Team:INSA-Lyon/Project/References

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<h3>References</h3>
<h3>References</h3>
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<dl>
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<dt><em>article</em><a name="Adhya1989"> (Adhya1989)</a></dt>
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<dd>Adhya, S.</dd>
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<dd>Multipartite genetic control elements: communication by DNA loop.</dd>
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<dd><em>Annu Rev Genet,</em></dd>
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<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>
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<dt><em>article</em><a name="Aguilera2008"> (Aguilera2008)</a></dt>
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<dd>Aguilera, L.; Campos, E.; Giménez, R.; Badía, J.; Aguilar, J. &amp; Baldoma, L.</dd>
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<dd>Dual role of LldR in regulation of the lldPRD operon, involved in L-lactate metabolism in Escherichia coli.</dd>
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<dd><em>J Bacteriol,</em></dd>
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<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>
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<dt><em>article</em><a name="Alberti1993"> (Alberti1993)</a></dt>
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<dd>Alberti, S.; Oehler, S.; von Wilcken-Bergmann, B. &amp; Müller-Hill, B.</dd>
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<dd>Genetic analysis of the leucine heptad repeats of Lac repressor: evidence for a 4-helical bundle.</dd>
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<dd><em>EMBO J,</em></dd>
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<dd><em>Institut für Genetik, Universität zu Köln, FRG., </em><b>1993</b><i>, 12</i>, 3227-3236</dd>
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<dt><em>article</em><a name="Allen2006"> (Allen2006)</a></dt>
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<dd>Allen, T. E.; Price, N. D.; Joyce, A. R. &amp; Palsson, B. Ø.</dd>
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<dd>Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.</dd>
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<dd><em>PLoS Comput Biol,</em></dd>
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<dd><em>Department of Bioengineering, University of California San Diego, La Jolla, California, USA., </em><b>2006</b><i>, 2</i>, e2</dd>
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<dt><em>article</em><a name="Alon2007"> (Alon2007)</a></dt>
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<dd>Alon, U.</dd>
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<dd>Network motifs: theory and experimental approaches.</dd>
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<dd><em>Nat Rev Genet,</em></dd>
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<dd><b>2007</b><i>, 8</i>, 450-461</dd>
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<dt><em>book</em><a name="Alon2006"> (Alon2006)</a></dt>
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<dd>Alon, U.</dd>
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<dd>An Introduction to Systems Biology</dd>
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<dd><em>Chapman &amp; Hall/CRC, </em><b>2006</b></dd>
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<dt><em>article</em><a name="Altan-Bonnet2003"> (Altan-Bonnet2003)</a></dt>
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<dd>Altan-Bonnet, G.; Libchaber, A. &amp; Krichevsky, O.</dd>
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<dd>Bubble dynamics in double-stranded DNA.</dd>
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<dd><em>Phys Rev Lett,</em></dd>
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<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>
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<dt><em>article</em><a name="Amouyal2005"> (Amouyal2005)</a></dt>
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<dd>Amouyal, M.</dd>
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<dd>Gene regulation at-a-distance in E. coli: new insights.</dd>
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<dd><em>C R Biol,</em></dd>
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<dd><b>2005</b><i>, 328</i>, 1-9</dd>
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<dt><em>article</em><a name="Amouyal1989"> (Amouyal1989)</a></dt>
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<dd>Amouyal, M.; Mortensen, L.; Buc, H. &amp; Hammer, K.</dd>
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<dd>Single and double loop formation when deoR repressor binds to its natural operator sites.</dd>
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<dd><em>Cell,</em></dd>
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<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>
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<dt><em>article</em><a name="Ansel2008"> (Ansel2008)</a></dt>
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<dd>Ansel, J.; Bottin, H.; Rodriguez-Beltran, C.; Damon, C.; Nagarajan, M.; Fehrmann, S.; François, J. &amp; Yvert, G.</dd>
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<dd>Cell-to-cell stochastic variation in gene expression is a complex genetic trait.</dd>
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<dd><em>PLoS Genet,</em></dd>
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<dd><em>Université de Lyon, Lyon, France., </em><b>2008</b><i>, 4</i>, e1000049</dd>
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<dt><em>article</em><a name="Atkinson2003"> (Atkinson2003)</a></dt>
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<dd>Atkinson, M. R.; Savageau, M. A.; Myers, J. T. &amp; Ninfa, A. J.</dd>
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<dd>Development of genetic circuitry exhibiting toggle switch or oscillatory behavior in Escherichia coli.</dd>
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<dd><em>Cell,</em></dd>
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<dd><b>2003</b><i>, 113</i>, 597-607</dd>
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<dt><em>article</em><a name="Atlung1997"> (Atlung1997)</a></dt>
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<dd>Atlung, T. &amp; Ingmer, H.</dd>
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<dd>H-NS: a modulator of environmentally regulated gene expression.</dd>
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<dd><em>Mol Microbiol,</em></dd>
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<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>
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<dt><em>article</em><a name="Bachellier1999"> (Bachellier1999)</a></dt>
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<dd>Bachellier, S.; Clément, J. M. &amp; Hofnung, M.</dd>
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<dd>Short palindromic repetitive DNA elements in enterobacteria: a survey.</dd>
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<dd><em>Res Microbiol,</em></dd>
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<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>
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<dt><em>mastersthesis</em><a name="Baglio2008"> (Baglio2008)</a></dt>
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<dd>Baglio, J.</dd>
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<dd>Dynamique du biopolym&eacute;re ADN en suivi de particule unique :simulations et exp&eacute;riences dans le cadre du s m&eacute;canisme de transposition.</dd>
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<dd><em>ENS, </em><b>2008</b></dd>
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<dt><em>article</em><a name="Bahloul2001"> (Bahloul2001)</a></dt>
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<dd>Bahloul, A.; Boubrik, F. &amp; Rouviere-Yaniv, J.</dd>
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<dd>Roles of Escherichia coli histone-like protein HU in DNA replication: HU-beta suppresses the thermosensitivity of dnaA46ts.</dd>
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<dd><em>Biochimie,</em></dd>
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<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>
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<dt><em>article</em><a name="Barkai2000"> (Barkai2000)</a></dt>
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<dd>Barkai, N. &amp; Leibler, S.</dd>
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<dd>Circadian clocks limited by noise.</dd>
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<dd><em>Nature,</em></dd>
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<dd><b>2000</b><i>, 403</i>, 267-268</dd>
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<dt><em>article</em><a name="Becskei2000"> (Becskei2000)</a></dt>
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<dd>Becskei, A. &amp; Serrano, L.</dd>
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<dd>Engineering stability in gene networks by autoregulation.</dd>
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<dd><em>Nature,</em></dd>
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<dd><b>2000</b><i>, 405</i>, 590-593</dd>
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<dt><em>article</em><a name="Behar2007"> (Behar2007)</a></dt>
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<dd>Behar, M.; Dohlman, H. G. &amp; Elston, T. C.</dd>
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<dd>Kinetic insulation as an effective mechanism for achieving pathway specificity in intracellular signaling networks.</dd>
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<dd><em>Proc Natl Acad Sci U S A,</em></dd>
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<dd><b>2007</b><i>, 104</i>, 16146-16151</dd>
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<dt><em>article</em><a name="Berg1981"> (Berg1981)</a></dt>
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<dd>Berg, O. G.; Winter, R. B. &amp; von Hippel, P. H.</dd>
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<dd>Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.</dd>
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<dd><em>Biochemistry,</em></dd>
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<dd><b>1981</b><i>, 20</i>, 6929-6948</dd>
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<dt><em>article</em><a name="Bergstrom1998"> (Bergstrom1998)</a></dt>
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<dd>Bergstrom, L. C.; Qin, L.; Harlocker, S. L.; Egger, L. A. &amp; Inouye, M.</dd>
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<dd>Hierarchical and co-operative binding of OmpR to a fusion construct containing the ompC and ompF upstream regulatory sequences of Escherichia coli.</dd>
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<dd><em>Genes Cells,</em></dd>
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<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>
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<dt><em>article</em><a name="Bhalla1999"> (Bhalla1999)</a></dt>
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<dd>Bhalla, U. S. &amp; Iyengar, R.</dd>
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<dd>Emergent properties of networks of biological signaling pathways.</dd>
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<dd><em>Science,</em></dd>
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<dd><b>1999</b><i>, 283</i>, 381-387</dd>
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<dt><em>article</em><a name="Blanco1986"> (Blanco1986)</a></dt>
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<dd>Blanco, C.; Ritzenthaler, P. &amp; Mata-Gilsinger, M.</dd>
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<dd>Negative dominant mutations of the uidR gene in Escherichia coli: genetic proof for a cooperative regulation of uidA expression.</dd>
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<dd><em>Genetics,</em></dd>
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<dd><b>1986</b><i>, 112</i>, 173-182</dd>
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<dt><em>article</em><a name="Blot2002"> (Blot2002)</a></dt>
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<dd>Blot, N.; Berrier, C.; Hugouvieux-Cotte-Pattat, N.; Ghazi, A. &amp; Condemine, G.</dd>
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<dd>The oligogalacturonate-specific porin KdgM of Erwinia chrysanthemi belongs to a new porin family.</dd>
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<dd><em>J Biol Chem,</em></dd>
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<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>
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<dt><em>article</em><a name="Bondarenko2003"> (Bondarenko2003)</a></dt>
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<dd>Bondarenko, V. A.; Liu, Y. V.; Jiang, Y. I. &amp; Studitsky, V. M.</dd>
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<dd>Communication over a large distance: enhancers and insulators.</dd>
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<dd><em>Biochem Cell Biol,</em></dd>
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<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>
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<dt><em>article</em><a name="Brunetti2001"> (Brunetti2001)</a></dt>
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<dd>Brunetti, R.; Prosseda, G.; Beghetto, E.; Colonna, B. &amp; Micheli, G.</dd>
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<dd>The looped domain organization of the nucleoid in histone-like protein defective Escherichia coli strains.</dd>
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<dd><em>Biochimie,</em></dd>
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<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>
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<dt><em>article</em><a name="Buchler2003"> (Buchler2003)</a></dt>
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<dd>Buchler, N. E.; Gerland, U. &amp; Hwa, T.</dd>
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<dd>On schemes of combinatorial transcription logic.</dd>
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<dd><em>Proc Natl Acad Sci U S A,</em></dd>
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<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>
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<dt><em>article</em><a name="Bundschuh2003"> (Bundschuh2003)</a></dt>
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<dd>Bundschuh, R.; Hayot, F. &amp; Jayaprakash, C.</dd>
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<dd>The role of dimerization in noise reduction of simple genetic networks.</dd>
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<dd><em>J Theor Biol,</em></dd>
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<dd><b>2003</b><i>, 220</i>, 261-269</dd>
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<dt><em>article</em><a name="Carew1972"> (Carew1972)</a></dt>
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<dd>Carew, T. J.; Pinsker, H. M. &amp; Kandel, E. R.</dd>
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<dd>Long-Term Habituation of a Defensive Withdrawal Reflex in Aplysia.</dd>
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<dd><em>Science,</em></dd>
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<dd><b>1972</b><i>, 175</i>, 451-454</dd>
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<dt><em>article</em><a name="Carlo2006"> (Carlo2006)</a></dt>
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<dd>Carlo, S. D.; Chen, B.; Hoover, T. R.; Kondrashkina, E.; Nogales, E. &amp; Nixon, B. T.</dd>
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<dd>The structural basis for regulated assembly and function of the transcriptional activator NtrC.</dd>
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<dd><em>Genes Dev,</em></dd>
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<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>
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<dt><em>article</em><a name="Carpentier2005"> (Carpentier2005)</a></dt>
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<dd>Carpentier, A.; Torrésani, B.; Grossmann, A. &amp; Hénaut, A.</dd>
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<dd>Decoding the nucleoid organisation of Bacillus subtilis and Escherichia coli through gene expression data.</dd>
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<dd><em>BMC Genomics,</em></dd>
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<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>
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<dt><em>article</em><a name="Castillo1998"> (Castillo1998)</a></dt>
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<dd>Castillo, A.; Nasser, W.; Condemine, G. &amp; Reverchon, S.</dd>
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<dd>The PecT repressor interacts with regulatory regions of pectate lyase genes in Erwinia chrysanthemi.</dd>
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<dd><em>Biochim Biophys Acta,</em></dd>
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<dd><b>1998</b><i>, 1442</i>, 148-160</dd>
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<dt><em>article</em><a name="Charlier1992"> (Charlier1992)</a></dt>
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<dd>Charlier, D.; Roovers, M.; Vliet, F. V.; Boyen, A.; Cunin, R.; Nakamura, Y.; Glansdorff, N. &amp; Piérard, A.</dd>
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<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>
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<dd><em>J Mol Biol,</em></dd>
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<dd><em>Research Institute of the CERIA-COOVI, Brussels, Belgium., </em><b>1992</b><i>, 226</i>, 367-386</dd>
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<dt><em>article</em><a name="Chen2010"> (Chen2010)</a></dt>
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<dd>Chen, Y.; Milstein, J. N. &amp; Meiners, J.</dd>
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<dd>Femtonewton entropic forces can control the formation of protein-mediated DNA loops.</dd>
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<dd><em>Phys Rev Lett,</em></dd>
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<dd><em>Department of Biomedical Engineering, University of Michigan, Ann Arbor, Michigan 48109, USA., </em><b>2010</b><i>, 104</i>, 048301</dd>
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<dt><em>article</em><a name="Cherry2000"> (Cherry2000)</a></dt>
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<dd>Cherry, J. L. &amp; Adler, F. R.</dd>
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<dd>How to make a biological switch.</dd>
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<dd><em>J Theor Biol,</em></dd>
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<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>
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<dt><em>article</em><a name="Chiam2007"> (Chiam2007)</a></dt>
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<dd>Chiam, K. &amp; Rajagopal, G.</dd>
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<dd>Oscillations in intracellular signaling cascades.</dd>
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<dd><em>Phys Rev E Stat Nonlin Soft Matter Phys,</em></dd>
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<dd><b>2007</b><i>, 75</i>, 061901</dd>
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<dt><em>article</em><a name="Ciliberti2007"> (Ciliberti2007)</a></dt>
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<dd>Ciliberti, S.; Martin, O. C. &amp; Wagner, A.</dd>
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<dd>Innovation and robustness in complex regulatory gene networks.</dd>
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<dd><em>Proc Natl Acad Sci U S A,</em></dd>
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<dd><b>2007</b><i>, 104</i>, 13591-13596</dd>
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<dt><em>article</em><a name="Ciliberto2005"> (Ciliberto2005)</a></dt>
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<dd>Ciliberto, A.; Novak, B. &amp; Tyson, J. J.</dd>
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<dd>Steady states and oscillations in the p53/Mdm2 network.</dd>
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<dd><em>Cell Cycle,</em></dd>
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<dd><b>2005</b><i>, 4</i>, 488-493</dd>
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<dt><em>article</em><a name="Condemine1992"> (Condemine1992)</a></dt>
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<dd>Condemine, G.; Dorel, C.; Hugouvieux-Cotte-Pattat, N. &amp; Robert-Baudouy, J.</dd>
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<dd>Some of the out genes involved in the secretion of pectate lyases in Erwinia chrysanthemi are regulated by kdgR.</dd>
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<dd><em>Mol Microbiol,</em></dd>
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<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>
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<dt><em>article</em><a name="Cook2002"> (Cook2002)</a></dt>
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<dd>Cook, P. R.</dd>
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<dd>Predicting three-dimensional genome structure from transcriptional activity.</dd>
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<dd><em>Nat Genet,</em></dd>
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<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>
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<dt><em>article</em><a name="Cox2006"> (Cox2006)</a></dt>
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<dd>Cox, C. D.; McCollum, J. M.; Austin, D. W.; Allen, M. S.; Dar, R. D. &amp; Simpson, M. L.</dd>
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<dd>Frequency domain analysis of noise in simple gene circuits.</dd>
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<dd><em>Chaos,</em></dd>
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<dd><b>2006</b><i>, 16</i>, 026102</dd>
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<dt><em>book</em><a name="Frederic2002"> (Frederic2002)</a></dt>
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<dd>Dardel, F. &amp; Képès, F.</dd>
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<dd>de l'Ecole Polytechnique, L. E. <i>(ed.)</i></dd>
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<dd>Bioinformatique Génomique et post-génomique</dd>
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<dd><b>2002</b></dd>
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<dt><em>article</em><a name="Dekker2008"> (Dekker2008)</a></dt>
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<dd>Dekker, J.</dd>
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<dd>Gene regulation in the third dimension.</dd>
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<dd><em>Science,</em></dd>
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<dd><b>2008</b><i>, 319</i>, 1793-1794</dd>
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<dt><em>article</em><a name="Dekker2002"> (Dekker2002)</a></dt>
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<dd>Dekker, J.; Rippe, K.; Dekker, M. &amp; Kleckner, N.</dd>
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<dd>Capturing chromosome conformation.</dd>
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<dd><em>Science,</em></dd>
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<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>
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<dt><em>article</em><a name="Delord2007"> (Delord2007)</a></dt>
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<dd>Delord, B.; Berry, H.; Guigon, E. &amp; Genet, S.</dd>
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<dd>A new principle for information storage in an enzymatic pathway model.</dd>
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<dd><em>PLoS Comput Biol,</em></dd>
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<dd><b>2007</b><i>, 3</i>, e124</dd>
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<dt><em>article</em><a name="Dolmetsch1998"> (Dolmetsch1998)</a></dt>
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<dd>Dolmetsch, R. E.; Xu, K. &amp; Lewis, R. S.</dd>
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<dd>Calcium oscillations increase the efficiency and specificity of gene expression.</dd>
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<dd><em>Nature,</em></dd>
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<dd><b>1998</b><i>, 392</i>, 933-936</dd>
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<dt><em>article</em><a name="Dostie2007"> (Dostie2007)</a></dt>
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<dd>Dostie, J.; Zhan, Y. &amp; Dekker, J.</dd>
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<dd>Chromosome conformation capture carbon copy technology.</dd>
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<dd><em>Curr Protoc Mol Biol,</em></dd>
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<dd><b>2007</b><i>, Chapter 21</i>, Unit 21.14</dd>
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<dt><em>article</em><a name="Dunlap2004"> (Dunlap2004)</a></dt>
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<dd>Dunlap, J. C. &amp; Loros, J. J.</dd>
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<dd>The neurospora circadian system.</dd>
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<dd><em>J Biol Rhythms,</em></dd>
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<dd><b>2004</b><i>, 19</i>, 414-424</dd>
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<dt><em>article</em><a name="Dunn1984"> (Dunn1984)</a></dt>
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<dd>Dunn, T. M.; Hahn, S.; Ogden, S. &amp; Schleif, R. F.</dd>
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<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>
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<dd><em>Proc Natl Acad Sci U S A,</em></dd>
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<dd><b>1984</b><i>, 81</i>, 5017-5020</dd>
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"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>

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