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Author Details

Lingyun Song
Center for Genomic & Computational Biology, Duke University
2004
58
33
Nathan Sheffield (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
38059622Epstein-Barr virus induces germinal center light zone chromatin architecture and promotes survival through enhancer looping at the <i>BCL2A1</i> locus.mBio2024
35179181Identification of enhancer regulatory elements that direct epicardial gene expression during zebrafish heart regeneration.Development2022
35609992Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data.Genome Res2022
35513710Enhancer selection dictates gene expression responses in remote organs during tissue regeneration.Nat Cell Biol2022
34429139Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains.Mol Neurodegener2021
33000793Electrochemical decarboxylative C3 alkylation of quinoxalin-2(1<i>H</i>)-ones with <i>N</i>-hydroxyphthalimide esters.Chem Commun (Camb)2020
32665240Identification and requirements of enhancers that direct gene expression during zebrafish fin regeneration.Development2020
31551426CommonMind Consortium provides transcriptomic and epigenomic data for Schizophrenia and Bipolar Disorder.Sci Data2019
33997167Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance.Genes Dis2019
31186305Open Chromatin Profiling in Adipose Tissue Marks Genomic Regions with Functional Roles in Cardiometabolic Traits.G3 (Bethesda)2019
29632383Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights.Nat Genet2018
30097539Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding.Genome Res2018
30139769Human cardiac <i>cis</i>-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.Genome Res2018
30087329Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia.Nat Commun2018
30031775Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.Cell Syst2018
30545853Transcriptome and epigenome landscape of human cortical development modeled in organoids.Science2018
28977539Incomplete MyoD-induced transdifferentiation is associated with chromatin remodeling deficiencies.Nucleic Acids Res2017
28087634Genome-wide identification of regulatory elements in Sertoli cells.Development2017
28385711Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.Genome Res2017
28369033CRISPR-Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome.Nat Biotechnol2017
27565349Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.Cell2016
27821050Stringent comparative sequence analysis reveals SOX10 as a putative inhibitor of glial cell differentiation.BMC Genomics2016
25569532Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.PLoS Genet2015
26501517Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements.Nat Methods2015
26307087Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus.Hum Mol Genet2015
26206884Genomic analysis reveals distinct mechanisms and functional classes of SOX10-regulated genes in melanocytes.Hum Mol Genet2015
25849986Regulation of chromatin accessibility and Zic binding at enhancers in the developing cerebellum.Nat Neurosci2015
26025803Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.Genome Res2015
24670287Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine.Epigenetics2014
25198066Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.PLoS One2014
25180270Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.Mol Hum Reprod2014
24905169Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency.Cell Stem Cell2014
23547170A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity.Genome Res2013
23916067DNA methylation and differentiation: HOX genes in muscle cells.Epigenetics Chromatin2013
24006278A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.Biol Reprod2013
23657885DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.Genome Res2013
23417056Early de novo DNA methylation and prolonged demethylation in the muscle lineage.Epigenetics2013
23482648Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions.Genome Res2013
22169360A genome-wide analysis of open chromatin in human tracheal epithelial cells reveals novel candidate regulatory elements for lung function.Thorax2012
23178118Site-specific silencing of regulatory elements as a mechanism of X inactivation.Cell2012
23034120Chromatin accessibility reveals insights into androgen receptor activation and transcriptional specificity.Genome Biol2012
22955617The accessible chromatin landscape of the human genome.Nature2012
22761590Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection.PLoS Genet2012
22912592Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes.PLoS Genet2012
22640407H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites.Genome Med2012
22300769Effects of sequence variation on differential allelic transcription factor occupancy and gene expression.Genome Res2012
22090374Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.Genome Res2012
21106903High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells.Genome Res2011
21795386Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration.Genome Res2011
21750106Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity.Genome Res2011
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Collaborators

Gregory E Crawford
Center for Genomic & Computational Biology, Duke University
Co-authored papers 53
Alexias Safi
Center for Genomic and Computational Biology, Duke University Medical Center
Co-authored papers 22
Terrence S Furey
University of North Carolina at Chapel Hill
Co-authored papers 16
Timothy E Reddy
Co-authored papers 9
Bum-Kyu Lee
Cancer Research Center, University at Albany, State University of New York
Co-authored papers 7
Vishwanath R Iyer
Indian Institute of Technology Bombay
Co-authored papers 7
Darin London
Co-authored papers 6
Nathan Sheffield (CM4AI)
University of Virginia
Co-authored papers 5
Alan P Boyle
University of Michigan ann arbor
Co-authored papers 5
Yoichiro Shibata
Center for Genomic and Computational Biology, Duke University.
Co-authored papers 5
Jason D Lieb
The University of Chicago
Co-authored papers 4
Ewan Birney
European Bioinformatics Institute
Co-authored papers 4
Stephen C J Parker
University of Michigan ann arbor
Co-authored papers 3
Allison E Ashley-Koch
Co-authored papers 3
Alok K Tewari
Dana-Farber Cancer Institute, Harvard Medical School
Co-authored papers 3
Patrick F Sullivan
University of North Carolina at Chapel Hill
Co-authored papers 3
Peter C Scacheri
Case Western Reserve University School of Medicine
Co-authored papers 3
Damian Keefe
University of Adelaide
Co-authored papers 3
Elliott H Margulies
National Human Genome Research Institute, National Institutes of Health
Co-authored papers 3
Zheng Liu
Chinese Academy of Agricultural Sciences
Co-authored papers 3
Ryan M McDaniell
The Children's Hospital of Philadelphia
Co-authored papers 3
Jason Gertz
Huntsman Cancer Institute, University of Utah
Co-authored papers 2
Zhancheng Zhang
Co-authored papers 2
Francis S Collins
University of Michigan ann arbor
Co-authored papers 2
Michael R Erdos
Center for Precision Health Research, National Human Genome Research Institute
Co-authored papers 2
John A Stamatoyannopoulos
Altius Institute for Biomedical Sciences
Co-authored papers 2
Panos Roussos
Co-authored papers 2
Gregory A Wray
Duke University
Co-authored papers 2
Laura J Scott
Co-authored papers 2
Jeremy M Simon
University of North Carolina
Co-authored papers 2
Release 1.2