Search | Genome Research

C. Thomas Caskey (1938–2022)

Richard A. Gibbs
Aravinda Chakravarti
Evan E. Eichler
Eric D. Green
Richard M. Myers
Anne C. Ferguson-Smith
Kateryna D. Makova
Hillary E. Sussman

First Published February 17, 2022

Deborah A. Nickerson (1954 –2021)

Aravinda Chakravarti
Evan E. Eichler
Richard A. Gibbs
Eric D. Green
Richard M. Myers
Hillary E. Sussman

First Published January 24, 2022

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

Jennifer F. Hughes
Helen Skaletsky
Tatyana Pyntikova
Natalia Koutseva
Terje Raudsepp
Laura G. Brown Daniel W. Bellott Ting-Jan Cho Shannon Dugan-Rocha Ziad Khan Colin Kremitzki Catrina Fronick Tina A. Graves-Lindsay Lucinda Fulton Wesley C. Warren Richard K. Wilson Elaine Owens James E. Womack William J. Murphy Donna M. Muzny
... [+15 authors] ...,
Kim C. Worley
Bhanu P. Chowdhary
Richard A. Gibbs
David C. Page

First Published November 18, 2020

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

Xian Fan
Mark Chaisson
Luay Nakhleh
Ken Chen

First Published January 19, 2017

Macaca mulatta) based on whole-genome sequences" > The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences

Cheng Xue
Muthuswamy Raveendran
R. Alan Harris
Gloria L. Fawcett
Xiaoming Liu
Simon White Mahmoud Dahdouli David Rio Deiros Jennifer E. Below William Salerno Laura Cox Guoping Fan Betsy Ferguson Julie Horvath Zach Johnson Sree Kanthaswamy H. Michael Kubisch Dahai Liu Michael Platt David G. Smith Binghua Sun Eric J. Vallender Feng Wang Roger W. Wiseman Rui Chen
... [+20 authors] ...,
Donna M. Muzny
Richard A. Gibbs
Fuli Yu
Jeffrey Rogers

First Published October 17, 2016

Postmortem genetic screening for the identification, verification, and reporting of genetic variants contributing to the sudden death of the young

D. Nicole R. Methner
Steven E. Scherer
Katherine Welch
Magdalena Walkiewicz
Christine M. Eng
John W. Belmont Mark C. Powell Viktoriya Korchina Harsha Vardhan Doddapaneni Donna M. Muzny
... [+5 authors] ...,
Richard A. Gibbs
Dwayne A. Wolf
Luis A. Sanchez
Roger Kahn

First Published July 19, 2016

The ethics of conducting molecular autopsies in cases of sudden death in the young

Amy L. McGuire
Quianta Moore
Mary Majumder
Magdalena Walkiewicz
Christine M. Eng
John W. Belmont Salma Nassef Sandra Darilek Katie Rutherford Stacey Pereira Steven E. Scherer V. Reid Sutton
... [+7 authors] ...,
Dwayne Wolf
Richard A. Gibbs
Roger Kahn
Luis A. Sanchez

First Published July 13, 2016

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

Eve Shinbrot
Erin E. Henninger
Nils Weinhold
Kyle R. Covington
A. Yasemin Göksenin
Nikolaus Schultz Hsu Chao HarshaVardhan Doddapaneni Donna M. Muzny
... [+4 authors] ...,
Richard A. Gibbs
Chris Sander
Zachary F. Pursell
David A. Wheeler

First Published September 16, 2014

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Zhen-Xia Chen
David Sturgill
Jiaxin Qu
Huaiyang Jiang
Soo Park
Nathan Boley Ana Maria Suzuki Anthony R. Fletcher David C. Plachetzki Peter C. FitzGerald Carlo G. Artieri Joel Atallah Olga Barmina James B. Brown Kerstin P. Blankenburg Emily Clough Abhijit Dasgupta Sai Gubbala Yi Han Joy C. Jayaseelan Divya Kalra Yoo-Ah Kim Christie L. Kovar Sandra L. Lee Mingmei Li James D. Malley John H. Malone Tittu Mathew Nicolas R. Mattiuzzo Mala Munidasa Donna M. Muzny Fiona Ongeri Lora Perales Teresa M. Przytycka Ling-Ling Pu Garrett Robinson Rebecca L. Thornton Nehad Saada Steven E. Scherer Harold E. Smith Charles Vinson Crystal B. Warner Kim C. Worley Yuan-Qing Wu Xiaoyan Zou Peter Cherbas Manolis Kellis Michael B. Eisen Fabio Piano Karin Kionte David H. Fitch Paul W. Sternberg Asher D. Cutter Michael O. Duff Roger A. Hoskins Brenton R. Graveley Richard A. Gibbs Peter J. Bickel Artyom Kopp
... [+54 authors] ...,
Piero Carninci
Susan E. Celniker
Brian Oliver
Stephen Richards

First Published July 1, 2014

Drosophila melanogaster Genetic Reference Panel lines" > Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Wen Huang
Andreas Massouras
Yutaka Inoue
Jason Peiffer
Miquel Ràmia
Aaron M. Tarone Lavanya Turlapati Thomas Zichner Dianhui Zhu Richard F. Lyman Michael M. Magwire Kerstin Blankenburg Mary Anna Carbone Kyle Chang Lisa L. Ellis Sonia Fernandez Yi Han Gareth Highnam Carl E. Hjelmen John R. Jack Mehwish Javaid Joy Jayaseelan Divya Kalra Sandy Lee Lora Lewis Mala Munidasa Fiona Ongeri Shohba Patel Lora Perales Agapito Perez LingLing Pu Stephanie M. Rollmann Robert Ruth Nehad Saada Crystal Warner Aneisa Williams Yuan-Qing Wu Akihiko Yamamoto Yiqing Zhang Yiming Zhu Robert R.H. Anholt Jan O. Korbel David Mittelman Donna M. Muzny Richard A. Gibbs Antonio Barbadilla J. Spencer Johnston
... [+42 authors] ...,
Eric A. Stone
Stephen Richards
Bart Deplancke
Trudy F.C. Mackay

First Published April 8, 2014

Reconstructing complex regions of genomes using long-read sequencing technology

John Huddleston
Swati Ranade
Maika Malig
Francesca Antonacci
Mark Chaisson
Lawrence Hon Peter H. Sudmant Tina A. Graves Can Alkan Megan Y. Dennis
... [+5 authors] ...,
Richard K. Wilson
Stephen W. Turner
Jonas Korlach
Evan E. Eichler

First Published January 13, 2014

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

Yi Wang
James Lu
Jin Yu
Richard A. Gibbs
Fuli Yu

First Published January 7, 2013

Strongylocentrotus purpuratus based on transcriptome analysis" > Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

Qiang Tu
R. Andrew Cameron
Kim C. Worley
Richard A. Gibbs
Eric H. Davidson

First Published June 18, 2012

A SNP discovery method to assess variant allele probability from next-generation resequencing data

Yufeng Shen
Zhengzheng Wan
Cristian Coarfa
Rafal Drabek
Lei Chen
Elizabeth A. Ostrowski Yue Liu
... [+2 authors] ...,
George M. Weinstock
David A. Wheeler
Richard A. Gibbs
Fuli Yu

First Published December 17, 2009

The completion of the Mammalian Gene Collection (MGC)

Gary Temple
Daniela S. Gerhard
Rebekah Rasooly
Elise A. Feingold
Peter J. Good
Cristen Robinson Allison Mandich Jeffrey G. Derge Jeanne Lewis Debonny Shoaf Francis S. Collins Wonhee Jang Lukas Wagner Carolyn M. Shenmen Leonie Misquitta Carl F. Schaefer Kenneth H. Buetow Tom I. Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L. Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D. Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L.G. Comstock Michael Stevens Chaochun Wei Marijke J. van Baren Kourosh Salehi-Ashtiani Ryan R. Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E. Gruber Mark R. Smith John McPherson Angela M. Garcia Preethi H. Gunaratne Jiaqian Wu Donna Muzny Richard A. Gibbs Alice C. Young Gerard G. Bouffard Robert W. Blakesley Jim Mullikin Eric D. Green Mark C. Dickson Alex C. Rodriguez Jane Grimwood Jeremy Schmutz Richard M. Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A. Moore Michael Mayo Sarah Munro Susan Wagner Steven J.M. Jones Robert A. Holt Marco A. Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C. Pulido Keith Robison Dominic Esposito James Hartley
... [+118 authors] ...,
Vanessa E. Wall
Ralph F. Hopkins
Osamu Ohara
Stefan Wiemann

First Published September 18, 2009

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

Oliver A. Hampton
Petra Den Hollander
Christopher A. Miller
David A. Delgado
Jian Li
Cristian Coarfa Ronald A. Harris Stephen Richards Steven E. Scherer
... [+4 authors] ...,
Donna M. Muzny
Richard A. Gibbs
Adrian V. Lee
Aleksandar Milosavljevic

First Published December 3, 2008

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes

Jeffrey G. Reid
Ankur K. Nagaraja
Francis C. Lynn
Rafal B. Drabek
Donna M. Muzny
Chad A. Shaw Michelle K. Weiss Arash O. Naghavi Mahjabeen Khan Huifeng Zhu Jayantha Tennakoon Gemunu H. Gunaratne David B. Corry Jonathan Miller Michael T. McManus
... [+10 authors] ...,
Michael S. German
Richard A. Gibbs
Martin M. Matzuk
Preethi H. Gunaratne

First Published July 9, 2008

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Webb Miller
Kate Rosenbloom
Ross C. Hardison
Minmei Hou
James Taylor
Brian Raney Richard Burhans David C. King Robert Baertsch Daniel Blankenberg Sergei L. Kosakovsky Pond Anton Nekrutenko Belinda Giardine Robert S. Harris Svitlana Tyekucheva Mark Diekhans Thomas H. Pringle William J. Murphy Arthur Lesk George M. Weinstock Kerstin Lindblad-Toh Richard A. Gibbs
... [+17 authors] ...,
Eric S. Lander
Adam Siepel
David Haussler
W. James Kent

First Published November 5, 2007

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Elliott H. Margulies
Gregory M. Cooper
George Asimenos
Daryl J. Thomas
Colin N. Dewey
Adam Siepel Ewan Birney Damian Keefe Ariel S. Schwartz Minmei Hou James Taylor Sergey Nikolaev Juan I. Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham James B. Brown Peter Bickel Ian Holmes James C. Mullikin Abel Ureta-Vidal Benedict Paten Eric A. Stone Kate R. Rosenbloom W. James Kent Gerard G. Bouffard Xiaobin Guan Nancy F. Hansen Jacquelyn R. Idol Valerie V.B. Maduro Baishali Maskeri Jennifer C. McDowell Morgan Park Pamela J. Thomas Alice C. Young Robert W. Blakesley Donna M. Muzny Erica Sodergren David A. Wheeler Kim C. Worley Huaiyang Jiang George M. Weinstock Richard A. Gibbs Tina Graves Robert Fulton Elaine R. Mardis Richard K. Wilson Michele Clamp James Cuff Sante Gnerre David B. Jaffe Jean L. Chang Kerstin Lindblad-Toh Eric S. Lander Angie Hinrichs Heather Trumbower Hiram Clawson Ann Zweig Robert M. Kuhn Galt Barber Rachel Harte Donna Karolchik Matthew A. Field Richard A. Moore Carrie A. Matthewson Jacqueline E. Schein Marco A. Marra Stylianos E. Antonarakis Serafim Batzoglou Nick Goldman Ross Hardison David Haussler
... [+68 authors] ...,
Webb Miller
Lior Pachter
Eric D. Green
Arend Sidow

First Published June 13, 2007

Community annotation: Procedures, protocols, and supporting tools

Christine G. Elsik
Kim C. Worley
Lan Zhang
Natalia V. Milshina
Huaiyang Jiang
Justin T. Reese Kevin L. Childs
... [+2 authors] ...,
Anand Venkatraman
C. Michael Dickens
George M. Weinstock
Richard A. Gibbs

First Published October 25, 2006

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects

Joël Savard
Diethard Tautz
Stephen Richards
George M. Weinstock
Richard A. Gibbs
John H. Werren
Hervé Tettelin
Martin J. Lercher

First Published October 25, 2006

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Adam Siepel
Gill Bejerano
Jakob S. Pedersen
Angie S. Hinrichs
Minmei Hou
Kate Rosenbloom Hiram Clawson John Spieth LaDeana W. Hillier Stephen Richards George M. Weinstock Richard K. Wilson
... [+7 authors] ...,
Richard A. Gibbs
W. James Kent
Webb Miller
David Haussler

First Published July 15, 2005

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay

Paul Hardenbol
Fuli Yu
John Belmont
Jennifer MacKenzie
Carsten Bruckner
Tiffany Brundage Andrew Boudreau Steve Chow Jim Eberle Ayca Erbilgin Mat Falkowski Ron Fitzgerald Sy Ghose Oleg Iartchouk Maneesh Jain George Karlin-Neumann Xiuhua Lu Xin Miao Bridget Moore Martin Moorhead Eugeni Namsaraev Shiran Pasternak Eunice Prakash Karen Tran Zhiyong Wang
... [+20 authors] ...,
Hywel B. Jones
Ronald W. Davis
Thomas D. Willis
Richard A. Gibbs

First Published February 1, 2005

Pooled genomic indexing of rhesus macaque

Aleksandar Milosavljevic
Ronald A. Harris
Erica J. Sodergren
Andrew R. Jackson
Ken J. Kalafus
Anne Hodgson Andrew Cree Weilie Dai Miklos Csuros
... [+4 authors] ...,
Baoli Zhu
Pieter J. de Jong
George M. Weinstock
Richard A. Gibbs

First Published February 1, 2005

Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution" > Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

Stephen Richards
Yue Liu
Brian R. Bettencourt
Pavel Hradecky
Stan Letovsky
Rasmus Nielsen Kevin Thornton Melissa J. Hubisz Rui Chen Richard P. Meisel Olivier Couronne Sujun Hua Mark A. Smith Peili Zhang Jing Liu Harmen J. Bussemaker Marinus F. van Batenburg Sally L. Howells Steven E. Scherer Erica Sodergren Beverly B. Matthews Madeline A. Crosby Andrew J. Schroeder Daniel Ortiz-Barrientos Catharine M. Rives Michael L. Metzker Donna M. Muzny Graham Scott David Steffen David A. Wheeler Kim C. Worley Paul Havlak K. James Durbin Amy Egan Rachel Gill Jennifer Hume Margaret B. Morgan George Miner Cerissa Hamilton Yanmei Huang Lenée Waldron Daniel Verduzco Kerstin P. Clerc-Blankenburg Inna Dubchak Mohamed A.F. Noor Wyatt Anderson Kevin P. White Andrew G. Clark
... [+43 authors] ...,
Stephen W. Schaeffer
William Gelbart
George M. Weinstock
Richard A. Gibbs

First Published January 3, 2005

The Atlas Genome Assembly System

Paul Havlak
Rui Chen
K. James Durbin
Amy Egan
Yanru Ren
Xing-Zhi Song
George M. Weinstock
Richard A. Gibbs

First Published April 1, 2004

Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome

Zhengdong Zhang
Paula E. Burch
Austin J. Cooney
Rainer B. Lanz
Fred A. Pereira
Jiaqian Wu
Richard A. Gibbs
George Weinstock
David A. Wheeler

First Published April 1, 2004

Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing

Jia Qian Wu
David Shteynberg
Manimozhiyan Arumugam
Richard A. Gibbs
Michael R. Brent

First Published April 1, 2004

Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project

Rui Chen
Erica Sodergren
George M. Weinstock
Richard A. Gibbs

First Published April 1, 2004

Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome

Rui Chen
John B. Bouck
George M. Weinstock
Richard A. Gibbs

First Published November 1, 2001

A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes

Wei-Wen Cai
Rui Chen
Richard A. Gibbs
Allan Bradley

First Published October 1, 2001

Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies

John Bouck
Webb Miller
James H. Gorrell
Donna Muzny
Richard A. Gibbs

First Published October 1, 1998

Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6

M. Ali Ansari-Lari
John C. Oeltjen
Scott Schwartz
Zheng Zhang
Donna M. Muzny
Jing Lu James H. Gorrell
... [+2 authors] ...,
A. Craig Chinault
John W. Belmont
Webb Miller
Richard A. Gibbs

First Published January 1, 1998

SNRPN Promoter: In Vitro Methylation Abolishes Promoter Activity" > Sequencing and Functional Analysis of the SNRPN Promoter: In Vitro Methylation Abolishes Promoter Activity

A.H.M. Mahbubul Huq
James S. Sutcliffe
Mitsuyoshi Nakao
Ying Shen
Richard A. Gibbs
Arthur L. Beaudet

First Published June 1, 1997

Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains

John C. Oeltjen
Tracy M. Malley
Donna M. Muzny
Webb Miller
Richard A. Gibbs
John W. Belmont

First Published April 1, 1997

Large-Scale Concatenation cDNA Sequencing

Wei Yu
Björn Andersson
Kim C. Worley
Donna M. Muzny
Yan Ding
Wen Liu
... [+1 authors] ...,
Jennifer Y. Ricafrente
Meredith A. Wentland
Greg Lennon
Richard A. Gibbs

First Published April 1, 1997

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Your search for returned 36 results

C. Thomas Caskey (1938–2022)

Deborah A. Nickerson (1954 –2021)

Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages" > Sequence analysis in Bos taurus reveals pervasiveness of X–Y arms races in mammalian lineages

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

Macaca mulatta) based on whole-genome sequences" > The population genomics of rhesus macaques (Macaca mulatta) based on whole-genome sequences

Postmortem genetic screening for the identification, verification, and reporting of genetic variants contributing to the sudden death of the young

The ethics of conducting molecular autopsies in cases of sudden death in the young

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

D. melanogaster modENCODE transcriptome annotation" > Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Drosophila melanogaster Genetic Reference Panel lines" > Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

Reconstructing complex regions of genomes using long-read sequencing technology

An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data

Strongylocentrotus purpuratus based on transcriptome analysis" > Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

A SNP discovery method to assess variant allele probability from next-generation resequencing data

The completion of the Mammalian Gene Collection (MGC)

A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes

28-Way vertebrate alignment and conservation track in the UCSC Genome Browser

Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome

Community annotation: Procedures, protocols, and supporting tools

Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

Highly multiplexed molecular inversion probe genotyping: Over 10,000 targeted SNPs genotyped in a single tube assay

Pooled genomic indexing of rhesus macaque

Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution" > Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution

The Atlas Genome Assembly System

Genomic Analysis of the Nuclear Receptor Family: New Insights Into Structure, Regulation, and Evolution From the Rat Genome

Identification of Rat Genes by TWINSCAN Gene Prediction, RT–PCR, and Direct Sequencing

Dynamic Building of a BAC Clone Tiling Path for the Rat Genome Sequencing Project

Comparing Vertebrate Whole-Genome Shotgun Reads to the Human Genome

A Clone-Array Pooled Shotgun Strategy for Sequencing Large Genomes

Analysis of the Quality and Utility of Random Shotgun Sequencing at Low Redundancies

Comparative Sequence Analysis of a Gene-Rich Cluster at Human Chromosome 12p13 and its Syntenic Region in Mouse Chromosome 6

SNRPN Promoter: In Vitro Methylation Abolishes Promoter Activity" > Sequencing and Functional Analysis of the SNRPN Promoter: In Vitro Methylation Abolishes Promoter Activity

Large-Scale Comparative Sequence Analysis of the Human and Murine Bruton’s Tyrosine Kinase Loci Reveals Conserved Regulatory Domains

Large-Scale Concatenation cDNA Sequencing

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Your search for returned 36 results