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Adam Frankish
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11
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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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Perspective
:
Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
Carolina Monzó
,
Adam Frankish
,
and
Ana Conesa
Genome Res.
April 2025
35
:
583
-
592
;
Published in Advance
March 3, 2025
,
doi:
10.1101/gr.279865.124
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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Resource
:
Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
Jonathan M. Mudge
,
Irwin Jungreis
,
Toby Hunt
,
Jose Manuel Gonzalez
,
James C. Wright
,
Mike Kay
,
Claire Davidson
,
Stephen Fitzgerald
,
Ruth Seal
,
Susan Tweedie
,
Liang He
,
Robert M. Waterhouse
,
Yue Li
,
Elspeth Bruford
,
Jyoti S. Choudhary
,
Adam Frankish
,
and
Manolis Kellis
Genome Res.
December 2019
29
:
2073
-
2087
;
Published in Advance
September 19, 2019
,
doi:
10.1101/gr.246462.118
Abstract
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Perspective
:
Functional transcriptomics in the post-ENCODE era
Jonathan M. Mudge
,
Adam Frankish
,
and
Jennifer Harrow
Genome Res.
December 2013
23
:
1961
-
1973
;
Published in Advance
October 30, 2013
,
doi:
10.1101/gr.161315.113
Abstract
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Method
:
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
Cédric Howald
,
Andrea Tanzer
,
Jacqueline Chrast
,
Felix Kokocinski
,
Thomas Derrien
,
Nathalie Walters
,
Jose M. Gonzalez
,
Adam Frankish
,
Bronwen L. Aken
,
Thibaut Hourlier
,
Jan-Hinnerk Vogel
,
Simon White
,
Stephen Searle
,
Jennifer Harrow
,
Tim J. Hubbard
,
Roderic Guigó
,
and
Alexandre Reymond
Genome Res.
September 2012
22
:
1698
-
1710
;
doi:
10.1101/gr.134478.111
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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Method
:
Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
Markus Brosch
,
Gary I. Saunders
,
Adam Frankish
,
Mark O. Collins
,
Lu Yu
,
James Wright
,
Ruth Verstraten
,
David J. Adams
,
Jennifer Harrow
,
Jyoti S. Choudhary
,
and
Tim Hubbard
Genome Res.
May 2011
21
:
756
-
767
;
Published in Advance
April 1, 2011
,
doi:
10.1101/gr.114272.110
Abstract
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Resource
:
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
Kim D. Pruitt
,
Jennifer Harrow
,
Rachel A. Harte
,
Craig Wallin
,
Mark Diekhans
,
Donna R. Maglott
,
Steve Searle
,
Catherine M. Farrell
,
Jane E. Loveland
,
Barbara J. Ruef
,
Elizabeth Hart
,
Marie-Marthe Suner
,
Melissa J. Landrum
,
Bronwen Aken
,
Sarah Ayling
,
Robert Baertsch
,
Julio Fernandez-Banet
,
Joshua L. Cherry
,
Val Curwen
,
Michael DiCuccio
,
Manolis Kellis
,
Jennifer Lee
,
Michael F. Lin
,
Michael Schuster
,
Andrew Shkeda
,
Clara Amid
,
Garth Brown
,
Oksana Dukhanina
,
Adam Frankish
,
Jennifer Hart
,
Bonnie L. Maidak
,
Jonathan Mudge
,
Michael R. Murphy
,
Terence Murphy
,
Jeena Rajan
,
Bhanu Rajput
,
Lillian D. Riddick
,
Catherine Snow
,
Charles Steward
,
David Webb
,
Janet A. Weber
,
Laurens Wilming
,
Wenyu Wu
,
Ewan Birney
,
David Haussler
,
Tim Hubbard
,
James Ostell
,
Richard Durbin
,
and
David Lipman
Genome Res.
July 2009
19
:
1316
-
1323
;
Published in Advance
June 4, 2009
,
doi:
10.1101/gr.080531.108
Abstract
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ARTICLE
:
Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
France Denoeud
,
Philipp Kapranov
,
Catherine Ucla
,
Adam Frankish
,
Robert Castelo
,
Jorg Drenkow
,
Julien Lagarde
,
Tyler Alioto
,
Caroline Manzano
,
Jacqueline Chrast
,
Sujit Dike
,
Carine Wyss
,
Charlotte N. Henrichsen
,
Nancy Holroyd
,
Mark C. Dickson
,
Ruth Taylor
,
Zahra Hance
,
Sylvain Foissac
,
Richard M. Myers
,
Jane Rogers
,
Tim Hubbard
,
Jennifer Harrow
,
Roderic Guigó
,
Thomas R. Gingeras
,
Stylianos E. Antonarakis
,
and
Alexandre Reymond
Genome Res.
June 2007
17
:
746
-
759
;
doi:
10.1101/gr.5660607
Abstract
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