teda Bio-X Research Center, College of Food Engineering and Biotechnology, Tianjin University of Science and Technology, No. 29, The 13th Avenue of Teda, Tianjin, PR China, 300457., 2007, 125, 281-285
- article (Wedel1990)
- Wedel, A.; Weiss, D. S.; Popham, D.; Dröge, P. & Kustu, S.
- A bacterial enhancer functions to tether a transcriptional activator near a promoter.
- Science,
- Department of Plant Pathology, University of California, Berkeley 94720., 1990, 248, 486-490
- article (Weissenborn1992)
- Weissenborn, D. L.; Wittekindt, N. & Larson, T. J.
- Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12.
- J Biol Chem,
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., 1992, 267, 6122-6131
- article (Weissenborn1992a)
- Weissenborn, D. L.; Wittekindt, N. & Larson, T. J.
- Structure and regulation of the glpFK operon encoding glycerol diffusion facilitator and glycerol kinase of Escherichia coli K-12.
- J Biol Chem,
- Department of Biochemistry and Nutrition, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308., 1992, 267, 6122-6131
- misc (Wikipedia)
- Wikipedia
- Microscope à force atomique
- article (Winder1998)
- Winder, D. G.; Mansuy, I. M.; Osman, M.; Moallem, T. M. & Kandel, E. R.
- Genetic and pharmacological evidence for a novel, intermediate phase of long-term potentiation suppressed by calcineurin.
- Cell,
- 1998, 92, 25-37
- article (Wolf2003)
- Wolf, D. M. & Arkin, A. P.
- Motifs, modules and games in bacteria.
- Curr Opin Microbiol,
- 2003, 6, 125-134
- article (Xiong2003)
- Xiong, W. & Ferrell, J. E.
- A positive-feedback-based bistable 'memory module' that governs a cell fate decision.
- Nature,
- 2003, 426, 460-465
- article (Yamamoto2003)
- Yamamoto, K. & Ishihama, A.
- Two different modes of transcription repression of the Escherichia coli acetate operon by IclR.
- Mol Microbiol,
- Department of Molecular Genetics, National Institute of Genetics, Mishima, Shizuoka 411-8504, Japan., 2003, 47, 183-194
- article (Yang1997)
- Yang, B.; Gerhardt, S. G. & Larson, T. J.
- Action at a distance for glp repressor control of glpTQ transcription in Escherichia coli K-12.
- Mol Microbiol,
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA., 1997, 24, 511-521
- article (Yang1996)
- Yang, B. & Larson, T. J.
- Action at a distance for negative control of transcription of the glpD gene encoding sn-glycerol 3-phosphate dehydrogenase of Escherichia coli K-12.
- J Bacteriol,
- Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg 24061-0308, USA., 1996, 178, 7090-7098
- article (Yang1988)
- Yang, Y. & Ames, G. F.
- DNA gyrase binds to the family of prokaryotic repetitive extragenic palindromic sequences.
- Proc Natl Acad Sci U S A,
- Department of Biochemistry, University of California, Berkeley 94720., 1988, 85, 8850-8854
- article (Yao2006)
- Yao, Y.; Martinez-Yamout, M. A.; Dickerson, T. J.; Brogan, A. P.; Wright, P. E. & Dyson, H. J.
- Structure of the Escherichia coli quorum sensing protein SdiA: activation of the folding switch by acyl homoserine lactones.
- J Mol Biol,
- Department of Molecular Biology and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA., 2006, 355, 262-273
- article (Yin1994)
- Yin, H.; Landick, R. & Gelles, J.
- Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule.
- Biophys J,
- Department of Biochemistry, Brandeis University, Waltham, Massachusetts 02254., 1994, 67, 2468-2478
- article (Yin1995)
- Yin, J. C.; Vecchio, M. D.; Zhou, H. & Tully, T.
- CREB as a memory modulator: induced expression of a dCREB2 activator isoform enhances long-term memory in Drosophila.
- Cell,
- 1995, 81, 107-115
- article (Yu2006)
- Yu, J.; Xiao, J.; Ren, X.; Lao, K. & Xie, X. S.
- Probing gene expression in live cells, one protein molecule at a time.
- Science,
- 2006, 311, 1600-1603
- article (Zhang2006)
- Zhang, Y.; McEwen, A. E.; Crothers, D. M. & Levene, S. D.
- Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping.
- PLoS One,
- Department of Chemistry, Yale University, New Haven, Connecticut, United States of America. ylzhang@lbl.gov, 2006, 1, e136
- article (Zhu2007)
- Zhu, C.; Zheng, Y. & Jia, Y.
- A theoretical study on activation of transcription factor modulated by intracellular Ca2+ oscillations.
- Biophys Chem,
- 2007, 129, 49-55
- article (Zurla2009)
- Zurla, C.; Manzo, C.; Dunlap, D.; Lewis, D. E. A.; Adhya, S. & Finzi, L.
- Direct demonstration and quantification of long-range DNA looping by the lambda bacteriophage repressor.
- Nucleic Acids Res,
- Physics Department, Emory University, Atlanta, GA 30322, USA., 2009, 37, 2789-2795
"Bacterial polyhydroxyalkanoate granules: biogenesis, structure, and potential use as nano-/micro-beads in biotechnological and biomedical applications." Grage K., Jahns A. C., Parlane N., Palanisamy R., Rasiah I. A., Atwood J. A. and Rehm B. H. A. 2009. Biomacromolecules 10, 660-669.
<b/> Modelling </b>
<p style="text-indent: 30px; text-align:justify;">“Recombinant Escherichia coli produces tailor-made biopolyester granules for applications in fluorescence activated cell sorting: functional display of the mouse interleukin-2 and myelin oligodendrocyte glycoprotein”, Thomas Bäckström, Jane A Brockelbank and Bernd HA Rehm. January 2007.BMC Biotechnology.
<p style="text-indent: 30px; text-align:justify;">“Polyhydroxyalkanoate Granules Are Complex Subcellular Organelles (Carbonosomes)” , Dieter Jendrossek ,May 2009, Journal Of Bacteriology,p. 3195–3202 .
<p style="text-indent: 30px; text-align:justify;">“Polyhydroxyalkanoate (PHA) homeostasis: the role of the PHA synthase” JoAnne Stubbe and Jiamin Tian, 2003, Nat. Prod. Rep.,20, 445–457.
<p style="text-indent: 30px; text-align:justify;"> <A NAME="et1" style="text-decoration:none">"Novel and economical purification of recombinant proteins: Intein-mediated protein purification using in vivo polyhydroxybutyrate (PHB)matrix association", Mahmoud Reza Banki, Tillman U.Gerngross and David W. Wood, 2005, Protein Science, 14:1387–1395 </A>
</div>
-moz-border-radius: 15px; -webkit-border-radius: 15px; border-radius: 15px;">
<a id="csb" href="http://fondation.insa-lyon.fr/"><img style="width: 120px; height: 60px; margin: 10px; padding-top: 15px; padding-bottom: 15px" src=""/></a>
<a id="csb" href="http://www.biomerieux.fr/"><img style="width: 120px; height: 90px; margin: 10px" src="http://www.biomerieux.fr/france/img/logo_home.png"/></a>
<a id="csb" href="http://www.insa-lyon.fr/en"><img style="width: 120px; height: 64.2px; margin: 15px; padding-top: 10px; padding-bottom: 10px" src="" /></a>
</html>