Search | Genome Research

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

Bin Zhao
John A. Lees
Hongjin Wu
Chao Yang
Daniel Falush

First Published May 30, 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

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

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 October 7, 2014

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

J. Gray Camp
Christopher L. Frank
Colin R. Lickwar
Harendra Guturu
Tomas Rube
Aaron M. Wenger
... [+1 authors] ...,
Jenny Chen
Gill Bejerano
Gregory E. Crawford
John F. Rawls

First Published June 24, 2014

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

Dynamic DNA methylation across diverse human cell lines and tissues

Katherine E. Varley
Jason Gertz
Kevin M. Bowling
Stephanie L. Parker
Timothy E. Reddy
Florencia Pauli-Behn Marie K. Cross Brian A. Williams John A. Stamatoyannopoulos
... [+4 authors] ...,
Gregory E. Crawford
Devin M. Absher
Barbara J. Wold
Richard M. Myers

First Published January 16, 2013

Predicting cell-type–specific gene expression from regions of open chromatin

Anirudh Natarajan
Galip Gürkan Yardımcı
Nathan C. Sheffield
Gregory E. Crawford
Uwe Ohler

First Published September 5, 2012

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

High-resolution mapping of open chromatin in the rice genome

Wenli Zhang
Yufeng Wu
James C. Schnable
Zixian Zeng
Michael Freeling
Gregory E. Crawford
Jiming Jiang

First Published November 22, 2011

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Bum-Kyu Lee
Akshay A. Bhinge
Anna Battenhouse
Ryan M. McDaniell
Zheng Liu
Lingyun Song Yunyun Ni Ewan Birney
... [+3 authors] ...,
Jason D. Lieb
Terrence S. Furey
Gregory E. Crawford
Vishwanath R. Iyer

First Published November 16, 2011

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Weisheng Wu
Yong Cheng
Cheryl A. Keller
Jason Ernst
Swathi Ashok Kumar
Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
... [+16 authors] ...,
Francesca Chiaromonte
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published July 27, 2011

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

Lingyun Song
Zhancheng Zhang
Linda L. Grasfeder
Alan P. Boyle
Paul G. Giresi
Bum-Kyu Lee Nathan C. Sheffield Stefan Gräf Mikael Huss Damian Keefe Zheng Liu Darin London Ryan M. McDaniell Yoichiro Shibata Kimberly A. Showers Jeremy M. Simon Teresa Vales Tianyuan Wang Deborah Winter Zhuzhu Zhang Neil D. Clarke Ewan Birney
... [+17 authors] ...,
Vishwanath R. Iyer
Gregory E. Crawford
Jason D. Lieb
Terrence S. Furey

First Published July 12, 2011

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Alan P. Boyle
Lingyun Song
Bum-Kyu Lee
Darin London
Damian Keefe
Ewan Birney
Vishwanath R. Iyer
Gregory E. Crawford
Terrence S. Furey

First Published November 24, 2010

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

Michael P. Schnetz
Cynthia F. Bartels
Kuntal Shastri
Dheepa Balasubramanian
Gabriel E. Zentner
Ravishankar Balaji Xiaodong Zhang Lingyun Song
... [+3 authors] ...,
Zhenghe Wang
Thomas LaFramboise
Gregory E. Crawford
Peter C. Scacheri

First Published February 27, 2009

Inferring genomic flux in bacteria

Xavier Didelot
Aaron Darling
Daniel Falush

First Published November 17, 2008

Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?" > A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?

Xavier Didelot
Mark Achtman
Julian Parkhill
Nicholas R. Thomson
Daniel Falush

First Published November 7, 2006

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

Gregory E. Crawford
Ingeborg E. Holt
James Whittle
Bryn D. Webb
Denise Tai
Sean Davis Elliott H. Margulies YiDong Chen John A. Bernat David Ginsburg Daixing Zhou Shujun Luo
... [+7 authors] ...,
Thomas J. Vasicek
Mark J. Daly
Tyra G. Wolfsberg
Francis S. Collins

First Published December 12, 2005

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Your search for returned 27 results

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

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

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

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

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

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

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

Mapping nucleosome positions using DNase-seq

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

Genome accessibility is widely preserved and locally modulated during mitosis

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

Microbiota modulate transcription in the intestinal epithelium without remodeling the accessible chromatin landscape

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

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

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

Dynamic DNA methylation across diverse human cell lines and tissues

Predicting cell-type–specific gene expression from regions of open chromatin

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

High-resolution mapping of open chromatin in the rice genome

Cell-type specific and combinatorial usage of diverse transcription factors revealed by genome-wide binding studies in multiple human cells

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

High-resolution genome-wide in vivo footprinting of diverse transcription factors in human cells

Genomic distribution of CHD7 on chromatin tracks H3K4 methylation patterns

Inferring genomic flux in bacteria

Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?" > A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?

Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS)

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Your search for returned 27 results