PMC Links for GEO DataSets (Select 200018927) - PMC

Select item 46667721.

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

Matthew T. Maurano, Eric Haugen, Richard Sandstrom, Jeff Vierstra, Anthony Shafer, Rajinder Kaul, John A. Stamatoyannopoulos

Nat Genet. Author manuscript; available in PMC 2016 May 18.

Published in final edited form as: Nat Genet. 2015 Dec; 47(12): 1393–1401. Published online 2015 Oct 26. doi: 10.1038/ng.3432

Correction in:: Nat Genet. 2016 Jan; 48(1): 101.

PMCID:: PMC4666772

Abstract Article PDF–2.0M

Select item 44990212.

Human Body Epigenome Maps Reveal Noncanonical DNA Methylation Variation

Matthew D. Schultz, Yupeng He, John W. Whitaker, Manoj Hariharan, Eran A. Mukamel, Danny Leung, Nisha Rajagopal, Joseph R. Nery, Mark A. Urich, Huaming Chen, Shin Lin, Yiing Lin, Inkyung Jung, Anthony D. Schmitt, Siddarth Selvaraj, Bing Ren, Terrence J. Sejnowski, Wei Wang, Joseph R. Ecker

Nature. Author manuscript; available in PMC 2016 Jan 9.

Published in final edited form as: Nature. 2015 Jul 9; 523(7559): 212–216. Published online 2015 Jun 1. doi: 10.1038/nature14465

Correction in:: Nature. 2016 Feb 11; 530(7589): 242.

PMCID:: PMC4499021

Abstract Article PDF–2.9M

Select item 44051753.

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

Paz Polak, Rosa Karlic, Amnon Koren, Robert Thurman, Richard Sandstrom, Michael Lawrence, Alex Reynolds, Eric Rynes, Kristian Vlahovicek, John A. Stamatoyannopoulos, Shamil R. Sunyaev

Nature. Author manuscript; available in PMC 2015 Aug 19.

Published in final edited form as: Nature. 2015 Feb 19; 518(7539): 360–364. doi: 10.1038/nature14221

PMCID:: PMC4405175

Abstract Article PDF–2.8M

Select item 41164844.

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

Paz Polak, Michael S. Lawrence, Eric Haugen, Nina Stoletzki, Petar Stojanov, Robert E Thurman, Levi A. Garraway, Sergei Mirkin, Gad Getz, John A. Stamatoyannopoulos, Shamil R. Sunyaev

Nat Biotechnol. Author manuscript; available in PMC 2014 Jul 30.

Published in final edited form as: Nat Biotechnol. 2014 Jan; 32(1): 71–75. Published online 2013 Dec 15. doi: 10.1038/nbt.2778

PMCID:: PMC4116484

Abstract Article PDF–565K

Select item 37715215.

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

Matthew T. Maurano, Richard Humbert, Eric Rynes, Robert E. Thurman, Eric Haugen, Hao Wang, Alex P. Reynolds, Richard Sandstrom, Hongzhu Qu, Jennifer Brody, Anthony Shafer, Fidencio Neri, Kristen Lee, Tanya Kutyavin, Sandra Stehling-Sun, Audra K. Johnson, Theresa K. Canfield, Erika Giste, Morgan Diegel, Daniel Bates, R. Scott Hansen, Shane Neph, Peter J. Sabo, Shelly Heimfeld, Antony Raubitschek, Steven Ziegler, Chris Cotsapas, Nona Sotoodehnia, Ian Glass, Shamil R. Sunyaev, Rajinder Kaul, John A. Stamatoyannopoulos

Science. Author manuscript; available in PMC 2013 Sep 12.

Published in final edited form as: Science. 2012 Sep 7; 337(6099): 1190–1195. Published online 2012 Sep 5. doi: 10.1126/science.1222794

PMCID:: PMC3771521

Abstract Article PDF–1.3M

Select item 37365826.

An expansive human regulatory lexicon encoded in transcription factor footprints

Shane Neph, Jeff Vierstra, Andrew B. Stergachis, Alex P. Reynolds, Eric Haugen, Benjamin Vernot, Robert E. Thurman, Richard Sandstrom, Audra K. Johnson, Matthew T. Maurano, Richard Humbert, Eric Rynes, Hao Wang, Shinny Vong, Kristen Lee, Daniel Bates, Morgan Diegel, Vaughn Roach, Douglas Dunn, Jun Neri, Anthony Schafer, R. Scott Hansen, Tanya Kutyavin, Erika Giste, Molly Weaver, Theresa Canfield, Peter Sabo, Miaohua Zhang, Gayathri Balasundaram, Rachel Byron, Michael J. MacCoss, Joshua M. Akey, Michael Bender, Mark Groudine, Rajinder Kaul, John A. Stamatoyannopoulos

Nature. Author manuscript; available in PMC 2013 Aug 7.

Published in final edited form as: Nature. 2012 Sep 6; 489(7414): 83–90. doi: 10.1038/nature11212

PMCID:: PMC3736582

Abstract Article PDF–2.8M

Select item 36316757.

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

Allan Lazarovici, Tianyin Zhou, Anthony Shafer, Ana Carolina Dantas Machado, Todd R. Riley, Richard Sandstrom, Peter J. Sabo, Yan Lu, Remo Rohs, John A. Stamatoyannopoulos, Harmen J. Bussemaker

Proc Natl Acad Sci U S A. 2013 Apr 16; 110(16): 6376–6381. Published online 2013 Apr 1. doi: 10.1073/pnas.1216822110

PMCID:: PMC3631675

Abstract Article PDF–1.1M

Select item 36072818.

The NIH Roadmap Epigenomics Mapping Consortium

Bradley E Bernstein, John A Stamatoyannopoulos, Joseph F Costello, Bing Ren, Aleksandar Milosavljevic, Alexander Meissner, Manolis Kellis, Marco A Marra, Arthur L Beaudet, Joseph R Ecker, Peggy J Farnham, Martin Hirst, Eric S Lander, Tarjei S Mikkelsen, James A Thomson

Nat Biotechnol. Author manuscript; available in PMC 2013 Mar 25.

Published in final edited form as: Nat Biotechnol. 2010 Oct; 28(10): 1045–1048. doi: 10.1038/nbt1010-1045

PMCID:: PMC3607281

Article PDF–797K

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