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Method

Unified integration of spatial transcriptomics across platforms with LLOKI

  • Ellie Haber
  • Ajinkya Deshpande
  • Jian Ma
  • Spencer Krieger
  • First Published November 13, 2025
Editorial

Innovations in computational biology: RECOMB 2024 Special Issue

  • Jian Ma
  • Bonnie Berger
  • First Published October 11, 2024
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
  • Andrew S. Belmont
  • First Published December 18, 2020
Method

MOCHI enables discovery of heterogeneous interactome modules in 3D nucleome

  • Dechao Tian
  • Ruochi Zhang
  • Yang Zhang
  • Xiaopeng Zhu
  • Jian Ma
  • First Published January 6, 2020
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
  • ... [+11 authors] ...,
  • Alexander S. Graphodatsky
  • Jian Ma
  • Harris A. Lewin
  • Denis M. Larkin
  • First Published February 13, 2019
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
  • ... [+8 authors] ...,
  • Xintian Hu
  • Yi Zhang
  • Xiangting Wang
  • Jiali Li
  • First Published July 7, 2017
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
  • ... [+17 authors] ...,
  • Michael Brudno
  • Inna Dubchak
  • David Haussler
  • Benedict Paten
  • First Published October 1, 2014
Research

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

  • Weisheng Wu
  • Yong Cheng
  • Cheryl A. Keller
  • Jason Ernst
  • Swathi Ashok Kumar
  • Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
  • ... [+16 authors] ...,
  • Francesca Chiaromonte
  • Gerd A. Blobel
  • Mitchell J. Weiss
  • Ross C. Hardison
  • First Published July 27, 2011
Method

Genome-wide identification of conserved regulatory function in diverged sequences

  • Leila Taher
  • David M. McGaughey
  • Samantha Maragh
  • Ivy Aneas
  • Seneca L. Bessling
  • Webb Miller
  • Marcelo A. Nobrega
  • Andrew S. McCallion
  • Ivan Ovcharenko
  • First Published May 31, 2011
Article

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

  • Yong Cheng
  • Weisheng Wu
  • Swathi Ashok Kumar
  • Duonan Yu
  • Wulan Deng
  • Tamara Tripic David C. King Kuan-Bei Chen Ying Zhang Daniela Drautz Belinda Giardine Stephan C. Schuster Webb Miller Francesca Chiaromonte
  • ... [+9 authors] ...,
  • Yu Zhang
  • Gerd A. Blobel
  • Mitchell J. Weiss
  • Ross C. Hardison
  • First Published November 3, 2009
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