Search | Genome Research

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang
Xi He
Belinda M. Giardine
Kathryn J. Isaac
Dylan J. Taylor
Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
... [+25 authors] ...,
Yu Zhang
Qunhua Li
Shaun Mahony
Ross C. Hardison

First Published July 1, 2024

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

Kelly Cochran
Divyanshi Srivastava
Avanti Shrikumar
Akshay Balsubramani
Ross C. Hardison
Anshul Kundaje
Shaun Mahony

First Published January 18, 2022

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

Guanjue Xiang
Cheryl A. Keller
Elisabeth Heuston
Belinda M. Giardine
Lin An
Alexander Q. Wixom Amber Miller April Cockburn Michael E.G. Sauria Kathryn Weaver Jens Lichtenberg Berthold Göttgens Qunhua Li David Bodine Shaun Mahony James Taylor Gerd A. Blobel Mitchell J. Weiss Yong Cheng Feng Yue
... [+15 authors] ...,
Jim Hughes
Douglas R. Higgs
Yu Zhang
Ross C. Hardison

First Published March 4, 2020

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Tao Yang
Feipeng Zhang
Galip Gürkan Yardımcı
Fan Song
Ross C. Hardison
William Stafford Noble
Feng Yue
Qunhua Li

First Published August 30, 2017

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

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

Maxim Pimkin
Andrew V. Kossenkov
Tejaswini Mishra
Christapher S. Morrissey
Weisheng Wu
Cheryl A. Keller Gerd A. Blobel
... [+2 authors] ...,
Dongwon Lee
Michael A. Beer
Ross C. Hardison
Mitchell J. Weiss

First Published October 15, 2014

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

Weisheng Wu
Christapher S. Morrissey
Cheryl A. Keller
Tejaswini Mishra
Maxim Pimkin
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published October 15, 2014

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

Ali Mortazavi
Shirley Pepke
Camden Jansen
Georgi K. Marinov
Jason Ernst
Manolis Kellis
Ross C. Hardison
Richard M. Myers
Barbara J. Wold

First Published October 29, 2013

$What fraction of the human genome is functional?$

What fraction of the human genome is functional?

Chris P. Ponting
Ross C. Hardison

First Published August 29, 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

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Yong Cheng
Weisheng Wu
Swathi Ashok Kumar
Duonan Yu
Wulan Deng
Tamara Tripic David C. King Kuan-Bei Chen Ying Zhang Daniela Drautz Belinda Giardine Stephan C. Schuster Webb Miller Francesca Chiaromonte
... [+9 authors] ...,
Yu Zhang
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published November 3, 2009

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Yong Cheng
David C. King
Louis C. Dore
Xinmin Zhang
Yuepin Zhou
Ying Zhang Christine Dorman Demesew Abebe Swathi A. Kumar Francesca Chiaromonte
... [+5 authors] ...,
Webb Miller
Roland D. Green
Mitchell J. Weiss
Ross C. Hardison

First Published September 25, 2008

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Webb Miller
Kate Rosenbloom
Ross C. Hardison
Minmei Hou
James Taylor
Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
... [+17 authors] ...,
Eric S. Lander
Adam Siepel
David Haussler
W. James Kent

First Published November 5, 2007

cis-regulatory elements using comparative genomics: Some lessons from ENCODE data" > Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

David C. King
James Taylor
Ying Zhang
Yong Cheng
Heather A. Lawson
Joel Martin
Francesca Chiaromonte
Webb Miller
Ross C. Hardison

First Published June 13, 2007

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Daniel Blankenberg
James Taylor
Ian Schenck
Jianbin He
Yi Zhang
Matthew Ghent Narayanan Veeraraghavan Istvan Albert
... [+3 authors] ...,
Webb Miller
Kateryna D. Makova
Ross C. Hardison
Anton Nekrutenko

First Published June 13, 2007

Accurate and reliable high-throughput detection of copy number variation in the human genome

Heike Fiegler
Richard Redon
Dan Andrews
Carol Scott
Robert Andrews
Carol Carder Richard Clark Oliver Dovey Peter Ellis Lars Feuk Lisa French Paul Hunt Dimitrios Kalaitzopoulos James Larkin Lyndal Montgomery George H. Perry Bob W. Plumb Keith Porter Rachel E. Rigby Diane Rigler Armand Valsesia Cordelia Langford Sean J. Humphray
... [+18 authors] ...,
Stephen W. Scherer
Charles Lee
Matthew E. Hurles
Nigel P. Carter

First Published November 22, 2006

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

James Taylor
Svitlana Tyekucheva
David C. King
Ross C. Hardison
Webb Miller
Francesca Chiaromonte

First Published October 19, 2006

cis-regulatory modules" > Experimental validation of predicted mammalian erythroid cis-regulatory modules

Hao Wang
Ying Zhang
Yong Cheng
Yuepin Zhou
David C. King
James Taylor Francesca Chiaromonte Jyotsna Kasturi Hanna Petrykowska Brian Gibb Christine Dorman Webb Miller
... [+7 authors] ...,
Louis C. Dore
John Welch
Mitchell J. Weiss
Ross C. Hardison

First Published October 12, 2006

Galaxy: A platform for interactive large-scale genome analysis

Belinda Giardine
Cathy Riemer
Ross C. Hardison
Richard Burhans
Laura Elnitski
Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
... [+4 authors] ...,
James Taylor
Webb Miller
W. James Kent
Anton Nekrutenko

First Published September 16, 2005

cis-regulatory modules in aligned mammalian genome sequences" > Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

David C. King
James Taylor
Laura Elnitski
Francesca Chiaromonte
Webb Miller
Ross C. Hardison

First Published July 15, 2005

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Ivan Ovcharenko
Gabriela G. Loots
Belinda M. Giardine
Minmei Hou
Jian Ma
Ross C. Hardison
Lisa Stubbs
Webb Miller

First Published December 8, 2004

Evolution and functional classification of vertebrate gene deserts

Ivan Ovcharenko
Gabriela G. Loots
Marcelo A. Nobrega
Ross C. Hardison
Webb Miller
Lisa Stubbs

First Published December 8, 2004

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

Shan Yang
Arian F. Smit
Scott Schwartz
Francesca Chiaromonte
Krishna M. Roskin
David Haussler
Webb Miller
Ross C. Hardison

First Published April 1, 2004

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

Ivan Ovcharenko
Gabriela G. Loots
Ross C. Hardison
Webb Miller
Lisa Stubbs

First Published March 1, 2004

GALA, a Database for Genomic Sequence Alignments and Annotations

Belinda Giardine
Laura Elnitski
Cathy Riemer
Izabela Makalowska
Scott Schwartz
Webb Miller
Ross C. Hardison

First Published April 1, 2003

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources

Kelly A. Frazer
Laura Elnitski
Deanna M. Church
Inna Dubchak
Ross C. Hardison

First Published January 1, 2003

First Published January 1, 2003

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Ross C. Hardison
Krishna M. Roskin
Shan Yang
Mark Diekhans
W. James Kent
Ryan Weber Laura Elnitski Jia Li Michael O'Connor Diana Kolbe Scott Schwartz Terrence S. Furey Simon Whelan Nick Goldman
... [+9 authors] ...,
Arian Smit
Webb Miller
Francesca Chiaromonte
David Haussler

First Published January 1, 2003

Human–Mouse Alignments with BLASTZ

Scott Schwartz
W. James Kent
Arian Smit
Zheng Zhang
Robert Baertsch
Ross C. Hardison
David Haussler
Webb Miller

First Published December 30, 2002

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

Ross C. Hardison
John Oeltjen
Webb Miller

First Published October 1, 1997

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Your search for returned 30 results

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding

An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

Genome accessibility is widely preserved and locally modulated during mitosis

Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

Integrating and mining the chromatin landscape of cell-type specificity using self-organizing maps

What fraction of the human genome is functional?

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

cis-regulatory elements using comparative genomics: Some lessons from ENCODE data" > Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Accurate and reliable high-throughput detection of copy number variation in the human genome

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

cis-regulatory modules" > Experimental validation of predicted mammalian erythroid cis-regulatory modules

Galaxy: A platform for interactive large-scale genome analysis

cis-regulatory modules in aligned mammalian genome sequences" > Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Evolution and functional classification of vertebrate gene deserts

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

GALA, a Database for Genomic Sequence Alignments and Annotations

Cross-Species Sequence Comparisons: A Review of Methods and Available Resources

Distinguishing Regulatory DNA From Neutral Sites

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Human–Mouse Alignments with BLASTZ

Long Human–Mouse Sequence Alignments Reveal Novel Regulatory Elements: A Reason to Sequence the Mouse Genome

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Your search for returned 30 results