Search | Genome Research

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

Aitor Serres-Armero
Brian W. Davis
Inna S. Povolotskaya
Carlos Morcillo-Suarez
Jocelyn Plassais
David Juan
Elaine A. Ostrander
Tomas Marques-Bonet

First Published April 16, 2021

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

A comparison of gene expression and DNA methylation patterns across tissues and species

Lauren E. Blake
Julien Roux
Irene Hernando-Herraez
Nicholas E. Banovich
Raquel Garcia Perez
Chiaowen Joyce Hsiao
... [+1 authors] ...,
Ittai Eres
Claudia Cuevas
Tomas Marques-Bonet
Yoav Gilad

First Published January 17, 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

Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Mario Ventura
Claudia R. Catacchio
Saba Sajjadian
Laura Vives
Peter H. Sudmant
Tomas Marques-Bonet
Tina A. Graves
Richard K. Wilson
Evan E. Eichler

First Published September 1, 2017

Worldwide patterns of genomic variation and admixture in gray wolves

Zhenxin Fan
Pedro Silva
Ilan Gronau
Shuoguo Wang
Aitor Serres Armero
Rena M. Schweizer Oscar Ramirez John Pollinger Marco Galaverni Diego Ortega Del-Vecchyo Lianming Du Wenping Zhang Zhihe Zhang Jinchuan Xing Carles Vilà
... [+10 authors] ...,
Tomas Marques-Bonet
Raquel Godinho
Bisong Yue
Robert K. Wayne

First Published December 17, 2015

Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)

Wesley C. Warren
Anna J. Jasinska
Raquel García-Pérez
Hannes Svardal
Chad Tomlinson
Mariano Rocchi Nicoletta Archidiacono Oronzo Capozzi Patrick Minx Michael J. Montague Kim Kyung LaDeana W. Hillier Milinn Kremitzki Tina Graves Colby Chiang Jennifer Hughes Nam Tran Yu Huang Vasily Ramensky Oi-wa Choi Yoon J. Jung Christopher A. Schmitt Nikoleta Juretic Jessica Wasserscheid Trudy R. Turner Roger W. Wiseman Jennifer J. Tuscher Julie A. Karl Jörn E. Schmitz Roland Zahn David H. O'Connor Eugene Redmond Alex Nisbett Béatrice Jacquelin Michaela C. Müller-Trutwin Jason M. Brenchley Michel Dione Martin Antonio Gary P. Schroth Jay R. Kaplan Matthew J. Jorgensen Gregg W.C. Thomas Matthew W. Hahn Brian J. Raney Bronwen Aken Rishi Nag Juergen Schmitz Gennady Churakov Angela Noll Roscoe Stanyon David Webb Francoise Thibaud-Nissen Magnus Nordborg Tomas Marques-Bonet
... [+49 authors] ...,
Ken Dewar
George M. Weinstock
Richard K. Wilson
Nelson B. Freimer

First Published September 16, 2015

DNA methylation contributes to natural human variation

Holger Heyn
Sebastian Moran
Irene Hernando-Herraez
Sergi Sayols
Antonio Gomez
Juan Sandoval Dave Monk
... [+2 authors] ...,
Kenichiro Hata
Tomas Marques-Bonet
Liewei Wang
Manel Esteller

First Published August 1, 2013

Evolution and diversity of copy number variation in the great ape lineage

Peter H. Sudmant
John Huddleston
Claudia R. Catacchio
Maika Malig
LaDeana W. Hillier
Carl Baker Kiana Mohajeri Ivanela Kondova Ronald E. Bontrop Stephan Persengiev Francesca Antonacci
... [+6 authors] ...,
Mario Ventura
Javier Prado-Martinez
Tomas Marques-Bonet
Evan E. Eichler

First Published July 3, 2013

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

LRRC37 gene family" > Evolutionary dynamism of the primate LRRC37 gene family

Giuliana Giannuzzi
Priscillia Siswara
Maika Malig
Tomas Marques-Bonet
James C. Mullikin
Mario Ventura
Evan E. Eichler

First Published October 11, 2012

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

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Mario Ventura
Claudia R. Catacchio
Saba Sajjadian
Laura Vives
Peter H. Sudmant
Tomas Marques-Bonet
Tina A. Graves
Richard K. Wilson
Evan E. Eichler

First Published March 14, 2012

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

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Mario Ventura
Claudia R. Catacchio
Can Alkan
Tomas Marques-Bonet
Saba Sajjadian
Tina A. Graves Fereydoun Hormozdiari Arcadi Navarro Maika Malig Carl Baker Choli Lee Emily H. Turner Lin Chen Jeffrey M. Kidd
... [+9 authors] ...,
Nicoletta Archidiacono
Jay Shendure
Richard K. Wilson
Evan E. Eichler

First Published June 17, 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

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Santhosh Girirajan
Lin Chen
Tina Graves
Tomas Marques-Bonet
Mario Ventura
Catrina Fronick Lucinda Fulton Mariano Rocchi
... [+3 authors] ...,
Robert S. Fulton
Richard K. Wilson
Elaine R. Mardis
Evan E. Eichler

First Published November 24, 2008

Copy number variation and evolution in humans and chimpanzees

George H. Perry
Fengtang Yang
Tomas Marques-Bonet
Carly Murphy
Tomas Fitzgerald
Arthur S. Lee Courtney Hyland Anne C. Stone Matthew E. Hurles Chris Tyler-Smith
... [+5 authors] ...,
Evan E. Eichler
Nigel P. Carter
Charles Lee
Richard Redon

First Published September 4, 2008

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 35 results

Copy number variation underlies complex phenotypes in domestic dog breeds and other canids

A limited set of transcriptional programs define major cell types

A comparison of gene expression and DNA methylation patterns across tissues and species

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

Corrigendum: The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Worldwide patterns of genomic variation and admixture in gray wolves

Chlorocebus aethiops sabaeus)" > The genome of the vervet (Chlorocebus aethiops sabaeus)

DNA methylation contributes to natural human variation

Evolution and diversity of copy number variation in the great ape lineage

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

LRRC37 gene family" > Evolutionary dynamism of the primate LRRC37 gene family

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

The evolution of African great ape subtelomeric heterochromatin and the fusion of human chromosome 2

Synthetic spike-in standards for RNA-seq experiments

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

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

Sequencing human–gibbon breakpoints of synteny reveals mosaic new insertions at rearrangement sites

Copy number variation and evolution in humans and chimpanzees

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 35 results