Searching journal content for Stephen B. Montgomery in author.

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  1. Resource: Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise
    • Aliza B. Rubenstein,
    • Gregory R. Smith,
    • Zidong Zhang,
    • Xi Chen,
    • Toby L. Chambers,
    • Frederique Ruf-Zamojski,
    • Natalia Mendelev,
    • Wan Sze Cheng,
    • Michel Zamojski,
    • Mary Anne S. Amper,
    • Venugopalan D. Nair,
    • Andrew R. Marderstein,
    • Stephen B. Montgomery,
    • Olga G. Troyanskaya,
    • Elena Zaslavsky,
    • Todd Trappe,
    • Scott Trappe,
    • and Stuart C. Sealfon
    Genome Res. July 2025 35: 1664-1677; Published in Advance May 20, 2025, doi:10.1101/gr.280051.124
  2. Method: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease
    • Tanner D. Jensen,
    • Bohan Ni,
    • Chloe M. Reuter,
    • John E. Gorzynski,
    • Sarah Fazal,
    • Devon Bonner,
    • Rachel A. Ungar,
    • Pagé C. Goddard,
    • Archana Raja,
    • Euan A. Ashley,
    • Jonathan A. Bernstein,
    • Stephan Zuchner,
    • Undiagnosed Diseases Network,
    • Michael D. Greicius,
    • Stephen B. Montgomery,
    • Michael C. Schatz,
    • Matthew T. Wheeler,
    • and Alexis Battle
    Genome Res. April 2025 35: 914-928; Published in Advance March 20, 2025, doi:10.1101/gr.279323.124
    OPEN ACCESS ARTICLE
  3. Resource: High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation
    • Jonas A. Gustafson,
    • Sophia B. Gibson,
    • Nikhita Damaraju,
    • Miranda P.G. Zalusky,
    • Kendra Hoekzema,
    • David Twesigomwe,
    • Lei Yang,
    • Anthony A. Snead,
    • Phillip A. Richmond,
    • Wouter De Coster,
    • Nathan D. Olson,
    • Andrea Guarracino,
    • Qiuhui Li,
    • Angela L. Miller,
    • Joy Goffena,
    • Zachary B. Anderson,
    • Sophie H.R. Storz,
    • Sydney A. Ward,
    • Maisha Sinha,
    • Claudia Gonzaga-Jauregui,
    • Wayne E. Clarke,
    • Anna O. Basile,
    • André Corvelo,
    • Catherine Reeves,
    • Adrienne Helland,
    • Rajeeva Lochan Musunuri,
    • Mahler Revsine,
    • Karynne E. Patterson,
    • Cate R. Paschal,
    • Christina Zakarian,
    • Sara Goodwin,
    • Tanner D. Jensen,
    • Esther Robb,
    • The 1000 Genomes ONT Sequencing Consortium,
    • University of Washington Center for Rare Disease Research (UW-CRDR),
    • Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) Consortium,
    • William Richard McCombie,
    • Fritz J. Sedlazeck,
    • Justin M. Zook,
    • Stephen B. Montgomery,
    • Erik Garrison,
    • Mikhail Kolmogorov,
    • Michael C. Schatz,
    • Richard N. McLaughlin, Jr.,
    • Harriet Dashnow,
    • Michael C. Zody,
    • Matt Loose,
    • Miten Jain,
    • Evan E. Eichler,
    • and Danny E. Miller
    Genome Res. November 2024 34: 2061-2073; Published in Advance October 2, 2024, doi:10.1101/gr.279273.124
    OPEN ACCESS ARTICLE
  4. Erratum: Erratum: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. November/December 2022 32: 2145; doi:10.1101/gr.277534.122
    OPEN ACCESS ARTICLE
  5. Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
  6. Method: Co-expression networks reveal the tissue-specific regulation of transcription and splicing
    • Ashis Saha,
    • Yungil Kim,
    • Ariel D.H. Gewirtz,
    • Brian Jo,
    • Chuan Gao,
    • Ian C. McDowell,
    • The GTEx Consortium,
    • Barbara E. Engelhardt,
    • and Alexis Battle
    Genome Res. November 2017 27: 1843-1858; Published in Advance October 11, 2017, doi:10.1101/gr.216721.116
    OPEN ACCESS ARTICLE
  7. Method: Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis
    • Fan Yang,
    • Jiebiao Wang,
    • The GTEx Consortium,
    • Brandon L. Pierce,
    • and Lin S. Chen
    Genome Res. November 2017 27: 1859-1871; Published in Advance October 11, 2017, doi:10.1101/gr.216754.116
  8. Research: Impact of the X Chromosome and sex on regulatory variation
    • Kimberly R. Kukurba,
    • Princy Parsana,
    • Brunilda Balliu,
    • Kevin S. Smith,
    • Zachary Zappala,
    • David A. Knowles,
    • Marie-Julie Favé,
    • Joe R. Davis,
    • Xin Li,
    • Xiaowei Zhu,
    • James B. Potash,
    • Myrna M. Weissman,
    • Jianxin Shi,
    • Anshul Kundaje,
    • Douglas F. Levinson,
    • Philip Awadalla,
    • Sara Mostafavi,
    • Alexis Battle,
    • and Stephen B. Montgomery
    Genome Res. June 2016 26: 768-777; Published in Advance April 21, 2016, doi:10.1101/gr.197897.115
    OPEN ACCESS ARTICLE
  9. Research: The landscape of genomic imprinting across diverse adult human tissues
    • Yael Baran,
    • Meena Subramaniam,
    • Anne Biton,
    • Taru Tukiainen,
    • Emily K. Tsang,
    • Manuel A. Rivas,
    • Matti Pirinen,
    • Maria Gutierrez-Arcelus,
    • Kevin S. Smith,
    • Kim R. Kukurba,
    • Rui Zhang,
    • Celeste Eng,
    • Dara G. Torgerson,
    • Cydney Urbanek,
    • the GTEx Consortium,
    • Jin Billy Li,
    • Jose R. Rodriguez-Santana,
    • Esteban G. Burchard,
    • Max A. Seibold,
    • Daniel G. MacArthur,
    • Stephen B. Montgomery,
    • Noah A. Zaitlen,
    • and Tuuli Lappalainen
    Genome Res. July 2015 25: 927-936; Published in Advance May 7, 2015, doi:10.1101/gr.192278.115
    OPEN ACCESS ARTICLE
  10. Research: Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals
    • Alexis Battle,
    • Sara Mostafavi,
    • Xiaowei Zhu,
    • James B. Potash,
    • Myrna M. Weissman,
    • Courtney McCormick,
    • Christian D. Haudenschild,
    • Kenneth B. Beckman,
    • Jianxin Shi,
    • Rui Mei,
    • Alexander E. Urban,
    • Stephen B. Montgomery,
    • Douglas F. Levinson,
    • and Daphne Koller
    Genome Res. January 2014 24: 14-24; Published in Advance October 3, 2013, doi:10.1101/gr.155192.113
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