TY - JOUR AU - Jacob, F. AU - Perrin, D. AU - Sánchez, C. AU - Monod, J. PY - 1960 DA - 1960// TI - Operon: a group of genes with the expression coordinated by an operator JO - CR Hebd Seances Acad Sci VL - 250 ID - Jacob1960 ER - TY - JOUR AU - Lercher, M. J. AU - Hurst, L. D. PY - 2006 DA - 2006// TI - Co-expressed yeast genes cluster over a long range but are not regularly spaced JO - J Mol Biol VL - 359 UR - https://doi.org/10.1016/j.jmb.2006.03.051 DO - 10.1016/j.jmb.2006.03.051 ID - Lercher2006 ER - TY - JOUR AU - Dossena, S. AU - Nofziger, C. AU - Bernardinelli, E. AU - Soyal, S. AU - Patsch, W. AU - Paulmichl, M. PY - 2013 DA - 2013// TI - Use of the operon structure of the C. elegans genome as a tool to identify functionally related proteins JO - Cell Physiol Biochem VL - 32 UR - https://doi.org/10.1159/000356623 DO - 10.1159/000356623 ID - Dossena2013 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Kondrashov, A. S. AU - Koonin, E. V. PY - 2001 DA - 2001// TI - Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context JO - Genome Res VL - 11 UR - https://doi.org/10.1101/gr.GR-1619R DO - 10.1101/gr.GR-1619R ID - Wolf2001 ER - TY - JOUR AU - Yin, Y. AU - Zhang, H. AU - Olman, V. AU - Xu, Y. PY - 2010 DA - 2010// TI - Genomic arrangement of bacterial operons is constrained by biological pathways encoded in the genome JO - Proc Natl Acad Sci USA VL - 107 UR - https://doi.org/10.1073/pnas.0911237107 DO - 10.1073/pnas.0911237107 ID - Yin2010 ER - TY - JOUR AU - Zhang, H. AU - Yin, Y. AU - Olman, V. AU - Xu, Y. PY - 2012 DA - 2012// TI - Genomic arrangement of regulons in bacterial genomes JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0029496 DO - 10.1371/journal.pone.0029496 ID - Zhang2012 ER - TY - JOUR AU - Dekker, J. AU - Marti-Renom, M. A. AU - Mirny, L. A. PY - 2013 DA - 2013// TI - Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data JO - Nat Rev Genet VL - 14 UR - https://doi.org/10.1038/nrg3454 DO - 10.1038/nrg3454 ID - Dekker2013 ER - TY - JOUR AU - Hakim, O. AU - Sung, M. -. H. AU - Voss, T. C. AU - Splinter, E. AU - John, S. AU - Sabo, P. J. PY - 2011 DA - 2011// TI - Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.111153.110 DO - 10.1101/gr.111153.110 ID - Hakim2011 ER - TY - JOUR AU - Krivega, I. AU - Dean, A. PY - 2012 DA - 2012// TI - Enhancer and promoter interactions—long distance calls JO - Curr Opin Genet Dev VL - 22 UR - https://doi.org/10.1016/j.gde.2011.11.001 DO - 10.1016/j.gde.2011.11.001 ID - Krivega2012 ER - TY - JOUR AU - Dixon, J. R. AU - Selvaraj, S. AU - Yue, F. AU - Kim, A. AU - Li, Y. AU - Shen, Y. PY - 2012 DA - 2012// TI - Topological domains in mammalian genomes identified by analysis of chromatin interactions JO - Nature VL - 485 UR - https://doi.org/10.1038/nature11082 DO - 10.1038/nature11082 ID - Dixon2012 ER - TY - JOUR AU - Sexton, T. AU - Yaffe, E. AU - Kenigsberg, E. AU - Bantignies, F. AU - Leblanc, B. AU - Hoichman, M. PY - 2012 DA - 2012// TI - Three-Dimensional folding and functional organization principles of the drosophila genome JO - Cell VL - 148 UR - https://doi.org/10.1016/j.cell.2012.01.010 DO - 10.1016/j.cell.2012.01.010 ID - Sexton2012 ER - TY - JOUR AU - Le, T. B. AU - Imakaev, M. V. AU - Mirny, L. A. AU - Laub, M. T. PY - 2013 DA - 2013// TI - High-resolution mapping of the spatial organization of a bacterial chromosome JO - Science VL - 342 UR - https://doi.org/10.1126/science.1242059 DO - 10.1126/science.1242059 ID - Le2013 ER - TY - JOUR AU - Cagliero, C. AU - Grand, R. S. AU - Jones, M. B. AU - Jin, D. J. AU - O’Sullivan, J. M. PY - 2013 DA - 2013// TI - Genome conformation capture reveals that the Escherichia coli chromosome is organized by replication and transcription JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt325 DO - 10.1093/nar/gkt325 ID - Cagliero2013 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Bardet, A. F. AU - He, Q. AU - Zeitlinger, J. AU - Stark, A. PY - 2011 DA - 2011// TI - A computational pipeline for comparative ChIP-seq analyses JO - Nat Protoc VL - 7 UR - https://doi.org/10.1038/nprot.2011.420 DO - 10.1038/nprot.2011.420 ID - Bardet2011 ER - TY - JOUR AU - Zhang, Y. AU - Liu, T. AU - Meyer, C. A. AU - Eeckhoute, J. AU - Johnson, D. S. AU - Bernstein, B. E. PY - 2008 DA - 2008// TI - Model-based analysis of ChIP-Seq (MACS) JO - Genome Biol VL - 9 UR - https://doi.org/10.1186/gb-2008-9-9-r137 DO - 10.1186/gb-2008-9-9-r137 ID - Zhang2008 ER - TY - JOUR AU - Rogozin, I. B. AU - Makarova, K. S. AU - Murvai, J. AU - Czabarka, E. AU - Wolf, Y. I. AU - Tatusov, R. L. PY - 2002 DA - 2002// TI - Connected gene neighborhoods in prokaryotic genomes JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.10.2212 DO - 10.1093/nar/30.10.2212 ID - Rogozin2002 ER - TY - JOUR AU - Williams, E. J. AU - Bowles, D. J. PY - 2004 DA - 2004// TI - Coexpression of neighboring genes in the genome of Arabidopsis thaliana JO - Genome Res VL - 14 UR - https://doi.org/10.1101/gr.2131104 DO - 10.1101/gr.2131104 ID - Williams2004 ER - TY - JOUR AU - Bhardwaj, N. AU - Lu, H. PY - 2005 DA - 2005// TI - Correlation between gene expression profiles and protein–protein interactions within and across genomes JO - Bioinformatics VL - 21 UR - https://doi.org/10.1093/bioinformatics/bti398 DO - 10.1093/bioinformatics/bti398 ID - Bhardwaj2005 ER - TY - JOUR AU - Overbeek, R. AU - Fonstein, M. AU - D’souza, M. AU - Pusch, G. D. AU - Maltsev, N. PY - 1999 DA - 1999// TI - The use of gene clusters to infer functional coupling JO - Proc Natl Acad Sci USA VL - 96 UR - https://doi.org/10.1073/pnas.96.6.2896 DO - 10.1073/pnas.96.6.2896 ID - Overbeek1999 ER - TY - JOUR AU - Salgado, H. AU - Moreno-Hagelsieb, G. AU - Smith, T. F. AU - Collado-Vides, J. PY - 2000 DA - 2000// TI - Operons in Escherichia coli: genomic analyses and predictions JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.110147297 DO - 10.1073/pnas.110147297 ID - Salgado2000 ER - 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 - Yaffe, E. AU - Tanay, A. PY - 2011 DA - 2011// TI - Probabilistic modeling of Hi-C contact maps eliminates systematic biases to characterize global chromosomal architecture JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.947 DO - 10.1038/ng.947 ID - Yaffe2011 ER - TY - JOUR AU - Ay, F. AU - Bunnik, E. M. AU - Varoquaux, N. AU - Bol, S. M. AU - Prudhomme, J. AU - Vert, J. -. P. PY - 2014 DA - 2014// TI - Three-dimensional modeling of the P. falciparum genome during the erythrocytic cycle reveals a strong connection between genome architecture and gene expression JO - Genome Res VL - 24 UR - https://doi.org/10.1101/gr.169417.113 DO - 10.1101/gr.169417.113 ID - Ay2014 ER - TY - JOUR AU - Rodley, C. D. AU - Grand, R. S. AU - Gehlen, L. R. AU - Greyling, G. AU - Jones, M. B. AU - O'Sullivan, J. M. PY - 2012 DA - 2012// TI - Mitochondrial-nuclear DNA interactions contribute to the regulation of nuclear transcript levels as part of the inter-organelle communication system JO - PLoS One VL - 7 UR - https://doi.org/10.1371/journal.pone.0030943 DO - 10.1371/journal.pone.0030943 ID - Rodley2012 ER - TY - JOUR AU - DePristo, M. A. AU - Banks, E. AU - Poplin, R. AU - Garimella, K. V. AU - Maguire, J. R. AU - Hartl, C. PY - 2011 DA - 2011// TI - A framework for variation discovery and genotyping using next-generation DNA sequencing data JO - Nat Genet VL - 43 UR - https://doi.org/10.1038/ng.806 DO - 10.1038/ng.806 ID - DePristo2011 ER - TY - JOUR AU - Mikkelsen, T. S. AU - Ku, M. AU - Jaffe, D. B. AU - Issac, B. AU - Lieberman, E. AU - Giannoukos, G. PY - 2007 DA - 2007// TI - Genome-wide maps of chromatin state in pluripotent and lineage-committed cells JO - Nature VL - 448 UR - https://doi.org/10.1038/nature06008 DO - 10.1038/nature06008 ID - Mikkelsen2007 ER - TY - JOUR AU - Karp, P. D. AU - Riley, M. AU - Saier, M. AU - Paulsen, I. T. AU - Collado-Vides, J. AU - Paley, S. M. PY - 2002 DA - 2002// TI - The ecocyc database JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.56 DO - 10.1093/nar/30.1.56 ID - Karp2002 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. 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 - JOUR AU - Faith, J. J. AU - Driscoll, M. E. AU - Fusaro, V. A. AU - Cosgrove, E. J. AU - Hayete, B. AU - Juhn, F. S. PY - 2008 DA - 2008// TI - Many Microbe Microarrays Database: uniformly normalized Affymetrix compendia with structured experimental metadata JO - Nucleic Acids Res VL - 36 ID - Faith2008 ER - TY - JOUR AU - Korbel, J. O. AU - Jensen, L. J. AU - Mering, C. AU - Bork, P. PY - 2004 DA - 2004// TI - Analysis of genomic context: prediction of functional associations from conserved bidirectionally transcribed gene pairs JO - Nat Biotechnol VL - 22 UR - https://doi.org/10.1038/nbt988 DO - 10.1038/nbt988 ID - Korbel2004 ER - TY - JOUR AU - Krom, N. AU - Ramakrishna, W. PY - 2010 DA - 2010// TI - Conservation, rearrangement, and deletion of gene pairs during the evolution of four grass genomes JO - DNA research VL - 17 UR - https://doi.org/10.1093/dnares/dsq022 DO - 10.1093/dnares/dsq022 ID - Krom2010 ER - TY - JOUR AU - Wagner, A. PY - 2000 DA - 2000// TI - Decoupled evolution of coding region and mRNA expression patterns after gene duplication: implications for the neutralist-selectionist debate JO - Proc Natl Acad Sci USA VL - 97 UR - https://doi.org/10.1073/pnas.110147097 DO - 10.1073/pnas.110147097 ID - Wagner2000 ER - TY - JOUR AU - Xenarios, I. AU - Rice, D. W. AU - Salwinski, L. AU - Baron, M. K. AU - Marcotte, E. M. AU - Eisenberg, D. PY - 2000 DA - 2000// TI - DIP: the database of interacting proteins JO - Nucleic Acids Res VL - 28 UR - https://doi.org/10.1093/nar/28.1.289 DO - 10.1093/nar/28.1.289 ID - Xenarios2000 ER - TY - JOUR AU - Consortium, U. PY - 2013 DA - 2013// TI - Update on activities at the Universal Protein Resource (UniProt) in 2013 JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gks1068 DO - 10.1093/nar/gks1068 ID - Consortium2013 ER -