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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
Method

Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome

  • Jakob Skou Pedersen
  • Eivind Valen
  • Amhed M. Vargas Velazquez
  • Brian J. Parker
  • Morten Rasmussen
  • Stinus Lindgreen Berit Lilje Desmond J. Tobin Theresa K. Kelly Søren Vang Robin Andersson Peter A. Jones Cindi A. Hoover Alexei Tikhonov Egor Prokhortchouk Edward M. Rubin Albin Sandelin
  • ... [+12 authors] ...,
  • M. Thomas P. Gilbert
  • Anders Krogh
  • Eske Willerslev
  • Ludovic Orlando
  • First Published December 3, 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
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
Method

True single-molecule DNA sequencing of a pleistocene horse bone

  • Ludovic Orlando
  • Aurelien Ginolhac
  • Maanasa Raghavan
  • Julia Vilstrup
  • Morten Rasmussen
  • Kim Magnussen Kathleen E. Steinmann Philipp Kapranov John F. Thompson Grant Zazula Duane Froese Ida Moltke Beth Shapiro
  • ... [+8 authors] ...,
  • Michael Hofreiter
  • Khaled A.S. Al-Rasheid
  • M. Thomas P. Gilbert
  • Eske Willerslev
  • First Published July 29, 2011
Research

Orcinus orca) indicates multiple species" > Complete mitochondrial genome phylogeographic analysis of killer whales (Orcinus orca) indicates multiple species

  • Phillip A. Morin
  • Frederick I. Archer
  • Andrew D. Foote
  • Julia Vilstrup
  • Eric E. Allen
  • Paul Wade John Durban Kim Parsons Robert Pitman Lewyn Li Pascal Bouffard Sandra C. Abel Nielsen
  • ... [+7 authors] ...,
  • Morten Rasmussen
  • Eske Willerslev
  • M. Thomas P. Gilbert
  • Timothy Harkins
  • First Published April 22, 2010
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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