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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

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

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

Valerie A. Schneider
Tina Graves-Lindsay
Kerstin Howe
Nathan Bouk
Hsiu-Chuan Chen
Paul A. Kitts Terence D. Murphy Kim D. Pruitt Françoise Thibaud-Nissen Derek Albracht Robert S. Fulton Milinn Kremitzki Vincent Magrini Chris Markovic Sean McGrath Karyn Meltz Steinberg Kate Auger William Chow Joanna Collins Glenn Harden Timothy Hubbard Sarah Pelan Jared T. Simpson Glen Threadgold James Torrance Jonathan M. Wood Laura Clarke Sergey Koren Matthew Boitano Paul Peluso Heng Li Chen-Shan Chin Adam M. Phillippy Richard Durbin
... [+29 authors] ...,
Richard K. Wilson
Paul Flicek
Evan E. Eichler
Deanna M. Church

First Published April 10, 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

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

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