Search | Genome Research

A limited set of transcriptional programs define major cell types

Alessandra Breschi
Manuel Muñoz-Aguirre
Valentin Wucher
Carrie A. Davis
Diego Garrido-Martín
Sarah Djebali Jesse Gillis Dmitri D. Pervouchine Anna Vlasova Alexander Dobin Chris Zaleski Jorg Drenkow Cassidy Danyko Alexandra Scavelli
... [+9 authors] ...,
Ferran Reverter
Michael P. Snyder
Thomas R. Gingeras
Roderic Guigó

First Published July 29, 2020

Dynamics of microRNA expression during mouse prenatal development

Sorena Rahmanian
Rabi Murad
Alessandra Breschi
Weihua Zeng
Mark Mackiewicz
Brian Williams Carrie A. Davis Brian Roberts Sarah Meadows Dianna Moore Diane Trout Chris Zaleski Alex Dobin Lei-Hoon Sei Jorg Drenkow Alex Scavelli Thomas R. Gingeras
... [+12 authors] ...,
Barbara J. Wold
Richard M. Myers
Roderic Guigó
Ali Mortazavi

First Published October 23, 2019

Alu elements suggests cell-type–specific enhancer function" > Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

Xiao-Ou Zhang
Thomas R. Gingeras
Zhiping Weng

First Published August 14, 2019

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

Felix Schlesinger
Andrew D. Smith
Thomas R. Gingeras
Gregory J. Hannon
Emily Hodges

First Published June 28, 2013

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

Chao Cheng
Roger Alexander
Renqiang Min
Jing Leng
Kevin Y. Yip
Joel Rozowsky Koon-Kiu Yan Xianjun Dong Sarah Djebali Yijun Ruan Carrie A. Davis Piero Carninci Timo Lassman Thomas R. Gingeras Roderic Guigó
... [+10 authors] ...,
Ewan Birney
Zhiping Weng
Michael Snyder
Mark Gerstein

First Published September 5, 2012

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

Thomas Derrien
Rory Johnson
Giovanni Bussotti
Andrea Tanzer
Sarah Djebali
Hagen Tilgner Gregory Guernec David Martin Angelika Merkel David G. Knowles Julien Lagarde Lavanya Veeravalli Xiaoan Ruan Yijun Ruan Timo Lassmann Piero Carninci James B. Brown Leonard Lipovich Jose M. Gonzalez Mark Thomas Carrie A. Davis Ramin Shiekhattar Thomas R. Gingeras
... [+18 authors] ...,
Tim J. Hubbard
Cedric Notredame
Jennifer Harrow
Roderic Guigó

First Published September 5, 2012

$Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs$

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

Hagen Tilgner
David G. Knowles
Rory Johnson
Carrie A. Davis
Sudipto Chakrabortty
Sarah Djebali
... [+1 authors] ...,
João Curado
Michael Snyder
Thomas R. Gingeras
Roderic Guigó

First Published September 5, 2012

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Philippe Batut
Alexander Dobin
Charles Plessy
Piero Carninci
Thomas R. Gingeras

First Published August 30, 2012

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent Earl
Keith Bradnam
John St. John
Aaron Darling
Dawei Lin
Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
... [+62 authors] ...,
Richard E. Green
David Haussler
Ian Korf
Benedict Paten

First Published September 16, 2011

Synthetic spike-in standards for RNA-seq experiments

Lichun Jiang
Felix Schlesinger
Carrie A. Davis
Yu Zhang
Renhua Li
Marc Salit
Thomas R. Gingeras
Brian Oliver

First Published August 4, 2011

Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines

Lucy Cherbas
Aarron Willingham
Dayu Zhang
Li Yang
Yi Zou
Brian D. Eads Joseph W. Carlson Jane M. Landolin Philipp Kapranov Jacqueline Dumais Anastasia Samsonova Jeong-Hyeon Choi Johnny Roberts Carrie A. Davis Haixu Tang Marijke J. van Baren Srinka Ghosh Alexander Dobin Kim Bell Wei Lin Laura Langton Michael O. Duff Aaron E. Tenney Chris Zaleski Michael R. Brent Roger A. Hoskins Thomas C. Kaufman Justen Andrews Brenton R. Graveley
... [+24 authors] ...,
Norbert Perrimon
Susan E. Celniker
Thomas R. Gingeras
Peter Cherbas

First Published December 22, 2010

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

David S. Johnson
Wei Li
D. Benjamin Gordon
Arindam Bhattacharjee
Bo Curry
Jayati Ghosh Leonardo Brizuela Jason S. Carroll Myles Brown Paul Flicek Christoph M. Koch Ian Dunham Mark Bieda Xiaoqin Xu Peggy J. Farnham Philipp Kapranov David A. Nix Thomas R. Gingeras Xinmin Zhang Heather Holster Nan Jiang Roland D. Green Jun S. Song Scott A. McCuine Elizabeth Anton Loan Nguyen Nathan D. Trinklein Zhen Ye Keith Ching David Hawkins Bing Ren Peter C. Scacheri Joel Rozowsky Alexander Karpikov Ghia Euskirchen Sherman Weissman Mark Gerstein Michael Snyder Annie Yang Zarmik Moqtaderi Heather Hirsch Hennady P. Shulha Yutao Fu Zhiping Weng
... [+39 authors] ...,
Kevin Struhl
Richard M. Myers
Jason D. Lieb
X. Shirley Liu

First Published February 7, 2008

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

Alvaro Rada-Iglesias
Adam Ameur
Philipp Kapranov
Stefan Enroth
Jan Komorowski
Thomas R. Gingeras
Claes Wadelius

First Published January 29, 2008

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

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions

France Denoeud
Philipp Kapranov
Catherine Ucla
Adam Frankish
Robert Castelo
Jorg Drenkow Julien Lagarde Tyler Alioto Caroline Manzano Jacqueline Chrast Sujit Dike Carine Wyss Charlotte N. Henrichsen Nancy Holroyd Mark C. Dickson Ruth Taylor Zahra Hance Sylvain Foissac Richard M. Myers Jane Rogers Tim Hubbard Jennifer Harrow
... [+17 authors] ...,
Roderic Guigó
Thomas R. Gingeras
Stylianos E. Antonarakis
Alexandre Reymond

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

Origin of phenotypes: Genes and transcripts

Thomas R. Gingeras

First Published June 13, 2007

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

Philipp Kapranov
Jorg Drenkow
Jill Cheng
Jeffrey Long
Gregg Helt
Sujit Dike
Thomas R. Gingeras

First Published July 5, 2005

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Dione Kampa
Jill Cheng
Philipp Kapranov
Mark Yamanaka
Shane Brubaker
Simon Cawley Jorg Drenkow Antonio Piccolboni
... [+3 authors] ...,
Stefan Bekiranov
Gregg Helt
Hari Tammana
Thomas R. Gingeras

First Published March 1, 2004

Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation

Shoulian Dong
Eugene Wang
Linda Hsie
Yanxiang Cao
Xiaogiong Chen
Thomas R. Gingeras

First Published July 12, 2001

Mycobacterium tuberculosis " > Comparing Genomes within the Species Mycobacterium tuberculosis

Midori Kato-Maeda
Jeanne T. Rhee
Thomas R. Gingeras
Hugh Salamon
Jorg Drenkow
Nat Smittipat
Peter M. Small

First Published April 1, 2001

Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data

Hugh Salamon
Midori Kato-Maeda
Peter M. Small
Jorg Drenkow
Thomas R. Gingeras

First Published November 21, 2000

Mycobacterium DNA Arrays" > Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays

Thomas R. Gingeras
Ghassan Ghandour
Eugene Wang
Anthony Berno
Peter M. Small
Francis Drobniewski
... [+1 authors] ...,
David Alland
Edward Desmond
Mark Holodniy
Jorg Drenkow

First Published May 1, 1998

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Your search for returned 24 results

A limited set of transcriptional programs define major cell types

Dynamics of microRNA expression during mouse prenatal development

Alu elements suggests cell-type–specific enhancer function" > Genome-wide analysis of polymerase III–transcribed Alu elements suggests cell-type–specific enhancer function

De novo DNA demethylation and noncoding transcription define active intergenic regulatory elements

Understanding transcriptional regulation by integrative analysis of transcription factor binding data

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs

High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Synthetic spike-in standards for RNA-seq experiments

Drosophila cell lines" > The transcriptional diversity of 25 Drosophila cell lines

Systematic evaluation of variability in ChIP-chip experiments using predefined DNA targets

Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders

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

Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in 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

Origin of phenotypes: Genes and transcripts

Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays

Novel RNAs Identified From an In-Depth Analysis of the Transcriptome of Human Chromosomes 21 and 22

Flexible Use of High-Density Oligonucleotide Arrays for Single-Nucleotide Polymorphism Discovery and Validation

Mycobacterium tuberculosis " > Comparing Genomes within the Species Mycobacterium tuberculosis

Detection of Deleted Genomic DNA Using a Semiautomated Computational Analysis of GeneChip Data

Mycobacterium DNA Arrays" > Simultaneous Genotyping and Species Identification Using Hybridization Pattern Recognition Analysis of Generic Mycobacterium DNA Arrays

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Your search for returned 24 results