Gregory E Crawford

Gregory E Crawford

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Gregory E Crawford

Gregory E Crawford

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Screening Regulatory Element Function with CRISPR/Cas9-based Epigenome Editing.

Methods Mol Biol 2018 ;1767:447-480

Department of Biomedical Engineering, Duke University, Durham, NC, USA.

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http://dx.doi.org/10.1007/978-1-4939-7774-1_25DOI Listing
February 2019

Human cardiac -regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.

Genome Res 2018 10 23;28(10):1577-1588. Epub 2018 Aug 23.

McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.

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http://dx.doi.org/10.1101/gr.234633.118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169896PMC
October 2018

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.

Cell Syst 2018 08 18;7(2):146-160.e7. Epub 2018 Jul 18.

University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.06.007DOI Listing
August 2018

Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids.

Cell Syst 2018 08 18;7(2):146-160.e7. Epub 2018 Jul 18.

University Program in Genetics and Genomics, Duke University, Durham, NC 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA; Computational Biology and Bioinformatics Graduate Program, Duke University, Durham, NC 27708, USA; Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, NC 27710, USA; Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA; Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, NC 27710, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cels.2018.06.007DOI Listing
August 2018

Tissue- and strain-specific effects of a genotoxic carcinogen 1,3-butadiene on chromatin and transcription.

Mamm Genome 2018 02 10;29(1-2):153-167. Epub 2018 Feb 10.

Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX, USA.

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http://dx.doi.org/10.1007/s00335-018-9739-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6095468PMC
February 2018

Genetic and epigenetic determinants of inter-individual variability in responses to toxicants.

Curr Opin Toxicol 2017 Oct 12;6:50-59. Epub 2017 Sep 12.

Department of Veterinary Integrative Biosciences, Texas A&M University, College Station, Texas.

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http://dx.doi.org/10.1016/j.cotox.2017.08.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5739339PMC
October 2017

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha.

Genome Res 2017 07 6;27(7):1195-1206. Epub 2017 Apr 6.

Department of Molecular Genetics and Microbiology, Center for the Genomics of Microbial Systems, Duke University, Durham, North Carolina 27710, USA.

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http://dx.doi.org/10.1101/gr.220111.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5495071PMC
July 2017

Genome-wide identification of regulatory elements in Sertoli cells.

Development 2017 02 13;144(4):720-730. Epub 2017 Jan 13.

Department of Cell Biology, Duke University, Durham, NC 27710, USA

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http://dx.doi.org/10.1242/dev.142554DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312035PMC
February 2017

Direct GR Binding Sites Potentiate Clusters of TF Binding across the Human Genome.

Cell 2016 Aug;166(5):1269-1281.e19

Center for Genomic & Computational Biology, Duke University, Durham, NC 27708, USA; Department of Biostatistics & Bioinformatics, Duke University, Durham, NC 27708, USA. Electronic address:

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5046229PMC
http://dx.doi.org/10.1016/j.cell.2016.07.049DOI Listing
August 2016

Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus.

Nucleic Acids Res 2016 Apr 15;44(7):3082-94. Epub 2015 Dec 15.

Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL 60614, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA

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http://dx.doi.org/10.1093/nar/gkv1358DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4838340PMC
April 2016

HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells.

Epigenetics Chromatin 2016 16;9:15. Epub 2016 Apr 16.

Center for Genomic and Computational Biology, Duke University, Durham, NC 27708 USA ; Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC 27708 USA.

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http://dx.doi.org/10.1186/s13072-016-0065-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4833939PMC
April 2016

Mapping nucleosome positions using DNase-seq.

Genome Res 2016 Mar 15;26(3):351-64. Epub 2016 Jan 15.

Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; Department of Computer Science, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Statistical Science, Duke University, Durham, North Carolina 27708, USA.

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http://dx.doi.org/10.1101/gr.195602.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4772017PMC
March 2016

Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma.

PLoS One 2014 8;9(9):e107156. Epub 2014 Sep 8.

Department of Pathology, The Pediatric Brain Tumor Foundation Institute, and The Preston Robert Tisch Brain Tumor Center at Duke, Duke University Medical Center, Durham, North Carolina, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0107156PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157845PMC
January 2016

The PsychENCODE project.

Nat Neurosci 2015 Dec;18(12):1707-12

Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1038/nn.4156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4675669PMC
December 2015

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators.

Genome Res 2015 Aug 29;25(8):1158-69. Epub 2015 May 29.

Department of Biomedical Engineering, Duke University, Durham, North Carolina 27708, USA; Center for Genomic and Computational Biology, Duke University, Durham, North Carolina 27708, USA; Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina 27710, USA.

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http://genome.cshlp.org/lookup/doi/10.1101/gr.179044.114
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http://dx.doi.org/10.1101/gr.179044.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4510000PMC
August 2015

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers.

Nat Biotechnol 2015 May 6;33(5):510-7. Epub 2015 Apr 6.

1] Department of Biomedical Engineering, Duke University, Durham, North Carolina, USA. [2] Center for Genomic &Computational Biology, Duke University, Durham, North Carolina, USA. [3] Department of Orthopaedic Surgery, Duke University Medical Center, Durham, North Carolina, USA.

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http://www.nature.com/articles/nbt.3199
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http://dx.doi.org/10.1038/nbt.3199DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430400PMC
May 2015

Interactions of chromatin context, binding site sequence content, and sequence evolution in stress-induced p53 occupancy and transactivation.

PLoS Genet 2015 Jan 8;11(1):e1004885. Epub 2015 Jan 8.

Environmental Genomics Group, Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1004885DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4287438PMC
January 2015

Open chromatin mapping identifies transcriptional networks regulating human epididymis epithelial function.

Mol Hum Reprod 2014 Dec 1;20(12):1198-207. Epub 2014 Sep 1.

Human Molecular Genetics Program, Lurie Children's Research Center, Chicago, IL, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA

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http://dx.doi.org/10.1093/molehr/gau075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4235575PMC
December 2014

Quantitative genetics of CTCF binding reveal local sequence effects and different modes of X-chromosome association.

PLoS Genet 2014 Nov 20;10(11):e1004798. Epub 2014 Nov 20.

The European Molecular Biology Laboratory, The European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1004798DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4238955PMC
November 2014

Explicit DNase sequence bias modeling enables high-resolution transcription factor footprint detection.

Nucleic Acids Res 2014 Oct 7;42(19):11865-78. Epub 2014 Oct 7.

Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA Max Delbruck Center for Molecular Medicine, 13125 Berlin, Germany

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http://dx.doi.org/10.1093/nar/gku810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4231734PMC
October 2014

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape.

Genome Res 2014 Sep 24;24(9):1504-16. Epub 2014 Jun 24.

Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA; Department of Molecular Genetics and Microbiology, Duke University, Durham, North Carolina 27710, USA;

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http://dx.doi.org/10.1101/gr.165845.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4158762PMC
September 2014

Notch signaling genes: myogenic DNA hypomethylation and 5-hydroxymethylcytosine.

Epigenetics 2014 Jun 26;9(6):842-50. Epub 2014 Mar 26.

Program in Human Genetics; Tulane Cancer Center; Center for Bioinformatics and Genomics; Tulane Health Sciences Center; New Orleans, LA USA.

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http://dx.doi.org/10.4161/epi.28597DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4065182PMC
June 2014

Epigenomic comparison reveals activation of "seed" enhancers during transition from naive to primed pluripotency.

Cell Stem Cell 2014 Jun;14(6):854-63

Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; Case Comprehensive Cancer Center, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA; National Center for Regenerative Medicine, Case Western Reserve University School of Medicine, Cleveland, OH 44106, USA. Electronic address:

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http://www.cell.com/cell-stem-cell/pdf/S1934-5909(14)00192-1
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http://www.cell.com/cms/attachment/2024866441/2044539278/mmc
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S193459091400192
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http://dx.doi.org/10.1016/j.stem.2014.05.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149284PMC
June 2014

Deletion of a conserved cis-element in the Ifng locus highlights the role of acute histone acetylation in modulating inducible gene transcription.

PLoS Genet 2014 Jan 9;10(1):e1003969. Epub 2014 Jan 9.

Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America ; Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1003969DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3886902PMC
January 2014

A genome-wide analysis of open chromatin in human epididymis epithelial cells reveals candidate regulatory elements for genes coordinating epididymal function.

Biol Reprod 2013 Oct 31;89(4):104. Epub 2013 Oct 31.

Human Molecular Genetics Program, Lurie Children's Research Center, and Department of Pediatrics, Northwestern University Feinberg School of Medicine Chicago, Illinois.

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http://dx.doi.org/10.1095/biolreprod.113.110403DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4076396PMC
October 2013

DNA methylation and differentiation: HOX genes in muscle cells.

Epigenetics Chromatin 2013 Aug 2;6(1):25. Epub 2013 Aug 2.

Hayward Human Genetics Program and Tulane Cancer Center, Tulane Health Sciences Center, New Orleans LA, USA.

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http://dx.doi.org/10.1186/1756-8935-6-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750649PMC
August 2013

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types.

Genome Res 2013 Jul 8;23(7):1118-29. Epub 2013 May 8.

Institute for Genome Sciences and Policy, Duke University, Durham, North Carolina 27708, USA.

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http://dx.doi.org/10.1101/gr.150482.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3698505PMC
July 2013

Site-specific silencing of regulatory elements as a mechanism of X inactivation.

Cell 2012 Nov;151(5):951-63

Department of Genetics, the Carolina Center for Genome Sciences, and the Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27599, USA.

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http://dx.doi.org/10.1016/j.cell.2012.10.037DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511858PMC
November 2012

Predicting cell-type-specific gene expression from regions of open chromatin.

Genome Res 2012 Sep;22(9):1711-22

Program in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.

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http://dx.doi.org/10.1101/gr.135129.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431488PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells.

Genome Res 2012 Jan 16;22(1):9-24. Epub 2011 Nov 16.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1101/gr.127597.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246210PMC
January 2012

High-resolution mapping of open chromatin in the rice genome.

Genome Res 2012 Jan 22;22(1):151-62. Epub 2011 Nov 22.

Department of Horticulture, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA.

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http://dx.doi.org/10.1101/gr.131342.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3246202PMC
January 2012

Gene expression during normal and FSHD myogenesis.

BMC Med Genomics 2011 Sep 27;4:67. Epub 2011 Sep 27.

Human Genetics Program, Tulane Medical School, New Orleans, LA, USA.

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http://dx.doi.org/10.1186/1755-8794-4-67DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3204225PMC
September 2011

Allele-specific and heritable chromatin signatures in humans.

Hum Mol Genet 2010 Oct 16;19(R2):R204-9. Epub 2010 Sep 16.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/hmg/ddq404DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2953746PMC
October 2010

Heritable individual-specific and allele-specific chromatin signatures in humans.

Science 2010 Apr 18;328(5975):235-9. Epub 2010 Mar 18.

Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, Section of Molecular Genetics and Microbiology, University of Texas, Austin, TX 78712, USA.

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http://dx.doi.org/10.1126/science.1184655DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2929018PMC
April 2010

DNase-seq: a high-resolution technique for mapping active gene regulatory elements across the genome from mammalian cells.

Cold Spring Harb Protoc 2010 Feb;2010(2):pdb.prot5384

Institute for Genome Sciences & Policy and Department of Pediatrics, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1101/pdb.prot5384DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627383PMC
February 2010

DNaseI hypersensitivity at gene-poor, FSH dystrophy-linked 4q35.2.

Nucleic Acids Res 2009 Dec;37(22):7381-93

Human Genetics Program and Department of Biochemistry and Tulane Cancer Center, Tulane Medical School, New Orleans, LA 70112, USA.

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http://dx.doi.org/10.1093/nar/gkp833DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2794184PMC
December 2009

Intronic enhancers coordinate epithelial-specific looping of the active CFTR locus.

Proc Natl Acad Sci U S A 2009 Nov 6;106(47):19934-9. Epub 2009 Nov 6.

Human Molecular Genetics Program, Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, 2300 Children's Plaza #211, Chicago, IL 60614, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0900946106
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http://dx.doi.org/10.1073/pnas.0900946106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785270PMC
November 2009

Mapping regulatory elements by DNaseI hypersensitivity chip (DNase-Chip).

Methods Mol Biol 2009 ;556:177-90

Institute for Genome Sciences & Policy, Duke University, Durham, NC, USA.

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http://dx.doi.org/10.1007/978-1-60327-192-9_13DOI Listing
September 2009

Discovering sequences with potential regulatory characteristics.

Genomics 2009 Apr 30;93(4):314-22. Epub 2008 Dec 30.

Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA.

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http://dx.doi.org/10.1016/j.ygeno.2008.11.008DOI Listing
April 2009

A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.

J Cell Mol Med 2009 Apr;13(4):680-92

Children's Memorial Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3822875PMC
http://dx.doi.org/10.1111/j.1582-4934.2008.00621.xDOI Listing
April 2009

F-Seq: a feature density estimator for high-throughput sequence tags.

Bioinformatics 2008 Nov 10;24(21):2537-8. Epub 2008 Sep 10.

Institute for Genome Sciences and Policy, Duke University, Durham, NC 27708, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn480DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2732284PMC
November 2008