Searching journal content for Michael R. Brent in author.

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  1. 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
    OPEN ACCESS ARTICLE
  2. 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
  3. 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
  4. 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
    OPEN ACCESS ARTICLE
  5. 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
    OPEN ACCESS ARTICLE
  6. 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
  7. 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
  8. 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
  9. 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
    OPEN ACCESS ARTICLE
  10. 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
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