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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

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

Drosophila cell lines" > Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

Jiayu Wen
Jaaved Mohammed
Diane Bortolamiol-Becet
Harrison Tsai
Nicolas Robine
Jakub O. Westholm Erik Ladewig Qi Dai Katsutomo Okamura Alex S. Flynt Dayu Zhang Justen Andrews Lucy Cherbas
... [+8 authors] ...,
Thomas C. Kaufman
Peter Cherbas
Adam Siepel
Eric C. Lai

First Published July 1, 2014

Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality

Daniel F. Simola
Lothar Wissler
Greg Donahue
Robert M. Waterhouse
Martin Helmkampf
Julien Roux Sanne Nygaard Karl M. Glastad Darren E. Hagen Lumi Viljakainen Justin T. Reese Brendan G. Hunt Dan Graur Eran Elhaik Evgenia V. Kriventseva Jiayu Wen Brian J. Parker Elizabeth Cash Eyal Privman Christopher P. Childers Monica C. Muñoz-Torres Jacobus J. Boomsma Erich Bornberg-Bauer Cameron R. Currie Christine G. Elsik Garret Suen Michael A.D. Goodisman Laurent Keller Jürgen Liebig Alan Rawls Danny Reinberg Chris D. Smith Chris R. Smith Neil Tsutsui
... [+29 authors] ...,
Yannick Wurm
Evgeny M. Zdobnov
Shelley L. Berger
Jürgen Gadau

First Published May 1, 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

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

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

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

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes

Brian J. Parker
Ida Moltke
Adam Roth
Stefan Washietl
Jiayu Wen
Manolis Kellis
Ronald Breaker
Jakob Skou Pedersen

First Published October 12, 2011

Signatures of RNA binding proteins globally coupled to effective microRNA target sites

Anders Jacobsen
Jiayu Wen
Debora S. Marks
Anders Krogh

First Published May 27, 2010

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