Search | Genome Research

In memoriam

Jim Watson (1928–2025): a genomics visionary

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

First Published July 23, 2026

In memoriam

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

In memoriam

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

Method

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

Fan Zhang
Matthew Flickinger
Sarah A. Gagliano Taliun
Gonçalo R. Abecasis
Laura J. Scott
Steven A. McCaroll
Carlos N. Pato
Michael Boehnke
Hyun Min Kang

First Published January 24, 2020

Method

An efficient and scalable analysis framework for variant extraction and refinement from population-scale DNA sequence data

Goo Jun
Mary Kate Wing
Gonçalo R. Abecasis
Hyun Min Kang

First Published April 16, 2015

Research

The influence of genomic context on mutation patterns in the human genome inferred from rare variants

Valerie M. Schaibley
Matthew Zawistowski
Daniel Wegmann
Margaret G. Ehm
Matthew R. Nelson
Pamela L. St. Jean
... [+1 authors] ...,
Gonçalo R. Abecasis
John Novembre
Sebastian Zöllner
Jun Z. Li

First Published August 29, 2013

Method

Genotype calling and haplotyping in parent-offspring trios

Wei Chen
Bingshan Li
Zhen Zeng
Serena Sanna
Carlo Sidore
Fabio Busonero
Hyun Min Kang
Yun Li
Gonçalo R. Abecasis

First Published October 11, 2012

Research

Comparative analysis of the primate X-inactivation center region and reconstruction of the ancestral primate XIST locus

Julie E. Horvath
Christina B. Sheedy
Stephanie L. Merrett
Abdoulaye Banire Diallo
David L. Swofford
NISC Comparative Sequencing Program
Eric D. Green
Huntington F. Willard

First Published April 25, 2011

Resource

Low-coverage sequencing: Implications for design of complex trait association studies

Yun Li
Carlo Sidore
Hyun Min Kang
Michael Boehnke
Gonçalo R. Abecasis

First Published April 1, 2011

Method

Systematic comparison of three genomic enrichment methods for massively parallel DNA sequencing

Jamie K. Teer
Lori L. Bonnycastle
Peter S. Chines
Nancy F. Hansen
Natsuyo Aoyama
Amy J. Swift Hatice Ozel Abaan Thomas J. Albert Elliott H. Margulies
... [+4 authors] ...,
Eric D. Green
Francis S. Collins
James C. Mullikin
Leslie G. Biesecker

First Published September 1, 2010

Resource

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

Resource

The ClinSeq Project: Piloting large-scale genome sequencing for research in genomic medicine

Leslie G. Biesecker
James C. Mullikin
Flavia M. Facio
Clesson Turner
Praveen F. Cherukuri
Robert W. Blakesley Gerard G. Bouffard Peter S. Chines Pedro Cruz Nancy F. Hansen Jamie K. Teer Baishali Maskeri Alice C. Young Teri A. Manolio Alexander F. Wilson Toren Finkel Paul Hwang Andrew Arai Alan T. Remaley
... [+14 authors] ...,
Vandana Sachdev
Robert Shamburek
Richard O. Cannon
Eric D. Green

First Published July 14, 2009

LETTER

Comparative sequence analysis of primate subtelomeres originating from a chromosome fission event

M. Katharine Rudd
RaeLynn M. Endicott
Cynthia Friedman
Megan Walker
Janet M. Young
Kazutoyo Osoegawa
Pieter J. de Jong
Eric D. Green
Barbara J. Trask

First Published October 24, 2008

ARTICLE

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

LETTER

Comparative sequence analyses reveal rapid and divergent evolutionary changes of the WFDC locus in the primate lineage

Belen Hurle
Willie Swanson
Eric D. Green

First Published January 31, 2007

RESOURCE

Sequencing and analysis of 10,967 full-length cDNA clones from Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling

Ryan D. Morin
Elbert Chang
Anca Petrescu
Nancy Liao
Malachi Griffith
Robert Kirkpatrick Yaron S. Butterfield Alice C. Young Jeffrey Stott Sarah Barber Ryan Babakaiff Mark C. Dickson Corey Matsuo David Wong George S. Yang Duane E. Smailus Keith D. Wetherby Peggy N. Kwong Jane Grimwood Charles P. Brinkley Mabel Brown-John Natalie D. Reddix-Dugue Michael Mayo Jeremy Schmutz Jaclyn Beland Morgan Park Susan Gibson Teika Olson Gerard G. Bouffard Miranda Tsai Ruth Featherstone Steve Chand Asim S. Siddiqui Wonhee Jang Ed Lee Steven L. Klein Robert W. Blakesley Barry R. Zeeberg Sudarshan Narasimhan John N. Weinstein Christa Prange Pennacchio Richard M. Myers Eric D. Green Lukas Wagner
... [+39 authors] ...,
Daniela S. Gerhard
Marco A. Marra
Steven J.M. Jones
Robert A. Holt

First Published May 3, 2006

LETTER

A preliminary comparative analysis of primate segmental duplications shows elevated substitution rates and a great-ape expansion of intrachromosomal duplications

Xinwei She
Ge Liu
Mario Ventura
Shaying Zhao
Doriana Misceo
Roberta Roberto Maria Francesca Cardone
... [+2 authors] ...,
Mariano Rocchi
Eric D. Green
Nicoletta Archidiacano
Evan E. Eichler

First Published April 10, 2006

LETTER

Sequence features in regions of weak and strong linkage disequilibrium

Albert V. Smith
Daryl J. Thomas
Heather M. Munro
Gonçalo R. Abecasis

First Published October 26, 2005

ARTICLE

Distribution and intensity of constraint in mammalian genomic sequence

Gregory M. Cooper
Eric A. Stone
George Asimenos
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published June 17, 2005

LETTER

Reconstructing large regions of an ancestral mammalian genome in silico

Mathieu Blanchette
Eric D. Green
Webb Miller
David Haussler

First Published December 1, 2004

LETTER

An intermediate grade of finished genomic sequence suitable for comparative analyses

Robert W. Blakesley
Nancy F. Hansen
James C. Mullikin
Pamela J. Thomas
Jennifer C. McDowell
Baishali Maskeri Alice C. Young Beatrice Benjamin Shelise Y. Brooks Bradley I. Coleman Jyoti Gupta Shi-Ling Ho Eric M. Karlins Quino L. Maduro Sirintorn Stantripop Cyrus Tsurgeon Jennifer L. Vogt Michelle A. Walker
... [+13 authors] ...,
Catherine A. Masiello
Xiaobin Guan
Gerard G. Bouffard
Eric D. Green

First Published October 12, 2004

RESOURCE

Aligning Multiple Genomic Sequences With the Threaded Blockset Aligner

Mathieu Blanchette
W. James Kent
Cathy Riemer
Laura Elnitski
Arian F.A. Smit
Krishna M. Roskin Robert Baertsch Kate Rosenbloom
... [+3 authors] ...,
Hiram Clawson
Eric D. Green
David Haussler
Webb Miller

First Published April 1, 2004

ARTICLE

Identification and Characterization of Multi-Species Conserved Sequences

Elliott H. Margulies
Mathieu Blanchette
David Haussler
Eric D. Green

First Published December 1, 2003

LETTER

Quantitative Estimates of Sequence Divergence for Comparative Analyses of Mammalian Genomes

Gregory M. Cooper
Michael Brudno
NISC Comparative Sequencing Program
Eric D. Green
Serafim Batzoglou
Arend Sidow

First Published May 1, 2003

METHODS

LAGAN and Multi-LAGAN: Efficient Tools for Large-Scale Multiple Alignment of Genomic DNA

Michael Brudno
Chuong B. Do
Gregory M. Cooper
Michael F. Kim
Eugene Davydov
NISC Comparative Sequencing Program
Eric D. Green
Arend Sidow
Serafim Batzoglou

First Published March 12, 2003

LETTER

Analysis of Primate Genomic Variation Reveals a Repeat-Driven Expansion of the Human Genome

Ge Liu
NISC Comparative Sequencing Program
Shaying Zhao
Jeffrey A. Bailey
S. Cenk Sahinalp
Can Alkan
Eray Tuzun
Eric D. Green
Evan E. Eichler

First Published March 1, 2003

LETTER

Pericentromeric Duplications in the Laboratory Mouse

James W. Thomas
Mary G. Schueler
Tyrone J. Summers
Robert W. Blakesley
Jennifer C. McDowell
Pamela J. Thomas Jacquelyn R. Idol Valerie V.B. Maduro Shih-Queen Lee-Lin Jeffrey W. Touchman
... [+5 authors] ...,
Gerard G. Bouffard
Stephen M. Beckstrom-Sternberg
NISC Comparative Sequencing Program
Eric D. Green

First Published December 30, 2002

METHODS

Parallel Construction of Orthologous Sequence-Ready Clone Contig Maps in Multiple Species

James W. Thomas
Arjun B. Prasad
Tyrone J. Summers
Shih-Queen Lee-Lin
Valerie V.B. Maduro
Jacquelyn R. Idol
... [+1 authors] ...,
Joseph F. Ryan
Pamela J. Thomas
Jennifer C. McDowell
Eric D. Green

First Published August 1, 2002

REPORT

Generation and Comparative Analysis of ∼3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome

Udaya DeSilva
Laura Elnitski
Jacquelyn R. Idol
Johannah L. Doyle
Weiniu Gan
James W. Thomas Scott Schwartz Nicole L. Dietrich Stephen M. Beckstrom-Sternberg Jennifer C. McDowell Robert W. Blakesley Gerard G. Bouffard
... [+7 authors] ...,
Pamela J. Thomas
Jeffrey W. Touchman
Webb Miller
Eric D. Green

First Published January 1, 2002

COMMENTARY

The Human Genome Sequence Expedition: Views from the “Base Camp”

Eric D. Green
Aravinda Chakravarti

First Published May 1, 2001

REPORT

Comparative Genome Mapping in the Sequence-based Era: Early Experience with Human Chromosome 7

James W. Thomas
Tyrone J. Summers
Shih-Queen Lee-Lin
Valerie V. Braden Maduro
Jacquelyn R. Idol
Stephen D. Mastrian
Joseph F. Ryan
D. Curtis Jamison
Eric D. Green

First Published May 1, 2000

REPORT

The Genomic Region Encompassing the Nephropathic Cystinosis Gene (CTNS): Complete Sequencing of a 200-kb Segment and Discovery of a Novel Gene within the Common Cystinosis-Causing Deletion

Jeffrey W. Touchman
Yair Anikster
Nicole L. Dietrich
Valerie V. Braden Maduro
Geraldine McDowell
Vorasuk Shotelersuk
... [+1 authors] ...,
Gerard G. Bouffard
Stephen M. Beckstrom-Sternberg
William A. Gahl
Eric D. Green

First Published February 1, 2000

LETTER

The CMT2D Locus: Refined Genetic Position and Construction of a Bacterial Clone-Based Physical Map

Rachel E. Ellsworth
Victor Ionasescu
Charles Searby
Val C. Sheffield
Valerie V. Braden
Tamara A. Kucaba
John D. McPherson
Marco A. Marra
Eric D. Green

First Published June 1, 1999

LETTER

Comparative Mapping of the Region of Human Chromosome 7 Deleted in Williams Syndrome

Udaya DeSilva
Hillary Massa
Barbara J. Trask
Eric D. Green

First Published May 1, 1999

LETTER

High Throughput Fingerprint Analysis of Large-Insert Clones

Marco A. Marra
Tamara A. Kucaba
Nicole L. Dietrich
Eric D. Green
Buddy Brownstein
Richard K. Wilson
... [+1 authors] ...,
Ken M. McDonald
LaDeana W. Hillier
John D. McPherson
Robert H. Waterston

First Published November 1, 1997

RESEARCH

A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb

Gerard G. Bouffard
Jacquelyn R. Idol
Valerie V. Braden
Leslie M. Iyer
Aimee F. Cunningham
Lauren A. Weintraub Jeffrey W. Touchman Rose M. Mohr-Tidwell Dale C. Peluso Robert S. Fulton
... [+5 authors] ...,
Melinda S. Ueltzen
Jean Weissenbach
Charles L. Magness
Eric D. Green

First Published July 1, 1997

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