David Fargo

David Fargo

UNVERIFIED PROFILE

Are you David Fargo?   Register this Author

Register author
David Fargo

David Fargo

Publications by authors named "David Fargo"

Are you David Fargo?   Register this Author

46Publications

985Reads

13Profile Views

ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.

PLoS Comput Biol 2020 01 24;16(1):e1007571. Epub 2020 Jan 24.

Office of Scientific Computing, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1007571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7001987PMC
January 2020

Genome-wide mutagenesis resulting from topoisomerase 1-processing of unrepaired ribonucleotides in DNA.

DNA Repair (Amst) 2019 12 3;84:102641. Epub 2019 Jul 3.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.dnarep.2019.102641DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6901746PMC
December 2019

Repair of multiple simultaneous double-strand breaks causes bursts of genome-wide clustered hypermutation.

PLoS Biol 2019 09 30;17(9):e3000464. Epub 2019 Sep 30.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, North Carolina, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pbio.3000464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6786661PMC
September 2019

Revealing a human p53 universe.

Nucleic Acids Res 2018 09;46(16):8153-8167

Genome Integrity & Structural Biology Laboratory, National Institute of Environmental Health Sciences/National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/nar/gky720DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6144829PMC
September 2018

Muver, a computational framework for accurately calling accumulated mutations.

BMC Genomics 2018 May 9;19(1):345. Epub 2018 May 9.

Integrative Bioinformatics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, Durham, NC, 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12864-018-4753-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944071PMC
May 2018

Widespread transcriptional pausing and elongation control at enhancers.

Genes Dev 2018 01 29;32(1):26-41. Epub 2018 Jan 29.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gad.309351.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5828392PMC
January 2018

A Novel Analytical Strategy to Identify Fusion Transcripts between Repetitive Elements and Protein Coding-Exons Using RNA-Seq.

PLoS One 2016 14;11(7):e0159028. Epub 2016 Jul 14.

National Institute of Environmental Health Sciences (NIEHS), 111 TW Alexander Drive, Building 101, Research Triangle Park, NC, 27709, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0159028PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4945064PMC
July 2017

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data.

Nucleic Acids Res 2017 Jun;45(10):5678-5690

Office of Scientific Computing, Division of Intramural Research, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article/45/10/5678/3603320
Publisher Site
http://dx.doi.org/10.1093/nar/gkx270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5449597PMC
June 2017

The phosphorylation status of T522 modulates tissue-specific functions of SIRT1 in energy metabolism in mice.

EMBO Rep 2017 05 31;18(5):841-857. Epub 2017 Mar 31.

Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC, USA

View Article

Download full-text PDF

Source
http://dx.doi.org/10.15252/embr.201643803DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5412809PMC
May 2017

Haploinsufficiency of SIRT1 Enhances Glutamine Metabolism and Promotes Cancer Development.

Curr Biol 2017 Feb 2;27(4):483-494. Epub 2017 Feb 2.

Signal Transduction Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2016.12.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5319916PMC
February 2017

CNOT3-Dependent mRNA Deadenylation Safeguards the Pluripotent State.

Stem Cell Reports 2016 11 13;7(5):897-910. Epub 2016 Oct 13.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stemcr.2016.09.007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5106518PMC
November 2016

The Impact of Environmental and Endogenous Damage on Somatic Mutation Load in Human Skin Fibroblasts.

PLoS Genet 2016 10 27;12(10):e1006385. Epub 2016 Oct 27.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, United States Of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006385DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5082821PMC
October 2016

RNA polymerase II promoter-proximal pausing in mammalian long non-coding genes.

Genomics 2016 08 16;108(2):64-77. Epub 2016 Jul 16.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health, Research Triangle Park, NC 27705, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ygeno.2016.07.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524647PMC
August 2016

Downstream Antisense Transcription Predicts Genomic Features That Define the Specific Chromatin Environment at Mammalian Promoters.

PLoS Genet 2016 08 3;12(8):e1006224. Epub 2016 Aug 3.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1006224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4972320PMC
August 2016

INO80 governs superenhancer-mediated oncogenic transcription and tumor growth in melanoma.

Genes Dev 2016 06;30(12):1440-53

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gad.277178.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4926866PMC
June 2016

A Serial shRNA Screen for Roadblocks to Reprogramming Identifies the Protein Modifier SUMO2.

Stem Cell Reports 2016 05 3;6(5):704-716. Epub 2016 Mar 3.

Department of Molecular Biology, Center for Regenerative Medicine and Cancer Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stemcr.2016.02.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4939549PMC
May 2016

An APOBEC3A hypermutation signature is distinguishable from the signature of background mutagenesis by APOBEC3B in human cancers.

Nat Genet 2015 Sep 10;47(9):1067-72. Epub 2015 Aug 10.

Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.3378DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4594173PMC
September 2015

Bidirectional Transcription Arises from Two Distinct Hubs of Transcription Factor Binding and Active Chromatin.

Mol Cell 2015 Jun 28;58(6):1101-12. Epub 2015 May 28.

Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address:

View Article

Download full-text PDF

Source
http://www.cell.com/molecular-cell/pdf/S1097-2765(15)00262-2
Web Search
http://linkinghub.elsevier.com/retrieve/pii/S109727651500262
Publisher Site
http://dx.doi.org/10.1016/j.molcel.2015.04.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4475495PMC
June 2015

Pausing of RNA polymerase II regulates mammalian developmental potential through control of signaling networks.

Mol Cell 2015 Apr 12;58(2):311-322. Epub 2015 Mar 12.

Laboratory of Epigenetics and Stem Cell Biology, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2015.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4402150PMC
April 2015

Post-transcriptional regulation of transcript abundance by a conserved member of the tristetraprolin family in Candida albicans.

Mol Microbiol 2015 Mar 30;95(6):1036-53. Epub 2015 Jan 30.

Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC, 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1111/mmi.12913DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4557868PMC
March 2015

Tracking replication enzymology in vivo by genome-wide mapping of ribonucleotide incorporation.

Nat Struct Mol Biol 2015 Mar 26;22(3):185-91. Epub 2015 Jan 26.

Genome Integrity &Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institute of Health (NIH), Research Triangle Park, North Carolina, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2957DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351163PMC
March 2015

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition.

Genome Res 2014 Nov 12;24(11):1751-64. Epub 2014 Sep 12.

Laboratory of Molecular Genetics, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA; Laboratory of Structural Biology, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, North Carolina 27709, USA;

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.178335.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4216917PMC
November 2014

TRIM28 regulates RNA polymerase II promoter-proximal pausing and pause release.

Nat Struct Mol Biol 2014 Oct 31;21(10):876-83. Epub 2014 Aug 31.

Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nsmb.2878DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4189995PMC
October 2014

SIRT1-mediated deacetylation of CRABPII regulates cellular retinoic acid signaling and modulates embryonic stem cell differentiation.

Mol Cell 2014 Sep 21;55(6):843-855. Epub 2014 Aug 21.

Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2014.07.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4228935PMC
September 2014

Novel DNA motif binding activity observed in vivo with an estrogen receptor α mutant mouse.

Mol Endocrinol 2014 Jun 8;28(6):899-911. Epub 2014 Apr 8.

Receptor Biology (S.C.H., W.W., K.J.H., B.P., K.S.K.), Laboratory of Reproductive and Developmental Toxicology, Biostatistics Branch (L.L.), Integrative Bioinformatics (S.A.G., D.F.), Laboratory of Structural Biology (L.C.P.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709; Department of Molecular and Cellular Biology (C.A.R., R.B.L., F.J.D.), Baylor College of Medicine, Houston, Texas 77030; and Department of Molecular Biology of the Cell (G.S.), German Cancer Research Center, 69121 Heidelberg, Germany.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1210/me.2014-1051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4042070PMC
June 2014

INO80 facilitates pluripotency gene activation in embryonic stem cell self-renewal, reprogramming, and blastocyst development.

Cell Stem Cell 2014 May;14(5):575-91

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, Research Triangle Park, NC 27709, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.stem.2014.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4154226PMC
May 2014

PAVIS: a tool for Peak Annotation and Visualization.

Bioinformatics 2013 Dec 4;29(23):3097-9. Epub 2013 Sep 4.

Biostatistics Branch and the Integrative Bioinformatics Group, National Institute of Environmental Health Sciences, Durham, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btt520DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3834791PMC
December 2013

Stable pausing by RNA polymerase II provides an opportunity to target and integrate regulatory signals.

Mol Cell 2013 Nov 31;52(4):517-28. Epub 2013 Oct 31.

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2013.10.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3845087PMC
November 2013

Life without TTP: apparent absence of an important anti-inflammatory protein in birds.

Am J Physiol Regul Integr Comp Physiol 2013 Oct 31;305(7):R689-700. Epub 2013 Jul 31.

Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina;

View Article

Download full-text PDF

Source
http://ajpregu.physiology.org/content/ajpregu/305/7/R689.ful
Web Search
http://ajpregu.physiology.org/content/ajpregu/early/2013/07/
Web Search
http://ajpregu.physiology.org/cgi/doi/10.1152/ajpregu.00310.
Publisher Site
http://dx.doi.org/10.1152/ajpregu.00310.2013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3798794PMC
October 2013

Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe.

Mol Cell Biol 2012 Oct 20;32(20):4206-14. Epub 2012 Aug 20.

Laboratory of Signal Transduction, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1128/MCB.00325-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3457339PMC
October 2012

Defining the status of RNA polymerase at promoters.

Cell Rep 2012 Oct 10;2(4):1025-35. Epub 2012 Oct 10.

Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2012.08.034DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3483431PMC
October 2012

Research resource: whole-genome estrogen receptor α binding in mouse uterine tissue revealed by ChIP-seq.

Mol Endocrinol 2012 May 22;26(5):887-98. Epub 2012 Mar 22.

Receptor Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1210/me.2011-1311DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3355558PMC
May 2012

Regulating the regulators: the pervasive effects of Pol II pausing on stimulus-responsive gene networks.

Genes Dev 2012 May;26(9):933-44

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gad.187781.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3347791PMC
May 2012

Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome.

Proc Natl Acad Sci U S A 2011 Jun 20;108(23):9715-20. Epub 2011 May 20.

Laboratory of Neurobiology, Library and Information Services, and Biostatistics Branch, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.1105713108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111303PMC
June 2011

Rapid activity-induced transcription of Arc and other IEGs relies on poised RNA polymerase II.

Nat Neurosci 2011 May 29;14(7):848-56. Epub 2011 May 29.

Laboratory of Neurobiology, National Institute of Environmental Health Sciences, US National Institutes of Health, Research Triangle Park, North Carolina, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nn.2839DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3125443PMC
May 2011

Pausing of RNA polymerase II disrupts DNA-specified nucleosome organization to enable precise gene regulation.

Cell 2010 Nov;143(4):540-51

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674100114
Publisher Site
http://dx.doi.org/10.1016/j.cell.2010.10.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2991113PMC
November 2010

Global analysis of short RNAs reveals widespread promoter-proximal stalling and arrest of Pol II in Drosophila.

Science 2010 Jan 10;327(5963):335-8. Epub 2009 Dec 10.

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://www.sciencemag.org/cgi/doi/10.1126/science.1181421
Publisher Site
http://dx.doi.org/10.1126/science.1181421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3435875PMC
January 2010

Using ChIP-chip and ChIP-seq to study the regulation of gene expression: genome-wide localization studies reveal widespread regulation of transcription elongation.

Methods 2009 Aug 9;48(4):398-408. Epub 2009 Mar 9.

Laboratory of Molecular Carcinogenesis, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC 27709, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.ymeth.2009.02.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431615PMC
August 2009