Search | Genome Research

Method

Highly accurate assembly polishing with DeepPolisher

Mira Mastoras
Mobin Asri
Lucas Brambrink
Prajna Hebbar
Alexey Kolesnikov
Daniel E. Cook Maria Nattestad Julian Lucas Taylor S. Won Pi-Chuan Chang Andrew Carroll Benedict Paten Kishwar Shafin Ahmad Abou Tayoun Derek Albracht Jamie Allen Alawi A. Alsheikh-Ali Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Edward A. Belter Halle D. Bender Andrew P. Blair Silvia Buonaiuto Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Richard Durbin Jana Ebler Evan E Eichler Jordan M. Eizenga Parsa Eskandar Eddie Ferro Anna-Sophie Fiston-Lavier Sarah M. Ford Willard W. Ford Giulio Formenti Adam Frankish Mallory A. Freeberg Qichen Fu Stephanie M. Fullerton Robert S. Fulton Yan Gao Gage H. Garcia Obed A. Garcia Joshua M.V. Gardner Shilpa Garg Erik Garrison Nanibaa' A. Garrison John Garza Mohammadmersad Ghorbani Tina Graves-Lindsay Richard E. Green Cristian Groza Andrea Guarracino Melissa Gymrek Leanne Haggerty Ira M. Hall Nancy F. Hansen Mohammad Amiruddin Hashmi Maximilian Haeussler David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Juan Jiang Jonathan LoTempio Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Ben Langmead Xiaoyu Zhuo Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Juan F. Macias-Velasco Maximillian G. Marin Franco L. Marsico Kateryna D. Makova Christopher Markovic Tobias Marschall Fergal J. Martin Mira Mastoras Capucine Mayoud Brandy McNulty Jack A. Medico Julian M. Menendez Karen H. Miga Anna Minkina Matthew W. Mitchell Saswat K. Mohanty Younes Mokrab Jean Monlong Shabir Moosa Avelina Moreno-Ochando Shinichi Morishita Jonathan M. Mudge Katherine M. Munson Njagi Mwaniki Nasna Nassir Chiara Natali Shloka Negi Lingbin Ni Adam M. Novak Chie Owa Sadye Paez Benedict Paten Hiram Clawson Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Farnaz Salehi Samuel Sacco Michael C. Schatz Laura B. Scheinfeldt Aarushi Sehgal William E. Seligmann Mahsa Shabani Kishwar Shafin Shadi Shahatit Ruhollah Shemirani Vikram S. Shivakumar Swati Sinha Jouni Sirén Linnéa Smeds Steven J. Solar Marco Sollitto Nicole Soranzo Andrew B. Stergachis Marie-Marthe Suner Yoshihiko Suzuki Arda Söylev Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Mitchell R. Vollger Brian P. Walenz Charles Wang Lisa E. Wang Ting Wang Aaron M. Wenger Conor V. Whelan Zilan Xin Zheng Xu Kai Ye DongAhn Yoo
... [+196 authors] ...,
Wenjin Zhang
Ying Zhou
Ivo Violich
Giulia Zunino

First Published May 19, 2025

Method

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease

Tanner D. Jensen
Bohan Ni
Chloe M. Reuter
John E. Gorzynski
Sarah Fazal
Devon Bonner Rachel A. Ungar Pagé C. Goddard Archana Raja Euan A. Ashley Jonathan A. Bernstein Stephan Zuchner Michael D. Greicius
... [+8 authors] ...,
Stephen B. Montgomery
Michael C. Schatz
Matthew T. Wheeler
Alexis Battle

First Published March 20, 2025

Perspective

Unraveling the hidden complexity of cancer through long-read sequencing

Qiuhui Li
Ayse G. Keskus
Justin Wagner
Michal B. Izydorczyk
Winston Timp
Fritz J. Sedlazeck
... [+1 authors] ...,
Alison P. Klein
Justin M. Zook
Mikhail Kolmogorov
Michael C. Schatz

First Published March 20, 2025

Method

Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

Sergey Koren
Zhigui Bao
Andrea Guarracino
Shujun Ou
Sara Goodwin
Katharine M. Jenike Julian Lucas Brandy McNulty Jimin Park Mikko Rautiainen Arang Rhie Dick Roelofs Harrie Schneiders Ilse Vrijenhoek Koen Nijbroek Olle Nordesjo Sergey Nurk Mike Vella Katherine R. Lawrence Doreen Ware Michael C. Schatz Erik Garrison Sanwen Huang
... [+18 authors] ...,
William Richard McCombie
Karen H. Miga
Alexander H.J. Wittenberg
Adam M. Phillippy

First Published November 6, 2024

Resource

High-coverage nanopore sequencing of samples from the 1000 Genomes Project to build a comprehensive catalog of human genetic variation

Jonas A. Gustafson
Sophia B. Gibson
Nikhita Damaraju
Miranda P.G. Zalusky
Kendra Hoekzema
David Twesigomwe Lei Yang Anthony A. Snead Phillip A. Richmond Wouter De Coster Nathan D. Olson Andrea Guarracino Qiuhui Li Angela L. Miller Joy Goffena Zachary B. Anderson Sophie H.R. Storz Sydney A. Ward Maisha Sinha Claudia Gonzaga-Jauregui Wayne E. Clarke Anna O. Basile André Corvelo Catherine Reeves Adrienne Helland Rajeeva Lochan Musunuri Mahler Revsine Karynne E. Patterson Cate R. Paschal Christina Zakarian Sara Goodwin Tanner D. Jensen Esther Robb William Richard McCombie Fritz J. Sedlazeck Justin M. Zook Stephen B. Montgomery Erik Garrison Mikhail Kolmogorov Michael C. Schatz Richard N. McLaughlin Harriet Dashnow Michael C. Zody
... [+38 authors] ...,
Matt Loose
Miten Jain
Evan E. Eichler
Danny E. Miller

First Published October 2, 2024

Research

Differences in activity and stability drive transposable element variation in tropical and temperate maize

Shujun Ou
Armin Scheben
Tyler Collins
Yinjie Qiu
Arun S. Seetharam
Claire C. Menard Nancy Manchanda Jonathan I. Gent
... [+3 authors] ...,
Michael C. Schatz
Sarah N. Anderson
Matthew B. Hufford
Candice N. Hirsch

First Published September 9, 2024

Resource

Interspecies regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes

Guanjue Xiang
Xi He
Belinda M. Giardine
Kathryn J. Isaac
Dylan J. Taylor
Rajiv C. McCoy Camden Jansen Cheryl A. Keller Alexander Q. Wixom April Cockburn Amber Miller Qian Qi Yanghua He Yichao Li Jens Lichtenberg Elisabeth F. Heuston Stacie M. Anderson Jing Luan Marit W. Vermunt Feng Yue Michael E.G. Sauria Michael C. Schatz James Taylor Berthold Göttgens Jim R. Hughes Douglas R. Higgs Mitchell J. Weiss Yong Cheng Gerd A. Blobel David M. Bodine
... [+25 authors] ...,
Yu Zhang
Qunhua Li
Shaun Mahony
Ross C. Hardison

First Published July 1, 2024

Perspective

Diversifying the genomic data science research community

Rosa Alcazar
Maria Alvarez
Rachel Arnold
Mentewab Ayalew
Lyle G. Best
Michael C. Campbell Kamal Chowdhury Katherine E.L. Cox Christina Daulton Youping Deng Carla Easter Karla Fuller Shazia Tabassum Hakim Ava M. Hoffman Natalie Kucher Andrew Lee Joslynn Lee Jeffrey T. Leek Robert Meller Loyda B. Méndez Miguel P. Méndez-González Stephen Mosher Michele Nishiguchi Siddharth Pratap Tiffany Rolle Sourav Roy Rachel Saidi Michael C. Schatz Shurjo K. Sen James Sniezek Edu Suarez Martinez Frederick J. Tan Jennifer Vessio Karriem Watson
... [+29 authors] ...,
Wendy Westbroek
Joseph Wilcox
Carrie Wright
Xianfa Xie

First Published July 20, 2022

Method

Targeted single-cell RNA sequencing of transcription factors enhances the identification of cell types and trajectories

Alexandra Pokhilko
Adam E. Handel
Fabiola Curion
Viola Volpato
Emma S. Whiteley
Sunniva Bøstrand Sarah E. Newey Colin J. Akerman
... [+3 authors] ...,
Caleb Webber
Michael B. Clark
Rory Bowden
M. Zameel Cader

First Published May 19, 2021

Method

Optimized sample selection for cost-efficient long-read population sequencing

T. Rhyker Ranallo-Benavidez
Zachary Lemmon
Sebastian Soyk
Sergey Aganezov
William J. Salerno
Rajiv C. McCoy
Zachary B. Lippman
Michael C. Schatz
Fritz J. Sedlazeck

First Published April 2, 2021

Research

Comprehensive analysis of structural variants in breast cancer genomes using single-molecule sequencing

Sergey Aganezov
Sara Goodwin
Rachel M. Sherman
Fritz J. Sedlazeck
Gayatri Arun
Sonam Bhatia Isac Lee Melanie Kirsche Robert Wappel Melissa Kramer Karen Kostroff
... [+6 authors] ...,
David L. Spector
Winston Timp
W. Richard McCombie
Michael C. Schatz

First Published September 4, 2020

Research

Complex rearrangements and oncogene amplifications revealed by long-read DNA and RNA sequencing of a breast cancer cell line

Maria Nattestad
Sara Goodwin
Karen Ng
Timour Baslan
Fritz J. Sedlazeck
Philipp Rescheneder Tyler Garvin Han Fang James Gurtowski Elizabeth Hutton Elizabeth Tseng Chen-Shan Chin Timothy Beck Yogi Sundaravadanam Melissa Kramer Eric Antoniou
... [+11 authors] ...,
John D. McPherson
James Hicks
W. Richard McCombie
Michael C. Schatz

First Published June 28, 2018

Research

The evolution of inflorescence diversity in the nightshades and heterochrony during meristem maturation

Zachary H. Lemmon
Soon Ju Park
Ke Jiang
Joyce Van Eck
Michael C. Schatz
Zachary B. Lippman

First Published November 7, 2016

Method

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

Sara Goodwin
James Gurtowski
Scott Ethe-Sayers
Panchajanya Deshpande
Michael C. Schatz
W. Richard McCombie

First Published October 7, 2015

Perspective

Biological data sciences in genome research

Michael C. Schatz

First Published October 1, 2015

Corrigendum

Corrigendum: Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Jennifer Y. Tan
Tamara Sirey
Frantisek Honti
Bryony Graham
Allison Piovesan
Matthias Merkenschlager
Caleb Webber
Chris P. Ponting
Ana C. Marques

First Published September 1, 2015

Research

The clustering of functionally related genes contributes to CNV-mediated disease

Tallulah Andrews
Frantisek Honti
Rolph Pfundt
Nicole de Leeuw
Jayne Hehir-Kwa
Anneke Vulto-van Silfhout
Bert de Vries
Caleb Webber

First Published April 17, 2015

Research

Extensive microRNA-mediated crosstalk between lncRNAs and mRNAs in mouse embryonic stem cells

Jennifer Y. Tan
Tamara Sirey
Frantisek Honti
Bryony Graham
Allison Piovesan
Matthias Merkenschlager
Caleb Webber
Chris P. Ponting
Ana C. Marques

First Published March 19, 2015

Resource

GAGE: A critical evaluation of genome assemblies and assembly algorithms

Steven L. Salzberg
Adam M. Phillippy
Aleksey Zimin
Daniela Puiu
Tanja Magoc
Sergey Koren Todd J. Treangen Michael C. Schatz Arthur L. Delcher
... [+4 authors] ...,
Michael Roberts
Guillaume Marçais
Mihai Pop
James A. Yorke

First Published December 6, 2011

Resource

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Dent Earl
Keith Bradnam
John St. John
Aaron Darling
Dawei Lin
Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
... [+62 authors] ...,
Richard E. Green
David Haussler
Ian Korf
Benedict Paten