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Your search for returned 32 results

Perspective

The Topological Regulatory Logic of noncoding RNA–mediated gene expression

Thomas R. Gingeras

First Published June 17, 2026

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

Resource

A limited set of transcriptional programs define major cell types

Alessandra Breschi
Manuel Muñoz-Aguirre
Valentin Wucher
Carrie A. Davis
Diego Garrido-Martín
Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
... [+9 authors] ...,
Ferran Reverter
Michael P. Snyder
Thomas R. Gingeras
Roderic Guigó

First Published July 29, 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

Resource

Dynamics of microRNA expression during mouse prenatal development

Sorena Rahmanian
Rabi Murad
Alessandra Breschi
Weihua Zeng
Mark Mackiewicz
Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
... [+12 authors] ...,
Barbara J. Wold
Richard M. Myers
Roderic Guigó
Ali Mortazavi

First Published October 23, 2019

Research

Alu elements suggests cell-type–specific enhancer function" > Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

Xiao-Ou Zhang
Thomas R. Gingeras
Zhiping Weng

First Published August 14, 2019

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

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