Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation
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Raymond K. Auerbach | M. Gerstein | A. Mortazavi | B. Wold | M. Snyder | E. Liu | T. Gingeras | W. Sung | Chia-Lin Wei | Y. Ruan | G. Euskirchen | Y. Orlov | Xiaoan Ruan | C. Davis | M. Fullwood | Huaien Wang | D. Raha | Guoliang Li | K. Sandhu | Meizhen Zheng | Ping Wang | H. Poh | Yufen Goh | Joanne Lim | Jingyao Zhang | Hui Shan Sim | Su Qin Peh | F. Mulawadi | Chin Thing Ong | Shuzhen Hong | Zhizhuo Zhang | S. Landt | W. Ge | Katherine I. Fisher-Aylor | Yi E. Sun | E. Cheung | C. Davis | Y. Sun | C. T. Ong
[1] J. Monod,et al. [Operon: a group of genes with the expression coordinated by an operator]. , 1960, Comptes rendus hebdomadaires des seances de l'Academie des sciences.
[2] D. Pauli,et al. An unusual split Drosophila heat shock gene expressed during embryogenesis, pupation and in testis. , 1988, Journal of molecular biology.
[3] AC Tose. Cell , 1993, Cell.
[4] Thomas Blumenthal,et al. Operons as a common form of chromosomal organization in C. elegans , 1994, Nature.
[5] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[6] P. Cook. The organization of replication and transcription. , 1999, Science.
[7] Thomas de Quincey. [C] , 2000, The Works of Thomas De Quincey, Vol. 1: Writings, 1799–1820.
[8] M. Lanotte,et al. Maturation sensitive and resistant t(15;17) NB4 cell lines as tools for APL physiopathology: nomenclature of cells and repertory of their known genetic alterations and phenotypes , 2001, Oncogene.
[9] T. Cremer,et al. Chromosome territories, nuclear architecture and gene regulation in mammalian cells , 2001, Nature Reviews Genetics.
[10] A. Orth,et al. Large-scale analysis of the human and mouse transcriptomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[11] Naoto Endo,et al. Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly , 2002, Proceedings of the National Academy of Sciences of the United States of America.
[12] H. Bussemaker,et al. The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes. , 2003, Genome research.
[13] E. Levanon,et al. Human housekeeping genes are compact. , 2003, Trends in genetics : TIG.
[14] M. Campbell,et al. PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.
[15] S. Batalov,et al. A gene atlas of the mouse and human protein-encoding transcriptomes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[16] K. H. Wolfe,et al. Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. , 2005, Molecular biology and evolution.
[17] James Taylor. Clues to function in gene deserts. , 2005, Trends in biotechnology.
[18] D. Brutlag,et al. A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters , 2006, Proceedings of the National Academy of Sciences of the United States of America.
[19] Giorgio Bernardi,et al. An isochore map of human chromosomes. , 2006, Genome research.
[20] Holger Fröhlich,et al. GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products , 2007, BMC Bioinformatics.
[21] Wouter de Laat,et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR) , 2007, Nature Protocols.
[22] L. Rivest,et al. Rcapture: Loglinear Models for Capture-Recapture in R , 2007 .
[23] Dustin E. Schones,et al. High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.
[24] Atif Shahab,et al. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). , 2007, Genome research.
[25] Robert Tibshirani,et al. Boolean implication networks derived from large scale, whole genome microarray datasets , 2008, Genome Biology.
[26] Clifford A. Meyer,et al. Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.
[27] E. Liu,et al. Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements* , 2008, Journal of Biological Chemistry.
[28] E. Liu,et al. An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.
[29] H. Tanabe,et al. Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. , 2009, Developmental cell.
[30] Ting Wang,et al. The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..
[31] W. Sung,et al. ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing , 2010, Genome Biology.
[32] A. Visel,et al. Genomic Views of Distant-Acting Enhancers , 2009, Nature.
[33] Nathaniel D. Heintzman,et al. Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.
[34] Peter Fraser,et al. The yin and yang of chromatin spatial organization , 2010, Genome Biology.
[35] Jennifer A. Mitchell,et al. Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.
[36] M. Snyder,et al. ChIP‐Seq: A Method for Global Identification of Regulatory Elements in the Genome , 2010, Current protocols in molecular biology.
[37] J. Dekker,et al. Genomics tools for the unraveling of chromosome architecture , 2010, Nature Biotechnology.
[38] G. Kreiman,et al. Widespread transcription at neuronal activity-regulated enhancers , 2010, Nature.
[39] M. Merkenschlager. Cohesin: a global player in chromosome biology with local ties to gene regulation. , 2010, Current opinion in genetics & development.
[40] Yijun Ruan,et al. Chromatin Interaction Analysis Using Paired‐End Tag Sequencing , 2010, Current protocols in molecular biology.
[41] Ryan Dale,et al. Cell type specificity of chromatin organization mediated by CTCF and cohesin , 2010, Proceedings of the National Academy of Sciences.
[42] N. D. Clarke,et al. Integrative model of genomic factors for determining binding site selection by estrogen receptor-α , 2010, Molecular systems biology.
[43] Mark Gerstein,et al. Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries , 2022 .
[44] Leighton J. Core,et al. A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells , 2011, Cell.
[45] Chee Seng Chan,et al. CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells , 2011, Nature Genetics.
[46] Christian Gieger,et al. Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile , 2011, Nature Genetics.
[47] Raymond K. Auerbach,et al. Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches , 2011, PLoS genetics.
[48] Lucas Lochovsky,et al. ACT: aggregation and correlation toolbox for analyses of genome tracks , 2011, Bioinform..
[49] J. Lawrence,et al. The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules , 2011, Nature Structural &Molecular Biology.