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Research

Regulation of endogenous retrovirus–derived regulatory elements by GATA2/3 and MSX2 in human trophoblast stem cells

Cui Du
Jing Jiang
Yuzhuo Li
Miao Yu
Jian Jin
Shuai Chen
... [+1 authors] ...,
Hairui Fan
Todd S. Macfarlan
Bin Cao
Ming-an Sun

First Published February 17, 2023

Research

Bacterial infection remodels the DNA methylation landscape of human dendritic cells

Alain Pacis
Ludovic Tailleux
Alexander M. Morin
John Lambourne
Julia L. MacIsaac
Vania Yotova Anne Dumaine Anne Danckaert Francesca Luca Jean-Christophe Grenier Kasper D. Hansen Brigitte Gicquel Miao Yu Athma Pai Chuan He Jenny Tung Tomi Pastinen
... [+12 authors] ...,
Michael S. Kobor
Roger Pique-Regi
Yoav Gilad
Luis B. Barreiro

First Published September 21, 2015

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

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

Lei Zhao
Ming-an Sun
Zejuan Li
Xue Bai
Miao Yu
Min Wang Liji Liang Xiaojian Shao Stephen Arnovitz Qianfei Wang
... [+5 authors] ...,
Chuan He
Xuemei Lu
Jianjun Chen
Hehuang Xie

First Published May 16, 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

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

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

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

Letter

Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes

David L. Goode
Gregory M. Cooper
Jeremy Schmutz
Mark Dickson
Eidelyn Gonzales
Ming Tsai Kalpana Karra
... [+2 authors] ...,
Eugene Davydov
Serafim Batzoglou
Richard M. Myers
Arend Sidow

First Published January 12, 2010

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