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Resource

A limited set of transcriptional programs define major cell types

Alessandra Breschi
Manuel Muñoz-Aguirre
Valentin Wucher
Carrie A. Davis
Diego Garrido-Martín
Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
... [+9 authors] ...,
Ferran Reverter
Michael P. Snyder
Thomas R. Gingeras
Roderic Guigó

First Published July 29, 2020

Resource

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

Method

Read clouds uncover variation in complex regions of the human genome

Alex Bishara
Yuling Liu
Ziming Weng
Dorna Kashef-Haghighi
Daniel E. Newburger
Robert West
Arend Sidow
Serafim Batzoglou

First Published August 18, 2015

Method

Parente2: a fast and accurate method for detecting identity by descent

Jesse M. Rodriguez
Sivan Bercovici
Lin Huang
Roy Frostig
Serafim Batzoglou

First Published October 1, 2014

Research

Genome evolution during progression to breast cancer

Daniel E. Newburger
Dorna Kashef-Haghighi
Ziming Weng
Raheleh Salari
Robert T. Sweeney
Alayne L. Brunner Shirley X. Zhu Xiangqian Guo Sushama Varma
... [+4 authors] ...,
Megan L. Troxell
Robert B. West
Serafim Batzoglou
Arend Sidow

First Published April 8, 2013

Research

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Chao Cheng
Roger Alexander
Renqiang Min
Jing Leng
Kevin Y. Yip
Joel Rozowsky Koon-Kiu Yan Xianjun Dong Sarah Djebali Yijun Ruan Carrie A. Davis Piero Carninci Timo Lassman Thomas R. Gingeras Roderic Guigó
... [+10 authors] ...,
Ewan Birney
Zhiping Weng
Michael Snyder
Mark Gerstein

First Published September 5, 2012

Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Anshul Kundaje
Sofia Kyriazopoulou-Panagiotopoulou
Max Libbrecht
Cheryl L. Smith
Debasish Raha
Elliott E. Winters
... [+1 authors] ...,
Steven M. Johnson
Michael Snyder
Serafim Batzoglou
Arend Sidow

First Published September 5, 2012

Method

Linking disease associations with regulatory information in the human genome

Marc A. Schaub
Alan P. Boyle
Anshul Kundaje
Serafim Batzoglou
Michael Snyder

First Published September 5, 2012

Resource

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

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