Publications by authors named "Philip Cayting"

14Publications

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Segmental duplications in the human genome reveal details of pseudogene formation.

Nucleic Acids Res 2010 Nov 8;38(20):6997-7007. Epub 2010 Jul 8.

Program in Computational Biology and Bioinformatics, Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.

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http://dx.doi.org/10.1093/nar/gkq587DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978362PMC
November 2010

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Nat Biotechnol 2010 Jan 27;28(1):47-55. Epub 2009 Dec 27.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://www.nature.com/articles/nbt.1600
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http://dx.doi.org/10.1038/nbt.1600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951730PMC
January 2010

Comparative analysis of processed ribosomal protein pseudogenes in four mammalian genomes.

Genome Biol 2009 5;10(1):R2. Epub 2009 Jan 5.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2009-10-1-r2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2687790PMC
September 2009

Pseudofam: the pseudogene families database.

Nucleic Acids Res 2009 Jan 28;37(Database issue):D738-43. Epub 2008 Oct 28.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1093/nar/gkn758DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2686518PMC
January 2009

Uncovering trends in gene naming.

Genome Biol 2008 Jan 31;9(1):401. Epub 2008 Jan 31.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2008-9-1-401DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395243PMC
January 2008

Analysis of nuclear receptor pseudogenes in vertebrates: how the silent tell their stories.

Mol Biol Evol 2008 Jan 7;25(1):131-43. Epub 2007 Dec 7.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA.

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http://dx.doi.org/10.1093/molbev/msm251DOI Listing
January 2008

Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation.

Nucleic Acids Res 2007 Jan 11;35(Database issue):D55-60. Epub 2006 Nov 11.

Center for Comparative Genomics and Bioinformatics, 506B Wartik, Pennsylvania State University, University Park, PA 16802, USA.

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http://dx.doi.org/10.1093/nar/gkl851DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1669708PMC
January 2007