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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

Albert J. Vilella
Jessica Severin
Abel Ureta-Vidal
Li Heng
Richard Durbin
Ewan Birney

First Published November 24, 2008

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

Benedict Paten
Javier Herrero
Kathryn Beal
Stephen Fitzgerald
Ewan Birney

First Published October 10, 2008

Genome-wide nucleotide-level mammalian ancestor reconstruction

Benedict Paten
Javier Herrero
Stephen Fitzgerald
Kathryn Beal
Paul Flicek
Ian Holmes
Ewan Birney

First Published October 10, 2008

Confounding between recombination and selection, and the Ped/Pop method for detecting selection

Paul F. O’Reilly
Ewan Birney
David J. Balding

First Published July 10, 2008

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Vardhman K. Rakyan
Thomas A. Down
Natalie P. Thorne
Paul Flicek
Eugene Kulesha
Stefan Gräf Eleni M. Tomazou Liselotte Bäckdahl Nathan Johnson Marlis Herberth Kevin L. Howe David K. Jackson Marcos M. Miretti Heike Fiegler John C. Marioni Ewan Birney
... [+11 authors] ...,
Tim J.P. Hubbard
Nigel P. Carter
Simon Tavaré
Stephan Beck

First Published June 24, 2008

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

Daniel R. Zerbino
Ewan Birney

First Published March 18, 2008

Identification of novel peptide hormones in the human proteome by hidden Markov model screening

Olivier Mirabeau
Emerald Perlas
Cinzia Severini
Enrica Audero
Olivier Gascuel
Roberta Possenti
Ewan Birney
Nadia Rosenthal
Cornelius Gross

First Published February 6, 2007

Academia-Industry Collaboration: An Integral Element for Building “Omic” Resources

David E. Hill
Michael A. Brasch
Anthony A. del Campo
Lynn Doucette-Stamm
James I. Garrels
Judith Glaven
... [+1 authors] ...,
James L. Hartley
James R. Hudson
Troy Moore
Marc Vidal

First Published October 15, 2004

C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions" > C. elegans ORFeome Version 3.1: Increasing the Coverage of ORFeome Resources With Improved Gene Predictions

Philippe Lamesch
Stuart Milstein
Tong Hao
Jennifer Rosenberg
Ning Li
Reynaldo Sequerra Stephanie Bosak
... [+2 authors] ...,
Lynn Doucette-Stamm
Jean Vandenhaute
David E. Hill
Marc Vidal

First Published October 15, 2004

Human ORFeome Version 1.1: A Platform for Reverse Proteomics

Jean-François Rual
Tomoko Hirozane-Kishikawa
Tong Hao
Nicolas Bertin
Siming Li
Amélie Dricot Ning Li Jennifer Rosenberg Philippe Lamesch Pierre-Olivier Vidalain Tracey R. Clingingsmith James L. Hartley Dominic Esposito David Cheo Troy Moore Blake Simmons Reynaldo Sequerra Stephanie Bosak Lynn Doucette-Stamm Christian Le Peuch Jean Vandenhaute
... [+16 authors] ...,
Michael E. Cusick
Joanna S. Albala
David E. Hill
Marc Vidal

First Published October 15, 2004

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