Tyrone Ryba

Tyrone Ryba

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Tyrone Ryba

Tyrone Ryba

Publications by authors named "Tyrone Ryba"

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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

Developmental control of replication timing defines a new breed of chromosomal domains with a novel mechanism of chromatin unfolding.

Nucleus 2012 Nov-Dec;3(6):500-7. Epub 2012 Sep 28.

Department of Biological Science; Florida State University, Tallahassee, FL, USA.

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http://dx.doi.org/10.4161/nucl.22318DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3515532PMC
May 2013

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia.

Genome Res 2012 Oct 24;22(10):1833-44. Epub 2012 May 24.

Department of Biological Science, Florida State University, Tallahassee, Florida 32306, USA.

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http://dx.doi.org/10.1101/gr.138511.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3460179PMC
October 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 2012

Chromatin-interaction compartment switch at developmentally regulated chromosomal domains reveals an unusual principle of chromatin folding.

Proc Natl Acad Sci U S A 2012 Jul 17;109(31):12574-9. Epub 2012 Jul 17.

Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.

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http://dx.doi.org/10.1073/pnas.1207185109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411983PMC
July 2012

Replication timing: a fingerprint for cell identity and pluripotency.

PLoS Comput Biol 2011 Oct 20;7(10):e1002225. Epub 2011 Oct 20.

Department of Biological Science, Florida State University, Tallahassee, Florida, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002225DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3197641PMC
October 2011

Genome-scale analysis of replication timing: from bench to bioinformatics.

Nat Protoc 2011 Jun 2;6(6):870-95. Epub 2011 Jun 2.

Department of Biological Science, Florida State University, Tallahassee, USA.

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http://dx.doi.org/10.1038/nprot.2011.328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3111951PMC
June 2011

G9a selectively represses a class of late-replicating genes at the nuclear periphery.

Proc Natl Acad Sci U S A 2009 Nov 4;106(46):19363-8. Epub 2009 Nov 4.

Department of Biological Science, Florida State University, Tallahassee, FL 32306, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0906142106
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http://dx.doi.org/10.1073/pnas.0906142106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2780741PMC
November 2009

ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data.

BMC Bioinformatics 2008 Dec 10;9:530. Epub 2008 Dec 10.

Department of Biological Sciences, Florida State University, Tallahassee, Florida 32306, USA.

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http://dx.doi.org/10.1186/1471-2105-9-530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2636809PMC
December 2008