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Review

Building genomic data structures from compressed representations using prefix-free parsing

  • Rahul Varki
  • Christina Boucher
  • First Published May 15, 2026
Method

Long-read reconstruction of many diverse haplotypes with devider

  • Jim Shaw
  • Christina Boucher
  • Yun William Yu
  • Noelle Noyes
  • Heng Li
  • First Published September 23, 2025
Method

Robust 16S rRNA classification based on a compressed LCA index

  • Omar Ahmed
  • Christina Boucher
  • Ben Langmead
  • First Published August 25, 2025
Method

r-index-based pangenome indexing" > Accurate short-read alignment through r-index-based pangenome indexing

  • Rahul Varki
  • Massimiliano Rossi
  • Eddie Ferro
  • Marco Oliva
  • Erik Garrison
  • Ben Langmead
  • Christina Boucher
  • First Published June 12, 2025
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

Factors impacting target-enriched long-read sequencing of resistomes and mobilomes

  • Ilya B. Slizovskiy
  • Nathalie Bonin
  • Jonathan E. Bravo
  • Peter M. Ferm
  • Jacob Singer
  • Christina Boucher
  • Noelle R. Noyes
  • First Published November 5, 2024
Research

Long-read genome sequencing and variant reanalysis increase diagnostic yield in neurodevelopmental disorders

  • Susan M. Hiatt
  • James M.J. Lawlor
  • Lori H. Handley
  • Donald R. Latner
  • Zachary T. Bonnstetter
  • Candice R. Finnila Michelle L. Thompson Lori Beth Boston Melissa Williams Ivan Rodriguez Nunez Jerry Jenkins Whitley V. Kelley E. Martina Bebin Michael A. Lopez Anna C.E. Hurst
  • ... [+10 authors] ...,
  • Bruce R. Korf
  • Jeremy Schmutz
  • Jane Grimwood
  • Gregory M. Cooper
  • First Published September 19, 2024
Resource

Allele-specific transcription factor binding across human brain regions offers mechanistic insight into eQTLs

  • Ashlyn G. Anderson
  • Belle A. Moyers
  • Jacob M. Loupe
  • Ivan Rodriguez-Nunez
  • Stephanie A. Felker
  • James M.J. Lawlor William E. Bunney Blynn G. Bunney Preston M. Cartagena Adolfo Sequeira Stanley J. Watson
  • ... [+6 authors] ...,
  • Huda Akil
  • Eric M. Mendenhall
  • Gregory M. Cooper
  • Richard M. Myers
  • First Published August 16, 2024
Method

cis-regulatory elements" > Probabilistic association of differentially expressed genes with cis-regulatory elements

  • Brian S. Roberts
  • Ashlyn G. Anderson
  • E. Christopher Partridge
  • Gregory M. Cooper
  • Richard M. Myers
  • First Published April 17, 2024
Method

Efficient taxa identification using a pangenome index

  • Omar Ahmed
  • Massimiliano Rossi
  • Christina Boucher
  • Ben Langmead
  • First Published May 31, 2023
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