John A Stamatoyannopoulos

John A Stamatoyannopoulos

UNVERIFIED PROFILE

Are you John A Stamatoyannopoulos?   Register this Author

Register author
John A Stamatoyannopoulos

John A Stamatoyannopoulos

Publications by authors named "John A Stamatoyannopoulos"

Are you John A Stamatoyannopoulos?   Register this Author

100Publications

3520Reads

6Profile Views

Operating on Genomic Ranges Using BEDOPS.

Methods Mol Biol 2016 ;1418:267-81

Altius Institute for Biomedical Sciences, 2211 Elliott Avenue, Seattle, WA, 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/978-1-4939-3578-9_14DOI Listing
December 2016

52 Genetic Loci Influencing Myocardial Mass.

Authors:
Pim van der Harst Jessica van Setten Niek Verweij Georg Vogler Lude Franke Matthew T Maurano Xinchen Wang Irene Mateo Leach Mark Eijgelsheim Nona Sotoodehnia Caroline Hayward Rossella Sorice Osorio Meirelles Leo-Pekka Lyytikäinen Ozren Polašek Toshiko Tanaka Dan E Arking Sheila Ulivi Stella Trompet Martina Müller-Nurasyid Albert V Smith Marcus Dörr Kathleen F Kerr Jared W Magnani Fabiola Del Greco M Weihua Zhang Ilja M Nolte Claudia T Silva Sandosh Padmanabhan Vinicius Tragante Tõnu Esko Gonçalo R Abecasis Michiel E Adriaens Karl Andersen Phil Barnett Joshua C Bis Rolf Bodmer Brendan M Buckley Harry Campbell Megan V Cannon Aravinda Chakravarti Lin Y Chen Alessandro Delitala Richard B Devereux Pieter A Doevendans Anna F Dominiczak Luigi Ferrucci Ian Ford Christian Gieger Tamara B Harris Eric Haugen Matthias Heinig Dena G Hernandez Hans L Hillege Joel N Hirschhorn Albert Hofman Norbert Hubner Shih-Jen Hwang Annamaria Iorio Mika Kähönen Manolis Kellis Ivana Kolcic Ishminder K Kooner Jaspal S Kooner Jan A Kors Edward G Lakatta Kasper Lage Lenore J Launer Daniel Levy Alicia Lundby Peter W Macfarlane Dalit May Thomas Meitinger Andres Metspalu Stefania Nappo Silvia Naitza Shane Neph Alex S Nord Teresa Nutile Peter M Okin Jesper V Olsen Ben A Oostra Josef M Penninger Len A Pennacchio Tune H Pers Siegfried Perz Annette Peters Yigal M Pinto Arne Pfeufer Maria Grazia Pilia Peter P Pramstaller Bram P Prins Olli T Raitakari Soumya Raychaudhuri Ken M Rice Elizabeth J Rossin Jerome I Rotter Sebastian Schafer David Schlessinger Carsten O Schmidt Jobanpreet Sehmi Herman H W Silljé Gianfranco Sinagra Moritz F Sinner Kamil Slowikowski Elsayed Z Soliman Timothy D Spector Wilko Spiering John A Stamatoyannopoulos Ronald P Stolk Konstantin Strauch Sian-Tsung Tan Kirill V Tarasov Bosco Trinh Andre G Uitterlinden Malou van den Boogaard Cornelia M van Duijn Wiek H van Gilst Jorma S Viikari Peter M Visscher Veronique Vitart Uwe Völker Melanie Waldenberger Christian X Weichenberger Harm-Jan Westra Cisca Wijmenga Bruce H Wolffenbuttel Jian Yang Connie R Bezzina Patricia B Munroe Harold Snieder Alan F Wright Igor Rudan Laurie A Boyer Folkert W Asselbergs Dirk J van Veldhuisen Bruno H Stricker Bruce M Psaty Marina Ciullo Serena Sanna Terho Lehtimäki James F Wilson Stefania Bandinelli Alvaro Alonso Paolo Gasparini J Wouter Jukema Stefan Kääb Vilmundur Gudnason Stephan B Felix Susan R Heckbert Rudolf A de Boer Christopher Newton-Cheh Andrew A Hicks John C Chambers Yalda Jamshidi Axel Visel Vincent M Christoffels Aaron Isaacs Nilesh J Samani Paul I W de Bakker

J Am Coll Cardiol 2016 09;68(13):1435-1448

Department of Medical Genetics, University Medical Center Utrecht, Utrecht, the Netherlands; Department of Epidemiology, University Medical Center Utrecht, Utrecht, the Netherlands.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.jacc.2016.07.729DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5478167PMC
September 2016

Cross-Platform DNA Encoding for Single-Cell Imaging of Gene Expression.

Angew Chem Int Ed Engl 2016 07 7;55(31):8975-8. Epub 2016 Jun 7.

Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1002/anie.201603945DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5036947PMC
July 2016

Genomic footprinting.

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

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

Role of DNA Methylation in Modulating Transcription Factor Occupancy.

Cell Rep 2015 Aug 6;12(7):1184-95. Epub 2015 Aug 6.

Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Oncology, Department of Medicine, University of Washington, Seattle, WA 98195, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.celrep.2015.07.024DOI Listing
August 2015

Taking Stock of Regulatory Variation.

Cell Syst 2015 Jul 29;1(1):18-21. Epub 2015 Jul 29.

Department of Genome Sciences, University of Washington, Seattle, WA 98115, USA; Division of Oncology, Department of Medicine, University of Washington, Seattle, WA 98115, USA. Electronic address:

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cels.2015.07.011DOI Listing
July 2015

Genomic discovery of potent chromatin insulators for human gene therapy.

Nat Biotechnol 2015 Feb 12;33(2):198-203. Epub 2015 Jan 12.

1] Division of Medical Genetics, University of Washington, Seattle, Washington, USA. [2] Department of Genome Sciences, University of Washington, Seattle, Washington, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.3062DOI Listing
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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4530010PMC
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.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nature14221DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405175PMC
February 2015

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.

View Article

Download full-text PDF

Source
https://www.nature.com/articles/nature13907.pdf
Web Search
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4317254/
Web Search
http://www.nature.com/articles/nature13907
Publisher Site
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

Inflammation-induced repression of chromatin bound by the transcription factor Foxp3 in regulatory T cells.

Nat Immunol 2014 Jun 13;15(6):580-587. Epub 2014 Apr 13.

Howard Hughes Medical Institute, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA.

View Article

Download full-text PDF

Source
http://www.nature.com/articles/ni.2868
Publisher Site
http://dx.doi.org/10.1038/ni.2868DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4112080PMC
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.

View Article

Download full-text PDF

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

Reduced local mutation density in regulatory DNA of cancer genomes is linked to DNA repair.

Nat Biotechnol 2014 Jan 15;32(1):71-5. Epub 2013 Dec 15.

1] Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA. [2] Harvard Medical School, Boston, Massachusetts, USA. [3] The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nbt.2778DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4116484PMC
January 2014

Epigenetic modifications and chromosome conformations of the beta globin locus throughout development.

Stem Cell Rev Rep 2013 Aug;9(4):397-407

Department of Medicine, Division of Hematology, University of Washington, NE Pacific St, Box 357710, Seattle, WA 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1007/s12015-012-9355-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398168PMC
August 2013

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis.

Dev Cell 2012 Oct 4;23(4):796-811. Epub 2012 Oct 4.

Division of Hematology/Oncology, Children's Hospital Boston and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Stem Cell Institute, Harvard Medical School, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.devcel.2012.09.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3477283PMC
October 2012

Widespread site-dependent buffering of human regulatory polymorphism.

PLoS Genet 2012 22;8(3):e1002599. Epub 2012 Mar 22.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1002599DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3310774PMC
September 2012

What does our genome encode?

Genome Res 2012 Sep;22(9):1602-11

Departments of Genome Sciences and Medicine, University of Washington School of Medicine, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.146506.112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3431477PMC
September 2012

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding.

Genome Biol 2011 7;12(4):R34. Epub 2011 Apr 7.

Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84-171, Berkeley, CA 94720, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1186/gb-2011-12-4-r34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218860PMC
February 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.

View Article

Download full-text PDF

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

Gammaretroviral vector integration occurs overwhelmingly within and near DNase hypersensitive sites.

Hum Gene Ther 2012 Feb 14;23(2):231-7. Epub 2011 Dec 14.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1089/hum.2010.177DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3277727PMC
February 2012

Rapid empirical discovery of optimal peptides for targeted proteomics.

Nat Methods 2011 Nov 6;8(12):1041-3. Epub 2011 Nov 6.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth.1770DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227787PMC
November 2011

Dynamic exchange at regulatory elements during chromatin remodeling underlies assisted loading mechanism.

Cell 2011 Aug 11;146(4):544-54. Epub 2011 Aug 11.

Laboratory of Receptor Biology and Gene Expression, Building 41, B602, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S00928674110076
Publisher Site
http://dx.doi.org/10.1016/j.cell.2011.07.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3210475PMC
August 2011

Transcription factor AP1 potentiates chromatin accessibility and glucocorticoid receptor binding.

Mol Cell 2011 Jul;43(1):145-55

Laboratory of Receptor Biology and Gene Expression, B602, Building 41, 41 Library Drive, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2011.06.016DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3138120PMC
July 2011

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements.

Genome Res 2011 May 6;21(5):697-706. Epub 2011 Apr 6.

Laboratory of Receptor Biology and Gene Expression, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892-5055, USA.

View Article

Download full-text PDF

Source
http://genome.cshlp.org/cgi/doi/10.1101/gr.111153.110
Publisher Site
http://dx.doi.org/10.1101/gr.111153.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3083086PMC
May 2011

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

Nat Genet 2011 Mar 23;43(3):264-8. Epub 2011 Jan 23.

Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.759DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6386452PMC
March 2011

Contribution of inherited mutations in the BRCA2-interacting protein PALB2 to familial breast cancer.

Cancer Res 2011 Mar 1;71(6):2222-9. Epub 2011 Feb 1.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1158/0008-5472.CAN-10-3958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3059378PMC
March 2011

Quantitative models of the mechanisms that control genome-wide patterns of transcription factor binding during early Drosophila development.

PLoS Genet 2011 Feb 3;7(2):e1001290. Epub 2011 Feb 3.

Department of Molecular and Cell Biology, California Institute of Quantitative Biosciences, University of California Berkeley, Berkeley, California, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pgen.1001290DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3033374PMC
February 2011

Cell-type-specific long-range looping interactions identify distant regulatory elements of the CFTR gene.

Nucleic Acids Res 2010 Jul 31;38(13):4325-36. Epub 2010 Mar 31.

Program in Gene Function and Expression and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605-0103, USA.

View Article

Download full-text PDF

Source
https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gkq175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910055PMC
July 2010

Illuminating eukaryotic transcription start sites.

Nat Methods 2010 Jul;7(7):501-3

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/nmeth0710-501DOI Listing
July 2010

Integrative meta-analysis of differential gene expression in acute myeloid leukemia.

PLoS One 2010 Mar 1;5(3):e9466. Epub 2010 Mar 1.

Department of Hematology, University of Washington, Seattle, Washington, United States of America.

View Article

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0009466PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830886PMC
March 2010

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.

View Article

Download full-text PDF

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

Human mutation rate associated with DNA replication timing.

Nat Genet 2009 Apr 15;41(4):393-5. Epub 2009 Mar 15.

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1038/ng.363DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914101PMC
April 2009

Power of deep, all-exon resequencing for discovery of human trait genes.

Proc Natl Acad Sci U S A 2009 Mar 6;106(10):3871-6. Epub 2009 Feb 6.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0812824106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2656172PMC
March 2009

Epigenomics at the tipping point. Foreword.

Pharmacogenomics 2008 Dec;9(12):1781-3

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

View Article

Download full-text PDF

Source
http://dx.doi.org/10.2217/14622416.9.12.1781DOI Listing
December 2008

Automated mapping of large-scale chromatin structure in ENCODE.

Bioinformatics 2008 Sep 30;24(17):1911-6. Epub 2008 Jun 30.

Division of Mathematical Sciences, SPMS, Nanyang Technological University, Singapore.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1093/bioinformatics/btn335DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2519158PMC
September 2008

Predicting human nucleosome occupancy from primary sequence.

PLoS Comput Biol 2008 Aug 22;4(8):e1000134. Epub 2008 Aug 22.

Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1371/journal.pcbi.1000134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2515632PMC
August 2008

Oct4 dependence of chromatin structure within the extended Nanog locus in ES cells.

Genes Dev 2008 Mar 18;22(5):575-80. Epub 2008 Feb 18.

Division of Hematology-Oncology, Children's Hospital and Dana Farber Cancer Institute, Harvard Medical School, Harvard Stem Cell Institute, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gad.1606308DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2259027PMC
March 2008

Interaction of the glucocorticoid receptor with the chromatin landscape.

Mol Cell 2008 Mar;29(5):611-24

Laboratory of Receptor Biology and Gene Expression, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892-5055, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.molcel.2008.02.010DOI Listing
March 2008

Nucleosome positioning signals in genomic DNA.

Genome Res 2007 Aug 9;17(8):1170-7. Epub 2007 Jul 9.

Bioinformatics Program, Boston University, Boston, MA 02215, USA.

View Article

Download full-text PDF

Source
http://www.genome.org/cgi/doi/10.1101/gr.6101007
Publisher Site
http://dx.doi.org/10.1101/gr.6101007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933512PMC
August 2007

Widely distributed noncoding purifying selection in the human genome.

Proc Natl Acad Sci U S A 2007 Jul 17;104(30):12410-5. Epub 2007 Jul 17.

Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1073/pnas.0705140104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1941483PMC
July 2007

Identification of higher-order functional domains in the human ENCODE regions.

Genome Res 2007 Jun;17(6):917-27

Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.

View Article

Download full-text PDF

Source
http://dx.doi.org/10.1101/gr.6081407DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1891350PMC
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