Search | Genome Research

Method

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Dmitry Antipov
Mikko Rautiainen
Sergey Nurk
Brian P. Walenz
Steven J. Solar
Adam M. Phillippy
Sergey Koren

First Published May 19, 2025

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

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

Method

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Ryan Lorig-Roach
Melissa Meredith
Jean Monlong
Miten Jain
Hugh E. Olsen
Brandy McNulty David Porubsky Tessa G. Montague Julian K. Lucas Chris Condon Jordan M. Eizenga Sissel Juul Sean K. McKenzie Sara E. Simmonds Jimin Park Mobin Asri Sergey Koren Evan E. Eichler Richard Axel
... [+14 authors] ...,
Bruce Martin
Paolo Carnevali
Karen H. Miga
Benedict Paten

First Published April 16, 2024

Method

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Sergey Nurk
Brian P. Walenz
Arang Rhie
Mitchell R. Vollger
Glennis A. Logsdon
Robert Grothe
... [+1 authors] ...,
Karen H. Miga
Evan E. Eichler
Adam M. Phillippy
Sergey Koren

First Published August 14, 2020

Method

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

Hagen Tilgner
Fereshteh Jahanbani
Ishaan Gupta
Paul Collier
Eric Wei
Morten Rasmussen
Michael Snyder

First Published December 1, 2017

Method

k-mer weighting and repeat separation" > Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Sergey Koren
Brian P. Walenz
Konstantin Berlin
Jason R. Miller
Nicholas H. Bergman
Adam M. Phillippy

First Published March 15, 2017

Method

Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm" > Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

Aleksey V. Zimin
Daniela Puiu
Ming-Cheng Luo
Tingting Zhu
Sergey Koren
Guillaume Marçais
James A. Yorke
Jan Dvořák
Steven L. Salzberg

First Published January 27, 2017

Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Anshul Kundaje
Sofia Kyriazopoulou-Panagiotopoulou
Max Libbrecht
Cheryl L. Smith
Debasish Raha
Elliott E. Winters
... [+1 authors] ...,
Steven M. Johnson
Michael Snyder
Serafim Batzoglou
Arend Sidow

First Published September 5, 2012

Method

Linking disease associations with regulatory information in the human genome

Marc A. Schaub
Alan P. Boyle
Anshul Kundaje
Serafim Batzoglou
Michael Snyder

First Published September 5, 2012

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Your search for returned 11 results

Method

Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding

Method

Highly accurate assembly polishing with DeepPolisher

Method

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

Method

Phased nanopore assembly with Shasta and modular graph phasing with GFAse

Method

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

Method

Microfluidic isoform sequencing shows widespread splicing coordination in the human transcriptome

Method

k-mer weighting and repeat separation" > Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

Method

Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm" > Hybrid assembly of the large and highly repetitive genome of Aegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

Method

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements

Method

Linking disease associations with regulatory information in the human genome

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Your search for returned 11 results

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