Search | Genome Research

Resource

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

Method

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

Research

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

Research

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

Research

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

Method

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

Research

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

Method

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

LETTER

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

LETTER

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

LETTER

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

Methods

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

ARTICLE

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

ARTICLE

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

PERSPECTIVE

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

LETTER

Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana" > Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Takeshi Itoh
Tsuyoshi Tanaka
Roberto A. Barrero
Chisato Yamasaki
Yasuyuki Fujii
Phillip B. Hilton Baltazar A. Antonio Hideo Aono Rolf Apweiler Richard Bruskiewich Thomas Bureau Frances Burr Antonio Costa de Oliveira Galina Fuks Takuya Habara Georg Haberer Bin Han Erimi Harada Aiko T. Hiraki Hirohiko Hirochika Douglas Hoen Hiroki Hokari Satomi Hosokawa Yue Hsing Hiroshi Ikawa Kazuho Ikeo Tadashi Imanishi Yukiyo Ito Pankaj Jaiswal Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Hiroaki Kawashima Jitendra P. Khurana Shoshi Kikuchi Setsuko Komatsu Kanako O. Koyanagi Hiromi Kubooka Damien Lieberherr Yao-Cheng Lin David Lonsdale Takashi Matsumoto Akihiro Matsuya W. Richard McCombie Joachim Messing Akio Miyao Nicola Mulder Yoshiaki Nagamura Jongmin Nam Nobukazu Namiki Hisataka Numa Shin Nurimoto Claire O’Donovan Hajime Ohyanagi Toshihisa Okido Satoshi OOta Naoki Osato Lance E. Palmer Francis Quetier Saurabh Raghuvanshi Naomi Saichi Hiroaki Sakai Yasumichi Sakai Katsumi Sakata Tetsuya Sakurai Fumihiko Sato Yoshiharu Sato Heiko Schoof Motoaki Seki Michie Shibata Yuji Shimizu Kazuo Shinozaki Yuji Shinso Nagendra K. Singh Brian Smith-White Jun-ichi Takeda Motohiko Tanino Tatiana Tatusova Supat Thongjuea Fusano Todokoro Mika Tsugane Akhilesh K. Tyagi Apichart Vanavichit Aihui Wang Rod A. Wing Kaori Yamaguchi Mayu Yamamoto Naoyuki Yamamoto Yeisoo Yu Hao Zhang Qiang Zhao
... [+86 authors] ...,
Kenichi Higo
Benjamin Burr
Takashi Gojobori
Takuji Sasaki