Searching journal content for Marco A. Marra 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: High-resolution structural genomics reveals new therapeutic vulnerabilities in glioblastoma
    • Michael J. Johnston,
    • Ana Nikolic,
    • Nicoletta Ninkovic,
    • Paul Guilhamon,
    • Florence M.G. Cavalli,
    • Steven Seaman,
    • Franz J. Zemp,
    • John Lee,
    • Aly Abdelkareem,
    • Katrina Ellestad,
    • Alex Murison,
    • Michelle M. Kushida,
    • Fiona J. Coutinho,
    • Yussanne Ma,
    • Andrew J. Mungall,
    • Richard Moore,
    • Marco A. Marra,
    • Michael D. Taylor,
    • Peter B. Dirks,
    • Trevor J. Pugh,
    • Sorana Morrissy,
    • Bradley St Croix,
    • Douglas J. Mahoney,
    • Mathieu Lupien,
    • and Marco Gallo
    Genome Res. August 2019 29: 1211-1222; Published in Advance June 27, 2019, doi:10.1101/gr.246520.118
    OPEN ACCESS ARTICLE
  3. Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
    • Roger A. Hoskins,
    • Joseph W. Carlson,
    • Kenneth H. Wan,
    • Soo Park,
    • Ivonne Mendez,
    • Samuel E. Galle,
    • Benjamin W. Booth,
    • Barret D. Pfeiffer,
    • Reed A. George,
    • Robert Svirskas,
    • Martin Krzywinski,
    • Jacqueline Schein,
    • Maria Carmela Accardo,
    • Elisabetta Damia,
    • Giovanni Messina,
    • María Méndez-Lago,
    • Beatriz de Pablos,
    • Olga V. Demakova,
    • Evgeniya N. Andreyeva,
    • Lidiya V. Boldyreva,
    • Marco Marra,
    • A. Bernardo Carvalho,
    • Patrizio Dimitri,
    • Alfredo Villasante,
    • Igor F. Zhimulev,
    • Gerald M. Rubin,
    • Gary H. Karpen,
    • and Susan E. Celniker
    Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
    OPEN ACCESS ARTICLE
  4. Method: TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
    • Gavin Ha,
    • Andrew Roth,
    • Jaswinder Khattra,
    • Julie Ho,
    • Damian Yap,
    • Leah M. Prentice,
    • Nataliya Melnyk,
    • Andrew McPherson,
    • Ali Bashashati,
    • Emma Laks,
    • Justina Biele,
    • Jiarui Ding,
    • Alan Le,
    • Jamie Rosner,
    • Karey Shumansky,
    • Marco A. Marra,
    • C. Blake Gilks,
    • David G. Huntsman,
    • Jessica N. McAlpine,
    • Samuel Aparicio,
    • and Sohrab P. Shah
    Genome Res. November 2014 24: 1881-1893; Published in Advance July 24, 2014, doi:10.1101/gr.180281.114
    OPEN ACCESS ARTICLE
  5. Method: Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm
    • Bo Zhang,
    • Yan Zhou,
    • Nan Lin,
    • Rebecca F. Lowdon,
    • Chibo Hong,
    • Raman P. Nagarajan,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Michael Stevens,
    • Hyung Joo Lee,
    • Xiaoyun Xing,
    • Jia Zhou,
    • Vasavi Sundaram,
    • GiNell Elliott,
    • Junchen Gu,
    • Taoping Shi,
    • Philippe Gascard,
    • Mahvash Sigaroudinia,
    • Thea D. Tlsty,
    • Theresa Kadlecek,
    • Arthur Weiss,
    • Henriette O’Geen,
    • Peggy J. Farnham,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Pamela A.F. Madden,
    • Angela Tam,
    • Richard Moore,
    • Martin Hirst,
    • Marco A. Marra,
    • Baoxue Zhang,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1522-1540; Published in Advance June 26, 2013, doi:10.1101/gr.156539.113
    OPEN ACCESS ARTICLE
  6. Method: Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods
    • Michael Stevens,
    • Jeffrey B. Cheng,
    • Daofeng Li,
    • Mingchao Xie,
    • Chibo Hong,
    • Cécile L. Maire,
    • Keith L. Ligon,
    • Martin Hirst,
    • Marco A. Marra,
    • Joseph F. Costello,
    • and Ting Wang
    Genome Res. September 2013 23: 1541-1553; Published in Advance June 26, 2013, doi:10.1101/gr.152231.112
  7. Method: Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
    • Gavin Ha,
    • Andrew Roth,
    • Daniel Lai,
    • Ali Bashashati,
    • Jiarui Ding,
    • Rodrigo Goya,
    • Ryan Giuliany,
    • Jamie Rosner,
    • Arusha Oloumi,
    • Karey Shumansky,
    • Suet-Feung Chin,
    • Gulisa Turashvili,
    • Martin Hirst,
    • Carlos Caldas,
    • Marco A. Marra,
    • Samuel Aparicio,
    • and Sohrab P. Shah
    Genome Res. October 2012 22: 1995-2007; Published in Advance May 25, 2012, doi:10.1101/gr.137570.112
    OPEN ACCESS ARTICLE
  8. Research: Extensive relationship between antisense transcription and alternative splicing in the human genome
    • A. Sorana Morrissy,
    • Malachi Griffith,
    • and Marco A. Marra
    Genome Res. August 2011 21: 1203-1212; Published in Advance June 30, 2011, doi:10.1101/gr.113431.110
  9. Research: Deep annotation of Drosophila melanogaster microRNAs yields insights into their processing, modification, and emergence
    • Eugene Berezikov,
    • Nicolas Robine,
    • Anastasia Samsonova,
    • Jakub O. Westholm,
    • Ammar Naqvi,
    • Jui-Hung Hung,
    • Katsutomo Okamura,
    • Qi Dai,
    • Diane Bortolamiol-Becet,
    • Raquel Martin,
    • Yongjun Zhao,
    • Phillip D. Zamore,
    • Gregory J. Hannon,
    • Marco A. Marra,
    • Zhiping Weng,
    • Norbert Perrimon,
    • and Eric C. Lai
    Genome Res. February 2011 21: 203-215; Published in Advance December 22, 2010, doi:10.1101/gr.116657.110
    OPEN ACCESS ARTICLE
  10. 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
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