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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

Genomic loci susceptible to systematic sequencing bias in clinical whole genomes

Timothy M. Freeman
Dennis Wang
Jason Harris
John C. Ambrose
Prabhu Arumugam
Emma L. Baple Marta Bleda Freya Boardman-Pretty Jeanne M. Boissiere Christopher R. Boustred Mark J. Caulfield Georgia C. Chan Clare E.H. Craig Louise C. Daugherty Anna de Burca Andrew Devereau Greg Elgar Rebecca E. Foulger Tom Fowler Pedro Furió-Tarí Joanne M. Hackett Dina Halai Angela Hamblin Shirley Henderson James E. Holman Tim J.P. Hubbard Kristina Ibáñez Rob Jackson Louise J. Jones Dalia Kasperaviciute Melis Kayikci Lea Lahnstein Kay Lawson Sarah E.A. Leigh Ivonne U.S. Leong Javier F. Lopez Fiona Maleady-Crowe Joanne Mason Ellen M. McDonagh Loukas Moutsianas Michael Mueller Nirupa Murugaesu Anna C. Need Chris A. Odhams Christine Patch Daniel Perez-Gil Dimitris Polychronopoulos John Pullinger Tahrima Rahim Augusto Rendon Pablo Riesgo-Ferreiro Tim Rogers Mina Ryten Kevin Savage Kushmita Sawant Richard H. Scott Afshan Siddiq Alexander Sieghart Damian Smedley Katherine R. Smith Alona Sosinsky William Spooner Helen E. Stevens Alexander Stuckey Razvan Sultana Ellen R.A. Thomas Simon R. Thompson Carolyn Tregidgo Arianna Tucci Emma Walsh Sarah A. Watters Matthew J. Welland
... [+67 authors] ...,
Eleanor Williams
Katarzyna Witkowska
Suzanne M. Wood
Magdalena Zarowiecki

First Published March 10, 2020

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

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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