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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

Drosophila melanogaster" > Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

Matthew Slattery
Lijia Ma
Rebecca F. Spokony
Robert K. Arthur
Pouya Kheradpour
Anshul Kundaje Nicolas Nègre Alex Crofts Ryan Ptashkin Jennifer Zieba Alexander Ostapenko Sarah Suchy Alec Victorsen Nader Jameel A. Jason Grundstad Wenxuan Gao Jennifer R. Moran
... [+12 authors] ...,
E. Jay Rehm
Robert L. Grossman
Manolis Kellis
Kevin P. White

First Published July 1, 2014

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

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

Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay

Pouya Kheradpour
Jason Ernst
Alexandre Melnikov
Peter Rogov
Li Wang
Xiaolan Zhang
Jessica Alston
Tarjei S. Mikkelsen
Manolis Kellis

First Published March 19, 2013

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

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

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

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes

Michael F. Lin
Pouya Kheradpour
Stefan Washietl
Brian J. Parker
Jakob S. Pedersen
Manolis Kellis

First Published October 12, 2011

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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