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Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Jiawei Shen
Siyuan Cheng
Deepak Purushotham
Xiaoyu Zhuo
Alan Y Du
Wenjin Zhang
Daofeng Li
Ting Wang

First Published February 21, 2025

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Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

Ashlyn G. Anderson
Belle A. Moyers
Jacob M. Loupe
Ivan Rodriguez-Nunez
Stephanie A. Felker
James M.J. Lawlor William E. Bunney Blynn G. Bunney Preston M. Cartagena Adolfo Sequeira Stanley J. Watson
... [+6 authors] ...,
Huda Akil
Eric M. Mendenhall
Gregory M. Cooper
Richard M. Myers

First Published August 16, 2024

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Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Xiaoyu Zhuo
Silas Hsu
Deepak Purushotham
Prashant Kumar Kuntala
Jessica K. Harrison
Alan Y. Du
Samuel Chen
Daofeng Li
Ting Wang

First Published May 8, 2023

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Dynamics of microRNA expression during mouse prenatal development

Sorena Rahmanian
Rabi Murad
Alessandra Breschi
Weihua Zeng
Mark Mackiewicz
Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
... [+12 authors] ...,
Barbara J. Wold
Richard M. Myers
Roderic Guigó
Ali Mortazavi

First Published October 23, 2019

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A genome-wide interactome of DNA-associated proteins in the human liver

Ryne C. Ramaker
Daniel Savic
Andrew A. Hardigan
Kimberly Newberry
Gregory M. Cooper
Richard M. Myers
Sara J. Cooper

First Published October 11, 2017

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Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Ali Mortazavi
Shirley Pepke
Camden Jansen
Georgi K. Marinov
Jason Ernst
Manolis Kellis
Ross C. Hardison
Richard M. Myers
Barbara J. Wold

First Published October 29, 2013

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Dynamic DNA methylation across diverse human cell lines and tissues

Katherine E. Varley
Jason Gertz
Kevin M. Bowling
Stephanie L. Parker
Timothy E. Reddy
Florencia Pauli-Behn Marie K. Cross Brian A. Williams John A. Stamatoyannopoulos
... [+4 authors] ...,
Gregory E. Crawford
Devin M. Absher
Barbara J. Wold
Richard M. Myers

First Published January 16, 2013

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Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Jie Wang
Jiali Zhuang
Sowmya Iyer
XinYing Lin
Troy W. Whitfield
Melissa C. Greven Brian G. Pierce Xianjun Dong Anshul Kundaje Yong Cheng Oliver J. Rando Ewan Birney
... [+7 authors] ...,
Richard M. Myers
William S. Noble
Michael Snyder
Zhiping Weng

First Published September 5, 2012

Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Stephen G. Landt
Georgi K. Marinov
Anshul Kundaje
Pouya Kheradpour
Florencia Pauli
Serafim Batzoglou Bradley E. Bernstein Peter Bickel James B. Brown Philip Cayting Yiwen Chen Gilberto DeSalvo Charles Epstein Katherine I. Fisher-Aylor Ghia Euskirchen Mark Gerstein Jason Gertz Alexander J. Hartemink Michael M. Hoffman Vishwanath R. Iyer Youngsook L. Jung Subhradip Karmakar Manolis Kellis Peter V. Kharchenko Qunhua Li Tao Liu X. Shirley Liu Lijia Ma Aleksandar Milosavljevic Richard M. Myers Peter J. Park Michael J. Pazin Marc D. Perry Debasish Raha Timothy E. Reddy Joel Rozowsky Noam Shoresh Arend Sidow Matthew Slattery John A. Stamatoyannopoulos Michael Y. Tolstorukov Kevin P. White Simon Xi
... [+38 authors] ...,
Peggy J. Farnham
Jason D. Lieb
Barbara J. Wold
Michael Snyder

First Published September 5, 2012

Resource

The completion of the Mammalian Gene Collection (MGC)

Gary Temple
Daniela S. Gerhard
Rebekah Rasooly
Elise A. Feingold
Peter J. Good
Cristen Robinson Allison Mandich Jeffrey G. Derge Jeanne Lewis Debonny Shoaf Francis S. Collins Wonhee Jang Lukas Wagner Carolyn M. Shenmen Leonie Misquitta Carl F. Schaefer Kenneth H. Buetow Tom I. Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L. Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D. Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L.G. Comstock Michael Stevens Chaochun Wei Marijke J. van Baren Kourosh Salehi-Ashtiani Ryan R. Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E. Gruber Mark R. Smith John McPherson Angela M. Garcia Preethi H. Gunaratne Jiaqian Wu Donna Muzny Richard A. Gibbs Alice C. Young Gerard G. Bouffard Robert W. Blakesley Jim Mullikin Eric D. Green Mark C. Dickson Alex C. Rodriguez Jane Grimwood Jeremy Schmutz Richard M. Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A. Moore Michael Mayo Sarah Munro Susan Wagner Steven J.M. Jones Robert A. Holt Marco A. Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C. Pulido Keith Robison Dominic Esposito James Hartley
... [+118 authors] ...,
Vanessa E. Wall
Ralph F. Hopkins
Osamu Ohara
Stefan Wiemann

First Published September 18, 2009

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Resource

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Resource

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

Resource

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Resource

Dynamics of microRNA expression during mouse prenatal development

Resource

A genome-wide interactome of DNA-associated proteins in the human liver

Resource

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Resource

Dynamic DNA methylation across diverse human cell lines and tissues

Resource

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

Resource

ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia

Resource

The completion of the Mammalian Gene Collection (MGC)

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