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Resource

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
Method

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
Resource

Precision environmental health monitoring by longitudinal exposome and multi-omics profiling

  • Peng Gao
  • Xiaotao Shen
  • Xinyue Zhang
  • Chao Jiang
  • Sai Zhang
  • Xin Zhou
  • Sophia Miryam Schüssler-Fiorenza Rose
  • Michael Snyder
  • First Published June 6, 2022
In memoriam

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022
In memoriam

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022
Research

RET regulatory code is disrupted in Hirschsprung disease" > A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease

  • Sumantra Chatterjee
  • Kameko M. Karasaki
  • Lauren E. Fries
  • Ashish Kapoor
  • Aravinda Chakravarti
  • First Published November 15, 2021
Method

Sequence-based correction of barcode bias in massively parallel reporter assays

  • Dongwon Lee
  • Ashish Kapoor
  • Changhee Lee
  • Michael Mudgett
  • Michael A. Beer
  • Aravinda Chakravarti
  • First Published July 20, 2021
Method

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
Resource

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
Method

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018
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