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High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation

  • Daniel Rico
  • Daniel Kent
  • Nefeli Karataraki
  • Aneta Mikulasova
  • Rolando Berlinguer-Palmini
  • Brian A. Walker
  • Biola M. Javierre
  • Lisa J. Russell
  • Chris A. Brackley
  • First Published July 21, 2022

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

Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers

  • Aneta Mikulasova
  • Daniel Kent
  • Marco Trevisan-Herraz
  • Nefeli Karataraki
  • Kent T.M. Fung
  • Cody Ashby Agata Cieslak Shmuel Yaccoby Frits van Rhee Maurizio Zangari Sharmilan Thanendrarajan Carolina Schinke Gareth J. Morgan Vahid Asnafi Salvatore Spicuglia Chris A. Brackley Anne E. Corcoran
  • ... [+12 authors] ...,
  • Sophie Hambleton
  • Brian A. Walker
  • Daniel Rico
  • Lisa J. Russell
  • First Published December 21, 2021

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

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

Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

  • Juan L. Mateo
  • Debbie L.C. van den Berg
  • Maximilian Haeussler
  • Daniela Drechsel
  • Zachary B. Gaber
  • Diogo S. Castro Paul Robson Q. Richard Lu Gregory E. Crawford Paul Flicek
  • ... [+5 authors] ...,
  • Laurence Ettwiller
  • Joachim Wittbrodt
  • François Guillemot
  • Ben Martynoga
  • First Published December 1, 2017

Microbiota regulate intestinal epithelial gene expression by suppressing the transcription factor Hepatocyte nuclear factor 4 alpha

  • James M. Davison
  • Colin R. Lickwar
  • Lingyun Song
  • Ghislain Breton
  • Gregory E. Crawford
  • John F. Rawls
  • First Published April 6, 2017

Corrigendum: Characterization of the neural stem cell gene regulatory network identifies OLIG2 as a multifunctional regulator of self-renewal

  • Juan L. Mateo
  • Debbie L.C. van den Berg
  • Maximilian Haeussler
  • Daniela Drechsel
  • Zachary B. Gaber
  • Diogo S. Castro Paul Robson Q. Richard Lu Gregory E. Crawford Paul Flicek
  • ... [+5 authors] ...,
  • Laurence Ettwiller
  • Joachim Wittbrodt
  • François Guillemot
  • Ben Martynoga
  • First Published November 1, 2016

Mapping nucleosome positions using DNase-seq

  • Jianling Zhong
  • Kaixuan Luo
  • Peter S. Winter
  • Gregory E. Crawford
  • Edwin S. Iversen
  • Alexander J. Hartemink
  • First Published January 15, 2016

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
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