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Research

Characterizing cytosine methylation of polymorphic transposable element insertions using the human pangenome resources

  • Xiaoyu Zhuo
  • Chad Tomlinson
  • Edward A. Belter
  • Prashant Kumar Kuntala
  • Wesley N. Saintilnord
  • Juan Jiang Tina Lindsay Juan F. Macias-Velasco Robert S. Fulton Ting Wang Derek Albracht Ivan A. Alexandrov Jamie Allen Alawi A. Alsheikh-Ali Nicolas Altemose Casey Andrews Dmitry Antipov Lucinda Antonacci-Fulton Mobin Asri Marcelo Ayllon Jennifer R. Balacco Floris P. Barthel Edward A. Belter Halle D. Bender Andrew P. Blair Davide Bolognini Katherine E. Bonini Christina Boucher Guillaume Bourque Silvia Buonaiuto Shuo Cao Andrew Carroll Ann M. Mc Cartney Monika Cechova Mark J.P. Chaisson Pi-Chuan Chang Xian Chang Jitender Cheema Haoyu Cheng Claudio Ciofi Hiram Clawson Sarah Cody Vincenza Colonna Holland C. Conwell Robert Cook-Deegan Mark Diekhans Maria Angela Diroma Daniel Doerr Zheng Dong Danilo Dubocanin 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 E. Garza Margarita Geleta Mohammadmersad Ghorbani Tina A. Graves-Lindsay Richard E. Green Cristian Groza Bida Gu Andrea Guarracino Melissa Gymrek Maximilian Haeussler Leanne Haggerty Ira M. Hall Nancy F. Hansen Yue Hao Mohammad Amiruddin Hashmi David Haussler Prajna Hebbar Peter Heringer Glenn Hickey Todd L. Hillaker S. Nakib Hossain Neng Huang Sarah E. Hunt Toby Hunt Alexander G. Ioannidis Nafiseh Jafarzadeh Nivesh Jain Erich D. Jarvis Maryam Jehangir Juan Jiang Eimear E. Kenny Juhyun Kim Bonhwang Koo Sergey Koren Milinn Kremitzki Charles H. Langley Ben Langmead Heather A. Lawson Daofeng Li Heng Li Wen-Wei Liao Jiadong Lin Tianjie Liu Glennis A. Logsdon Ryan Lorig-Roach Jonathan LoTempio Hailey Loucks Jane E. Loveland Jianguo Lu Shuangjia Lu Julian K. Lucas Walfred Ma Juan F. Macias-Velasco Kateryna D. Makova Maximillian G. Marin Christopher Markovic Tobias Marschall Franco L. Marsico 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 Pilar N. Ossorio Chie Owa Sadye Paez Benedict Paten Clelia Peano Adam M. Phillippy Brandon D. Pickett Laura Pignata Nadia Pisanti David Porubsky Pjotr Prins Anandi Radhakrishnan T. Rhyker Ranallo-Benavidez Brian J. Raney Mikko Rautiainen Alessandro Raveane Luyao Ren Arang Rhie Fedor Ryabov Samuel Sacco Farnaz Salehi 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 Ahmad Abou Tayoun Jack A.S. Tierney Chad Tomlinson Francesca Floriana Tricomi Mohammed Uddin Matteo Tommaso Ungaro Rahul Varki Flavia Villani Ivo Violich 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
  • ... [+208 authors] ...,
  • Wenjin Zhang
  • Ying Zhou
  • Xiaoyu Zhuo
  • Giulia Zunino
  • First Published May 14, 2026
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
Method

Accurate allocation of multimapped reads enables regulatory element analysis at repeats

  • Alexis Morrissey
  • Jeffrey Shi
  • Daniela Q. James
  • Shaun Mahony
  • First Published July 10, 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
Method

Size-based expectation maximization for characterizing nucleosome positions and subtypes

  • Jianyu Yang
  • Kuangyu Yen
  • Shaun Mahony
  • First Published June 17, 2024
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