TY - JOUR AU - Cook, P. R. PY - 2010 DA - 2010// TI - A model for all genomes: the role of transcription factories JO - J Mol Biol VL - 395 UR - https://doi.org/10.1016/j.jmb.2009.10.031 DO - 10.1016/j.jmb.2009.10.031 ID - Cook2010 ER - TY - JOUR AU - Huynen, M. A. AU - Snel, B. PY - 2000 DA - 2000// TI - Gene and context: integrative approaches to genome analysis JO - Adv Protein Chem VL - 54 UR - https://doi.org/10.1016/S0065-3233(00)54010-8 DO - 10.1016/S0065-3233(00)54010-8 ID - Huynen2000 ER - TY - JOUR AU - Képès, F. PY - 2004 DA - 2004// TI - Periodic transcriptional organization of the E.coli genome JO - J Mol Biol VL - 340 UR - https://doi.org/10.1016/j.jmb.2004.05.039 DO - 10.1016/j.jmb.2004.05.039 ID - Képès2004 ER - TY - JOUR AU - Képès, F. PY - 2003 DA - 2003// TI - Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites JO - J Mol Biol VL - 329 UR - https://doi.org/10.1016/S0022-2836(03)00535-7 DO - 10.1016/S0022-2836(03)00535-7 ID - Képès2003 ER - TY - STD TI - Bouyioukos C, Elati M, Képès F. Hydrocarbon and Lipid Microbiology Protocols Springer Protocols Handbooks In: McGenity TJ, Timmis KN, Nogales Fernández B, editors. Heidelberg: Humana Press: 2015. p. 1–16, doi:http://dx.doi.org/10.1007/8623_2015_92. http://link.springer.com/protocol/10.1007%8623_2015_92. UR - http://link.springer.com/protocol/10.1007%8623_2015_92 ID - ref5 ER - TY - JOUR AU - Jeong, K. S. AU - Ahn, J. AU - Khodursky, A. B. PY - 2004 DA - 2004// TI - Spatial patterns of transcriptional activity in the chromosome of Escherichia coli JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-11-r86 DO - 10.1186/gb-2004-5-11-r86 ID - Jeong2004 ER - TY - JOUR AU - Junier, I. AU - Hérisson, J. AU - Képès, F. PY - 2012 DA - 2012// TI - Genomic organization of evolutionarily correlated genes in bacteria: limits and strategies JO - J Mol Biol VL - 419 UR - https://doi.org/10.1016/j.jmb.2012.03.009 DO - 10.1016/j.jmb.2012.03.009 ID - Junier2012 ER - TY - JOUR AU - Wright, M. A. AU - Kharchenko, P. AU - Church, G. M. AU - Segré, D. PY - 2007 DA - 2007// TI - Chromosomal periodicity of evolutionarily conserved gene pairs JO - Proc Natl Acad Sci U S A VL - 104 UR - https://doi.org/10.1073/pnas.0610776104 DO - 10.1073/pnas.0610776104 ID - Wright2007 ER - TY - JOUR AU - Dekker, J. PY - 2008 DA - 2008// TI - Gene regulation in the third dimension JO - Science VL - 319 UR - https://doi.org/10.1126/science.1152850 DO - 10.1126/science.1152850 ID - Dekker2008 ER - TY - JOUR AU - Spilianakis, C. G. AU - Lalioti, M. D. AU - Town, T. AU - Lee, G. R. AU - Flavell, R. A. PY - 2005 DA - 2005// TI - Interchromosomal associations between alternatively expressed loci JO - Nature VL - 435 UR - https://doi.org/10.1038/nature03574 DO - 10.1038/nature03574 ID - Spilianakis2005 ER - TY - JOUR AU - Papantonis, A. AU - Cook, P. R. PY - 2013 DA - 2013// TI - Transcription factories: genome organization and gene regulation JO - Chem Rev VL - 113 UR - https://doi.org/10.1021/cr300513p DO - 10.1021/cr300513p ID - Papantonis2013 ER - TY - JOUR AU - Junier, I. AU - Hérisson, J. AU - Képès, F. PY - 2010 DA - 2010// TI - Periodic pattern detection in sparse boolean sequences JO - Algorithm Mol Biol VL - 5 UR - https://doi.org/10.1186/1748-7188-5-31 DO - 10.1186/1748-7188-5-31 ID - Junier2010 ER - TY - STD TI - Elati M, Fekih R, Nicolle R, Junier I, Herisson J, Kepes F. Boosting binding sites prediction using gene positions. Lect Notes Comput Sci. 2011:92–103. doi:http://dx.doi.org/10.1007/978-3-642-23038-7_9. UR - http://dx.doi.org/10.1007/978-3-642-23038-7_9 ID - ref13 ER - TY - JOUR AU - Képès, F. AU - Vaillant, C. PY - 2003 DA - 2003// TI - Transcription-based solenoidal model of chromosomes JO - ComPlexUs VL - 1 UR - https://doi.org/10.1159/000082184 DO - 10.1159/000082184 ID - Képès2003 ER - TY - JOUR AU - Dorman, C. J. PY - 2013 DA - 2013// TI - Genome architecture and global gene regulation in bacteria: making progress towards a unified model? JO - Nat Rev Microbiol VL - 11 UR - https://doi.org/10.1038/nrmicro3007 DO - 10.1038/nrmicro3007 ID - Dorman2013 ER - TY - JOUR AU - Dillon, S. C. AU - Dorman, C. J. PY - 2010 DA - 2010// TI - Bacterial nucleoid-associated proteins, nucleoid structure and gene expression JO - Nat Rev Microbiol VL - 8 UR - https://doi.org/10.1038/nrmicro2261 DO - 10.1038/nrmicro2261 ID - Dillon2010 ER - TY - STD TI - Weng X, Xiao J. Spatial organization of transcription in bacterial cells. Trends Genet. 2014. doi:http://dx.doi.org/10.1016/j.tig.2014.04.008. UR - http://dx.doi.org/10.1016/j.tig.2014.04.008 ID - ref17 ER - TY - JOUR AU - Sutherland, H. AU - Bickmore, W. A. PY - 2009 DA - 2009// TI - Transcription factories: gene expression in unions? JO - Nat Rev Genet VL - 10 UR - https://doi.org/10.1038/nrg2592 DO - 10.1038/nrg2592 ID - Sutherland2009 ER - TY - JOUR AU - Képès, F. AU - Jester, B. C. AU - Lepage, T. AU - Rafiei, N. AU - Rosu, B. AU - Junier, I. PY - 2012 DA - 2012// TI - The layout of a bacterial genome JO - FEBS Lett VL - 586 UR - https://doi.org/10.1016/j.febslet.2012.03.051 DO - 10.1016/j.febslet.2012.03.051 ID - Képès2012 ER - TY - CHAP AU - Ester, M. AU - Kriegel, H. -. p. AU - Jörg, S. AU - Xu, X. PY - 1996 DA - 1996// TI - A density-based algorithm for discovering clusters in large spatial databases with noise BT - Proceedings of the Second International Conference on Knowledge Discovery and Data Mining (KDD-96) PB - AAAI Press CY - Palo Alto ID - Ester1996 ER - TY - BOOK PY - 2015 DA - 2015// TI - R: A Language and Environment for Statistical Computing PB - R Foundation for Statistical Computing CY - Vienna ID - ref21 ER - TY - JOUR AU - Schapire, R. E. AU - Singer, Y. PY - 1999 DA - 1999// TI - Improved boosting algorithms using confidence-rated predictions JO - Mach Learn VL - 37 UR - https://doi.org/10.1023/A:1007614523901 DO - 10.1023/A:1007614523901 ID - Schapire1999 ER - TY - JOUR AU - Valens, M. AU - Penaud, S. AU - Rossignol, M. AU - Cornet, F. AU - Boccard, F. PY - 2004 DA - 2004// TI - Macrodomain organization of the Escherichia coli chromosome JO - EMBO J VL - 23 UR - https://doi.org/10.1038/sj.emboj.7600434 DO - 10.1038/sj.emboj.7600434 ID - Valens2004 ER - TY - JOUR AU - Salgado, H. AU - Peralta-Gil, M. AU - Gama-Castro, S. AU - Santos-Zavaleta, A. AU - Muñiz-Rascado, L. AU - García-Sotelo, J. S. AU - Weiss, V. AU - Solano-Lira, H. AU - Martínez-Flores, I. AU - Medina-Rivera, A. AU - Salgado-Osorio, G. AU - Alquicira-Hernández, S. AU - Alquicira-Hernández, K. AU - López-Fuentes, A. AU - Porrón-Sotelo, L. AU - Huerta, A. M. AU - Bonavides-Martínez, C. AU - Balderas-Martínez, Y. I. AU - Pannier, L. AU - Olvera, M. AU - Labastida, A. AU - Jiménez-Jacinto, V. AU - Vega-Alvarado, L. AU - Del Moral-Chávez, V. AU - Hernández-Alvarez, A. AU - Morett, E. AU - Collado-Vides, J. PY - 2013 DA - 2013// TI - Regulondb v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1201 DO - 10.1093/nar/gks1201 ID - Salgado2013 ER - TY - STD TI - Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I. The ecocyc database. EcoSal Plus. 2014; 2014. doi:http://dx.doi.org/10.1128/ecosalplus.ESP-0009-2013. UR - http://dx.doi.org/10.1128/ecosalplus.ESP-0009-2013 ID - ref25 ER - TY - JOUR AU - Thomas-Chollier, M. AU - Defrance, M. AU - Medina-Rivera, A. AU - Sand, O. AU - Herrmann, C. AU - Thieffry, D. AU - van Helden, J. PY - 2011 DA - 2011// TI - RSAT 2011: Regulatory sequence analysis tools JO - Nucleic Acids Res VL - 39 UR - https://doi.org/10.1093/nar/gkr377 DO - 10.1093/nar/gkr377 ID - Thomas-Chollier2011 ER - TY - STD TI - Riley M, Abe T, Arnaud MB, Berlyn MKB, Blattner FR, Chaudhuri RR, Glasner JD, Horiuchi T, Keseler IM, Kosuge T, Mori H, Perna NT, Plunkett 3rd G, Rudd KE, Serres MH, Thomas GH, Thomson NR, Wishart D, Wanner BL. Escherichia coli k-12: a cooperatively developed annotation snapshot–2005. Nucleic Acids Res. 2006; 34(1):1–9. doi:http://dx.doi.org/10.1093/nar/gkj405. UR - http://dx.doi.org/10.1093/nar/gkj405 ID - ref27 ER - TY - JOUR AU - Junier, I. AU - Martin, O. AU - Képès, F. PY - 2010 DA - 2010// TI - Spatial and topological organization of dna chains induced by gene co-localization JO - PLoS Comput Biol VL - 6 UR - https://doi.org/10.1371/journal.pcbi.1000678 DO - 10.1371/journal.pcbi.1000678 ID - Junier2010 ER - TY - JOUR AU - Cook, P. R. PY - 2002 DA - 2002// TI - Predicting three-dimensional genome structure from transcriptional activity JO - Nat Genet VL - 32 UR - https://doi.org/10.1038/ng1102-347 DO - 10.1038/ng1102-347 ID - Cook2002 ER - TY - JOUR AU - Elati, M. AU - Nicolle, R. AU - Junier, I. AU - Fernández, D. AU - Fekih, R. AU - Font, J. AU - Képès, F. PY - 2013 DA - 2013// TI - PreCisIon: PREdiction of CIS-regulatory elements improved by gene’s positION JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1286 DO - 10.1093/nar/gks1286 ID - Elati2013 ER - TY - JOUR AU - Hotteling, H. PY - 1936 DA - 1936// TI - Relations between two sets of variates JO - Biometrika VL - 28 UR - https://doi.org/10.1093/biomet/28.3-4.321 DO - 10.1093/biomet/28.3-4.321 ID - Hotteling1936 ER - TY - JOUR AU - Lê Cao, K. -. A. AU - González, I. AU - Déjean, S. PY - 2009 DA - 2009// TI - integrOmics: an R package to unravel relationships between two omics datasets. JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp515 DO - 10.1093/bioinformatics/btp515 ID - Lê Cao2009 ER -