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High-fidelity bidirectional translation between single-cell transcriptomes and DNA methylomes with scBOND

  • Kehan Lang
  • Chenyang Jia
  • Siyu Li
  • Yi Guo
  • Dingjun Hu
  • Shengquan Chen
  • First Published March 26, 2026

Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data

  • Kaixuan Luo
  • Jianling Zhong
  • Alexias Safi
  • Linda K. Hong
  • Alok K. Tewari
  • Lingyun Song
  • ... [+1 authors] ...,
  • Timothy E. Reddy
  • Li Ma
  • Gregory E. Crawford
  • Alexander J. Hartemink
  • First Published May 24, 2022

Correcting signal biases and detecting regulatory elements in STARR-seq data

  • Young-Sook Kim
  • Graham D. Johnson
  • Jungkyun Seo
  • Alejandro Barrera
  • Thomas N. Cowart
  • William H. Majoros
  • Alejandro Ochoa
  • Andrew S. Allen
  • Timothy E. Reddy
  • First Published March 15, 2021

AP-1 subunits converge promiscuously at enhancers to potentiate transcription

  • Jungkyun Seo
  • D. Dewran Koçak
  • Luke C. Bartelt
  • Courtney A. Williams
  • Alejandro Barrera
  • Charles A. Gersbach
  • Timothy E. Reddy
  • First Published March 5, 2021

Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding

  • Ian C. McDowell
  • Alejandro Barrera
  • Anthony M. D'Ippolito
  • Christopher M. Vockley
  • Linda K. Hong
  • Sarah M. Leichter Luke C. Bartelt William H. Majoros Lingyun Song Alexias Safi D. Dewran Koçak Charles A. Gersbach
  • ... [+7 authors] ...,
  • Alexander J. Hartemink
  • Gregory E. Crawford
  • Barbara E. Engelhardt
  • Timothy E. Reddy
  • First Published August 10, 2018

Genomic approaches for understanding the genetics of complex disease

  • William L. Lowe
  • Timothy E. Reddy
  • First Published October 1, 2015

Read clouds uncover variation in complex regions of the human genome

  • Alex Bishara
  • Yuling Liu
  • Ziming Weng
  • Dorna Kashef-Haghighi
  • Daniel E. Newburger
  • Robert West
  • Arend Sidow
  • Serafim Batzoglou
  • First Published August 18, 2015

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

  • Christopher M. Vockley
  • Cong Guo
  • William H. Majoros
  • Michael Nodzenski
  • Denise M. Scholtens
  • M. Geoffrey Hayes
  • William L. Lowe
  • Timothy E. Reddy
  • First Published June 17, 2015

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

  • Lauren R. Polstein
  • Pablo Perez-Pinera
  • D. Dewran Kocak
  • Christopher M. Vockley
  • Peggy Bledsoe
  • Lingyun Song
  • ... [+1 authors] ...,
  • Alexias Safi
  • Gregory E. Crawford
  • Timothy E. Reddy
  • Charles A. Gersbach
  • First Published May 29, 2015

Discovery of recurrent structural variants in nasopharyngeal carcinoma

  • Anton Valouev
  • Ziming Weng
  • Robert T. Sweeney
  • Sushama Varma
  • Quynh-Thu Le
  • Christina Kong
  • Arend Sidow
  • Robert B. West
  • First Published November 8, 2013
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