Search | Genome Research

The impact of long-read sequencing on human population-scale genomics

Tobias Rausch
Tobias Marschall
Jan O. Korbel

First Published April 14, 2025

An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes

Chong Li
Marc Jan Bonder
Sabriya Syed
Matthew Jensen
Mark B. Gerstein
Michael C. Zody Mark J.P. Chaisson Michael E. Talkowski Tobias Marschall
... [+4 authors] ...,
Jan O. Korbel
Evan E. Eichler
Charles Lee
Xinghua Shi

First Published December 5, 2024

Gaps and complex structurally variant loci in phased genome assemblies

David Porubsky
Mitchell R. Vollger
William T. Harvey
Allison N. Rozanski
Peter Ebert
Glenn Hickey Patrick Hasenfeld Ashley D. Sanders Catherine Stober Jan O. Korbel Benedict Paten Tobias Marschall Evan E. Eichler Haley J. Abel Lucinda L. Antonacci-Fulton Mobin Asri Gunjan Baid Carl A. Baker Anastasiya Belyaeva Konstantinos Billis Guillaume Bourque Silvia Buonaiuto Andrew Carroll Mark J.P. Chaisson Pi-Chuan Chang Xian H. Chang Haoyu Cheng Justin Chu Sarah Cody Vincenza Colonna Daniel E. Cook Robert M. Cook-Deegan Omar E. Cornejo Mark Diekhans Daniel Doerr Peter Ebert Jana Ebler Evan E. Eichler Jordan M. Eizenga Susan Fairley Olivier Fedrigo Adam L. Felsenfeld Xiaowen Feng Christian Fischer Paul Flicek Giulio Formenti Adam Frankish Robert S. Fulton Yan Gao Shilpa Garg Erik Garrison Nanibaa’ A. Garrison Carlos Garcia Giron Richard E. Green Cristian Groza Andrea Guarracino Leanne Haggerty Ira M. Hall William T. Harvey Marina Haukness David Haussler Simon Heumos Glenn Hickey Kendra Hoekzema Thibaut Hourlier Kerstin Howe Miten Jain Erich D. Jarvis Hanlee P. Ji Eimear E. Kenny Barbara A. Koenig Alexey Kolesnikov Jan O. Korbel Jennifer Kordosky Sergey Koren HoJoon Lee Alexandra P. Lewis Heng Li Wen-Wei Liao Shuangjia Lu Tsung-Yu Lu Julian K. Lucas Hugo Magalhães Santiago Marco-Sola Pierre Marijon Charles Markello Tobias Marschall Fergal J. Martin Ann McCartney Jennifer McDaniel Karen H. Miga Matthew W. Mitchell Jean Monlong Jacquelyn Mountcastle Katherine M. Munson Moses Njagi Mwaniki Maria Nattestad Adam M. Novak Sergey Nurk Hugh E. Olsen Nathan D. Olson Benedict Paten Trevor Pesout Adam M. Phillippy Alice B. Popejoy David Porubsky Pjotr Prins Daniela Puiu Mikko Rautiainen Allison A. Regier Arang Rhie Samuel Sacco Ashley D. Sanders Valerie A. Schneider Baergen I. Schultz Kishwar Shafin Jonas A. Sibbesen Jouni Sirén Michael W. Smith Heidi J. Sofia Ahmad N. Abou Tayoun Françoise Thibaud-Nissen Chad Tomlinson Francesca Floriana Tricomi Flavia Villani Mitchell R. Vollger Justin Wagner Brian Walenz
... [+123 authors] ...,
Ting Wang
Jonathan M.D. Wood
Aleksey V. Zimin
Justin M. Zook

First Published May 10, 2023

A high-resolution map of small-scale inversions in the gibbon genome

Ludovica Mercuri
Donato Palmisano
Alberto L'Abbate
Pietro D'Addabbo
Francesco Montinaro
Claudia Rita Catacchio Patrick Hasenfeld Mario Ventura
... [+3 authors] ...,
Jan O. Korbel
Ashley D. Sanders
Flavia Angela Maria Maggiolini
Francesca Antonacci

First Published September 30, 2022

Somatic structural variant formation is guided by and influences genome architecture

Nikos Sidiropoulos
Balca R. Mardin
F. Germán Rodríguez-González
Ivan D. Bochkov
Shilpa Garg
Adrian M. Stütz
Jan O. Korbel
Erez Lieberman Aiden
Joachim Weischenfeldt

First Published February 17, 2022

Pan-cancer analysis distinguishes transcriptional changes of aneuploidy from proliferation

Christopher Buccitelli
Lorena Salgueiro
Konstantina Rowald
Rocio Sotillo
Balca R. Mardin
Jan O. Korbel

First Published March 20, 2017

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

Drosophila melanogaster based on population-scale sequencing" > Impact of genomic structural variation in Drosophila melanogaster based on population-scale sequencing

Thomas Zichner
David A. Garfield
Tobias Rausch
Adrian M. Stütz
Enrico Cannavó
Martina Braun
Eileen E.M. Furlong
Jan O. Korbel

First Published December 6, 2012

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

Andreas Schlattl
Simon Anders
Sebastian M. Waszak
Wolfgang Huber
Jan O. Korbel

First Published August 23, 2011

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Weisheng Wu
Yong Cheng
Cheryl A. Keller
Jason Ernst
Swathi Ashok Kumar
Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
... [+16 authors] ...,
Francesca Chiaromonte
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published July 27, 2011

Genome-wide identification of conserved regulatory function in diverged sequences

Leila Taher
David M. McGaughey
Samantha Maragh
Ivy Aneas
Seneca L. Bessling
Webb Miller
Marcelo A. Nobrega
Andrew S. McCallion
Ivan Ovcharenko

First Published May 31, 2011

Erythroid GATA1 function revealed by genome-wide analysis of transcription factor occupancy, histone modifications, and mRNA expression

Yong Cheng
Weisheng Wu
Swathi Ashok Kumar
Duonan Yu
Wulan Deng
Tamara Tripic David C. King Kuan-Bei Chen Ying Zhang Daniela Drautz Belinda Giardine Stephan C. Schuster Webb Miller Francesca Chiaromonte
... [+9 authors] ...,
Yu Zhang
Gerd A. Blobel
Mitchell J. Weiss
Ross C. Hardison

First Published November 3, 2009

Thylacinus cynocephalus)" > The mitochondrial genome sequence of the Tasmanian tiger (Thylacinus cynocephalus)

Webb Miller
Daniela I. Drautz
Jan E. Janecka
Arthur M. Lesk
Aakrosh Ratan
Lynn P. Tomsho Mike Packard Yeting Zhang Lindsay R. McClellan Ji Qi Fangqing Zhao M. Thomas P. Gilbert Love Dalén Juan Luis Arsuaga Per G.P. Ericson Daniel H. Huson
... [+11 authors] ...,
Kristofer M. Helgen
William J. Murphy
Anders Götherström
Stephan C. Schuster

First Published January 12, 2009

MSB: A mean-shift-based approach for the analysis of structural variation in the genome

Lu-yong Wang
Alexej Abyzov
Jan O. Korbel
Michael Snyder
Mark Gerstein

First Published November 26, 2008

Analysis of copy number variants and segmental duplications in the human genome: Evidence for a change in the process of formation in recent evolutionary history

Philip M. Kim
Hugo Y.K. Lam
Alexander E. Urban
Jan O. Korbel
Jason Affourtit
Fabian Grubert
... [+1 authors] ...,
Xueying Chen
Sherman Weissman
Michael Snyder
Mark B. Gerstein

First Published October 8, 2008

Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif

Yong Cheng
David C. King
Louis C. Dore
Xinmin Zhang
Yuepin Zhou
Ying Zhang Christine Dorman Demesew Abebe Swathi A. Kumar Francesca Chiaromonte
... [+5 authors] ...,
Webb Miller
Roland D. Green
Mitchell J. Weiss
Ross C. Hardison

First Published September 25, 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

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

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

cis-regulatory elements using comparative genomics: Some lessons from ENCODE data" > Finding cis-regulatory elements using comparative genomics: Some lessons from ENCODE data

David C. King
James Taylor
Ying Zhang
Yong Cheng
Heather A. Lawson
Joel Martin
Francesca Chiaromonte
Webb Miller
Ross C. Hardison

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

A framework for collaborative analysis of ENCODE data: Making large-scale analyses biologist-friendly

Daniel Blankenberg
James Taylor
Ian Schenck
Jianbin He
Yi Zhang
Matthew Ghent Narayanan Veeraraghavan Istvan Albert
... [+3 authors] ...,
Webb Miller
Kateryna D. Makova
Ross C. Hardison
Anton Nekrutenko

First Published June 13, 2007

What is a gene, post-ENCODE? History and updated definition

Mark B. Gerstein
Can Bruce
Joel S. Rozowsky
Deyou Zheng
Jiang Du
Jan O. Korbel
... [+1 authors] ...,
Olof Emanuelsson
Zhengdong D. Zhang
Sherman Weissman
Michael Snyder

First Published June 13, 2007

Using genomic data to unravel the root of the placental mammal phylogeny

William J. Murphy
Thomas H. Pringle
Tess A. Crider
Mark S. Springer
Webb Miller

First Published February 23, 2007

ESPERR: Learning strong and weak signals in genomic sequence alignments to identify functional elements

James Taylor
Svitlana Tyekucheva
David C. King
Ross C. Hardison
Webb Miller
Francesca Chiaromonte

First Published October 19, 2006

cis-regulatory modules" > Experimental validation of predicted mammalian erythroid cis-regulatory modules

Hao Wang
Ying Zhang
Yong Cheng
Yuepin Zhou
David C. King
James Taylor Francesca Chiaromonte Jyotsna Kasturi Hanna Petrykowska Brian Gibb Christine Dorman Webb Miller
... [+7 authors] ...,
Louis C. Dore
John Welch
Mitchell J. Weiss
Ross C. Hardison

First Published October 12, 2006

Reconstructing contiguous regions of an ancestral genome

Jian Ma
Louxin Zhang
Bernard B. Suh
Brian J. Raney
Richard C. Burhans
W. James Kent
Mathieu Blanchette
David Haussler
Webb Miller

First Published September 18, 2006

Galaxy: A platform for interactive large-scale genome analysis

Belinda Giardine
Cathy Riemer
Ross C. Hardison
Richard Burhans
Laura Elnitski
Prachi Shah Yi Zhang Daniel Blankenberg Istvan Albert
... [+4 authors] ...,
James Taylor
Webb Miller
W. James Kent
Anton Nekrutenko

First Published September 16, 2005

cis-regulatory modules in aligned mammalian genome sequences" > Evaluation of regulatory potential and conservation scores for detecting cis-regulatory modules in aligned mammalian genome sequences

David C. King
James Taylor
Laura Elnitski
Francesca Chiaromonte
Webb Miller
Ross C. Hardison

First Published July 15, 2005

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

Mulan: Multiple-sequence local alignment and visualization for studying function and evolution

Ivan Ovcharenko
Gabriela G. Loots
Belinda M. Giardine
Minmei Hou
Jian Ma
Ross C. Hardison
Lisa Stubbs
Webb Miller

First Published December 8, 2004

Evolution and functional classification of vertebrate gene deserts

Ivan Ovcharenko
Gabriela G. Loots
Marcelo A. Nobrega
Ross C. Hardison
Webb Miller
Lisa Stubbs

First Published December 8, 2004

Reconstructing large regions of an ancestral mammalian genome in silico

Mathieu Blanchette
Eric D. Green
Webb Miller
David Haussler

First Published December 1, 2004

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

Comparative Analysis of the α-Like Globin Clusters in Mouse, Rat, and Human Chromosomes Indicates a Mechanism Underlying Breaks in Conserved Synteny

Cristina Tufarelli
Ross Hardison
Webb Miller
Jim Hughes
Kevin Clark
Nicki Ventress
Anna Maria Frischauf
Douglas R. Higgs

First Published April 1, 2004

Regulatory Potential Scores From Genome-Wide Three-Way Alignments of Human, Mouse, and Rat

Diana Kolbe
James Taylor
Laura Elnitski
Pallavi Eswara
Jia Li
Webb Miller
Ross Hardison
Francesca Chiaromonte

First Published April 1, 2004

Patterns of Insertions and Their Covariation With Substitutions in the Rat, Mouse, and Human Genomes

Shan Yang
Arian F. Smit
Scott Schwartz
Francesca Chiaromonte
Krishna M. Roskin
David Haussler
Webb Miller
Ross C. Hardison

First Published April 1, 2004

zPicture: Dynamic Alignment and Visualization Tool for Analyzing Conservation Profiles

Ivan Ovcharenko
Gabriela G. Loots
Ross C. Hardison
Webb Miller
Lisa Stubbs

First Published March 1, 2004

GALA, a Database for Genomic Sequence Alignments and Annotations

Belinda Giardine
Laura Elnitski
Cathy Riemer
Izabela Makalowska
Scott Schwartz
Webb Miller
Ross C. Hardison

First Published April 1, 2003

First Published January 1, 2003

Covariation in Frequencies of Substitution, Deletion, Transposition, and Recombination During Eutherian Evolution

Ross C. Hardison
Krishna M. Roskin
Shan Yang
Mark Diekhans
W. James Kent
Ryan Weber Laura Elnitski Jia Li Michael O'Connor Diana Kolbe Scott Schwartz Terrence S. Furey Simon Whelan Nick Goldman
... [+9 authors] ...,
Arian Smit
Webb Miller
Francesca Chiaromonte
David Haussler

First Published January 1, 2003

Gene Length and Proximity to Neighbors Affect Genome-Wide Expression Levels

Francesca Chiaromonte
Webb Miller
Eric E. Bouhassira,

First Published January 1, 2003

Human–Mouse Alignments with BLASTZ

Scott Schwartz
W. James Kent
Arian Smit
Zheng Zhang
Robert Baertsch
Ross C. Hardison
David Haussler
Webb Miller

First Published December 30, 2002

3.3 Mb of Mouse Genomic Sequence Orthologous to the Region of Human Chromosome 7q11.23 Implicated in Williams Syndrome " > 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