John W Whitaker

John W Whitaker

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John W Whitaker

John W Whitaker

Publications by authors named "John W Whitaker"

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Identification of DNA motifs that regulate DNA methylation.

Nucleic Acids Res 2019 07;47(13):6753-6768

Bioinformatics and Systems Biology Graduate Program, University of California, San Diego, La Jolla, CA, USA.

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http://dx.doi.org/10.1093/nar/gkz483DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6649826PMC
July 2019

Epigenomic analysis reveals DNA motifs regulating histone modifications in human and mouse.

Proc Natl Acad Sci U S A 2019 02 12;116(9):3668-3677. Epub 2019 Feb 12.

Graduate Program of Bioinformatics and Systems Biology, University of California, San Diego, La Jolla, CA 92093-0359;

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http://dx.doi.org/10.1073/pnas.1813565116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6397554PMC
February 2019

The Transcriptional Response to DNA-Double-Strand Breaks in Physcomitrella patens.

PLoS One 2016 18;11(8):e0161204. Epub 2016 Aug 18.

Centre for Plant Sciences, Faculty of Biological Sciences, Leeds University, Leeds LS2 9JT, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0161204PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4990234PMC
July 2017

Epipolymorphisms associated with the clinical outcome of autoimmune arthritis affect CD4+ T cell activation pathways.

Proc Natl Acad Sci U S A 2016 11 14;113(48):13845-13850. Epub 2016 Nov 14.

SingHealth Translational Immunology and Inflammation Centre, SingHealth, Singapore 169856.

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http://dx.doi.org/10.1073/pnas.1524056113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137722PMC
November 2016

Integrative omics analysis of rheumatoid arthritis identifies non-obvious therapeutic targets.

PLoS One 2015 22;10(4):e0124254. Epub 2015 Apr 22.

Division of Rheumatology, Allergy and Immunology, University of California San Diego, La Jolla, California, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124254PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406750PMC
April 2016

Integrative genomic deconvolution of rheumatoid arthritis GWAS loci into gene and cell type associations.

Genome Biol 2016 Apr 30;17:79. Epub 2016 Apr 30.

Immunology, Janssen Research and Development, LLC., 1400 McKean Rd., Spring House, PA, 19477, USA.

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http://dx.doi.org/10.1186/s13059-016-0948-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4853861PMC
April 2016

Constructing 3D interaction maps from 1D epigenomes.

Nat Commun 2016 Mar 10;7:10812. Epub 2016 Mar 10.

Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0359, USA.

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http://dx.doi.org/10.1038/ncomms10812DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792925PMC
March 2016

Human body epigenome maps reveal noncanonical DNA methylation variation.

Nature 2015 Jul 1;523(7559):212-6. Epub 2015 Jun 1.

1] Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, California 92037, USA [2] Howard Hughes Medical Institute, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.

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http://dx.doi.org/10.1038/nature14465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4499021PMC
July 2015

Predicting the human epigenome from DNA motifs.

Nat Methods 2015 Mar 21;12(3):265-72, 7 p following 272. Epub 2014 Sep 21.

1] Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California, USA. [2] Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California, USA.

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http://dx.doi.org/10.1038/nmeth.3065DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4344378PMC
March 2015

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
February 2015

Computational schemes for the prediction and annotation of enhancers from epigenomic assays.

Methods 2015 Jan 15;72:86-94. Epub 2014 Oct 15.

Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093-0359, United States; Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA 92093-0359, United States. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2014.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4778972PMC
January 2015

An imprinted rheumatoid arthritis methylome signature reflects pathogenic phenotype.

Genome Med 2013 30;5(4):40. Epub 2013 Apr 30.

Division of Rheumatology, Allergy and Immunology, UCSD School of Medicine, La Jolla, CA, USA.

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http://dx.doi.org/10.1186/gm444DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3706831PMC
May 2014

Predicting enhancer transcription and activity from chromatin modifications.

Nucleic Acids Res 2013 Dec 12;41(22):10032-43. Epub 2013 Sep 12.

Department of Chemistry and Biochemistry, UCSD, La Jolla 92093, CA, USA and Department of Cellular and Molecular Medicine, UCSD, La Jolla, CA 92093-0359, USA.

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http://dx.doi.org/10.1093/nar/gkt826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3905895PMC
December 2013

STAR: an integrated solution to management and visualization of sequencing data.

Bioinformatics 2013 Dec 27;29(24):3204-10. Epub 2013 Sep 27.

Department of Chemistry and Biochemistry, University of California, San Diego, CA 92093, USA, Department of Neuroscience, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA, The ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Crawley, Western Australia 6009, Australia, Key Laboratory for Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China, Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA 92037, USA, Department of Cellular and Molecular Medicine, University of California, San Diego, CA 92093, USA and Ludwig Institute for Cancer Research, La Jolla, CA 92093, USA.

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http://bioinformatics.oxfordjournals.org/content/early/2013/
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http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bio
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http://dx.doi.org/10.1093/bioinformatics/btt558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3842760PMC
December 2013

DNA methylome signature in rheumatoid arthritis.

Ann Rheum Dis 2013 Jan 26;72(1):110-7. Epub 2012 Jun 26.

Department of Medicine, University of California, San Diego School of Medicine, La Jolla, CA, USA.

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http://dx.doi.org/10.1136/annrheumdis-2012-201526DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3549371PMC
January 2013

Global identification of transcriptional regulators of pluripotency and differentiation in embryonic stem cells.

Nucleic Acids Res 2012 Sep 22;40(17):8199-209. Epub 2012 Jun 22.

Department of Genetics, The Institute for Diabetes, Obesity and Metabolism, Perelman School of Medicine at the University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104, USA.

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http://dx.doi.org/10.1093/nar/gks584DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3458541PMC
September 2012

Mutagen structure and transcriptional response: induction of distinct transcriptional profiles in Salmonella TA100 by the drinking-water mutagen MX and its homologues.

Environ Mol Mutagen 2010 Jan;51(1):69-79

Integrated Systems Toxicology Division, U.S. Environmental Protection Agency, Research Triangle Park, North Carolina 27711, USA.

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http://doi.wiley.com/10.1002/em.20512
Publisher Site
http://dx.doi.org/10.1002/em.20512DOI Listing
January 2010

The transferome of metabolic genes explored: analysis of the horizontal transfer of enzyme encoding genes in unicellular eukaryotes.

Genome Biol 2009 15;10(4):R36. Epub 2009 Apr 15.

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK.

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http://dx.doi.org/10.1186/gb-2009-10-4-r36DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688927PMC
September 2009

Alio intuitu: the automated reconstruction of the metabolic networks of parasites.

Trends Parasitol 2009 Sep 28;25(9):396-7. Epub 2009 Aug 28.

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http://dx.doi.org/10.1016/j.pt.2009.06.001DOI Listing
September 2009

Prediction of horizontal gene transfers in eukaryotes: approaches and challenges.

Biochem Soc Trans 2009 Aug;37(Pt 4):792-5

Institute of Molecular and Cellular Biology, University of Leeds, Leeds, West Yorkshire LS2 9JT, UK.

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http://dx.doi.org/10.1042/BST0370792DOI Listing
August 2009

metaTIGER: a metabolic evolution resource.

Nucleic Acids Res 2009 Jan 25;37(Database issue):D531-8. Epub 2008 Oct 25.

Institute of Molecular and Cellular Biology, Garstang Building, University of Leeds, Leeds, W. Yorks, LS2 9JT, UK.

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http://dx.doi.org/10.1093/nar/gkn826DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686446PMC
January 2009