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David Haussler
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31
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Method
:
Highly accurate assembly polishing with DeepPolisher
Mira Mastoras
,
Mobin Asri
,
Lucas Brambrink
,
Prajna Hebbar
,
Alexey Kolesnikov
,
Daniel E. Cook
,
Maria Nattestad
,
Julian Lucas
,
Taylor S. Won
,
Pi-Chuan Chang
,
Andrew Carroll
,
Benedict Paten
,
Kishwar Shafin
,
and
and the Human Pangenome Reference Consortium
Genome Res.
July 2025
35
:
1595
-
1608
;
Published in Advance
May 19, 2025
,
doi:
10.1101/gr.280149.124
Abstract
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Research
:
Gaps and complex structurally variant loci in phased genome assemblies
David Porubsky
,
Mitchell R. Vollger
,
William T. Harvey
,
Allison N. Rozanski
,
Peter Ebert
,
Glenn Hickey
,
Patrick Hasenfeld
,
Ashley D. Sanders
,
Catherine Stober
,
Human Pangenome Reference Consortium
,
Jan O. Korbel
,
Benedict Paten
,
Tobias Marschall
,
and
Evan E. Eichler
Genome Res.
April 2023
33
:
496
-
510
;
Published in Advance
May 10, 2023
,
doi:
10.1101/gr.277334.122
Abstract
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Method
:
A complete pedigree-based graph workflow for rare candidate variant analysis
Charles Markello
,
Charles Huang
,
Alex Rodriguez
,
Andrew Carroll
,
Pi-Chuan Chang
,
Jordan Eizenga
,
Thomas Markello
,
David Haussler
,
and
Benedict Paten
Genome Res.
May 2022
32
:
893
-
903
;
Published in Advance
April 28, 2022
,
doi:
10.1101/gr.276387.121
Abstract
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Research
:
A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
Elisabeth J. van Bree
,
Rita L.F.P. Guimarães
,
Mischa Lundberg
,
Elena R. Blujdea
,
Jimi L. Rosenkrantz
,
Fred T.G. White
,
Josse Poppinga
,
Paula Ferrer-Raventós
,
Anne-Fleur E. Schneider
,
Isabella Clayton
,
David Haussler
,
Marcel J.T. Reinders
,
Henne Holstege
,
Adam D. Ewing
,
Colette Moses
,
and
Frank M.J. Jacobs
Genome Res.
April 2022
32
:
656
-
670
;
Published in Advance
March 24, 2022
,
doi:
10.1101/gr.275515.121
Abstract
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Research
:
Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
James A. Cahill
,
Joel Armstrong
,
Alden Deran
,
Carolyn J. Khoury
,
Benedict Paten
,
David Haussler
,
and
Erich D. Jarvis
Genome Res.
November 2021
31
:
2035
-
2049
;
Published in Advance
October 19, 2021
,
doi:
10.1101/gr.275989.121
Abstract
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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
,
Evan E. Eichler
,
David Haussler
,
Mario Stanke
,
and
Benedict Paten
Genome Res.
July 2018
28
:
1029
-
1038
;
Published in Advance
June 8, 2018
,
doi:
10.1101/gr.233460.117
Abstract
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Method
:
Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
Nicholas H. Putnam
,
Brendan L. O'Connell
,
Jonathan C. Stites
,
Brandon J. Rice
,
Marco Blanchette
,
Robert Calef
,
Christopher J. Troll
,
Andrew Fields
,
Paul D. Hartley
,
Charles W. Sugnet
,
David Haussler
,
Daniel S. Rokhsar
,
and
Richard E. Green
Genome Res.
March 2016
26
:
342
-
350
;
Published in Advance
February 4, 2016
,
doi:
10.1101/gr.193474.115
Abstract
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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
,
Michael Brudno
,
Inna Dubchak
,
David Haussler
,
and
Benedict Paten
Genome Res.
December 2014
24
:
2077
-
2089
;
Published in Advance
October 1, 2014
,
doi:
10.1101/gr.174920.114
Abstract
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Resource
:
GENCODE: The reference human genome annotation for The ENCODE Project
Jennifer Harrow
,
Adam Frankish
,
Jose M. Gonzalez
,
Electra Tapanari
,
Mark Diekhans
,
Felix Kokocinski
,
Bronwen L. Aken
,
Daniel Barrell
,
Amonida Zadissa
,
Stephen Searle
,
If Barnes
,
Alexandra Bignell
,
Veronika Boychenko
,
Toby Hunt
,
Mike Kay
,
Gaurab Mukherjee
,
Jeena Rajan
,
Gloria Despacio-Reyes
,
Gary Saunders
,
Charles Steward
,
Rachel Harte
,
Michael Lin
,
Cédric Howald
,
Andrea Tanzer
,
Thomas Derrien
,
Jacqueline Chrast
,
Nathalie Walters
,
Suganthi Balasubramanian
,
Baikang Pei
,
Michael Tress
,
Jose Manuel Rodriguez
,
Iakes Ezkurdia
,
Jeltje van Baren
,
Michael Brent
,
David Haussler
,
Manolis Kellis
,
Alfonso Valencia
,
Alexandre Reymond
,
Mark Gerstein
,
Roderic Guigó
,
and
Tim J. Hubbard
Genome Res.
September 2012
22
:
1760
-
1774
;
doi:
10.1101/gr.135350.111
Abstract
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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
Abstract
Full Text
Full Text (PDF)
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OPEN ACCESS ARTICLE
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