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Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Ju Heon Maeng
H. Josh Jang
Alan Y. Du
Shin-Cheng Tzeng
Ting Wang

First Published December 8, 2023

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

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

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

DNase-seq predicts regions of rotational nucleosome stability across diverse human cell types

Deborah R. Winter
Lingyun Song
Sayan Mukherjee
Terrence S. Furey
Gregory E. Crawford

First Published May 8, 2013

A dynamic H3K27ac signature identifies VEGFA-stimulated endothelial enhancers and requires EP300 activity

Bing Zhang
Daniel S. Day
Joshua W. Ho
Lingyun Song
Jingjing Cao
Danos Christodoulou
... [+1 authors] ...,
Jonathan G. Seidman
Gregory E. Crawford
Peter J. Park
William T. Pu

First Published April 1, 2013

Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions

Nathan C. Sheffield
Robert E. Thurman
Lingyun Song
Alexias Safi
John A. Stamatoyannopoulos
Boris Lenhard
Gregory E. Crawford
Terrence S. Furey

First Published March 12, 2013

Effects of sequence variation on differential allelic transcription factor occupancy and gene expression

Timothy E. Reddy
Jason Gertz
Florencia Pauli
Katerina S. Kucera
Katherine E. Varley
Kimberly M. Newberry Georgi K. Marinov Ali Mortazavi Brian A. Williams Lingyun Song
... [+5 authors] ...,
Gregory E. Crawford
Barbara Wold
Huntington F. Willard
Richard M. Myers

First Published February 2, 2012

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