TY - JOUR AU - Eisen, M. B. AU - Spellman, P. T. AU - Brown, P. O. AU - Botstein, D. PY - 1998 DA - 1998// TI - Cluster analysis and display of genome-wide expression patterns JO - Proc Natl Acad Sci USA VL - 95 UR - https://doi.org/10.1073/pnas.95.25.14863 DO - 10.1073/pnas.95.25.14863 ID - Eisen1998 ER - TY - JOUR AU - Osbourn, A. E. AU - Field, B. PY - 2009 DA - 2009// TI - Operons JO - Cell Mol Life Sci VL - 66 UR - https://doi.org/10.1007/s00018-009-0114-3 DO - 10.1007/s00018-009-0114-3 ID - Osbourn2009 ER - TY - JOUR AU - Cohen, B. A. AU - Mitra, R. D. AU - Hughes, J. D. AU - Church, G. M. PY - 2000 DA - 2000// TI - A computational analysis of whole-genome expression data reveals chromosomal domains of gene expression JO - Nat Genet VL - 26 UR - https://doi.org/10.1038/79896 DO - 10.1038/79896 ID - Cohen2000 ER - TY - JOUR AU - Boutanaev, A. M. AU - Kalmykova, A. I. AU - Shevelyov, Y. Y. AU - Nurminsky, D. I. PY - 2002 DA - 2002// TI - Large clusters of co-expressed genes in the Drosophila genome JO - Nature VL - 420 UR - https://doi.org/10.1038/nature01216 DO - 10.1038/nature01216 ID - Boutanaev2002 ER - TY - JOUR AU - Roy, P. J. AU - Stuart, J. M. AU - Lund, J. AU - Kim, S. K. PY - 2002 DA - 2002// TI - Chromosomal clustering of muscle-expressed genes in caenorhabditis elegans JO - Nature VL - 418 ID - Roy2002 ER - TY - JOUR AU - Park, C. S. AU - Gong, R. AU - Stuart, J. AU - Tang, S. J. PY - 2006 DA - 2006// TI - Molecular network and chromosomal clustering of genes involved in synaptic plasticity in the hippocampus JO - J Biol Chem VL - 281 UR - https://doi.org/10.1074/jbc.M605876200 DO - 10.1074/jbc.M605876200 ID - Park2006 ER - TY - JOUR AU - Lercher, M. J. AU - Urrutia, A. O. AU - Hurst, L. D. PY - 2002 DA - 2002// TI - Clustering of housekeeping genes provides a unified model of gene order in the human genome JO - Nat Genet VL - 31 UR - https://doi.org/10.1038/ng887 DO - 10.1038/ng887 ID - Lercher2002 ER - TY - JOUR AU - Hurst, L. D. AU - Pal, C. AU - Lercher, M. J. PY - 2004 DA - 2004// TI - The evolutionary dynamics of eukaryotic gene order JO - Nat Rev Genet VL - 5 UR - https://doi.org/10.1038/nrg1319 DO - 10.1038/nrg1319 ID - Hurst2004 ER - TY - JOUR AU - Semon, M. AU - Duret, L. PY - 2006 DA - 2006// TI - Evolutionary origin and maintenance of coexpressed gene clusters in mammals JO - Mol Biol Evol VL - 23 UR - https://doi.org/10.1093/molbev/msl034 DO - 10.1093/molbev/msl034 ID - Semon2006 ER - TY - JOUR AU - Caron, H. AU - van Schaik, B. AU - van der Mee, M. AU - Baas, F. AU - Riggins, G. AU - van Sluis, P. AU - Hermus, M. C. AU - van Asperen, R. AU - Boon, K. AU - Voute, P. A. PY - 2001 DA - 2001// TI - The human transcriptome map: clustering of highly expressed genes in chromosomal domains JO - Science VL - 291 UR - https://doi.org/10.1126/science.1056794 DO - 10.1126/science.1056794 ID - Caron2001 ER - TY - JOUR AU - Versteeg, R. AU - van Schaik, B. D. AU - van Batenburg, M. F. AU - Roos, M. AU - Monajemi, R. AU - Caron, H. AU - Bussemaker, H. J. AU - van Kampen, A. H. PY - 2003 DA - 2003// TI - The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1649303 DO - 10.1101/gr.1649303 ID - Versteeg2003 ER - TY - JOUR AU - Goetze, S. AU - Mateos-Langerak, J. AU - Gierman, H. J. AU - de Leeuw, W. AU - Giromus, O. AU - Indemans, M. H. AU - Koster, J. AU - Ondrej, V. AU - Versteeg, R. AU - van Driel, R. PY - 2007 DA - 2007// TI - The three-dimensional structure of human interphase chromosomes is related to the transcriptome map JO - Mol Cell Biol VL - 27 UR - https://doi.org/10.1128/MCB.00208-07 DO - 10.1128/MCB.00208-07 ID - Goetze2007 ER - TY - JOUR AU - Prieto, C. AU - Risueno, A. AU - Fontanillo, C. AU - De las Rivas, J. PY - 2008 DA - 2008// TI - Human gene coexpression landscape: confident network derived from tissue transcriptomic profiles JO - PLoS One VL - 3 UR - https://doi.org/10.1371/journal.pone.0003911 DO - 10.1371/journal.pone.0003911 ID - Prieto2008 ER - TY - JOUR AU - Meaburn, K. J. AU - Misteli, T. PY - 2007 DA - 2007// TI - Cell biology: chromosome territories JO - Nature VL - 445 UR - https://doi.org/10.1038/445379a DO - 10.1038/445379a ID - Meaburn2007 ER - TY - JOUR AU - Cremer, T. AU - Cremer, C. PY - 2006 DA - 2006// TI - Rise, fall and resurrection of chromosome territories: a historical perspective. Part II. Fall and resurrection of chromosome territories during the 1950s to 1980s. Part III. Chromosome territories and the functional nuclear architecture: experiments and models from the 1990s to the present JO - Eur J Histochem VL - 50 ID - Cremer2006 ER - TY - JOUR AU - Cremer, T. AU - Cremer, C. PY - 2006 DA - 2006// TI - Rise, fall and resurrection of chromosome territories: a historical perspective. Part I. The rise of chromosome territories JO - Eur J Histochem VL - 50 ID - Cremer2006 ER - TY - JOUR AU - Olsson, I. AU - Bjerling, P. PY - 2011 DA - 2011// TI - Advancing our understanding of functional genome organisation through studies in the fission yeast JO - Curr Genet VL - 57 UR - https://doi.org/10.1007/s00294-010-0327-x DO - 10.1007/s00294-010-0327-x ID - Olsson2011 ER - TY - JOUR AU - Duan, Z. AU - Andronescu, M. AU - Schutz, K. AU - McIlwain, S. AU - Kim, Y. J. AU - Lee, C. AU - Shendure, J. AU - Fields, S. AU - Blau, C. A. AU - Noble, W. S. PY - 2010 DA - 2010// TI - A three-dimensional model of the yeast genome JO - Nature VL - 465 UR - https://doi.org/10.1038/nature08973 DO - 10.1038/nature08973 ID - Duan2010 ER - TY - JOUR AU - Lieberman-Aiden, E. AU - van Berkum, N. L. AU - Williams, L. AU - Imakaev, M. AU - Ragoczy, T. AU - Telling, A. AU - Amit, I. AU - Lajoie, B. R. AU - Sabo, P. J. AU - Dorschner, M. O. PY - 2009 DA - 2009// TI - Comprehensive mapping of long-range interactions reveals folding principles of the human genome JO - Science VL - 326 UR - https://doi.org/10.1126/science.1181369 DO - 10.1126/science.1181369 ID - Lieberman-Aiden2009 ER - TY - JOUR AU - Schoenfelder, S. AU - Sexton, T. AU - Chakalova, L. AU - Cope, N. F. AU - Horton, A. AU - Andrews, S. AU - Kurukuti, S. AU - Mitchell, J. A. AU - Umlauf, D. AU - Dimitrova, D. S. PY - 2010 DA - 2010// TI - Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells JO - Nat Genet VL - 42 UR - https://doi.org/10.1038/ng.496 DO - 10.1038/ng.496 ID - Schoenfelder2010 ER - TY - JOUR AU - Branco, M. R. AU - Pombo, A. PY - 2006 DA - 2006// TI - Intermingling of chromosome territories in interphase suggests role in translocations and transcription-dependent associations JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040138 DO - 10.1371/journal.pbio.0040138 ID - Branco2006 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 - Mitchell, J. A. AU - Fraser, P. PY - 2008 DA - 2008// TI - Transcription factories are nuclear subcompartments that remain in the absence of transcription JO - Genes Dev VL - 22 UR - https://doi.org/10.1101/gad.454008 DO - 10.1101/gad.454008 ID - Mitchell2008 ER - TY - JOUR AU - Geyer, P. K. AU - Vitalini, M. W. AU - Wallrath, L. L. PY - 2011 DA - 2011// TI - Nuclear organization: taking a position on gene expression JO - Curr Opin Cell Biol VL - 23 UR - https://doi.org/10.1016/j.ceb.2011.03.002 DO - 10.1016/j.ceb.2011.03.002 ID - Geyer2011 ER - TY - JOUR AU - Cavalli, G. PY - 2007 DA - 2007// TI - Chromosome kissing JO - Curr Opin Genet Dev VL - 17 UR - https://doi.org/10.1016/j.gde.2007.08.013 DO - 10.1016/j.gde.2007.08.013 ID - Cavalli2007 ER - TY - JOUR AU - Kleckner, N. AU - Weiner, B. M. PY - 1993 DA - 1993// TI - Potential advantages of unstable interactions for pairing of chromosomes in meiotic, somatic, and premeiotic cells JO - Cold Spring Harb Symp Quant Biol VL - 58 UR - https://doi.org/10.1101/SQB.1993.058.01.062 DO - 10.1101/SQB.1993.058.01.062 ID - Kleckner1993 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 - Khalil, A. AU - Grant, J. L. AU - Caddle, L. B. AU - Atzema, E. AU - Mills, K. D. AU - Arneodo, A. PY - 2007 DA - 2007// TI - Chromosome territories have a highly nonspherical morphology and nonrandom positioning JO - Chromosome Res VL - 15 UR - https://doi.org/10.1007/s10577-007-1172-8 DO - 10.1007/s10577-007-1172-8 ID - Khalil2007 ER - TY - JOUR AU - Tanabe, H. AU - Kupper, K. AU - Ishida, T. AU - Neusser, M. AU - Mizusawa, H. PY - 2005 DA - 2005// TI - Inter- and intra-specific gene-density-correlated radial chromosome territory arrangements are conserved in Old World monkeys JO - Cytogenet Genome Res VL - 108 UR - https://doi.org/10.1159/000080824 DO - 10.1159/000080824 ID - Tanabe2005 ER - TY - JOUR AU - Parada, L. A. AU - McQueen, P. G. AU - Misteli, T. PY - 2004 DA - 2004// TI - Tissue-specific spatial organization of genomes JO - Genome Biol VL - 5 UR - https://doi.org/10.1186/gb-2004-5-7-r44 DO - 10.1186/gb-2004-5-7-r44 ID - Parada2004 ER - TY - JOUR AU - Peric-Hupkes, D. AU - Meuleman, W. AU - Pagie, L. AU - Bruggeman, S. W. AU - Solovei, I. AU - Brugman, W. AU - Graf, S. AU - Flicek, P. AU - Kerkhoven, R. M. AU - van Lohuizen, M. PY - 2010 DA - 2010// TI - Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation JO - Mol Cell VL - 38 UR - https://doi.org/10.1016/j.molcel.2010.03.016 DO - 10.1016/j.molcel.2010.03.016 ID - Peric-Hupkes2010 ER - TY - JOUR AU - Janga, S. C. AU - Collado-Vides, J. AU - Babu, M. M. PY - 2008 DA - 2008// TI - Transcriptional regulation constrains the organization of genes on eukaryotic chromosomes JO - Proc Natl Acad Sci USA VL - 105 UR - https://doi.org/10.1073/pnas.0806317105 DO - 10.1073/pnas.0806317105 ID - Janga2008 ER - TY - JOUR AU - Veron, A. S. AU - Lemaitre, C. AU - Gautier, C. AU - Lacroix, V. AU - Sagot, M. F. PY - 2011 DA - 2011// TI - Close 3D proximity of evolutionary breakpoints argues for the notion of spatial synteny JO - BMC Genomics VL - 12 UR - https://doi.org/10.1186/1471-2164-12-303 DO - 10.1186/1471-2164-12-303 ID - Veron2011 ER - TY - JOUR AU - Woo, Y. H. AU - Walker, M. AU - Churchill, G. A. PY - 2010 DA - 2010// TI - Coordinated expression domains in mammalian genomes JO - PLoS One VL - 5 UR - https://doi.org/10.1371/journal.pone.0012158 DO - 10.1371/journal.pone.0012158 ID - Woo2010 ER - TY - JOUR AU - Van ‘t Veer, L. J. AU - Dai, H. AU - Van De Vijver, M. J. AU - He, Y. D. AU - Hart, A. A. AU - Mao, M. AU - Peterse, H. L. AU - Van Der Kooy, K. AU - Marton, M. J. AU - Witteveen, A. T. PY - 2002 DA - 2002// TI - Gene expression profiling predicts clinical outcome of breast cancer JO - Nature VL - 415 UR - https://doi.org/10.1038/415530a DO - 10.1038/415530a ID - Van ‘t Veer2002 ER - TY - JOUR AU - Elkon, R. AU - Linhart, C. AU - Sharan, R. AU - Shamir, R. AU - Shiloh, Y. PY - 2003 DA - 2003// TI - Genome-wide in silico identification of transcriptional regulators controlling the cell cycle in human cells JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.947203 DO - 10.1101/gr.947203 ID - Elkon2003 ER - TY - JOUR AU - Yan, X. AU - Mehan, M. R. AU - Huang, Y. AU - Waterman, M. S. AU - Yu, P. S. AU - Zhou, X. J. PY - 2007 DA - 2007// TI - A graph-based approach to systematically reconstruct human transcriptional regulatory modules JO - Bioinformatics VL - 23 UR - https://doi.org/10.1093/bioinformatics/btm227 DO - 10.1093/bioinformatics/btm227 ID - Yan2007 ER - TY - JOUR AU - Su, A. I. AU - Wiltshire, T. AU - Batalov, S. AU - Lapp, H. AU - Ching, K. A. AU - Block, D. AU - Zhang, J. AU - Soden, R. AU - Hayakawa, M. AU - Kreiman, G. PY - 2004 DA - 2004// TI - A gene atlas of the mouse and human protein-encoding transcriptomes JO - Proc Natl Acad Sci USA VL - 101 UR - https://doi.org/10.1073/pnas.0400782101 DO - 10.1073/pnas.0400782101 ID - Su2004 ER - TY - BOOK AU - Zhang, Y. AU - Zha, H. AU - Wang, J. Z. AU - Chu, C. H. PY - 2004 DA - 2004// TI - Gene Co-regulation vs. Co-expression PB - Poster Proceedings of the International Conference on Research in Computational Molecular Biology (RECOMB) CY - San Diego, CA ID - Zhang2004 ER - TY - JOUR AU - Sanyal, A. AU - Lajoie, B. R. AU - Jain, G. AU - Dekker, J. PY - 2012 DA - 2012// TI - The long-range interaction landscape of gene promoters JO - Nature VL - 489 UR - https://doi.org/10.1038/nature11279 DO - 10.1038/nature11279 ID - Sanyal2012 ER - TY - JOUR AU - da Huang, W. AU - Sherman, B. T. AU - Lempicki, R. A. PY - 2009 DA - 2009// TI - Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources JO - Nat Protoc VL - 4 UR - https://doi.org/10.1038/nprot.2008.211 DO - 10.1038/nprot.2008.211 ID - da Huang2009 ER -