Ghia Euskirchen

Ghia Euskirchen

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Ghia Euskirchen

Ghia Euskirchen

Publications by authors named "Ghia Euskirchen"

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41Publications

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Transcriptome Signature and Regulation in Human Somatic Cell Reprogramming.

Stem Cell Reports 2015 Jun 21;4(6):1125-39. Epub 2015 May 21.

Department of Genetics, Yale Stem Cell Center, Yale School of Medicine, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.stemcr.2015.04.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4471828PMC
June 2015

Integrated systems analysis reveals a molecular network underlying autism spectrum disorders.

Mol Syst Biol 2014 Dec 30;10:774. Epub 2014 Dec 30.

Department of Genetics, Stanford Center for Genomics and Personalized Medicine Stanford University School of Medicine, Stanford, CA, USA

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300495PMC
http://dx.doi.org/10.15252/msb.20145487DOI Listing
December 2014

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

SWI/SNF chromatin-remodeling factors: multiscale analyses and diverse functions.

J Biol Chem 2012 Sep 5;287(37):30897-905. Epub 2012 Sep 5.

Department of Genetics, Stanford University School of Medicine, Stanford, California 94305-5120, USA.

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http://dx.doi.org/10.1074/jbc.R111.309302DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3438922PMC
September 2012

Performance comparison of exome DNA sequencing technologies.

Nat Biotechnol 2011 Sep 25;29(10):908-14. Epub 2011 Sep 25.

Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.

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http://dx.doi.org/10.1038/nbt.1975DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4127531PMC
September 2011

Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project.

Authors:
Mark B Gerstein Zhi John Lu Eric L Van Nostrand Chao Cheng Bradley I Arshinoff Tao Liu Kevin Y Yip Rebecca Robilotto Andreas Rechtsteiner Kohta Ikegami Pedro Alves Aurelien Chateigner Marc Perry Mitzi Morris Raymond K Auerbach Xin Feng Jing Leng Anne Vielle Wei Niu Kahn Rhrissorrakrai Ashish Agarwal Roger P Alexander Galt Barber Cathleen M Brdlik Jennifer Brennan Jeremy Jean Brouillet Adrian Carr Ming-Sin Cheung Hiram Clawson Sergio Contrino Luke O Dannenberg Abby F Dernburg Arshad Desai Lindsay Dick Andréa C Dosé Jiang Du Thea Egelhofer Sevinc Ercan Ghia Euskirchen Brent Ewing Elise A Feingold Reto Gassmann Peter J Good Phil Green Francois Gullier Michelle Gutwein Mark S Guyer Lukas Habegger Ting Han Jorja G Henikoff Stefan R Henz Angie Hinrichs Heather Holster Tony Hyman A Leo Iniguez Judith Janette Morten Jensen Masaomi Kato W James Kent Ellen Kephart Vishal Khivansara Ekta Khurana John K Kim Paulina Kolasinska-Zwierz Eric C Lai Isabel Latorre Amber Leahey Suzanna Lewis Paul Lloyd Lucas Lochovsky Rebecca F Lowdon Yaniv Lubling Rachel Lyne Michael MacCoss Sebastian D Mackowiak Marco Mangone Sheldon McKay Desirea Mecenas Gennifer Merrihew David M Miller Andrew Muroyama John I Murray Siew-Loon Ooi Hoang Pham Taryn Phippen Elicia A Preston Nikolaus Rajewsky Gunnar Rätsch Heidi Rosenbaum Joel Rozowsky Kim Rutherford Peter Ruzanov Mihail Sarov Rajkumar Sasidharan Andrea Sboner Paul Scheid Eran Segal Hyunjin Shin Chong Shou Frank J Slack Cindie Slightam Richard Smith William C Spencer E O Stinson Scott Taing Teruaki Takasaki Dionne Vafeados Ksenia Voronina Guilin Wang Nicole L Washington Christina M Whittle Beijing Wu Koon-Kiu Yan Georg Zeller Zheng Zha Mei Zhong Xingliang Zhou Julie Ahringer Susan Strome Kristin C Gunsalus Gos Micklem X Shirley Liu Valerie Reinke Stuart K Kim LaDeana W Hillier Steven Henikoff Fabio Piano Michael Snyder Lincoln Stein Jason D Lieb Robert H Waterston

Science 2010 Dec 22;330(6012):1775-87. Epub 2010 Dec 22.

Program in Computational Biology and Bioinformatics, Yale University, Bass 432, 266 Whitney Avenue, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1126/science.1196914DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3142569PMC
December 2010

Comprehensive annotation of the transcriptome of the human fungal pathogen Candida albicans using RNA-seq.

Genome Res 2010 Oct 1;20(10):1451-8. Epub 2010 Sep 1.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520, USA.

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http://dx.doi.org/10.1101/gr.109553.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2945194PMC
October 2010

Evidence against a genomic code for nucleosome positioning. Reply to "Nucleosome sequence preferences influence in vivo nucleosome organization.".

Nat Struct Mol Biol 2010 Aug;17(8):920-3

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb0810-920DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4742340PMC
August 2010

Molecular mechanisms of ethanol-induced pathogenesis revealed by RNA-sequencing.

PLoS Pathog 2010 Apr 1;6(4):e1000834. Epub 2010 Apr 1.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, United States of America.

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http://dx.doi.org/10.1371/journal.ppat.1000834DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2848557PMC
April 2010

Mapping accessible chromatin regions using Sono-Seq.

Proc Natl Acad Sci U S A 2009 Sep 18;106(35):14926-31. Epub 2009 Aug 18.

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

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http://dx.doi.org/10.1073/pnas.0905443106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736440PMC
September 2009

Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo.

Nat Struct Mol Biol 2009 Aug 20;16(8):847-52. Epub 2009 Jul 20.

Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts, USA.

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http://dx.doi.org/10.1038/nsmb.1636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2823114PMC
August 2009

PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls.

Nat Biotechnol 2009 Jan 4;27(1):66-75. Epub 2009 Jan 4.

Molecular Biophysics & Biochemistry Dept., Yale University, PO Box 208114, New Haven, Connecticut 06520-8114, USA.

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http://dx.doi.org/10.1038/nbt.1518DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2924752PMC
January 2009

Efficient yeast ChIP-Seq using multiplex short-read DNA sequencing.

BMC Genomics 2009 Jan 21;10:37. Epub 2009 Jan 21.

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/1471-2164-10-37DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656530PMC
January 2009

Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome.

Genome Biol 2008 Jan 3;9(1):R3. Epub 2008 Jan 3.

Molecular, Cellular and Developmental Biology Department, KBT918, Yale University, New Haven, Connecticut 06511, USA.

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http://dx.doi.org/10.1186/gb-2008-9-1-r3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395237PMC
January 2008

Mapping the chromosomal targets of STAT1 by Sequence Tag Analysis of Genomic Enrichment (STAGE).

Genome Res 2007 Jun;17(6):910-6

Institute for Cellular and Molecular Biology, Center for Systems and Synthetic Biology, Section of Molecular Genetics and Microbiology, University of Texas at Austin, Austin, Texas 78712, USA.

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http://dx.doi.org/10.1101/gr.5574907DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891349PMC
June 2007

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

Integrative approaches in molecular medicine.

Authors:
Ghia Euskirchen

Pharmacogenomics 2004 Jun;5(4):357-60

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA.

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http://dx.doi.org/10.1517/14622416.5.4.357DOI Listing
June 2004

CREB binds to multiple loci on human chromosome 22.

Mol Cell Biol 2004 May;24(9):3804-14

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8005, USA>

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC387762PMC
http://dx.doi.org/10.1128/mcb.24.9.3804-3814.2004DOI Listing
May 2004

A plethora of sites.

Nat Genet 2004 Apr;36(4):325-6

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http://dx.doi.org/10.1038/ng0404-325DOI Listing
April 2004

Distribution of NF-kappaB-binding sites across human chromosome 22.

Proc Natl Acad Sci U S A 2003 Oct 3;100(21):12247-52. Epub 2003 Oct 3.

Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520-8005, USA.

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http://dx.doi.org/10.1073/pnas.2135255100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC218744PMC
October 2003

The transcriptional activity of human Chromosome 22.

Genes Dev 2003 Feb;17(4):529-40

Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.

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http://dx.doi.org/10.1101/gad.1055203DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC195998PMC
February 2003

Nnf1p, Dsn1p, Mtw1p, and Nsl1p: a new group of proteins important for chromosome segregation in Saccharomyces cerevisiae.

Eukaryot Cell 2002 Apr;1(2):229-40

Department of Biological Sciences, Columbia University, New York, New York 10027, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC118027PMC
http://dx.doi.org/10.1128/ec.1.2.229-240.2002DOI Listing
April 2002