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

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

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

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

Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome

Timothy Ravasi
Harukazu Suzuki
Ken C. Pang
Shintaro Katayama
Masaaki Furuno
Rie Okunishi Shiro Fukuda Kelin Ru Martin C. Frith M. Milena Gongora
... [+5 authors] ...,
Sean M. Grimmond
David A. Hume
Yoshihide Hayashizaki
John S. Mattick

First Published December 12, 2005

ARTICLE

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

LETTER

The Mouse Secretome: Functional Classification of the Proteins Secreted Into the Extracellular Environment

Sean M. Grimmond
Kevin C. Miranda
Zheng Yuan
Melissa J. Davis
David A. Hume
Ken Yagi Naoko Tominaga
... [+2 authors] ...,
Hidemasa Bono
Yoshihide Hayashizaki
Yasushi Okazaki
Rohan D. Teasdale

First Published June 2, 2003

LETTER

Continued Discovery of Transcriptional Units Expressed in Cells of the Mouse Mononuclear Phagocyte Lineage

Christine A. Wells
Timothy Ravasi
Razvan Sultana
Ken Yagi
Piero Carninci
Hidemasa Bono Geoffrey Faulkner
... [+2 authors] ...,
Yasushi Okazaki
John Quackenbush
David A. Hume
Paul A. Lyons

First Published June 2, 2003

LETTER

Phosphoregulators: Protein Kinases and Protein Phosphatases of Mouse

Alistair R.R. Forrest
Timothy Ravasi
Darrin Taylor
Thomas Huber
David A. Hume
Sean Grimmond

First Published June 2, 2003

LETTER

Identification and Analysis of Chromodomain-Containing Proteins Encoded in the Mouse Transcriptome

Khairina Tajul-Arifin
Rohan Teasdale
Timothy Ravasi
David A. Hume
John S. Mattick

First Published June 2, 2003

LETTER

Systematic Characterization of the Zinc-Finger-Containing Proteins in the Mouse Transcriptome

Timothy Ravasi
Thomas Huber
Mihaela Zavolan
Alistair Forrest
Terry Gaasterland
Sean Grimmond
David A. Hume

First Published June 2, 2003

COMMENTARY

A Guide to the Mammalian Genome

Yasushi Okazaki
David A. Hume

First Published June 2, 2003

LETTER

Systematic Expression Profiling of the Mouse Transcriptome Using RIKEN cDNA Microarrays

Hidemasa Bono
Ken Yagi
Takeya Kasukawa
Itoshi Nikaido
Naoko Tominaga
Rika Miki Yosuke Mizuno Yasuhiro Tomaru Hitoshi Goto Hiroyuki Nitanda Daisuke Shimizu Hirochika Makino Tomoyuki Morita Junshin Fujiyama Takehito Sakai
... [+10 authors] ...,
Takashi Shimoji
David A. Hume
Yoshihide Hayashizaki
Yasushi Okazaki

First Published June 2, 2003

RESOURCE

Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System

Takeya Kasukawa
Masaaki Furuno
Itoshi Nikaido
Hidemasa Bono
David A. Hume
Carol Bult David P. Hill Richard Baldarelli Julian Gough Alexander Kanapin Hideo Matsuda
... [+6 authors] ...,
Lynn M. Schriml
Yoshihide Hayashizaki
Yasushi Okazaki
John Quackenbush

First Published June 2, 2003

ARTICLE

Targeting a Complex Transcriptome: The Construction of the Mouse Full-Length cDNA Encyclopedia

Piero Carninci
Kazunori Waki
Toshiyuki Shiraki
Hideaki Konno
Kazuhiro Shibata
Masayoshi Itoh Katsunori Aizawa Takahiro Arakawa Yoshiyuki Ishii Daisuke Sasaki Hidemasa Bono Shinji Kondo Yuichi Sugahara Rintaro Saito Naoki Osato Shiro Fukuda Kenjiro Sato Akira Watahiki Tomoko Hirozane-Kishikawa Mari Nakamura Yuko Shibata Ayako Yasunishi Noriko Kikuchi Atsushi Yoshiki Moriaki Kusakabe Stefano Gustincich Kirk Beisel William Pavan Vassilis Aidinis Akira Nakagawara William A. Held Hiroo Iwata Tomohiro Kono Hiromitsu Nakauchi Paul Lyons Christine Wells David A. Hume Michela Fagiolini Takao K. Hensch Michelle Brinkmeier Sally Camper Junji Hirota Peter Mombaerts
... [+38 authors] ...,
Masami Muramatsu
Yasushi Okazaki
Jun Kawai
Yoshihide Hayashizaki