Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

[1]  Christian Gieger,et al.  Genetic variation near IRS1 associates with reduced adiposity and an impaired metabolic profile , 2011, Nature Genetics.

[2]  Chee Seng Chan,et al.  CTCF-Mediated Functional Chromatin Interactome in Pluripotent Cells , 2011, Nature Genetics.

[3]  Leighton J. Core,et al.  A Rapid, Extensive, and Transient Transcriptional Response to Estrogen Signaling in Breast Cancer Cells , 2011, Cell.

[4]  Raymond K. Auerbach,et al.  Diverse Roles and Interactions of the SWI/SNF Chromatin Remodeling Complex Revealed Using Global Approaches , 2011, PLoS genetics.

[5]  Lucas Lochovsky,et al.  ACT: aggregation and correlation toolbox for analyses of genome tracks , 2011, Bioinform..

[6]  M. Merkenschlager.  Cohesin: a global player in chromosome biology with local ties to gene regulation. , 2010, Current opinion in genetics & development.

[7]  J. Dekker,et al.  Genomics tools for the unraveling of chromosome architecture , 2010, Nature Biotechnology.

[8]  M. Snyder,et al.  ChIP‐Seq: A Method for Global Identification of Regulatory Elements in the Genome , 2010, Current protocols in molecular biology.

[9]  Peter Fraser,et al.  The yin and yang of chromatin spatial organization , 2010, Genome Biology.

[10]  W. Sung,et al.  ChIA-PET tool for comprehensive chromatin interaction analysis with paired-end tag sequencing , 2010, Genome Biology.

[11]  Ryan Dale,et al.  Cell type specificity of chromatin organization mediated by CTCF and cohesin , 2010, Proceedings of the National Academy of Sciences.

[12]  Yijun Ruan,et al.  Chromatin Interaction Analysis Using Paired‐End Tag Sequencing , 2010, Current protocols in molecular biology.

[13]  E. Liu,et al.  An Oestrogen Receptor α-bound Human Chromatin Interactome , 2009, Nature.

[14]  A. Visel,et al.  Genomic Views of Distant-Acting Enhancers , 2009, Nature.

[15]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[16]  H. Tanabe,et al.  Chromosomal dynamics at the Shh locus: limb bud-specific differential regulation of competence and active transcription. , 2009, Developmental cell.

[17]  E. Liu,et al.  Regulation of Estrogen Receptor-mediated Long Range Transcription via Evolutionarily Conserved Distal Response Elements* , 2008, Journal of Biological Chemistry.

[18]  Ting Wang,et al.  The UCSC Genome Browser Database: update 2009 , 2008, Nucleic Acids Res..

[19]  Robert Tibshirani,et al.  Boolean implication networks derived from large scale, whole genome microarray datasets , 2008, Genome Biology.

[20]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[21]  Wouter de Laat,et al.  Quantitative analysis of chromosome conformation capture assays (3C-qPCR) , 2007, Nature Protocols.

[22]  Atif Shahab,et al.  Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). , 2007, Genome research.

[23]  Holger Fröhlich,et al.  GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products , 2007, BMC Bioinformatics.

[24]  Dustin E. Schones,et al.  High-Resolution Profiling of Histone Methylations in the Human Genome , 2007, Cell.

[25]  L. Rivest,et al.  Rcapture: Loglinear Models for Capture-Recapture in R , 2007 .

[26]  Giorgio Bernardi,et al.  An isochore map of human chromosomes. , 2006, Genome research.

[27]  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.

[28]  James Taylor.  Clues to function in gene deserts. , 2005, Trends in biotechnology.

[29]  K. H. Wolfe,et al.  Clusters of co-expressed genes in mammalian genomes are conserved by natural selection. , 2005, Molecular biology and evolution.

[30]  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.

[31]  M. Campbell,et al.  PANTHER: a library of protein families and subfamilies indexed by function. , 2003, Genome research.

[32]  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.

[33]  E. Levanon,et al.  Human housekeeping genes are compact. , 2003, Trends in genetics : TIG.

[34]  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.

[35]  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.

[36]  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.

[37]  P. Cook.  The organization of replication and transcription. , 1999, Science.

[38]  Thomas Blumenthal,et al.  Operons as a common form of chromosomal organization in C. elegans , 1994, Nature.

[39]  D. Pauli,et al.  An unusual split Drosophila heat shock gene expressed during embryogenesis, pupation and in testis. , 1988, Journal of molecular biology.

[40]  J. Lawrence,et al.  The three-dimensional folding of the α-globin gene domain reveals formation of chromatin globules , 2011, Nature Structural &Molecular Biology.

[41]  M. Huss,et al.  Supplementary information for Integrative model of genomic factors for determining binding site selection by estrogen receptor α , 2010 .

[42]  Jennifer A. Mitchell,et al.  Preferential associations between co-regulated genes reveal a transcriptional interactome in erythroid cells , 2010, Nature Genetics.

[43]  C. Cremer.  NUCLEAR ARCHITECTURE AND GENE REGULATION IN MAMMALIAN CELLS , 2001 .

[44]  Y. Benjamini,et al.  Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .

[45]  Mark Gerstein,et al.  Bioinformatics Applications Note Gene Expression Rseqtools: a Modular Framework to Analyze Rna-seq Data Using Compact, Anonymized Data Summaries , 2022 .