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Research"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"900","DOI":"10.1101\/gr.070276.107","article-title":"Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-\/AT-tracts","volume":"18","author":"BK Cho","year":"2008","journal-title":"Genome research"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.jmb.2007.11.101","article-title":"Functional characterization of the Escherichia coli Fis-DNA binding sequence","volume":"376","author":"Y Shao","year":"2008","journal-title":"Journal of Molecular Biology"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1006\/jmbi.1998.2160","article-title":"A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K-12 genome","volume":"284","author":"K Robison","year":"1998","journal-title":"Journal of Molecular Biology"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"2073","DOI":"10.1093\/nar\/gkq934","article-title":"Direct and indirect effects of H-NS and Fis on global gene expression control in Escherichia coli","volume":"39","author":"C Kahramanoglou","year":"2011","journal-title":"Nucleic Acids Research"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"1790","DOI":"10.1093\/nar\/gkp1084","article-title":"DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation","volume":"38","author":"BS Alexandrov","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1103\/PhysRevE.58.3585","article-title":"Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains","volume":"58","author":"A Campa","year":"1998","journal-title":"Phys Rev E"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"165103","DOI":"10.1063\/1.3654958","article-title":"Determining the DNA stability parameters for the breathing dynamics of heterogeneous DNA by stochastic optimization","volume":"135","author":"S Talukder","year":"2011","journal-title":"The Journal of chemical physics"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.gene.2007.12.011","article-title":"DNA sequence and structural properties as predictors of human and mouse promoters","volume":"410","author":"P Akan","year":"2008","journal-title":"Gene"},{"key":"ref65","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1007\/s10867-009-9125-4","article-title":"Nonlinearity in DNA and its relation to specific functions","volume":"35","author":"B Alexandrov","year":"2009","journal-title":"Journal of biological physics"},{"key":"ref66","doi-asserted-by":"crossref","first-page":"D583","DOI":"10.1093\/nar\/gkq1143","article-title":"EcoCyc: a 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O6-methylguanine","volume":"29","author":"SL Ginell","year":"1990","journal-title":"Biochemistry"},{"key":"ref70","doi-asserted-by":"crossref","first-page":"9573","DOI":"10.1073\/pnas.87.24.9573","article-title":"High-resolution structure of a mutagenic lesion in DNA","volume":"87","author":"GA Leonard","year":"1990","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref71","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1021\/bi00353a012","article-title":"Structural studies of the O6meG.C interaction in the d(C-G-C-G-A-A-T-T-C-O6meG-C-G) duplex","volume":"25","author":"DJ Patel","year":"1986","journal-title":"Biochemistry"},{"key":"ref72","doi-asserted-by":"crossref","first-page":"6182","DOI":"10.1021\/bi00441a009","article-title":"O6-ethylguanine carcinogenic lesions in DNA: an NMR study of O6etG.C pairing in dodecanucleotide duplexes","volume":"28","author":"MW Kalnik","year":"1989","journal-title":"Biochemistry"},{"key":"ref73","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1128\/MMBR.54.4.342-380.1990","article-title":"The single-stranded DNA-binding protein of Escherichia coli","volume":"54","author":"RR Meyer","year":"1990","journal-title":"Microbiological reviews"},{"key":"ref74","doi-asserted-by":"crossref","first-page":"283","DOI":"10.1016\/j.sbi.2004.05.004","article-title":"Structure and evolution of transcriptional regulatory networks","volume":"14","author":"MM Babu","year":"2004","journal-title":"Current opinion in structural biology"},{"key":"ref75","doi-asserted-by":"crossref","first-page":"13577","DOI":"10.1073\/pnas.93.24.13577","article-title":"Cocrystal structure of YY1 bound to the adeno-associated virus P5 initiator","volume":"93","author":"HB Houbaviy","year":"1996","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref76","doi-asserted-by":"crossref","first-page":"1115","DOI":"10.1016\/0092-8674(94)90387-5","article-title":"TATA-binding protein-independent initiation: YY1, TFIIB, and RNA polymerase II direct basal transcription on supercoiled template DNA","volume":"76","author":"A Usheva","year":"1994","journal-title":"Cell"},{"key":"ref77","first-page":"459","article-title":"Steroid hormone receptors: interaction with deoxyribonucleic acid and transcription factors","volume":"14","author":"M Truss","year":"1993","journal-title":"Endocrine reviews"},{"key":"ref78","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.1093\/nar\/25.18.3733","article-title":"Binding of NF1 to the MMTV promoter in nucleosomes: influence of rotational phasing, translational positioning and histone H1","volume":"25","author":"K Eisfeld","year":"1997","journal-title":"Nucleic Acids Research"},{"key":"ref79","doi-asserted-by":"crossref","first-page":"2090","DOI":"10.1101\/gr.094144.109","article-title":"Distinguishing direct versus indirect transcription factor-DNA interactions","volume":"19","author":"R Gordan","year":"2009","journal-title":"Genome research"},{"key":"ref80","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1093\/nar\/25.18.3559","article-title":"Transcription factor access to chromatin","volume":"25","author":"M Beato","year":"1997","journal-title":"Nucleic Acids Research"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"427","DOI":"10.1146\/annurev.bi.58.070189.002235","article-title":"DNA conformation and protein binding","volume":"58","author":"AA Travers","year":"1989","journal-title":"Annual Review of Biochemistry"},{"key":"ref82","doi-asserted-by":"crossref","first-page":"7231","DOI":"10.1073\/pnas.85.19.7231","article-title":"Energetic coupling between DNA bending and base pair opening","volume":"85","author":"J Ramstein","year":"1988","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref83","doi-asserted-by":"crossref","first-page":"021903","DOI":"10.1103\/PhysRevE.86.021903","article-title":"Breathing, bubbling, and bending: DNA flexibility from multimicrosecond simulations","volume":"86","author":"MRM Ari Zeida","year":"2012","journal-title":"Phys Rev E"},{"key":"ref84","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1224139","article-title":"Extreme Bendability of DNA Less than 100 Base Pairs Long Revealed by Single-Molecule Cyclization","volume":"337","author":"R Vafabakhsh","year":"2012","journal-title":"Science"},{"key":"ref85","doi-asserted-by":"crossref","first-page":"6332","DOI":"10.1073\/pnas.85.17.6332","article-title":"Structure of an alternating-B DNA helix and its relationship to A-tract DNA","volume":"85","author":"C Yoon","year":"1988","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref86","doi-asserted-by":"crossref","first-page":"1460","DOI":"10.1073\/pnas.95.4.1460","article-title":"A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics","volume":"95","author":"J SantaLucia Jr","year":"1998","journal-title":"Proceedings of the National Academy of Sciences of the United States of America"},{"key":"ref87","doi-asserted-by":"crossref","first-page":"6770","DOI":"10.1093\/nar\/gkg882","article-title":"Conservation of DNA curvature signals in regulatory regions of prokaryotic genes","volume":"31","author":"R Jauregui","year":"2003","journal-title":"Nucleic Acids Research"},{"key":"ref88","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1146\/annurev.micro.51.1.593","article-title":"Clues and consequences of DNA bending in transcription","volume":"51","author":"J Perez-Martin","year":"1997","journal-title":"Annual review of microbiology"},{"key":"ref89","doi-asserted-by":"crossref","first-page":"128105","DOI":"10.1103\/PhysRevLett.97.128105","article-title":"Sequence sensitivity of breathing dynamics in heteropolymer DNA","volume":"97","author":"T Ambjornsson","year":"2006","journal-title":"Physical review letters"},{"key":"ref90","doi-asserted-by":"crossref","first-page":"2674","DOI":"10.1529\/biophysj.106.095935","article-title":"Breathing dynamics in heteropolymer DNA","volume":"92","author":"T Ambjornsson","year":"2007","journal-title":"Biophysical journal"},{"key":"ref91","doi-asserted-by":"crossref","first-page":"863","DOI":"10.1016\/j.dnarep.2006.04.007","article-title":"Ultra-violet light induced changes in DNA dynamics may enhance TT-dimer recognition","volume":"5","author":"KB Blagoev","year":"2006","journal-title":"DNA repair"},{"key":"ref92","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1063\/1.1699114","article-title":"Equations of state calculations by fast computing machines","volume":"21","author":"N Metropolis","year":"1953","journal-title":"J Chem Phys"},{"key":"ref93","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1016\/j.jmb.2004.02.072","article-title":"Bubble nucleation and cooperativity in DNA melting","volume":"339","author":"Y Zeng","year":"2004","journal-title":"Journal of Molecular Biology"},{"key":"ref94","doi-asserted-by":"crossref","first-page":"64","DOI":"10.1016\/j.mrfmmm.2011.06.004","article-title":"O(6)-methylguanine-DNA methyltransferase (MGMT): impact on cancer risk in response to tobacco smoke","volume":"736","author":"M Christmann","year":"2012","journal-title":"Mutation research"},{"key":"ref95","doi-asserted-by":"crossref","first-page":"5881","DOI":"10.1021\/bi00440a026","article-title":"Thermodynamic Comparison of the Base-Pairs Formed by the Carcinogenic Lesion O-6-Methylguanine with Reference Both to Watson-Crick Pairs and to Mismatched Pairs","volume":"28","author":"BL Gaffney","year":"1989","journal-title":"Biochemistry"},{"key":"ref96","doi-asserted-by":"crossref","first-page":"D355","DOI":"10.1093\/nar\/gkp896","article-title":"KEGG for representation and analysis of molecular networks involving diseases and drugs","volume":"38","author":"M Kanehisa","year":"2010","journal-title":"Nucleic Acids Research"},{"key":"ref97","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1016\/S0022-2836(77)80200-3","article-title":"The Protein Data Bank: a computer-based archival file for macromolecular structures","volume":"112","author":"FC Bernstein","year":"1977","journal-title":"Journal of Molecular Biology"},{"key":"ref98","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1016\/0263-7855(96)00018-5","article-title":"VMD: visual molecular dynamics","volume":"14","author":"W Humphrey","year":"1996","journal-title":"Journal of molecular graphics"},{"key":"ref99","doi-asserted-by":"crossref","first-page":"27:21","DOI":"10.1145\/1961189.1961199","article-title":"LIBSVM: A library for support vector machines","volume":"2","author":"C Chang","year":"2011","journal-title":"ACM Transactions on Intelligent Systems and Technology"}],"container-title":["PLoS Computational 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