Searching journal content for J B Fan in author.

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  1. Method: Tree-based differential testing using inferential uncertainty for RNA-seq
    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    OPEN ACCESS ARTICLE
  2. 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
  3. 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
  4. Method: Characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomic data with nonuniform cellular densities
    • Brendan F. Miller,
    • Dhananjay Bambah-Mukku,
    • Catherine Dulac,
    • Xiaowei Zhuang,
    • and Jean Fan
    Genome Res. October 2021 31: 1843-1855; Published in Advance May 25, 2021, doi:10.1101/gr.271288.120
    OPEN ACCESS ARTICLE
  5. Method: Linking transcriptional and genetic tumor heterogeneity through allele analysis of single-cell RNA-seq data
    • Jean Fan,
    • Hae-Ock Lee,
    • Soohyun Lee,
    • Da-eun Ryu,
    • Semin Lee,
    • Catherine Xue,
    • Seok Jin Kim,
    • Kihyun Kim,
    • Nikolaos Barkas,
    • Peter J. Park,
    • Woong-Yang Park,
    • and Peter V. Kharchenko
    Genome Res. August 2018 28: 1217-1227; Published in Advance June 13, 2018, doi:10.1101/gr.228080.117
  6. Research: Integrated single-cell genetic and transcriptional analysis suggests novel drivers of chronic lymphocytic leukemia
    • Lili Wang,
    • Jean Fan,
    • Joshua M. Francis,
    • George Georghiou,
    • Sarah Hergert,
    • Shuqiang Li,
    • Rutendo Gambe,
    • Chensheng W. Zhou,
    • Chunxiao Yang,
    • Sheng Xiao,
    • Paola Dal Cin,
    • Michaela Bowden,
    • Dylan Kotliar,
    • Sachet A. Shukla,
    • Jennifer R. Brown,
    • Donna Neuberg,
    • Dario R. Alessi,
    • Cheng-Zhong Zhang,
    • Peter V. Kharchenko,
    • Kenneth J. Livak,
    • and Catherine J. Wu
    Genome Res. August 2017 27: 1300-1311; Published in Advance July 5, 2017, doi:10.1101/gr.217331.116
  7. Method: Modeling cis-regulation with a compendium of genome-wide histone H3K27ac profiles
    • Su Wang,
    • Chongzhi Zang,
    • Tengfei Xiao,
    • Jingyu Fan,
    • Shenglin Mei,
    • Qian Qin,
    • Qiu Wu,
    • Xujuan Li,
    • Kexin Xu,
    • Housheng Hansen He,
    • Myles Brown,
    • Clifford A. Meyer,
    • and X. Shirley Liu
    Genome Res. October 2016 26: 1417-1429; Published in Advance July 27, 2016, doi:10.1101/gr.201574.115
  8. Method: Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq
    • Saiful Islam,
    • Una Kjällquist,
    • Annalena Moliner,
    • Pawel Zajac,
    • Jian-Bing Fan,
    • Peter Lönnerberg,
    • and Sten Linnarsson
    Genome Res. July 2011 21: 1160-1167; Published in Advance May 4, 2011, doi:10.1101/gr.110882.110
  9. LETTER: Human embryonic stem cells have a unique epigenetic signature
    • Marina Bibikova,
    • Eugene Chudin,
    • Bonnie Wu,
    • Lixin Zhou,
    • Eliza Wickham Garcia,
    • Ying Liu,
    • Soojung Shin,
    • Todd W. Plaia,
    • Jonathan M. Auerbach,
    • Dan E. Arking,
    • Rodolfo Gonzalez,
    • Jeremy Crook,
    • Bruce Davidson,
    • Thomas C. Schulz,
    • Allan Robins,
    • Aparna Khanna,
    • Peter Sartipy,
    • Johan Hyllner,
    • Padmavathy Vanguri,
    • Smita Savant-Bhonsale,
    • Alan K. Smith,
    • Aravinda Chakravarti,
    • Anirban Maitra,
    • Mahendra Rao,
    • David L. Barker,
    • Jeanne F. Loring,
    • and Jian-Bing Fan
    Genome Res. September 2006 16: 1075-1083; Published in Advance August 9, 2006, doi:10.1101/gr.5319906
    OPEN ACCESS ARTICLE
  10. Methods: High-throughput DNA methylation profiling using universal bead arrays
    • Marina Bibikova,
    • Zhenwu Lin,
    • Lixin Zhou,
    • Eugene Chudin,
    • Eliza Wickham Garcia,
    • Bonnie Wu,
    • Dennis Doucet,
    • Neal J. Thomas,
    • Yunhua Wang,
    • Ekkehard Vollmer,
    • Torsten Goldmann,
    • Carola Seifart,
    • Wei Jiang,
    • David L. Barker,
    • Mark S. Chee,
    • Joanna Floros,
    • and Jian-Bing Fan
    Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
    OPEN ACCESS ARTICLE
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