Publications by authors named "Richard Sandstrom"

52Publications

The birth of a human-specific neural gene by incomplete duplication and gene fusion.

Genome Biol 2017 03 9;18(1):49. Epub 2017 Mar 9.

Department of Genome Sciences, University of Washington School of Medicine, 3720 15 Ave NE, S413C, Box 355065, Seattle, WA, 98195-5065, USA.

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http://dx.doi.org/10.1186/s13059-017-1163-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5345166PMC
March 2017

Cross-species Analyses Unravel the Complexity of H3K27me3 and H4K20me3 in the Context of Neural Stem Progenitor Cells.

Neuroepigenetics 2016 Jun 3;6:10-25. Epub 2016 May 3.

Department of Biology, University of Texas at San Antonio, San Antonio, Texas 78249, USA; Neuroscience Institute, University of Texas at San Antonio, San Antonio, Texas 78249, USA.

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http://dx.doi.org/10.1016/j.nepig.2016.04.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4941106PMC
June 2016

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

Genome-wide comparative analysis reveals human-mouse regulatory landscape and evolution.

BMC Genomics 2015 Feb 14;16:87. Epub 2015 Feb 14.

Department of Mathematics and Computer Science, Emory University, Atlanta, GA, 30322, USA.

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http://www.biomedcentral.com/1471-2164/16/87
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http://dx.doi.org/10.1186/s12864-015-1245-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333152PMC
February 2015

Cell-of-origin chromatin organization shapes the mutational landscape of cancer.

Nature 2015 Feb;518(7539):360-364

Division of Genetics, Department of Medicine, Brigham & Women's Hospital and Harvard Medical School, Boston, MA, 02115.

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http://dx.doi.org/10.1038/nature14221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405175PMC
February 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

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

Resolving the complexity of the human genome using single-molecule sequencing.

Nature 2015 Jan 10;517(7536):608-11. Epub 2014 Nov 10.

1] Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA.

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https://www.nature.com/articles/nature13907.pdf
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https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/
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http://www.nature.com/articles/nature13907
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http://dx.doi.org/10.1038/nature13907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254PMC
January 2015

A genome-wide map of adeno-associated virus-mediated human gene targeting.

Nat Struct Mol Biol 2014 Nov 5;21(11):969-75. Epub 2014 Oct 5.

1] Department of Medicine, University of Washington, Seattle, Washington, USA. [2] Department of Biochemistry, University of Washington, Seattle, Washington, USA.

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http://dx.doi.org/10.1038/nsmb.2895DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405182PMC
November 2014

Molecular targets of chromatin repressive mark H3K9me3 in primate progenitor cells within adult neurogenic niches.

Front Genet 2014 30;5:252. Epub 2014 Jul 30.

Department of Biology, University of Texas at San Antonio San Antonio, TX, USA ; Neurobiology, Neuroscience Institute, University of Texas at San Antonio San Antonio, TX, USA.

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http://dx.doi.org/10.3389/fgene.2014.00252DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4115620PMC
August 2014

Epigenetic regulation by chromatin activation mark H3K4me3 in primate progenitor cells within adult neurogenic niche.

Sci Rep 2014 Jun 20;4:5371. Epub 2014 Jun 20.

1] Department of Biology, University of Texas at San Antonio, One UTSA Circle, San Antonio, Texas 78249, USA [2] Neuroscience Institute, University of Texas at San Antonio, San Antonio, Texas 78249, USA.

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http://dx.doi.org/10.1038/srep05371DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064326PMC
June 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

Probing DNA shape and methylation state on a genomic scale with DNase I.

Proc Natl Acad Sci U S A 2013 Apr 1;110(16):6376-81. Epub 2013 Apr 1.

Department of Electrical Engineering and Biological Sciences, Columbia University, New York, NY 10027, USA.

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http://dx.doi.org/10.1073/pnas.1216822110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631675PMC
April 2013

Circuitry and dynamics of human transcription factor regulatory networks.

Cell 2012 Sep 5;150(6):1274-86. Epub 2012 Sep 5.

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

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http://dx.doi.org/10.1016/j.cell.2012.04.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3679407PMC
September 2012

An encyclopedia of mouse DNA elements (Mouse ENCODE).

August 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

Zebrafish globin switching occurs in two developmental stages and is controlled by the LCR.

Dev Biol 2012 Jun 19;366(2):185-94. Epub 2012 Apr 19.

Stem Cell Program and Division of Hematology/Oncology, Children's Hospital and Dana Farber Cancer Institute, and Harvard Stem Cell Institute, Harvard Medical School, 1 Blackfan Cir., Karp 7, Boston, MA 02115, USA.

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http://dx.doi.org/10.1016/j.ydbio.2012.03.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378398PMC
June 2012

Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.

Genome Biol 2011 11;12(5):R43. Epub 2011 May 11.

Department of Genome Sciences, University of Washington, Foege S310A, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1186/gb-2011-12-5-r43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3219966PMC
February 2012

Sequencing newly replicated DNA reveals widespread plasticity in human replication timing.

Proc Natl Acad Sci U S A 2010 Jan 4;107(1):139-44. Epub 2009 Dec 4.

Department of Medicine, Division of Medical Genetics, University of Washington School of Medicine, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1073/pnas.0912402107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2806781PMC
January 2010

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007