Search | Genome Research

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

Matthias H. Weissensteiner
Marzia A. Cremona
Wilfried M. Guiblet
Nicholas Stoler
Robert S. Harris
Monika Cechova
... [+1 authors] ...,
Kristin A. Eckert
Francesca Chiaromonte
Yi-Fei Huang
Kateryna D. Makova

First Published July 11, 2023

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

Wilfried M. Guiblet
Michael DeGiorgio
Xiaoheng Cheng
Francesca Chiaromonte
Kristin A. Eckert
Yi-Fei Huang
Kateryna D. Makova

First Published June 29, 2021

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

Wilfried M. Guiblet
Marzia A. Cremona
Monika Cechova
Robert S. Harris
Iva Kejnovská
Eduard Kejnovsky
Kristin Eckert
Francesca Chiaromonte
Kateryna D. Makova

First Published November 6, 2018

Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Arkarachai Fungtammasan
Erin Walsh
Francesca Chiaromonte
Kristin A. Eckert
Kateryna D. Makova

First Published October 3, 2016

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Arkarachai Fungtammasan
Erin Walsh
Francesca Chiaromonte
Kristin A. Eckert
Kateryna D. Makova

First Published March 28, 2012

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

George H. Perry
Páll Melsted
John C. Marioni
Ying Wang
Russell Bainer
Joseph K. Pickrell Katelyn Michelini Sarah Zehr
... [+3 authors] ...,
Anne D. Yoder
Matthew Stephens
Jonathan K. Pritchard
Yoav Gilad

First Published December 29, 2011

A matter of life or death: How microsatellites emerge in and vanish from the human genome

Yogeshwar D. Kelkar
Kristin A. Eckert
Francesca Chiaromonte
Kateryna D. Makova

First Published October 12, 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

Windshield splatter analysis with the Galaxy metagenomic pipeline

Sergei Kosakovsky Pond
Samir Wadhawan
Francesca Chiaromonte
Guruprasad Ananda
Wen-Yu Chung
James Taylor
Anton Nekrutenko

First Published October 9, 2009

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

Erika M. Kvikstad
Francesca Chiaromonte
Kateryna D. Makova

First Published June 5, 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

Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs

Julie E. Horvath
David W. Weisrock
Stephanie L. Embry
Isabella Fiorentino
James P. Balhoff
Peter Kappeler
Gregory A. Wray
Huntington F. Willard
Anne D. Yoder

First Published February 1, 2008

The genome-wide determinants of human and chimpanzee microsatellite evolution

Yogeshwar D. Kelkar
Svitlana Tyekucheva
Francesca Chiaromonte
Kateryna D. Makova

First Published November 21, 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

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

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

Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

Diana Kolbe
James Taylor
Laura Elnitski
Pallavi Eswara
Jia Li
Webb Miller
Ross Hardison
Francesca Chiaromonte

First Published April 1, 2004

Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents

Kateryna D. Makova
Shan Yang
Francesca Chiaromonte

First Published April 1, 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

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

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels

Francesca Chiaromonte
Webb Miller
Eric E. Bouhassira,

First Published January 1, 2003

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Your search for returned 24 results

Accurate sequencing of DNA motifs able to form alternative (non-B) structures

Selection and thermostability suggest G-quadruplexes are novel functional elements of the human genome

Long-read sequencing technology indicates genome-wide effects of non-B DNA on polymerization speed and error rate

Corrigendum: A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

A genome-wide analysis of common fragile sites: What features determine chromosomal instability in the human genome?

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

A matter of life or death: How microsatellites emerge in and vanish from the human genome

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

Windshield splatter analysis with the Galaxy metagenomic pipeline

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

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

Development and application of a phylogenomic toolkit: Resolving the evolutionary history of Madagascar’s lemurs

The genome-wide determinants of human and chimpanzee microsatellite evolution

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

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

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

Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

Insertions and Deletions Are Male Biased Too: A Whole-Genome Analysis in Rodents

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

Distinguishing Regulatory DNA From Neutral Sites

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

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels

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Your search for returned 24 results