David R Kelley

David R Kelley

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David R Kelley

David R Kelley

Publications by authors named "David R Kelley"

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Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.

Genome Res 2016 07 3;26(7):990-9. Epub 2016 May 3.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA;

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http://dx.doi.org/10.1101/gr.200535.115DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4937568PMC
July 2016

Widespread RNA binding by chromatin-associated proteins.

Genome Biol 2016 Feb 16;17:28. Epub 2016 Feb 16.

Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, 02138, USA.

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http://dx.doi.org/10.1186/s13059-016-0878-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4756407PMC
February 2016

Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre.

Nat Struct Mol Biol 2014 Feb 26;21(2):198-206. Epub 2014 Jan 26.

1] Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts, USA. [2] Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Massachusetts, USA. [3] Department of Pathology, Beth Israel Deaconess Medical Center, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.2764DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3950333PMC
February 2014

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.

PLoS One 2012 3;7(8):e42680. Epub 2012 Aug 3.

Institute for Physical Science and Technology, University of Maryland, College Park, Maryland, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0042680PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411808PMC
January 2013

Gene prediction with Glimmer for metagenomic sequences augmented by classification and clustering.

Nucleic Acids Res 2012 Jan 18;40(1):e9. Epub 2011 Nov 18.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, Department of Computer Science, 3115 Biomolecular Sciences Building 296, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1093/nar/gkr1067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245904PMC
January 2012

Quake: quality-aware detection and correction of sequencing errors.

Genome Biol 2010 29;11(11):R116. Epub 2010 Nov 29.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, and Department of Computer Science, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/gb-2010-11-11-r116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3156955PMC
June 2011

Extracting between-pathway models from E-MAP interactions using expected graph compression.

J Comput Biol 2011 Mar;18(3):379-90

Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, USA.

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http://dx.doi.org/10.1089/cmb.2010.0268DOI Listing
March 2011

Clustering metagenomic sequences with interpolated Markov models.

BMC Bioinformatics 2010 Nov 2;11:544. Epub 2010 Nov 2.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/1471-2105-11-544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098094PMC
November 2010

Detection and correction of false segmental duplications caused by genome mis-assembly.

Genome Biol 2010 10;11(3):R28. Epub 2010 Mar 10.

Center for Bioinformatics and Computational Biology, Institute for Advanced Computer Studies, University of Maryland, College Park, MD 20742, USA.

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http://dx.doi.org/10.1186/gb-2010-11-3-r28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864568PMC
September 2010