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David B. Jaffe
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12
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Corrigendum
:
Corrigendum: Direct determination of diploid genome sequences
Neil I. Weisenfeld
,
Vijay Kumar
,
Preyas Shah
,
Deanna M. Church
,
and
David B. Jaffe
Genome Res.
April 2018
28
:
606.1
;
doi:
10.1101/gr.235812.118
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Method
:
Direct determination of diploid genome sequences
Neil I. Weisenfeld
,
Vijay Kumar
,
Preyas Shah
,
Deanna M. Church
,
and
David B. Jaffe
Genome Res.
May 2017
27
:
757
-
767
;
Published in Advance
April 5, 2017
,
doi:
10.1101/gr.214874.116
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Method
:
Paired-end sequencing of Fosmid libraries by Illumina
Louise J.S. Williams
,
Diana G. Tabbaa
,
Na Li
,
Aaron M. Berlin
,
Terrance P. Shea
,
Iain MacCallum
,
Michael S. Lawrence
,
Yotam Drier
,
Gad Getz
,
Sarah K. Young
,
David B. Jaffe
,
Chad Nusbaum
,
and
Andreas Gnirke
Genome Res.
November 2012
22
:
2241
-
2249
;
Published in Advance
July 16, 2012
,
doi:
10.1101/gr.138925.112
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Method
:
Finished bacterial genomes from shotgun sequence data
Filipe J. Ribeiro
,
Dariusz Przybylski
,
Shuangye Yin
,
Ted Sharpe
,
Sante Gnerre
,
Amr Abouelleil
,
Aaron M. Berlin
,
Anna Montmayeur
,
Terrance P. Shea
,
Bruce J. Walker
,
Sarah K. Young
,
Carsten Russ
,
Chad Nusbaum
,
Iain MacCallum
,
and
David B. Jaffe
Genome Res.
November 2012
22
:
2270
-
2277
;
Published in Advance
July 24, 2012
,
doi:
10.1101/gr.141515.112
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Resource
:
Assemblathon 1: A competitive assessment of de novo short read assembly methods
Dent Earl
,
Keith Bradnam
,
John St. John
,
Aaron Darling
,
Dawei Lin
,
Joseph Fass
,
Hung On Ken Yu
,
Vince Buffalo
,
Daniel R. Zerbino
,
Mark Diekhans
,
Ngan Nguyen
,
Pramila Nuwantha Ariyaratne
,
Wing-Kin Sung
,
Zemin Ning
,
Matthias Haimel
,
Jared T. Simpson
,
Nuno A. Fonseca
,
İnanç Birol
,
T. Roderick Docking
,
Isaac Y. Ho
,
Daniel S. Rokhsar
,
Rayan Chikhi
,
Dominique Lavenier
,
Guillaume Chapuis
,
Delphine Naquin
,
Nicolas Maillet
,
Michael C. Schatz
,
David R. Kelley
,
Adam M. Phillippy
,
Sergey Koren
,
Shiaw-Pyng Yang
,
Wei Wu
,
Wen-Chi Chou
,
Anuj Srivastava
,
Timothy I. Shaw
,
J. Graham Ruby
,
Peter Skewes-Cox
,
Miguel Betegon
,
Michelle T. Dimon
,
Victor Solovyev
,
Igor Seledtsov
,
Petr Kosarev
,
Denis Vorobyev
,
Ricardo Ramirez-Gonzalez
,
Richard Leggett
,
Dan MacLean
,
Fangfang Xia
,
Ruibang Luo
,
Zhenyu Li
,
Yinlong Xie
,
Binghang Liu
,
Sante Gnerre
,
Iain MacCallum
,
Dariusz Przybylski
,
Filipe J. Ribeiro
,
Shuangye Yin
,
Ted Sharpe
,
Giles Hall
,
Paul J. Kersey
,
Richard Durbin
,
Shaun D. Jackman
,
Jarrod A. Chapman
,
Xiaoqiu Huang
,
Joseph L. DeRisi
,
Mario Caccamo
,
Yingrui Li
,
David B. Jaffe
,
Richard E. Green
,
David Haussler
,
Ian Korf
,
and
Benedict Paten
Genome Res.
December 2011
21
:
2224
-
2241
;
Published in Advance
September 16, 2011
,
doi:
10.1101/gr.126599.111
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Research
:
Integrative analysis of the melanoma transcriptome
Michael F. Berger
,
Joshua Z. Levin
,
Krishna Vijayendran
,
Andrey Sivachenko
,
Xian Adiconis
,
Jared Maguire
,
Laura A. Johnson
,
James Robinson
,
Roel G. Verhaak
,
Carrie Sougnez
,
Robert C. Onofrio
,
Liuda Ziaugra
,
Kristian Cibulskis
,
Elisabeth Laine
,
Jordi Barretina
,
Wendy Winckler
,
David E. Fisher
,
Gad Getz
,
Matthew Meyerson
,
David B. Jaffe
,
Stacey B. Gabriel
,
Eric S. Lander
,
Reinhard Dummer
,
Andreas Gnirke
,
Chad Nusbaum
,
and
Levi A. Garraway
Genome Res.
April 2010
20
:
413
-
427
;
Published in Advance
February 23, 2010
,
doi:
10.1101/gr.103697.109
Abstract
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RESOURCE
:
ALLPATHS: De novo assembly of whole-genome shotgun microreads
Jonathan Butler
,
Iain MacCallum
,
Michael Kleber
,
Ilya A. Shlyakhter
,
Matthew K. Belmonte
,
Eric S. Lander
,
Chad Nusbaum
,
and
David B. Jaffe
Genome Res.
May 2008
18
:
810
-
820
;
Published in Advance
March 13, 2008
,
doi:
10.1101/gr.7337908
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Methods
:
Quality scores and SNP detection in sequencing-by-synthesis systems
William Brockman
,
Pablo Alvarez
,
Sarah Young
,
Manuel Garber
,
Georgia Giannoukos
,
William L. Lee
,
Carsten Russ
,
Eric S. Lander
,
Chad Nusbaum
,
and
David B. Jaffe
Genome Res.
May 2008
18
:
763
-
770
;
Published in Advance
January 22, 2008
,
doi:
10.1101/gr.070227.107
Abstract
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ARTICLE
:
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
Elliott H. Margulies
,
Gregory M. Cooper
,
George Asimenos
,
Daryl J. Thomas
,
Colin N. Dewey
,
Adam Siepel
,
Ewan Birney
,
Damian Keefe
,
Ariel S. Schwartz
,
Minmei Hou
,
James Taylor
,
Sergey Nikolaev
,
Juan I. Montoya-Burgos
,
Ari Löytynoja
,
Simon Whelan
,
Fabio Pardi
,
Tim Massingham
,
James B. Brown
,
Peter Bickel
,
Ian Holmes
,
James C. Mullikin
,
Abel Ureta-Vidal
,
Benedict Paten
,
Eric A. Stone
,
Kate R. Rosenbloom
,
W. James Kent
,
Gerard G. Bouffard
,
Xiaobin Guan
,
Nancy F. Hansen
,
Jacquelyn R. Idol
,
Valerie V.B. Maduro
,
Baishali Maskeri
,
Jennifer C. McDowell
,
Morgan Park
,
Pamela J. Thomas
,
Alice C. Young
,
Robert W. Blakesley
,
Donna M. Muzny
,
Erica Sodergren
,
David A. Wheeler
,
Kim C. Worley
,
Huaiyang Jiang
,
George M. Weinstock
,
Richard A. Gibbs
,
Tina Graves
,
Robert Fulton
,
Elaine R. Mardis
,
Richard K. Wilson
,
Michele Clamp
,
James Cuff
,
Sante Gnerre
,
David B. Jaffe
,
Jean L. Chang
,
Kerstin Lindblad-Toh
,
Eric S. Lander
,
Angie Hinrichs
,
Heather Trumbower
,
Hiram Clawson
,
Ann Zweig
,
Robert M. Kuhn
,
Galt Barber
,
Rachel Harte
,
Donna Karolchik
,
Matthew A. Field
,
Richard A. Moore
,
Carrie A. Matthewson
,
Jacqueline E. Schein
,
Marco A. Marra
,
Stylianos E. Antonarakis
,
Serafim Batzoglou
,
Nick Goldman
,
Ross Hardison
,
David Haussler
,
Webb Miller
,
Lior Pachter
,
Eric D. Green
,
and
Arend Sidow
Genome Res.
June 2007
17
:
760
-
774
;
doi:
10.1101/gr.6034307
Abstract
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Methods
:
Assembly of polymorphic genomes: Algorithms and application to
Ciona savignyi
Jade P. Vinson
,
David B. Jaffe
,
Keith O'Neill
,
Elinor K. Karlsson
,
Nicole Stange-Thomann
,
Scott Anderson
,
Jill P. Mesirov
,
Nori Satoh
,
Yutaka Satou
,
Chad Nusbaum
,
Bruce Birren
,
James E. Galagan
,
and
Eric S. Lander
Genome Res.
August 2005
15
:
1127
-
1135
;
doi:
10.1101/gr.3722605
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