Search | Genome Research

Research

Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T

Luis F. Paulin
Jeremy Fan
Kieran O'Neill
Erin Pleasance
Vanessa L. Porter
Steven J.M. Jones
Fritz J. Sedlazeck

First Published March 17, 2025

Research

Rearrangements of viral and human genomes at human papillomavirus integration events and their allele-specific impacts on cancer genome regulation

Vanessa L. Porter
Michelle Ng
Kieran O'Neill
Signe MacLennan
Richard D. Corbett
Luka Culibrk Zeid Hamadeh Marissa Iden Rachel Schmidt Shirng-Wern Tsaih Carolyn Nakisige Martin Origa Jackson Orem Glenn Chang Jeremy Fan Ka Ming Nip Vahid Akbari Simon K. Chan James Hopkins Richard A. Moore Eric Chuah Karen L. Mungall Andrew J. Mungall
... [+18 authors] ...,
Inanc Birol
Steven J.M. Jones
Janet S. Rader
Marco A. Marra

First Published December 5, 2024

Research

XIST locus" > 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

Research

Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver

Brad G. Hoffman
Gordon Robertson
Bogard Zavaglia
Mike Beach
Rebecca Cullum
Sam Lee Galina Soukhatcheva Leping Li Elizabeth D. Wederell Nina Thiessen Mikhail Bilenky Timothee Cezard Angela Tam Baljit Kamoh Inanc Birol Derek Dai YongJun Zhao Martin Hirst C. Bruce Verchere
... [+14 authors] ...,
Cheryl D. Helgason
Marco A. Marra
Steven J.M. Jones
Pamela A. Hoodless

First Published June 15, 2010

Research

The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance

Santosh S. Atanur
İnanç Birol
Victor Guryev
Martin Hirst
Oliver Hummel
Catherine Morrissey Jacques Behmoaras Xose M. Fernandez-Suarez Michelle D. Johnson William M. McLaren Giannino Patone Enrico Petretto Charles Plessy Kathleen S. Rockland Charles Rockland Kathrin Saar Yongjun Zhao Piero Carninci Paul Flicek Ted Kurtz Edwin Cuppen Michal Pravenec
... [+17 authors] ...,
Norbert Hubner
Steven J.M. Jones
Ewan Birney
Timothy J. Aitman

First Published April 29, 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

ABySS: A parallel assembler for short read sequence data

Jared T. Simpson
Kim Wong
Shaun D. Jackman
Jacqueline E. Schein
Steven J.M. Jones
İnanç Birol

First Published February 27, 2009

LETTER

Genome-wide relationship between histone H3 lysine 4 mono- and tri-methylation and transcription factor binding

A. Gordon Robertson
Mikhail Bilenky
Angela Tam
Yongjun Zhao
Thomas Zeng
Nina Thiessen Timothee Cezard Anthony P. Fejes Elizabeth D. Wederell Rebecca Cullum Ghia Euskirchen Martin Krzywinski Inanc Birol Michael Snyder
... [+9 authors] ...,
Pamela A. Hoodless
Martin Hirst
Marco A. Marra
Steven J.M. Jones

First Published September 11, 2008

Next-Generation DNA Sequencing/Review

The new paradigm of flow cell sequencing

Robert A. Holt
Steven J.M. Jones

First Published June 2, 2008

LETTER

Caenorhabditis elegans operons" > Identification and analysis of internal promoters in Caenorhabditis elegans operons

Peiming Huang
Erin D. Pleasance
Jason S. Maydan
Rebecca Hunt-Newbury
Nigel J. O’Neil
Allan Mah
... [+1 authors] ...,
David L. Baillie
Marco A. Marra
Donald G. Moerman
Steven J.M. Jones

First Published August 21, 2007

REVIEW

Locating mammalian transcription factor binding sites: A survey of computational and experimental techniques

Laura Elnitski
Victor X. Jin
Peggy J. Farnham
Steven J.M. Jones

First Published October 19, 2006

Methods

Physical map-assisted whole-genome shotgun sequence assemblies

René L. Warren
Dmitry Varabei
Darren Platt
Xiaoqiu Huang
David Messina
Shiaw-Pyng Yang James W. Kronstad Martin Krzywinski Wesley C. Warren John W. Wallis LaDeana W. Hillier Asif T. Chinwalla Jacqueline E. Schein
... [+8 authors] ...,
Asim S. Siddiqui
Marco A. Marra
Richard K. Wilson
Steven J.M. Jones

First Published June 1, 2006

RESOURCE

Xenopus laevis and Xenopus tropicalis reveals post-tetraploidization transcriptome remodeling" > 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

ARTICLE

C. elegans daf-2 mutants using serial analysis of gene expression" > Analysis of long-lived C. elegans daf-2 mutants using serial analysis of gene expression

Julius Halaschek-Wiener
Jaswinder S. Khattra
Sheldon McKay
Anatoli Pouzyrev
Jeff M. Stott
George S. Yang Robert A. Holt
... [+2 authors] ...,
Steven J.M. Jones
Marco A. Marra
Angela R. Brooks-Wilson
Donald L. Riddle

First Published April 18, 2005

Methods

Mapping segmental and sequence variations among laboratory mice using BAC array CGH

Antoine M. Snijders
Norma J. Nowak
Bing Huey
Jane Fridlyand
Sindy Law
Jeffrey Conroy Taku Tokuyasu Kubilay Demir Readman Chiu Jian-Hua Mao Ajay N. Jain
... [+6 authors] ...,
Steven J.M. Jones
Allan Balmain
Daniel Pinkel
Donna G. Albertson

First Published February 1, 2005

ENSEMBL Special

Sockeye: A 3D Environment for Comparative Genomics

Stephen B. Montgomery
Tamara Astakhova
Mikhail Bilenky
Ewan Birney
Tony Fu
Maik Hassel Craig Melsopp Marcin Rak
... [+3 authors] ...,
A. Gordon Robertson
Monica Sleumer
Asim S. Siddiqui
Steven J.M. Jones

First Published May 3, 2004

RESOURCE

Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

Matthew L. Rise
Kristian R. von Schalburg
Gordon D. Brown
Melanie A. Mawer
Robert H. Devlin
Nathanael Kuipers Maura Busby Marianne Beetz-Sargent Roberto Alberto A. Ross Gibbs Peter Hunt Robert Shukin Jeffrey A. Zeznik Colleen Nelson Simon R.M. Jones Duane E. Smailus Steven J.M. Jones Jacqueline E. Schein Marco A. Marra Yaron S.N. Butterfield
... [+15 authors] ...,
Jeff M. Stott
Siemon H.S. Ng
William S. Davidson
Ben F. Koop

First Published February 12, 2004

RESOURCE

Internet Contig Explorer (iCE)—A Tool for Visualizing Clone Fingerprint Maps

Christopher D. Fjell
Ian Bosdet
Jacqueline E. Schein
Steven J.M. Jones
Marco A. Marra

First Published June 1, 2003

Methods

Assessment of SAGE in Transcript Identification

Erin D. Pleasance
Marco A. Marra
Steven J.M. Jones

First Published May 12, 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

Software for Automated Analysis of DNA Fingerprinting Gels

Daniel R. Fuhrmann
Martin I. Krzywinski
Readman Chiu
Parvaneh Saeedi
Jacqueline E. Schein
Ian E. Bosdet Asif Chinwalla LaDeana W. Hillier
... [+3 authors] ...,
Robert H. Waterston
John D. McPherson
Steven J.M. Jones
Marco A. Marra

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

LETTER

Cryptococcus neoformans " > Temperature-Regulated Transcription in the Pathogenic Fungus Cryptococcus neoformans

Barbara R. Steen
Tian Lian
Scott Zuyderduyn
William Kim MacDonald
Marco Marra
Steven J.M. Jones
James W. Kronstad

First Published September 1, 2002

RESOURCE

Cryptococcus neoformans " > Physical Maps for Genome Analysis of Serotype A and D Strains of the Fungal Pathogen Cryptococcus neoformans

Jacqueline E. Schein
Kristin L. Tangen
Readman Chiu
Heesun Shin
Klaus B. Lengeler
William Kim MacDonald Ian Bosdet
... [+2 authors] ...,
Joseph Heitman
Steven J.M. Jones
Marco A. Marra
James W. Kronstad

First Published August 21, 2002

LETTER

Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast" > Evidence That Plant-Like Genes in Chlamydia Species Reflect an Ancestral Relationship between Chlamydiaceae, Cyanobacteria, and the Chloroplast

Fiona S.L. Brinkman
Jeffrey L. Blanchard
Artem Cherkasov
Yossef Av-Gay
Robert C. Brunham
Rachel C. Fernandez B. Brett Finlay Sarah P. Otto B.F. Francis Ouellette
... [+4 authors] ...,
Patrick J. Keeling
Ann M. Rose
Robert E.W. Hancock
Steven J.M. Jones

First Published July 19, 2002

ARTICLE

Caenorhabditis elegans " > Changes in Gene Expression Associated with Developmental Arrest and Longevity in Caenorhabditis elegans

Steven J.M. Jones
Donald L. Riddle
Anatoli T. Pouzyrev
Victor E. Velculescu
LaDeana Hillier
Sean R. Eddy
... [+1 authors] ...,
Shawn L. Stricklin
David L. Baillie
Robert Waterston
Marco A. Marra

First Published July 12, 2001

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