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

Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes

Iris Zhu
David Landsman

First Published October 26, 2023

Mediator dynamics during heat shock in budding yeast

Debasish Sarkar
Z. Iris Zhu
Elizabeth R. Knoll
Emily Paul
David Landsman
Randall H. Morse

First Published November 16, 2021

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

Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers

Tao Deng
Z. Iris Zhu
Shaofei Zhang
Yuri Postnikov
Di Huang
Marion Horsch Takashi Furusawa Johannes Beckers Jan Rozman Martin Klingenspor Oana Amarie Jochen Graw Birgit Rathkolb Eckhard Wolf Thure Adler Dirk H. Busch Valérie Gailus-Durner Helmut Fuchs Martin Hrabě de Angelis Arjan van der Velde
... [+15 authors] ...,
Lino Tessarollo
Ivan Ovcherenko
David Landsman
Michael Bustin

First Published July 8, 2015

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

Weishi Yu
Carl McIntosh
Ryan Lister
Iris Zhu
Yixing Han
Jianke Ren David Landsman Eunice Lee Victorino Briones
... [+4 authors] ...,
Minoru Terashima
Robert Leighty
Joseph R. Ecker
Kathrin Muegge

First Published August 28, 2014

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

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

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

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

Retroposed Copies of the HMG Genes: A Window to Genome Dynamics

Liora Z. Strichman-Almashanu
Michael Bustin
David Landsman

First Published May 1, 2003

Drosophila Genome: Evaluation of Potential Dimerization Partners" > B-ZIP Proteins Encoded by the Drosophila Genome: Evaluation of Potential Dimerization Partners

Jan Fassler
David Landsman
Asha Acharya
Jonathan R. Moll
Maria Bonovich
Charles Vinson

First Published August 1, 2002

Saccharomyces cerevisiae " > Candidate Regulatory Sequence Elements for Cell Cycle-Dependent Transcription in Saccharomyces cerevisiae

Tyra G. Wolfsberg
Andrei E. Gabrielian
Michael J. Campbell
Raymond J. Cho
John L. Spouge
David Landsman

First Published August 1, 1999

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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

Clustered and diverse transcription factor binding underlies cell type specificity of enhancers for housekeeping genes

Mediator dynamics during heat shock in budding yeast

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

Pangolin genomes and the evolution of mammalian scales and immunity

Functional compensation among HMGN variants modulates the DNase I hypersensitive sites at enhancers

Genome-wide DNA methylation patterns in LSH mutant reveals de-repression of repeat elements and redundant epigenetic silencing pathways

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

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

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

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

Retroposed Copies of the HMG Genes: A Window to Genome Dynamics

Drosophila Genome: Evaluation of Potential Dimerization Partners" > B-ZIP Proteins Encoded by the Drosophila Genome: Evaluation of Potential Dimerization Partners

Saccharomyces cerevisiae " > Candidate Regulatory Sequence Elements for Cell Cycle-Dependent Transcription in Saccharomyces cerevisiae

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Your search for returned 25 results