Search | Genome Research

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

Charting the regulatory landscape of TP53 on transposable elements in cancer

Xuan Qu
Yonghao Liang
Colin McCornack
Xiaoyun Xing
Heather Schmidt
Chad Tomlinson
... [+1 authors] ...,
Catrina Fronick
Edward A. Belter
Juan F. Macias-Velasco
Ting Wang

First Published May 13, 2025

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Jiawei Shen
Siyuan Cheng
Deepak Purushotham
Xiaoyu Zhuo
Alan Y Du
Wenjin Zhang
Daofeng Li
Ting Wang

First Published February 21, 2025

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

Yujie Chen
Yiran Hou
Qinglin Zeng
Irene Wang
Meiru Shang
Kwangdeok Shin Christopher Hemauer
... [+2 authors] ...,
Xiaoyun Xing
Junsu Kang
Guoyan Zhao
Ting Wang

First Published January 14, 2025

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Ju Heon Maeng
H. Josh Jang
Alan Y. Du
Shin-Cheng Tzeng
Ting Wang

First Published December 8, 2023

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

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Xiaoyu Zhuo
Silas Hsu
Deepak Purushotham
Prashant Kumar Kuntala
Jessica K. Harrison
Alan Y. Du
Samuel Chen
Daofeng Li
Ting Wang

First Published May 8, 2023

Functional characterization of enhancer activity during a long terminal repeat's evolution

Alan Y. Du
Xiaoyu Zhuo
Vasavi Sundaram
Nicholas O. Jensen
Hemangi G. Chaudhari
Nancy L. Saccone
Barak A. Cohen
Ting Wang

First Published October 3, 2022

cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish" > Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish

Hyung Joo Lee
Yiran Hou
Ju Heon Maeng
Nakul M. Shah
Yujie Chen
Heather A. Lawson
Hongbo Yang
Feng Yue
Ting Wang

First Published June 1, 2022

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

Wanqing Shao
Ting Wang

First Published December 21, 2020

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Xiaoyu Zhuo
Alan Y. Du
Erica C. Pehrsson
Daofeng Li
Ting Wang

First Published December 10, 2020

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Jin Li
Yan Li
Wei Li
Huaibing Luo
Yanping Xi
Shihua Dong Ming Gao Peng Xu Baolong Zhang Ying Liang Qingping Zou Xin Hu Lina Peng Dan Zou Ting Wang Hongbo Yang
... [+11 authors] ...,
Cizhong Jiang
Shaoliang Peng
Feizhen Wu
Wenqiang Yu

First Published January 22, 2019

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Vasavi Sundaram
Yong Cheng
Zhihai Ma
Daofeng Li
Xiaoyun Xing
Peter Edge
Michael P. Snyder
Ting Wang

First Published October 15, 2014

Recurrent epimutations activate gene body promoters in primary glioblastoma

Raman P. Nagarajan
Bo Zhang
Robert J.A. Bell
Brett E. Johnson
Adam B. Olshen
Vasavi Sundaram Daofeng Li Ashley E. Graham Aaron Diaz Shaun D. Fouse Ivan Smirnov
... [+6 authors] ...,
Jun Song
Pamela L. Paris
Ting Wang
Joseph F. Costello

First Published April 7, 2014

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Bo Zhang
Yan Zhou
Nan Lin
Rebecca F. Lowdon
Chibo Hong
Raman P. Nagarajan Jeffrey B. Cheng Daofeng Li Michael Stevens Hyung Joo Lee Xiaoyun Xing Jia Zhou Vasavi Sundaram GiNell Elliott Junchen Gu Taoping Shi Philippe Gascard Mahvash Sigaroudinia Thea D. Tlsty Theresa Kadlecek Arthur Weiss Henriette O’Geen Peggy J. Farnham Cécile L. Maire Keith L. Ligon Pamela A.F. Madden Angela Tam Richard Moore Martin Hirst
... [+24 authors] ...,
Marco A. Marra
Baoxue Zhang
Joseph F. Costello
Ting Wang

First Published June 26, 2013

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Michael Stevens
Jeffrey B. Cheng
Daofeng Li
Mingchao Xie
Chibo Hong
Cécile L. Maire Keith L. Ligon
... [+2 authors] ...,
Martin Hirst
Marco A. Marra
Joseph F. Costello
Ting Wang

First Published June 26, 2013

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

Pengfei Yu
Shu Xiao
Xiaoyun Xin
Chun-Xiao Song
Wei Huang
Darina McDee
... [+1 authors] ...,
Tetsuya Tanaka
Ting Wang
Chuan He
Sheng Zhong

First Published October 2, 2012

Spark: A navigational paradigm for genomic data exploration

Cydney B. Nielsen
Hamid Younesy
Henriette O'Geen
Xiaoqin Xu
Andrew R. Jackson
Aleksandar Milosavljevic Ting Wang
... [+2 authors] ...,
Joseph F. Costello
Martin Hirst
Peggy J. Farnham
Steven J.M. Jones

First Published September 7, 2012

Leishmania" > Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

Matthew B. Rogers
James D. Hilley
Nicholas J. Dickens
Jon Wilkes
Paul A. Bates
Daniel P. Depledge David Harris Yerim Her Pawel Herzyk Hideo Imamura Thomas D. Otto Mandy Sanders Kathy Seeger Jean-Claude Dujardin
... [+9 authors] ...,
Matthew Berriman
Deborah F. Smith
Christiane Hertz-Fowler
Jeremy C. Mottram

First Published October 28, 2011

Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype" > Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

Robert A. Kingsley
Chisomo L. Msefula
Nicholas R. Thomson
Samuel Kariuki
Kathryn E. Holt
Melita A. Gordon David Harris Louise Clarke Sally Whitehead Vartul Sangal Kevin Marsh Mark Achtman Malcolm E. Molyneux Martin Cormican
... [+9 authors] ...,
Julian Parkhill
Calman A. MacLennan
Robert S. Heyderman
Gordon Dougan

First Published November 9, 2009

Candida dubliniensis and Candida albicans" > Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

Andrew P. Jackson
John A. Gamble
Tim Yeomans
Gary P. Moran
David Saunders
David Harris Martin Aslett Jamie F. Barrell Geraldine Butler Francesco Citiulo David C. Coleman Piet W.J. de Groot Tim J. Goodwin Michael A. Quail Jacqueline McQuillan Carol A. Munro Arnab Pain Russell T. Poulter Marie-Adèle Rajandream Hubert Renauld Martin J. Spiering Adrian Tivey
... [+17 authors] ...,
Neil A.R. Gow
Barclay Barrell
Derek J. Sullivan
Matthew Berriman

First Published September 10, 2009

Pseudomonas aeruginosa" > Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

Craig Winstanley
Morgan G.I. Langille
Joanne L. Fothergill
Irena Kukavica-Ibrulj
Catherine Paradis-Bleau
François Sanschagrin Nicholas R. Thomson Geoff L. Winsor Michael A. Quail Nicola Lennard Alexandra Bignell Louise Clarke Kathy Seeger David Saunders David Harris
... [+10 authors] ...,
Julian Parkhill
Robert E.W. Hancock
Fiona S.L. Brinkman
Roger C. Levesque

First Published December 1, 2008

Toxoplasma gondii" > Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

Asis Khan
Ulrike Böhme
Krystyna A. Kelly
Ellen Adlem
Karen Brooks
Mark Simmonds Karen Mungall Michael A. Quail Claire Arrowsmith Tracey Chillingworth Carol Churcher David Harris Matthew Collins Nigel Fosker Audrey Fraser Zahra Hance Kay Jagels Sharon Moule Lee Murphy Susan O'Neil Marie-Adele Rajandream David Saunders Kathy Seeger Sally Whitehead Thomas Mayr Xuenan Xuan Junichi Watanabe Yutaka Suzuki Hiroyuki Wakaguri Sumio Sugano Chihiro Sugimoto Ian Paulsen Aaron J. Mackey David S. Roos Neil Hall
... [+30 authors] ...,
Matthew Berriman
Bart Barrell
L. David Sibley
James W. Ajioka

First Published August 10, 2006

X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies" > From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

Panayiotis V. Benos
Melanie K. Gatt
Lee Murphy
David Harris
Bart Barrell
Concepcion Ferraz Sophie Vidal Christine Brun Jacques Demaille Edouard Cadieu Stephane Dreano Stéphanie Gloux Valerie Lelaure Stephanie Mottier Francis Galibert Dana Borkova Belen Miñana Fotis C. Kafatos Slava Bolshakov Inga Sidén-Kiamos George Papagiannakis Lefteris Spanos Christos Louis Encarnación Madueño Beatriz de Pablos Juan Modolell Annette Peter Petra Schöttler Meike Werner Fotini Mourkioti Nicole Beinert Gordon Dowe Ulrich Schäfer Herbert Jäckle Alain Bucheton Debbie Callister Lorna Campbell Nadine S. Henderson Paul J. McMillan Cathy Salles Evelyn Tait Phillipe Valenti Robert D.C. Saunders
... [+38 authors] ...,
Alain Billaud
Lior Pachter
David M. Glover
Michael Ashburner

First Published May 1, 2001

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Your search for returned 24 results

Highly accurate assembly polishing with DeepPolisher

Charting the regulatory landscape of TP53 on transposable elements in cancer

Exploring the epigenome profiles of repetitive elements with the WashU Repeat Browser

Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution

Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome

Gaps and complex structurally variant loci in phased genome assemblies

Comparing genomic and epigenomic features across species using the WashU Comparative Epigenome Browser

Functional characterization of enhancer activity during a long terminal repeat's evolution

cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish" > Epigenomic analysis reveals prevalent contribution of transposable elements to cis-regulatory elements, tissue-specific expression, and alternative promoters in zebrafish

Transcript assembly improves expression quantification of transposable elements in single-cell RNA-seq data

Epigenomic differences in the human and chimpanzee genomes are associated with structural variation

Guide Positioning Sequencing identifies aberrant DNA methylation patterns that alter cell identity and tumor-immune surveillance networks

Widespread contribution of transposable elements to the innovation of gene regulatory networks

Recurrent epimutations activate gene body promoters in primary glioblastoma

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

Estimating absolute methylation levels at single-CpG resolution from methylation enrichment and restriction enzyme sequencing methods

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

Spark: A navigational paradigm for genomic data exploration

Leishmania" > Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype" > Epidemic multiple drug resistant Salmonella Typhimurium causing invasive disease in sub-Saharan Africa have a distinct genotype

Candida dubliniensis and Candida albicans" > Comparative genomics of the fungal pathogens Candida dubliniensis and Candida albicans

Pseudomonas aeruginosa" > Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa

Toxoplasma gondii" > Common inheritance of chromosome Ia associated with clonal expansion of Toxoplasma gondii

X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies" > From First Base: The Sequence of the Tip of the X Chromosome of Drosophila melanogaster, a Comparison of Two Sequencing Strategies

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Your search for returned 24 results