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Research

Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes

Iris Zhu
David Landsman

First Published October 26, 2023

Research

Mediator dynamics during heat shock in budding yeast

Debasish Sarkar
Z. Iris Zhu
Elizabeth R. Knoll
Emily Paul
David Landsman
Randall H. Morse

First Published November 16, 2021

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

Research

Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers

Tao Deng
Z. Iris Zhu
Shaofei Zhang
Yuri Postnikov
Di Huang
Marion Horsch Takashi Furusawa Johannes Beckers Jan Rozman Martin Klingenspor Oana Amarie Jochen Graw Birgit Rathkolb Eckhard Wolf Thure Adler Dirk H. Busch Valérie Gailus-Durner Helmut Fuchs Martin Hrabě de Angelis Arjan van der Velde
... [+15 authors] ...,
Lino Tessarollo
Ivan Ovcherenko
David Landsman
Michael Bustin

First Published July 8, 2015

Research

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

Weishi Yu
Carl McIntosh
Ryan Lister
Iris Zhu
Yixing Han
Jianke Ren David Landsman Eunice Lee Victorino Briones
... [+4 authors] ...,
Minoru Terashima
Robert Leighty
Joseph R. Ecker
Kathrin Muegge

First Published August 28, 2014

Method

Discovery of recurrent structural variants in nasopharyngeal carcinoma

Anton Valouev
Ziming Weng
Robert T. Sweeney
Sushama Varma
Quynh-Thu Le
Christina Kong
Arend Sidow
Robert B. West

First Published November 8, 2013

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

The origin, evolution, and functional impact of short insertion–deletion variants identified in 179 human genomes

Stephen B. Montgomery
David L. Goode
Erika Kvikstad
Cornelis A. Albers
Zhengdong D. Zhang
Xinmeng Jasmine Mu Guruprasad Ananda Bryan Howie Konrad J. Karczewski Kevin S. Smith Vanessa Anaya Rhea Richardson Joe Davis Daniel G. MacArthur Arend Sidow Laurent Duret Mark Gerstein
... [+12 authors] ...,
Kateryna D. Makova
Jonathan Marchini
Gil McVean
Gerton Lunter

First Published March 11, 2013

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

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

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