Searching journal content for Jian Ma in author.

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  1. Method: Unified integration of spatial transcriptomics across platforms with LLOKI
    • Ellie Haber,
    • Ajinkya Deshpande,
    • Jian Ma,
    • and Spencer Krieger
    Genome Res. December 2025 35: 2722-2733; Published in Advance November 13, 2025, doi:10.1101/gr.280803.125
    OPEN ACCESS ARTICLE
  2. Editorial: Innovations in computational biology: RECOMB 2024 Special Issue
    • Jian Ma and
    • Bonnie Berger
    Genome Res. September 2024 34: vii-viii; doi:10.1101/gr.280036.124
  3. Method: TSA-seq reveals a largely conserved genome organization relative to nuclear speckles with small position changes tightly correlated with gene expression changes
    • Liguo Zhang,
    • Yang Zhang,
    • Yu Chen,
    • Omid Gholamalamdari,
    • Yuchuan Wang,
    • Jian Ma,
    • and Andrew S. Belmont
    Genome Res. February 2021 31: 251-264; Published in Advance December 18, 2020, doi:10.1101/gr.266239.120
  4. Method: MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome
    • Dechao Tian,
    • Ruochi Zhang,
    • Yang Zhang,
    • Xiaopeng Zhu,
    • and Jian Ma
    Genome Res. February 2020 30: 227-238; Published in Advance January 6, 2020, doi:10.1101/gr.250316.119
  5. Research: Evolution of gene regulation in ruminants differs between evolutionary breakpoint regions and homologous synteny blocks
    • Marta Farré,
    • Jaebum Kim,
    • Anastasia A. Proskuryakova,
    • Yang Zhang,
    • Anastasia I. Kulemzina,
    • Qiye Li,
    • Yang Zhou,
    • Yingqi Xiong,
    • Jennifer L. Johnson,
    • Polina L. Perelman,
    • Warren E. Johnson,
    • Wesley C. Warren,
    • Anna V. Kukekova,
    • Guojie Zhang,
    • Stephen J. O'Brien,
    • Oliver A. Ryder,
    • Alexander S. Graphodatsky,
    • Jian Ma,
    • Harris A. Lewin,
    • and Denis M. Larkin
    Genome Res. April 2019 29: 576-589; Published in Advance February 13, 2019, doi:10.1101/gr.239863.118
  6. Resource: Annotation and cluster analysis of spatiotemporal- and sex-related lncRNA expression in rhesus macaque brain
    • Siling Liu,
    • Zhengbo Wang,
    • Dong Chen,
    • Bowen Zhang,
    • Ren-Rong Tian,
    • Jing Wu,
    • Ying Zhang,
    • Kaiyu Xu,
    • Liu-Meng Yang,
    • Chao Cheng,
    • Jian Ma,
    • Longbao Lv,
    • Yong-Tang Zheng,
    • Xintian Hu,
    • Yi Zhang,
    • Xiangting Wang,
    • and Jiali Li
    Genome Res. September 2017 27: 1608-1620; Published in Advance July 7, 2017, doi:10.1101/gr.217463.116
    OPEN ACCESS ARTICLE
  7. Resource: Alignathon: a competitive assessment of whole-genome alignment methods
    • Dent Earl,
    • Ngan Nguyen,
    • Glenn Hickey,
    • Robert S. Harris,
    • Stephen Fitzgerald,
    • Kathryn Beal,
    • Igor Seledtsov,
    • Vladimir Molodtsov,
    • Brian J. Raney,
    • Hiram Clawson,
    • Jaebum Kim,
    • Carsten Kemena,
    • Jia-Ming Chang,
    • Ionas Erb,
    • Alexander Poliakov,
    • Minmei Hou,
    • Javier Herrero,
    • William James Kent,
    • Victor Solovyev,
    • Aaron E. Darling,
    • Jian Ma,
    • Cedric Notredame,
    • Michael Brudno,
    • Inna Dubchak,
    • David Haussler,
    • and Benedict Paten
    Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
    OPEN ACCESS ARTICLE
  8. Methods: Reconstructing contiguous regions of an ancestral genome
    • Jian Ma,
    • Louxin Zhang,
    • Bernard B. Suh,
    • Brian J. Raney,
    • Richard C. Burhans,
    • W. James Kent,
    • Mathieu Blanchette,
    • David Haussler,
    • and Webb Miller
    Genome Res. December 2006 16: 1557-1565; Published in Advance September 18, 2006, doi:10.1101/gr.5383506
    OPEN ACCESS ARTICLE
  9. Chicken Special/Resources: Mulan: Multiple-sequence local alignment and visualization for studying function and evolution
    • Ivan Ovcharenko,
    • Gabriela G. Loots,
    • Belinda M. Giardine,
    • Minmei Hou,
    • Jian Ma,
    • Ross C. Hardison,
    • Lisa Stubbs,
    • and Webb Miller
    Genome Res. January 2005 15: 184-194; Published in Advance December 8, 2004, doi:10.1101/gr.3007205
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