Integrative analysis of haplotype-resolved epigenomes across human tissues

[1]  G. Bourque,et al.  The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity , 2014, Nature Structural &Molecular Biology.

[2]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[3]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[4]  Bing Ren,et al.  Whole-genome haplotype reconstruction using proximity-ligation and shotgun sequencing , 2013, Nature Biotechnology.

[5]  Leighton J. Core,et al.  Coordinated Effects of Sequence Variation on DNA Binding, Chromatin Structure, and Transcription , 2013, Science.

[6]  Jonathan K. Pritchard,et al.  Identification of Genetic Variants That Affect Histone Modifications in Human Cells , 2013, Science.

[7]  C. Glass,et al.  Impact of natural genetic variation on enhancer selection and function , 2013, Nature.

[8]  Dan Xie,et al.  Extensive Variation in Chromatin States Across Humans , 2013, Science.

[9]  B. Ren,et al.  Mapping Human Epigenomes , 2013, Cell.

[10]  Pedro G. Ferreira,et al.  Transcriptome and genome sequencing uncovers functional variation in humans , 2013, Nature.

[11]  Shane J. Neph,et al.  Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes , 2013, Cell.

[12]  Keith L. Ligon,et al.  DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape , 2013, Nature Genetics.

[13]  Michael Q. Zhang,et al.  Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells , 2013, Cell.

[14]  F. Real,et al.  Nr5a2 heterozygosity sensitises to, and cooperates with, inflammation in KRasG12V-driven pancreatic tumourigenesis , 2013, Gut.

[15]  Wei Xie,et al.  RFECS: A Random-Forest Based Algorithm for Enhancer Identification from Chromatin State , 2013, PLoS Comput. Biol..

[16]  Bradley E. Bernstein,et al.  Genome-wide Chromatin State Transitions Associated with Developmental and Environmental Cues , 2013, Cell.

[17]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[18]  Matthew D Dean,et al.  Genomic landscape of human allele-specific DNA methylation , 2012, Proceedings of the National Academy of Sciences.

[19]  Monika S. Kowalczyk,et al.  Intragenic enhancers act as alternative promoters. , 2012, Molecular cell.

[20]  José Vicente Castell,et al.  Foxa1 Reduces Lipid Accumulation in Human Hepatocytes and Is Down-Regulated in Nonalcoholic Fatty Liver , 2012, PloS one.

[21]  Daniel A. Skelly,et al.  A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data. , 2011, Genome research.

[22]  E. Huang,et al.  Loss of nuclear factor E2-related factor 1 in the brain leads to dysregulation of proteasome gene expression and neurodegeneration , 2011, Proceedings of the National Academy of Sciences.

[23]  R. Young,et al.  Histone H3K27ac separates active from poised enhancers and predicts developmental state , 2010, Proceedings of the National Academy of Sciences.

[24]  G. Bourque,et al.  Transposable elements have rewired the core regulatory network of human embryonic stem cells , 2010, Nature Genetics.

[25]  Bernd Fritzsch,et al.  Neurod1 regulates survival and formation of connections in mouse ear and brain , 2010, Cell and Tissue Research.

[26]  Seung U. Kim,et al.  Transplantation of human neural stem cells transduced with Olig2 transcription factor improves locomotor recovery and enhances myelination in the white matter of rat spinal cord following contusive injury , 2009, BMC Neuroscience.

[27]  John N. Hutchinson,et al.  Widespread Monoallelic Expression on Human Autosomes , 2007, Science.

[28]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[29]  Inna Dubchak,et al.  VISTA Enhancer Browser—a database of tissue-specific human enhancers , 2006, Nucleic Acids Res..

[30]  S. Nishikawa,et al.  Involvement of Runx1 in the down-regulation of fetal liver kinase-1 expression during transition of endothelial cells to hematopoietic cells. , 2005, Blood.