Publications by authors named "Jeff Vierstra"

23Publications

Unbiased phenotypic identification of functionally distinct hematopoietic progenitors.

J Biol Res (Thessalon) 2019 Dec 18;26. Epub 2019 Jul 18.

1Altius Institute for Biomedical Sciences, Seattle, WA 98121 USA.

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http://dx.doi.org/10.1186/s40709-019-0097-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6639971PMC
December 2019

Genomic footprinting.

Nat Methods 2016 Mar;13(3):213-21

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.3768DOI Listing
March 2016

Methylated Cytosines Mutate to Transcription Factor Binding Sites that Drive Tetrapod Evolution.

Genome Biol Evol 2015 Oct 27;7(11):3155-69. Epub 2015 Oct 27.

Laboratory of Metabolism, National Cancer Institute, National Institutes of Health, Bethesda, Maryland

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http://dx.doi.org/10.1093/gbe/evv205DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4994754PMC
October 2015

Large-scale identification of sequence variants influencing human transcription factor occupancy in vivo.

Nat Genet 2015 Dec 26;47(12):1393-401. Epub 2015 Oct 26.

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/ng.3432DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4666772PMC
December 2015

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

Coupling transcription factor occupancy to nucleosome architecture with DNase-FLASH.

Nat Methods 2014 Jan 3;11(1):66-72. Epub 2013 Nov 3.

1] Department of Genome Sciences, University of Washington, Seattle, Washington, USA. [2] Department of Medicine, Division of Oncology, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nmeth.2713DOI Listing
January 2014

Genome-scale mapping of DNase I hypersensitivity.

Curr Protoc Mol Biol 2013 Jul;Chapter 27:Unit 21.27

Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1002/0471142727.mb2127s103DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405172PMC
July 2013

Personal and population genomics of human regulatory variation.

Genome Res 2012 Sep;22(9):1689-97

Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.

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http://dx.doi.org/10.1101/gr.134890.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431486PMC
September 2012

BEDOPS: high-performance genomic feature operations.

Bioinformatics 2012 Jul 9;28(14):1919-20. Epub 2012 May 9.

Department of Genome Sciences and Department of Medicine, University of Washington, Seattle, Washington, DC 98195, USA.

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http://dx.doi.org/10.1093/bioinformatics/bts277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3389768PMC
July 2012