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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

Partial alignment of multislice spatially resolved transcriptomics data

  • Xinhao Liu
  • Ron Zeira
  • Benjamin J. Raphael
  • First Published August 8, 2023
Research

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
Method

Reconstruction of clone- and haplotype-specific cancer genome karyotypes from bulk tumor samples

  • Sergey Aganezov
  • Benjamin J. Raphael
  • First Published September 4, 2020
Resource

A chromosome-level assembly of the Atlantic herring genome—detection of a supergene and other signals of selection

  • Mats E. Pettersson
  • Christina M. Rochus
  • Fan Han
  • Junfeng Chen
  • Jason Hill
  • Ola Wallerman Guangyi Fan Xiaoning Hong Qiwu Xu He Zhang Shanshan Liu Xin Liu Leanne Haggerty Toby Hunt Fergal J. Martin
  • ... [+10 authors] ...,
  • Paul Flicek
  • Ignas Bunikis
  • Arild Folkvord
  • Leif Andersson
  • First Published October 24, 2019
Method

Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors

  • Jack Kuipers
  • Katharina Jahn
  • Benjamin J. Raphael
  • Niko Beerenwinkel
  • First Published October 13, 2017
Resource

GenomeVIP: a cloud platform for genomic variant discovery and interpretation

  • R. Jay Mashl
  • Adam D. Scott
  • Kuan-lin Huang
  • Matthew A. Wyczalkowski
  • Christopher J. Yoon
  • Beifang Niu Erin DeNardo Venkata D. Yellapantula Robert E. Handsaker Ken Chen Daniel C. Koboldt Kai Ye
  • ... [+7 authors] ...,
  • David Fenyö
  • Benjamin J. Raphael
  • Michael C. Wendl
  • Li Ding
  • First Published May 18, 2017
Method

De novo discovery of mutated driver pathways in cancer

  • Fabio Vandin
  • Eli Upfal
  • Benjamin J. Raphael
  • First Published June 7, 2011
Methods

Decoding the fine-scale structure of a breast cancer genome and transcriptome

  • Stanislav Volik
  • Benjamin J. Raphael
  • Guiqing Huang
  • Michael R. Stratton
  • Graham Bignel
  • John Murnane John H. Brebner Krystyna Bajsarowicz Pamela L. Paris Quanzhou Tao David Kowbel Anna Lapuk Dmitri A. Shagin Irina A. Shagina Joe W. Gray
  • ... [+10 authors] ...,
  • Jan-Fang Cheng
  • Pieter J. de Jong
  • Pavel Pevzner
  • Colin Collins
  • First Published February 3, 2006
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