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Method

Identification of complex genomic rearrangements in cancers using CouGaR

  • Misko Dzamba
  • Arun K. Ramani
  • Pawel Buczkowicz
  • Yue Jiang
  • Man Yu
  • Cynthia Hawkins
  • Michael Brudno
  • First Published November 14, 2016
Resource

Alignathon: a competitive assessment of whole-genome alignment methods

  • Dent Earl
  • Ngan Nguyen
  • Glenn Hickey
  • Robert S. Harris
  • Stephen Fitzgerald
  • Kathryn Beal Igor Seledtsov Vladimir Molodtsov Brian J. Raney Hiram Clawson Jaebum Kim Carsten Kemena Jia-Ming Chang Ionas Erb Alexander Poliakov Minmei Hou Javier Herrero William James Kent Victor Solovyev Aaron E. Darling Jian Ma Cedric Notredame
  • ... [+17 authors] ...,
  • Michael Brudno
  • Inna Dubchak
  • David Haussler
  • Benedict Paten
  • First Published October 1, 2014
Method

iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

  • Aziz M. Mezlini
  • Eric J.M. Smith
  • Marc Fiume
  • Orion Buske
  • Gleb L. Savich
  • Sohrab Shah
  • ... [+1 authors] ...,
  • Sam Aparicio
  • Derek Y. Chiang
  • Anna Goldenberg
  • Michael Brudno
  • First Published November 29, 2012
Resource

Detecting copy number variation with mated short reads

  • Paul Medvedev
  • Marc Fiume
  • Misko Dzamba
  • Tim Smith
  • Michael Brudno
  • First Published August 30, 2010
Resource

Multiple whole-genome alignments without a reference organism

  • Inna Dubchak
  • Alexander Poliakov
  • Andrey Kislyuk
  • Michael Brudno
  • First Published January 28, 2009
RESOURCE

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

  • Webb Miller
  • Kate Rosenbloom
  • Ross C. Hardison
  • Minmei Hou
  • James Taylor
  • Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
  • ... [+17 authors] ...,
  • Eric S. Lander
  • Adam Siepel
  • David Haussler
  • W. James Kent
  • First Published November 5, 2007
RESOURCE

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

  • Daniel Blankenberg
  • James Taylor
  • Ian Schenck
  • Jianbin He
  • Yi Zhang
  • Matthew Ghent Narayanan Veeraraghavan Istvan Albert
  • ... [+3 authors] ...,
  • Webb Miller
  • Kateryna D. Makova
  • Ross C. Hardison
  • Anton Nekrutenko
  • First Published June 13, 2007
RESOURCE

Galaxy: A platform for interactive large-scale genome analysis

  • Belinda Giardine
  • Cathy Riemer
  • Ross C. Hardison
  • Richard Burhans
  • Laura Elnitski
  • Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
  • ... [+4 authors] ...,
  • James Taylor
  • Webb Miller
  • W. James Kent
  • Anton Nekrutenko
  • First Published September 16, 2005
Methods

Automated Whole-Genome Multiple Alignment of Rat, Mouse, and Human

  • Michael Brudno
  • Alexander Poliakov
  • Asaf Salamov
  • Gregory M. Cooper
  • Arend Sidow
  • Edward M. Rubin
  • Victor Solovyev
  • Serafim Batzoglou
  • Inna Dubchak
  • First Published April 1, 2004
LETTER

Characterization of Evolutionary Rates and Constraints in Three Mammalian Genomes

  • Gregory M. Cooper
  • Michael Brudno
  • Eric A. Stone
  • Inna Dubchak
  • Serafim Batzoglou
  • Arend Sidow
  • First Published April 1, 2004
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