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

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

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

Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus

Bharat Panwar
Benjamin J. Schmiedel
Shu Liang
Brandie White
Enrique Rodriguez
Kenneth Kalunian Andrew J. McKnight
... [+2 authors] ...,
Rachel Soloff
Gregory Seumois
Pandurangan Vijayanand
Ferhat Ay

First Published March 5, 2021

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

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

Shilin Zhang
Yichen Wang
Lin Jia
Xue Wen
Zhonghua Du
Cong Wang Yajing Hao Dehai Yu Lei Zhou Naifei Chen Jingcheng Chen Huiling Chen Hui Zhang Ilkay Celik Günhan Gülsoy Jianjun Luo Baoming Qin Xueling Cui Zhonghui Liu Songling Zhang Miguel A. Esteban Ferhat Ay Wei Xu Runsheng Chen
... [+19 authors] ...,
Wei Li
Andrew R. Hoffman
Ji-Fan Hu
Jiuwei Cui

First Published July 17, 2019

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

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Maxwell W. Libbrecht
Ferhat Ay
Michael M. Hoffman
David M. Gilbert
Jeffrey A. Bilmes
William Stafford Noble

First Published February 12, 2015

Method

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

Ferhat Ay
Timothy L. Bailey
William Stafford Noble

First Published February 5, 2014

Method

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Daniel Marbach
Sushmita Roy
Ferhat Ay
Patrick E. Meyer
Rogerio Candeias
Tamer Kahveci
Christopher A. Bristow
Manolis Kellis

First Published March 28, 2012

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Your search for returned 10 results

Method

Highly accurate assembly polishing with DeepPolisher

Method

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

Method

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

Method

Multi–cell type gene coexpression network analysis reveals coordinated interferon response and cross–cell type correlations in systemic lupus erythematosus

Method

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

Method

Profiling the long noncoding RNA interaction network in the regulatory elements of target genes by chromatin in situ reverse transcription sequencing

Method

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

Method

Joint annotation of chromatin state and chromatin conformation reveals relationships among domain types and identifies domains of cell-type-specific expression

Method

Statistical confidence estimation for Hi-C data reveals regulatory chromatin contacts

Method

Drosophila melanogaster by integrative inference of transcriptional networks" > Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

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