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Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise

Aliza B. Rubenstein
Gregory R. Smith
Zidong Zhang
Xi Chen
Toby L. Chambers
Frederique Ruf-Zamojski Natalia Mendelev Wan Sze Cheng Michel Zamojski Mary Anne S. Amper Venugopalan D. Nair Andrew R. Marderstein Stephen B. Montgomery Olga G. Troyanskaya
... [+9 authors] ...,
Elena Zaslavsky
Todd Trappe
Scott Trappe
Stuart C. Sealfon

First Published May 20, 2025

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang
Xi He
Belinda M. Giardine
Kathryn J. Isaac
Dylan J. Taylor
Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
... [+25 authors] ...,
Yu Zhang
Qunhua Li
Shaun Mahony
Ross C. Hardison

First Published July 1, 2024

Data integration and inference of gene regulation using single-cell temporal multimodal data with scTIE

Yingxin Lin
Tung-Yu Wu
Xi Chen
Sheng Wan
Brian Chao
Jingxue Xin
Jean Y.H. Yang
Wing H. Wong
Y.X. Rachel Wang

First Published December 15, 2023

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Kelly Cochran
Divyanshi Srivastava
Avanti Shrikumar
Akshay Balsubramani
Ross C. Hardison
Anshul Kundaje
Shaun Mahony

First Published January 18, 2022

Time course regulatory analysis based on paired expression and chromatin accessibility data

Zhana Duren
Xi Chen
Jingxue Xin
Yong Wang
Wing Hung Wong

First Published March 18, 2020

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Guanjue Xiang
Cheryl A. Keller
Elisabeth Heuston
Belinda M. Giardine
Lin An
Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
... [+15 authors] ...,
Jim Hughes
Douglas R. Higgs
Yu Zhang
Ross C. Hardison

First Published March 4, 2020

GenTree, an integrated resource for analyzing the evolution and function of primate-specific coding genes

Yi Shao
Chunyan Chen
Hao Shen
Bin Z. He
Daqi Yu
Shuai Jiang Shilei Zhao Zhiqiang Gao Zhenglin Zhu Xi Chen Yan Fu
... [+6 authors] ...,
Hua Chen
Ge Gao
Manyuan Long
Yong E. Zhang

First Published March 12, 2019

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang
Feipeng Zhang
Galip Gürkan Yardımcı
Fan Song
Ross C. Hardison
William Stafford Noble
Feng Yue
Qunhua Li

First Published August 30, 2017

Genome accessibility is widely preserved and locally modulated during mitosis

Chris C.-S. Hsiung
Christapher S. Morrissey
Maheshi Udugama
Christopher L. Frank
Cheryl A. Keller
Songjoon Baek Belinda Giardine
... [+2 authors] ...,
Gregory E. Crawford
Myong-Hee Sung
Ross C. Hardison
Gerd A. Blobel

First Published November 4, 2014

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

Maxim Pimkin
Andrew V. Kossenkov
Tejaswini Mishra
Christapher S. Morrissey
Weisheng Wu
Cheryl A. Keller Gerd A. Blobel
... [+2 authors] ...,
Dongwon Lee
Michael A. Beer
Ross C. Hardison
Mitchell J. Weiss

First Published October 15, 2014

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