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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

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

Partial alignment of multislice spatially resolved transcriptomics data

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

Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci

  • Jonathan M. Mudge
  • Irwin Jungreis
  • Toby Hunt
  • Jose Manuel Gonzalez
  • James C. Wright
  • Mike Kay Claire Davidson Stephen Fitzgerald Ruth Seal Susan Tweedie Liang He Robert M. Waterhouse Yue Li
  • ... [+8 authors] ...,
  • Elspeth Bruford
  • Jyoti S. Choudhary
  • Adam Frankish
  • Manolis Kellis
  • First Published September 19, 2019
Research

An AR-ERG transcriptional signature defined by long-range chromatin interactomes in prostate cancer cells

  • Zhizhuo Zhang
  • Kern Rei Chng
  • Shreyas Lingadahalli
  • Zikai Chen
  • Mei Hui Liu
  • Huy Hoang Do Shaojiang Cai Nicola Rinaldi Huay Mei Poh Guoliang Li Ying Ying Sung Charlie L. Heng Leighton J. Core Si Kee Tan Xiaoan Ruan John T. Lis
  • ... [+11 authors] ...,
  • Manolis Kellis
  • Yijun Ruan
  • Wing-Kin Sung
  • Edwin Cheung
  • First Published January 3, 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
Method

cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis" > Identifying cis-mediators for trans-eQTLs across many human tissues using genomic mediation analysis

  • Fan Yang
  • Jiebiao Wang
  • Brandon L. Pierce
  • Lin S. Chen
  • François Aguet
  • Kristin G. Ardlie Beryl B. Cummings Ellen T. Gelfand Gad Getz Kane Hadley Robert E. Handsaker Katherine H. Huang Seva Kashin Konrad J. Karczewski Monkol Lek Xiao Li Daniel G. MacArthur Jared L. Nedzel Duyen T. Nguyen Michael S. Noble Ayellet V. Segrè Casandra A. Trowbridge Taru Tukiainen Nathan S. Abell Brunilda Balliu Ruth Barshir Omer Basha Alexis Battle Gireesh K. Bogu Andrew Brown Christopher D. Brown Stephane E. Castel Lin S. Chen Colby Chiang Donald F. Conrad Nancy J. Cox Farhan N. Damani Joe R. Davis Olivier Delaneau Emmanouil T. Dermitzakis Barbara E. Engelhardt Eleazar Eskin Pedro G. Ferreira Laure Frésard Eric R. Gamazon Diego Garrido-Martín Ariel D.H. Gewirtz Genna Gliner Michael J. Gloudemans Roderic Guigo Ira M. Hall Buhm Han Yuan He Farhad Hormozdiari Cedric Howald Hae Kyung Im Brian Jo Eun Yong Kang Yungil Kim Sarah Kim-Hellmuth Tuuli Lappalainen Gen Li Xin Li Boxiang Liu Serghei Mangul Mark I. McCarthy Ian C. McDowell Pejman Mohammadi Jean Monlong Stephen B. Montgomery Manuel Muñoz-Aguirre Anne W. Ndungu Dan L. Nicolae Andrew B. Nobel Meritxell Oliva Halit Ongen John J. Palowitch Nikolaos Panousis Panagiotis Papasaikas YoSon Park Princy Parsana Anthony J. Payne Christine B. Peterson Jie Quan Ferran Reverter Chiara Sabatti Ashis Saha Michael Sammeth Alexandra J. Scott Andrey A. Shabalin Reza Sodaei Matthew Stephens Barbara E. Stranger Benjamin J. Strober Jae Hoon Sul Emily K. Tsang Sarah Urbut Martijn van de Bunt Gao Wang Xiaoquan Wen Fred A. Wright Hualin S. Xi Esti Yeger-Lotem Zachary Zappala Judith B. Zaugg Yi-Hui Zhou Joshua M. Akey Daniel Bates Joanne Chan Lin S. Chen Melina Claussnitzer Kathryn Demanelis Morgan Diegel Jennifer A. Doherty Andrew P. Feinberg Marian S. Fernando Jessica Halow Kasper D. Hansen Eric Haugen Peter F. Hickey Lei Hou Farzana Jasmine Ruiqi Jian Lihua Jiang Audra Johnson Rajinder Kaul Manolis Kellis Muhammad G. Kibriya Kristen Lee Jin Billy Li Qin Li Xiao Li Jessica Lin Shin Lin Sandra Linder Caroline Linke Yaping Liu Matthew T. Maurano Benoit Molinie Stephen B. Montgomery Jemma Nelson Fidencio J. Neri Meritxell Oliva Yongjin Park Brandon L. Pierce Nicola J. Rinaldi Lindsay F. Rizzardi Richard Sandstrom Andrew Skol Kevin S. Smith Michael P. Snyder John Stamatoyannopoulos Barbara E. Stranger Hua Tang Emily K. Tsang Li Wang Meng Wang Nicholas Van Wittenberghe Fan Wu Rui Zhang Concepcion R. Nierras Philip A. Branton Latarsha J. Carithers Ping Guan Helen M. Moore Abhi Rao Jimmie B. Vaught Sarah E. Gould Nicole C. Lockart Casey Martin Jeffery P. Struewing Simona Volpi Anjene M. Addington Susan E. Koester A. Roger Little Lori E. Brigham Richard Hasz Marcus Hunter Christopher Johns Mark Johnson Gene Kopen William F. Leinweber John T. Lonsdale Alisa McDonald Bernadette Mestichelli Kevin Myer Brian Roe Michael Salvatore Saboor Shad Jeffrey A. Thomas Gary Walters Michael Washington Joseph Wheeler Jason Bridge Barbara A. Foster Bryan M. Gillard Ellen Karasik Rachna Kumar Mark Miklos Michael T. Moser Scott D. Jewell Robert G. Montroy Daniel C. Rohrer Dana R. Valley David A. Davis Deborah C. Mash Anita H. Undale Anna M. Smith David E. Tabor Nancy V. Roche Jeffrey A. McLean Negin Vatanian Karna L. Robinson Leslie Sobin Mary E. Barcus Kimberly M. Valentino Liqun Qi Steven Hunter Pushpa Hariharan Shilpi Singh Ki Sung Um Takunda Matose Maria M. Tomaszewski Laura K. Barker Maghboeba Mosavel Laura A. Siminoff Heather M. Traino Paul Flicek Thomas Juettemann Magali Ruffier Dan Sheppard Kieron Taylor Stephen J. Trevanion Daniel R. Zerbino Brian Craft Mary Goldman Maximilian Haeussler W. James Kent Christopher M. Lee
  • ... [+234 authors] ...,
  • Benedict Paten
  • Kate R. Rosenbloom
  • John Vivian
  • Jingchun Zhu
  • First Published October 11, 2017
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