Search | Genome Research

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Chong Li
Marc Jan Bonder
Sabriya Syed
Matthew Jensen
Mark B. Gerstein
Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
... [+4 authors] ...,
Jan O. Korbel
Evan E. Eichler
Charles Lee
Xinghua Shi

First Published December 5, 2024

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases

Prashant S. Emani
Maya N. Geradi
Gamze Gürsoy
Monica R. Grasty
Andrew Miranker
Mark B. Gerstein

First Published December 14, 2023

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

Vladimir Despic
Mario Dejung
Mengting Gu
Jayanth Krishnan
Jing Zhang
Lydia Herzel
... [+1 authors] ...,
Korinna Straube
Mark B. Gerstein
Falk Butter
Karla M. Neugebauer

First Published April 5, 2017

Pangolin genomes and the evolution of mammalian scales and immunity

Siew Woh Choo
Mike Rayko
Tze King Tan
Ranjeev Hari
Aleksey Komissarov
Wei Yee Wee Andrey A. Yurchenko Sergey Kliver Gaik Tamazian Agostinho Antunes Richard K. Wilson Wesley C. Warren Klaus-Peter Koepfli Patrick Minx Ksenia Krasheninnikova Antoinette Kotze Desire L. Dalton Elaine Vermaak Ian C. Paterson Pavel Dobrynin Frankie Thomas Sitam Jeffrine J. Rovie-Ryan Warren E. Johnson Aini Mohamed Yusoff Shu-Jin Luo Kayal Vizi Karuppannan Gang Fang Deyou Zheng
... [+23 authors] ...,
Mark B. Gerstein
Leonard Lipovich
Stephen J. O'Brien
Guat Jah Wong

First Published August 10, 2016

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

Justin Cotney
Jing Leng
Sunghee Oh
Laura E. DeMare
Steven K. Reilly
Mark B. Gerstein
James P. Noonan

First Published March 15, 2012

C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

Zhi John Lu
Kevin Y. Yip
Guilin Wang
Chong Shou
LaDeana W. Hillier
Ekta Khurana Ashish Agarwal Raymond Auerbach Joel Rozowsky Chao Cheng Masaomi Kato David M. Miller Frank Slack
... [+8 authors] ...,
Michael Snyder
Robert H. Waterston
Valerie Reinke
Mark B. Gerstein

First Published December 22, 2010

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

Dorothee Pflueger
Stéphane Terry
Andrea Sboner
Lukas Habegger
Raquel Esgueva
Pei-Chun Lin Maria A. Svensson Naoki Kitabayashi Benjamin J. Moss Theresa Y. MacDonald Xuhong Cao Terrence Barrette Ashutosh K. Tewari Mark S. Chee Arul M. Chinnaiyan
... [+10 authors] ...,
David S. Rickman
Francesca Demichelis
Mark B. Gerstein
Mark A. Rubin

First Published October 29, 2010

Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families

Prianka V. Patel
Tara A. Gianoulis
Robert D. Bjornson
Kevin Y. Yip
Donald M. Engelman
Mark B. Gerstein

First Published April 29, 2010

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Kevin Judd McKernan
Heather E. Peckham
Gina L. Costa
Stephen F. McLaughlin
Yutao Fu
Eric F. Tsung Christopher R. Clouser Cisyla Duncan Jeffrey K. Ichikawa Clarence C. Lee Zheng Zhang Swati S. Ranade Eileen T. Dimalanta Fiona C. Hyland Tanya D. Sokolsky Lei Zhang Andrew Sheridan Haoning Fu Cynthia L. Hendrickson Bin Li Lev Kotler Jeremy R. Stuart Joel A. Malek Jonathan M. Manning Alena A. Antipova Damon S. Perez Michael P. Moore Kathleen C. Hayashibara Michael R. Lyons Robert E. Beaudoin Brittany E. Coleman Michael W. Laptewicz Adam E. Sannicandro Michael D. Rhodes Rajesh K. Gottimukkala Shan Yang Vineet Bafna Ali Bashir Andrew MacBride Can Alkan Jeffrey M. Kidd
... [+36 authors] ...,
Evan E. Eichler
Martin G. Reese
Francisco M. De La Vega
Alan P. Blanchard

First Published June 22, 2009

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Philip M. Kim
Hugo Y.K. Lam
Alexander E. Urban
Jan O. Korbel
Jason Affourtit
Fabian Grubert
... [+1 authors] ...,
Xueying Chen
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published October 8, 2008

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Laurie Gordon
Shan Yang
Mary Tran-Gyamfi
Dan Baggott
Mari Christensen
Aaron Hamilton Richard Crooijmans
... [+2 authors] ...,
Martien Groenen
Susan Lucas
Ivan Ovcharenko
Lisa Stubbs

First Published October 5, 2007

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

Nathan D. Trinklein
Ulaş Karaöz
Jiaqian Wu
Anason Halees
Shelley Force Aldred
Patrick J. Collins Deyou Zheng Zhengdong D. Zhang
... [+3 authors] ...,
Mark B. Gerstein
Michael Snyder
Richard M. Myers
Zhiping Weng

First Published June 13, 2007

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

Joel S. Rozowsky
Daniel Newburger
Fred Sayward
Jiaqian Wu
Greg Jordan
Jan O. Korbel Ugrappa Nagalakshmi Jin Yang Deyou Zheng Roderic Guigó Thomas R. Gingeras
... [+6 authors] ...,
Sherman Weissman
Perry Miller
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Zhengdong D. Zhang
Alberto Paccanaro
Yutao Fu
Sherman Weissman
Zhiping Weng
Joseph Chang
Michael Snyder
Mark B. Gerstein

First Published June 13, 2007

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Deyou Zheng
Adam Frankish
Robert Baertsch
Philipp Kapranov
Alexandre Reymond
Siew Woh Choo Yontao Lu France Denoeud Stylianos E. Antonarakis Michael Snyder Yijun Ruan Chia-Lin Wei
... [+7 authors] ...,
Thomas R. Gingeras
Roderic Guigó
Jennifer Harrow
Mark B. Gerstein

First Published June 13, 2007

Structured RNAs in the ENCODE selected regions of the human genome

Stefan Washietl
Jakob S. Pedersen
Jan O. Korbel
Claudia Stocsits
Andreas R. Gruber
Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Reiche Andrea Tanzer Catherine Ucla Carine Wyss Stylianos E. Antonarakis France Denoeud Julien Lagarde Jorg Drenkow Philipp Kapranov Thomas R. Gingeras Roderic Guigó Michael Snyder
... [+15 authors] ...,
Mark B. Gerstein
Alexandre Reymond
Ivo L. Hofacker
Peter F. Stadler

First Published June 13, 2007

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Ghia M. Euskirchen
Joel S. Rozowsky
Chia-Lin Wei
Wah Heng Lee
Zhengdong D. Zhang
Stephen Hartman Olof Emanuelsson Viktor Stolc
... [+3 authors] ...,
Sherman Weissman
Mark B. Gerstein
Yijun Ruan
Michael Snyder

First Published June 13, 2007

What is a gene, post-ENCODE? History and updated definition

Mark B. Gerstein
Can Bruce
Joel S. Rozowsky
Deyou Zheng
Jiang Du
Jan O. Korbel
... [+1 authors] ...,
Olof Emanuelsson
Zhengdong D. Zhang
Sherman Weissman
Michael Snyder

First Published June 13, 2007

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

Olof Emanuelsson
Ugrappa Nagalakshmi
Deyou Zheng
Joel S. Rozowsky
Alexander E. Urban
Jiang Du Zheng Lian
... [+2 authors] ...,
Viktor Stolc
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published November 21, 2006

A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors

Stuart Huntley
Daniel M. Baggott
Aaron T. Hamilton
Mary Tran-Gyamfi
Shan Yang
Joomyeong Kim
Laurie Gordon
Elbert Branscomb
Lisa Stubbs

First Published April 10, 2006

Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon

Anuj Kumar
Michael Seringhaus
Matthew C. Biery
Robert J. Sarnovsky
Lara Umansky
Stacy Piccirillo Matthew Heidtman Kei-Hoi Cheung
... [+3 authors] ...,
Craig J. Dobry
Mark B. Gerstein
Nancy L. Craig
Michael Snyder

First Published October 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

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Your search for returned 25 results

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Assessing and mitigating privacy risks of sparse, noisy genotypes by local alignment to haplotype databases

Dynamic RNA–protein interactions underlie the zebrafish maternal-to-zygotic transition

Pangolin genomes and the evolution of mammalian scales and immunity

Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data" > Prediction and characterization of noncoding RNAs in C. elegans by integrating conservation, secondary structure, and high-throughput sequencing and array data

Discovery of non-ETS gene fusions in human prostate cancer using next-generation RNA sequencing

Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two-base encoding

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

Integrated analysis of experimental data sets reveals many novel promoters in 1% of the human genome

The DART classification of unannotated transcription within the ENCODE regions: Associating transcription with known and novel loci

Statistical analysis of the genomic distribution and correlation of regulatory elements in the ENCODE regions

Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution

Structured RNAs in the ENCODE selected regions of the human genome

Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

What is a gene, post-ENCODE? History and updated definition

Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome

A comprehensive catalog of human KRAB-associated zinc finger genes: Insights into the evolutionary history of a large family of transcriptional repressors

Large-Scale Mutagenesis of the Yeast Genome Using a Tn7-Derived Multipurpose Transposon

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

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Your search for returned 25 results