Searching journal content for Steven Jones in author.

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  1. Research: Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation
    • Vanessa L. Porter,
    • Michelle Ng,
    • Kieran O'Neill,
    • Signe MacLennan,
    • Richard D. Corbett,
    • Luka Culibrk,
    • Zeid Hamadeh,
    • Marissa Iden,
    • Rachel Schmidt,
    • Shirng-Wern Tsaih,
    • Carolyn Nakisige,
    • Martin Origa,
    • Jackson Orem,
    • Glenn Chang,
    • Jeremy Fan,
    • Ka Ming Nip,
    • Vahid Akbari,
    • Simon K. Chan,
    • James Hopkins,
    • Richard A. Moore,
    • Eric Chuah,
    • Karen L. Mungall,
    • Andrew J. Mungall,
    • Inanc Birol,
    • Steven J.M. Jones,
    • Janet S. Rader,
    • and Marco A. Marra
    Genome Res. April 2025 35: 653-670; Published in Advance December 5, 2024, doi:10.1101/gr.279041.124
    OPEN ACCESS ARTICLE
  2. Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
    • Luis F. Paulin,
    • Jeremy Fan,
    • Kieran O'Neill,
    • Erin Pleasance,
    • Vanessa L. Porter,
    • Steven J.M. Jones,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
  3. Method: Spark: A navigational paradigm for genomic data exploration
    • Cydney B. Nielsen,
    • Hamid Younesy,
    • Henriette O'Geen,
    • Xiaoqin Xu,
    • Andrew R. Jackson,
    • Aleksandar Milosavljevic,
    • Ting Wang,
    • Joseph F. Costello,
    • Martin Hirst,
    • Peggy J. Farnham,
    • and Steven J.M. Jones
    Genome Res. November 2012 22: 2262-2269; Published in Advance September 7, 2012, doi:10.1101/gr.140665.112
  4. Research: Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver
    • Brad G. Hoffman,
    • Gordon Robertson,
    • Bogard Zavaglia,
    • Mike Beach,
    • Rebecca Cullum,
    • Sam Lee,
    • Galina Soukhatcheva,
    • Leping Li,
    • Elizabeth D. Wederell,
    • Nina Thiessen,
    • Mikhail Bilenky,
    • Timothee Cezard,
    • Angela Tam,
    • Baljit Kamoh,
    • Inanc Birol,
    • Derek Dai,
    • YongJun Zhao,
    • Martin Hirst,
    • C. Bruce Verchere,
    • Cheryl D. Helgason,
    • Marco A. Marra,
    • Steven J.M. Jones,
    • and Pamela A. Hoodless
    Genome Res. August 2010 20: 1037-1051; Published in Advance June 15, 2010, doi:10.1101/gr.104356.109
    OPEN ACCESS ARTICLE
  5. Research: The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance
    • Santosh S. Atanur,
    • İnanç Birol,
    • Victor Guryev,
    • Martin Hirst,
    • Oliver Hummel,
    • Catherine Morrissey,
    • Jacques Behmoaras,
    • Xose M. Fernandez-Suarez,
    • Michelle D. Johnson,
    • William M. McLaren,
    • Giannino Patone,
    • Enrico Petretto,
    • Charles Plessy,
    • Kathleen S. Rockland,
    • Charles Rockland,
    • Kathrin Saar,
    • Yongjun Zhao,
    • Piero Carninci,
    • Paul Flicek,
    • Ted Kurtz,
    • Edwin Cuppen,
    • Michal Pravenec,
    • Norbert Hubner,
    • Steven J.M. Jones,
    • Ewan Birney,
    • and Timothy J. Aitman
    Genome Res. June 2010 20: 791-803; Published in Advance April 29, 2010, doi:10.1101/gr.103499.109
  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: Next-generation tag sequencing for cancer gene expression profiling
    • A. Sorana Morrissy,
    • Ryan D. Morin,
    • Allen Delaney,
    • Thomas Zeng,
    • Helen McDonald,
    • Steven Jones,
    • Yongjun Zhao,
    • Martin Hirst,
    • and Marco A. Marra
    Genome Res. October 2009 19: 1825-1835; Published in Advance June 18, 2009, doi:10.1101/gr.094482.109
  8. Resource: Circos: An information aesthetic for comparative genomics
    • Martin Krzywinski,
    • Jacqueline Schein,
    • İnanç Birol,
    • Joseph Connors,
    • Randy Gascoyne,
    • Doug Horsman,
    • Steven J. Jones,
    • and Marco A. Marra
    Genome Res. September 2009 19: 1639-1645; Published in Advance June 18, 2009, doi:10.1101/gr.092759.109
  9. Resource: ABySS: A parallel assembler for short read sequence data
    • Jared T. Simpson,
    • Kim Wong,
    • Shaun D. Jackman,
    • Jacqueline E. Schein,
    • Steven J.M. Jones,
    • and İnanç Birol
    Genome Res. June 2009 19: 1117-1123; Published in Advance February 27, 2009, doi:10.1101/gr.089532.108
    OPEN ACCESS ARTICLE
  10. LETTER: Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding
    • A. Gordon Robertson,
    • Mikhail Bilenky,
    • Angela Tam,
    • Yongjun Zhao,
    • Thomas Zeng,
    • Nina Thiessen,
    • Timothee Cezard,
    • Anthony P. Fejes,
    • Elizabeth D. Wederell,
    • Rebecca Cullum,
    • Ghia Euskirchen,
    • Martin Krzywinski,
    • Inanc Birol,
    • Michael Snyder,
    • Pamela A. Hoodless,
    • Martin Hirst,
    • Marco A. Marra,
    • and Steven J.M. Jones
    Genome Res. December 2008 18: 1906-1917; Published in Advance September 11, 2008, doi:10.1101/gr.078519.108
    OPEN ACCESS ARTICLE
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