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Bibliography (39 total) : Review Only   Up

• 2013


• Cournac A, Plumbridge J (2013) DNA looping in prokaryotes: experimental and theoretical approaches. J Bacteriol 195:1109-19



• Cipriano MJ, Novichkov PN, Kazakov AE, Rodionov DA, Arkin AP, Gelfand MS, Dubchak I (2013) RegTransBase - a database of regulatory sequences and interactions based on literature: a resource for investigating transcriptional regulation in prokaryotes. BMC Genomics 14:213



• Weiss V, Medina-Rivera A, Huerta AM, Santos-Zavaleta A, Salgado H, Morett E, Collado-Vides J (2013) Evidence classification of high-throughput protocols and confidence integration in RegulonDB. Database (Oxford) 2013:bas059



• 2012


• Antiqueira L, Janga SC, Costa Lda F (2012) Extensive cross-talk and global regulators identified from an analysis of the integrated transcriptional and signaling network in Escherichia coli. Mol Biosyst 8:3028-35



• Martínez-Antonio A, Velázquez-Ramírez DA, Sánchez-Mondragón J, Santillán M (2012) Hierarchical dynamics of a transcription factors network in E. coli. Mol Biosyst 8:2932-6



• Iyer LM, Aravind L (2012) Insights from the architecture of the bacterial transcription apparatus. J Struct Biol 179:299-319



• Hussein R, Lim HN (2012) Direct comparison of small RNA and transcription factor signaling. Nucleic Acids Res 40:7269-79



• Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R (2012) Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Cell Rep 2:150-61



• Hammar P, Leroy P, Mahmutovic A, Marklund EG, Berg OG, Elf J (2012) The lac repressor displays facilitated diffusion in living cells. Science 336:1595-8



• Ishihama A (2012) Prokaryotic genome regulation: a revolutionary paradigm. Proc Jpn Acad Ser B Phys Biol Sci 88:485-508



• Tsoy OV, Pyatnitskiy MA, Kazanov MD, Gelfand MS (2012) Evolution of transcriptional regulation in closely related bacteria. BMC Evol Biol 12:200



• 2011


• Rubinstein ND, Zeevi D, Oren Y, Segal G, Pupko T (2011) The operonic location of auto-transcriptional repressors is highly conserved in bacteria. Mol Biol Evol 28:3309-18



• Bendtsen KM, Erdossy J, Csiszovszki Z, Svenningsen SL, Sneppen K, Krishna S, Semsey S (2011) Direct and indirect effects in the regulation of overlapping promoters. Nucleic Acids Res 39:6879-85



• Zare H, Kaveh M, Khodursky A (2011) Inferring a transcriptional regulatory network from gene expression data using nonlinear manifold embedding. PLoS One 6:e21969



• Gama-Castro S, Salgado H, Peralta-Gil M, Santos-Zavaleta A, Muñiz-Rascado L, Solano-Lira H, Jimenez-Jacinto V, Weiss V, García-Sotelo JS, López-Fuentes A, Porrón-Sotelo L, Alquicira-Hernández S, Medina-Rivera A, Martínez-Flores I, Alquicira-Hernández K, Martínez-Adame R, Bonavides-Martínez C, Miranda-Rios J, Huerta AM, Mendoza-Vargas A, Collado-Torres L, Taboada B, Vega-Alvarado L, Olvera M, Olvera L, Grande R, Morett E, Collado-Vides J (2011) RegulonDB version 7.0: transcriptional regulation of Escherichia coli K-12 integrated within genetic sensory response units (Gensor Units). Nucleic Acids Res 39:D98-105



• 2010


• Pomerantz RT, O'Donnell M (2010) Polymerase trafficking: A role for transcription factors in preventing replication fork arrest. Transcription 1:136-139



• Janga SC, Contreras-Moreira B (2010) Dissecting the expression patterns of transcription factors across conditions using an integrated network-based approach. Nucleic Acids Res 38:6841-56



• Asif HM, Rolfe MD, Green J, Lawrence ND, Rattray M, Sanguinetti G (2010) TFInfer: a tool for probabilistic inference of transcription factor activities. Bioinformatics 26:2635-6



• Ishihama A (2010) Prokaryotic genome regulation: multifactor promoters, multitarget regulators and hierarchic networks. FEMS Microbiol Rev 34:628-45 Review



• Langlois RE, Lu H (2010) Boosting the prediction and understanding of DNA-binding domains from sequence. Nucleic Acids Res 38:3149-58



• Kinney JB, Murugan A, Callan CG, Cox EC (2010) Using deep sequencing to characterize the biophysical mechanism of a transcriptional regulatory sequence. Proc Natl Acad Sci U S A 107:9158-63



• Xiao R, Roman-Sanchez R, Moore DD (2010) DamIP: a novel method to identify DNA binding sites in vivo. Nucl Recept Signal 8:e003



• Li G, Liu B, Xu Y (2010) Accurate recognition of cis-regulatory motifs with the correct lengths in prokaryotic genomes. Nucleic Acids Res 38:e12



• Martínez-Núñez MA, Perez-Rueda E, Gutierrez-Ríos RM, Merino E (2010) New insights into the regulatory networks of paralogous genes in bacteria. Microbiology 156:14-22 Review



• 2009


• Li GW, Elf J (2009) Single molecule approaches to transcription factor kinetics in living cells. FEBS Lett 583:3979-83 Review



• Huttenhower C, Mutungu KT, Indik N, Yang W, Schroeder M, Forman JJ, Troyanskaya OG, Coller HA (2009) Detailing regulatory networks through large scale data integration. Bioinformatics 25:3267-74



• Grainger DC, Lee DJ, Busby SJ (2009) Direct methods for studying transcription regulatory proteins and RNA polymerase in bacteria. Curr Opin Microbiol 12:531-5 Review



• Mendoza-Vargas A, Olvera L, Olvera M, Grande R, Vega-Alvarado L, Taboada B, Jimenez-Jacinto V, Salgado H, Juárez K, Contreras-Moreira B, Huerta AM, Collado-Vides J, Morett E (2009) Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS One 4:e7526



• Chan TM, Li G, Leung KS, Lee KH (2009) Discovering multiple realistic TFBS motifs based on a generalized model. BMC Bioinformatics 10:321



• Pérez AG, Angarica VE, Collado-Vides J, Vasconcelos AT (2009) From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters. BMC Mol Biol 10:92



• Keilwagen J, Baumbach J, Kohl TA, Grosse I (2009) MotifAdjuster: a tool for computational reassessment of transcription factor binding site annotations. Genome Biol 10:R46



• Browning D, Savery N, Kolb A, Busby S (2009) Assays for transcription factor activity. Methods Mol Biol 543:369-87



• 2008


• Cho BK, Barrett CL, Knight EM, Park YS, Palsson Ø (2008) Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli. Proc Natl Acad Sci U S A 105:19462-7



• Ernst J, Beg QK, Kay KA, Balázsi G, Oltvai ZN, Bar-Joseph Z (2008) A semi-supervised method for predicting transcription factor-gene interactions in Escherichia coli. PLoS Comput Biol 4:e1000044



• Grainger DC, Busby SJ (2008) Global regulators of transcription in Escherichia coli: mechanisms of action and methods for study. Adv Appl Microbiol 65:93-113 Review



• Wang H, Benham CJ (2008) Superhelical destabilization in regulatory regions of stress response genes. PLoS Comput Biol 4:e17



• 2007


• Koschützki D, Schwöbbermeyer H, Schreiber F (2007) Ranking of network elements based on functional substructures. J Theor Biol 248:471-9



• Price MN, Dehal PS, Arkin AP (2007) Orthologous transcription factors in bacteria have different functions and regulate different genes. PLoS Comput Biol 3:1739-50



• Salgado H, Martínez-Antonio A, Janga SC (2007) Conservation of transcriptional sensing systems in prokaryotes: a perspective from Escherichia coli. FEBS Lett 581:3499-506