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Michael R. Brent
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Displaying results 1-10 of
15
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Method
:
Dual threshold optimization and network inference reveal convergent evidence from TF binding locations and TF perturbation responses
Yiming Kang
,
Nikhil R. Patel
,
Christian Shively
,
Pamela Samantha Recio
,
Xuhua Chen
,
Bernd J. Wranik
,
Griffin Kim
,
R. Scott McIsaac
,
Robi Mitra
,
and
Michael R. Brent
Genome Res.
March 2020
30
:
459
-
471
;
Published in Advance
February 14, 2020
,
doi:
10.1101/gr.259655.119
Abstract
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Method
:
Model-driven mapping of transcriptional networks reveals the circuitry and dynamics of virulence regulation
Ezekiel J. Maier
,
Brian C. Haynes
,
Stacey R. Gish
,
Zhuo A. Wang
,
Michael L. Skowyra
,
Alyssa L. Marulli
,
Tamara L. Doering
,
and
Michael R. Brent
Genome Res.
May 2015
25
:
690
-
700
;
Published in Advance
February 2, 2015
,
doi:
10.1101/gr.184101.114
Abstract
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Method
:
Mapping functional transcription factor networks from gene expression data
Brian C. Haynes
,
Ezekiel J. Maier
,
Michael H. Kramer
,
Patricia I. Wang
,
Holly Brown
,
and
Michael R. Brent
Genome Res.
August 2013
23
:
1319
-
1328
;
Published in Advance
May 1, 2013
,
doi:
10.1101/gr.150904.112
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
:
The transcriptional diversity of 25
Drosophila
cell lines
Lucy Cherbas
,
Aarron Willingham
,
Dayu Zhang
,
Li Yang
,
Yi Zou
,
Brian D. Eads
,
Joseph W. Carlson
,
Jane M. Landolin
,
Philipp Kapranov
,
Jacqueline Dumais
,
Anastasia Samsonova
,
Jeong-Hyeon Choi
,
Johnny Roberts
,
Carrie A. Davis
,
Haixu Tang
,
Marijke J. van Baren
,
Srinka Ghosh
,
Alexander Dobin
,
Kim Bell
,
Wei Lin
,
Laura Langton
,
Michael O. Duff
,
Aaron E. Tenney
,
Chris Zaleski
,
Michael R. Brent
,
Roger A. Hoskins
,
Thomas C. Kaufman
,
Justen Andrews
,
Brenton R. Graveley
,
Norbert Perrimon
,
Susan E. Celniker
,
Thomas R. Gingeras
,
and
Peter Cherbas
Genome Res.
February 2011
21
:
301
-
314
;
Published in Advance
December 22, 2010
,
doi:
10.1101/gr.112961.110
Abstract
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Resource
:
The completion of the Mammalian Gene Collection (MGC)
The MGC Project Team
,
Gary Temple
,
Daniela S. Gerhard
,
Rebekah Rasooly
,
Elise A. Feingold
,
Peter J. Good
,
Cristen Robinson
,
Allison Mandich
,
Jeffrey G. Derge
,
Jeanne Lewis
,
Debonny Shoaf
,
Francis S. Collins
,
Wonhee Jang
,
Lukas Wagner
,
Carolyn M. Shenmen
,
Leonie Misquitta
,
Carl F. Schaefer
,
Kenneth H. Buetow
,
Tom I. Bonner
,
Linda Yankie
,
Ming Ward
,
Lon Phan
,
Alex Astashyn
,
Garth Brown
,
Catherine Farrell
,
Jennifer Hart
,
Melissa Landrum
,
Bonnie L. Maidak
,
Michael Murphy
,
Terence Murphy
,
Bhanu Rajput
,
Lillian Riddick
,
David Webb
,
Janet Weber
,
Wendy Wu
,
Kim D. Pruitt
,
Donna Maglott
,
Adam Siepel
,
Brona Brejova
,
Mark Diekhans
,
Rachel Harte
,
Robert Baertsch
,
Jim Kent
,
David Haussler
,
Michael Brent
,
Laura Langton
,
Charles L.G. Comstock
,
Michael Stevens
,
Chaochun Wei
,
Marijke J. van Baren
,
Kourosh Salehi-Ashtiani
,
Ryan R. Murray
,
Lila Ghamsari
,
Elizabeth Mello
,
Chenwei Lin
,
Christa Pennacchio
,
Kirsten Schreiber
,
Nicole Shapiro
,
Amber Marsh
,
Elizabeth Pardes
,
Troy Moore
,
Anita Lebeau
,
Mike Muratet
,
Blake Simmons
,
David Kloske
,
Stephanie Sieja
,
James Hudson
,
Praveen Sethupathy
,
Michael Brownstein
,
Narayan Bhat
,
Joseph Lazar
,
Howard Jacob
,
Chris E. Gruber
,
Mark R. Smith
,
John McPherson
,
Angela M. Garcia
,
Preethi H. Gunaratne
,
Jiaqian Wu
,
Donna Muzny
,
Richard A. Gibbs
,
Alice C. Young
,
Gerard G. Bouffard
,
Robert W. Blakesley
,
Jim Mullikin
,
Eric D. Green
,
Mark C. Dickson
,
Alex C. Rodriguez
,
Jane Grimwood
,
Jeremy Schmutz
,
Richard M. Myers
,
Martin Hirst
,
Thomas Zeng
,
Kane Tse
,
Michelle Moksa
,
Merinda Deng
,
Kevin Ma
,
Diana Mah
,
Johnson Pang
,
Greg Taylor
,
Eric Chuah
,
Athena Deng
,
Keith Fichter
,
Anne Go
,
Stephanie Lee
,
Jing Wang
,
Malachi Griffith
,
Ryan Morin
,
Richard A. Moore
,
Michael Mayo
,
Sarah Munro
,
Susan Wagner
,
Steven J.M. Jones
,
Robert A. Holt
,
Marco A. Marra
,
Sun Lu
,
Shuwei Yang
,
James Hartigan
,
Marcus Graf
,
Ralf Wagner
,
Stanley Letovksy
,
Jacqueline C. Pulido
,
Keith Robison
,
Dominic Esposito
,
James Hartley
,
Vanessa E. Wall
,
Ralph F. Hopkins
,
Osamu Ohara
,
and
Stefan Wiemann
Genome Res.
December 2009
19
:
2324
-
2333
;
Published in Advance
September 18, 2009
,
doi:
10.1101/gr.095976.109
Abstract
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Methods
:
Targeted discovery of novel human exons by comparative genomics
Adam Siepel
,
Mark Diekhans
,
Broňa Brejová
,
Laura Langton
,
Michael Stevens
,
Charles L.G. Comstock
,
Colleen Davis
,
Brent Ewing
,
Shelly Oommen
,
Christopher Lau
,
Hung-Chun Yu
,
Jianfeng Li
,
Bruce A. Roe
,
Phil Green
,
Daniela S. Gerhard
,
Gary Temple
,
David Haussler
,
and
Michael R. Brent
Genome Res.
December 2007
17
:
1763
-
1773
;
Published in Advance
November 7, 2007
,
doi:
10.1101/gr.7128207
Abstract
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Methods
:
A tale of two templates: Automatically resolving double traces has many applications, including efficient PCR-based elucidation of alternative splices
Aaron E. Tenney
,
Jia Qian Wu
,
Laura Langton
,
Paul Klueh
,
Ralph Quatrano
,
and
Michael R. Brent
Genome Res.
February 2007
17
:
212
-
218
;
Published in Advance
January 8, 2007
,
doi:
10.1101/gr.5661407
Abstract
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RESOURCE
:
Iterative gene prediction and pseudogene removal improves genome annotation
Marijke J. van Baren
and
Michael R. Brent
Genome Res.
May 2006
16
:
678
-
685
;
doi:
10.1101/gr.4766206
Abstract
Full Text
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PERSPECTIVE
:
Genome annotation past, present, and future: How to define an ORF at each locus
Michael R. Brent
Genome Res.
December 2005
15
:
1777
-
1786
;
doi:
10.1101/gr.3866105
Abstract
Full Text
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