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Method

Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation

  • Ian T. Fiddes
  • Joel Armstrong
  • Mark Diekhans
  • Stefanie Nachtweide
  • Zev N. Kronenberg
  • Jason G. Underwood David Gordon Dent Earl Thomas Keane
  • ... [+4 authors] ...,
  • Evan E. Eichler
  • David Haussler
  • Mario Stanke
  • Benedict Paten
  • First Published June 8, 2018
Corrigendum

Corrigendum: Direct determination of diploid genome sequences

  • Neil I. Weisenfeld
  • Vijay Kumar
  • Preyas Shah
  • Deanna M. Church
  • David B. Jaffe
  • First Published April 2, 2018
Corrigendum

Corrigendum: Discovery and genotyping of structural variation from long-read haploid genome sequence data

  • John Huddleston
  • Mark J.P. Chaisson
  • Karyn Meltz Steinberg
  • Wes Warren
  • Kendra Hoekzema
  • David Gordon Tina A. Graves-Lindsay Katherine M. Munson Zev N. Kronenberg Laura Vives Paul Peluso Matthew Boitano
  • ... [+7 authors] ...,
  • Chen-Shin Chin
  • Jonas Korlach
  • Richard K. Wilson
  • Evan E. Eichler
  • First Published January 2, 2018
Method

Direct determination of diploid genome sequences

  • Neil I. Weisenfeld
  • Vijay Kumar
  • Preyas Shah
  • Deanna M. Church
  • David B. Jaffe
  • First Published April 5, 2017
Research

Discovery and genotyping of structural variation from long-read haploid genome sequence data

  • John Huddleston
  • Mark J.P. Chaisson
  • Karyn Meltz Steinberg
  • Wes Warren
  • Kendra Hoekzema
  • David Gordon Tina A. Graves-Lindsay Katherine M. Munson Zev N. Kronenberg Laura Vives Paul Peluso Matthew Boitano
  • ... [+7 authors] ...,
  • Chen-Shin Chin
  • Jonas Korlach
  • Richard K. Wilson
  • Evan E. Eichler
  • First Published November 28, 2016
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
  • ... [+6 authors] ...,
  • Carsten Russ
  • Chad Nusbaum
  • Iain MacCallum
  • David B. Jaffe
  • First Published July 24, 2012
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
  • ... [+4 authors] ...,
  • Sarah K. Young
  • David B. Jaffe
  • Chad Nusbaum
  • Andreas Gnirke
  • First Published July 16, 2012
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
  • ... [+62 authors] ...,
  • Richard E. Green
  • David Haussler
  • Ian Korf
  • Benedict Paten
  • First Published September 16, 2011
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
  • ... [+17 authors] ...,
  • Reinhard Dummer
  • Andreas Gnirke
  • Chad Nusbaum
  • Levi A. Garraway
  • First Published February 23, 2010
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
  • David B. Jaffe
  • First Published March 13, 2008
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