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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
Resource

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

  • Chong Li
  • Marc Jan Bonder
  • Sabriya Syed
  • Matthew Jensen
  • Mark B. Gerstein
  • Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
  • ... [+4 authors] ...,
  • Jan O. Korbel
  • Evan E. Eichler
  • Charles Lee
  • Xinghua Shi
  • First Published December 5, 2024
Editorial

Innovations in computational biology: RECOMB 2024 Special Issue

  • Jian Ma
  • Bonnie Berger
  • First Published October 11, 2024
Method

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases

  • Prashant S. Emani
  • Maya N. Geradi
  • Gamze Gürsoy
  • Monica R. Grasty
  • Andrew Miranker
  • Mark B. Gerstein
  • First Published December 14, 2023
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
Research

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

  • Vladimir Despic
  • Mario Dejung
  • Mengting Gu
  • Jayanth Krishnan
  • Jing Zhang
  • Lydia Herzel
  • ... [+1 authors] ...,
  • Korinna Straube
  • Mark B. Gerstein
  • Falk Butter
  • Karla M. Neugebauer
  • First Published April 5, 2017
Research

Pangolin genomes and the evolution of mammalian scales and immunity

  • Siew Woh Choo
  • Mike Rayko
  • Tze King Tan
  • Ranjeev Hari
  • Aleksey Komissarov
  • Wei Yee Wee Andrey A. Yurchenko Sergey Kliver Gaik Tamazian Agostinho Antunes Richard K. Wilson Wesley C. Warren Klaus-Peter Koepfli Patrick Minx Ksenia Krasheninnikova Antoinette Kotze Desire L. Dalton Elaine Vermaak Ian C. Paterson Pavel Dobrynin Frankie Thomas Sitam Jeffrine J. Rovie-Ryan Warren E. Johnson Aini Mohamed Yusoff Shu-Jin Luo Kayal Vizi Karuppannan Gang Fang Deyou Zheng
  • ... [+23 authors] ...,
  • Mark B. Gerstein
  • Leonard Lipovich
  • Stephen J. O'Brien
  • Guat Jah Wong
  • First Published August 10, 2016
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