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Method

Multicondition and multimodal temporal profile inference during mouse embryonic development

  • Ran Zhang
  • Chengxiang Qiu
  • Galina N. Filippova
  • Gang Li
  • Jay Shendure
  • Jean-Philippe Vert
  • Xinxian Deng
  • William Stafford Noble
  • Christine M. Disteche
  • First Published August 14, 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

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

Enzymatic methyl sequencing detects DNA methylation at single-base resolution from picograms of DNA

  • Romualdas Vaisvila
  • V.K. Chaithanya Ponnaluri
  • Zhiyi Sun
  • Bradley W. Langhorst
  • Lana Saleh
  • Shengxi Guan Nan Dai Matthew A. Campbell Brittany S. Sexton Katherine Marks Mala Samaranayake James C. Samuelson Heidi E. Church Esta Tamanaha Ivan R. Corrêa Sriharsa Pradhan
  • ... [+11 authors] ...,
  • Eileen T. Dimalanta
  • Thomas C. Evans
  • Louise Williams
  • Theodore B. Davis
  • First Published June 17, 2021
Resource

Caenorhabditis elegans nematodes" > Comprehensive characterization of tissue-specific chromatin accessibility in L2 Caenorhabditis elegans nematodes

  • Timothy J. Durham
  • Riza M. Daza
  • Louis Gevirtzman
  • Darren A. Cusanovich
  • Olubusayo Bolonduro
  • William Stafford Noble
  • Jay Shendure
  • Robert H. Waterston
  • First Published April 22, 2021
Research

Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands

  • Brian S. Roberts
  • E. Christopher Partridge
  • Bryan A. Moyers
  • Vikram Agarwal
  • Kimberly M. Newberry
  • Beth K. Martin
  • Jay Shendure
  • Richard M. Myers
  • Gregory M. Cooper
  • First Published April 20, 2021
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
Research

Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology" > Suppressor mutations in Mecp2-null mice implicate the DNA damage response in Rett syndrome pathology

  • Adebola Enikanolaiye
  • Julie Ruston
  • Rong Zeng
  • Christine Taylor
  • Marijke Schrock
  • Christie M. Buchovecky
  • Jay Shendure
  • Elif Acar
  • Monica J. Justice
  • First Published April 21, 2020
Corrigendum

Corrigendum: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity

  • Fumitaka Inoue
  • Martin Kircher
  • Beth Martin
  • Gregory M. Cooper
  • Daniela M. Witten
  • Michael T. McManus
  • Nadav Ahituv
  • Jay Shendure
  • First Published May 1, 2018
Method

k-mer weighting and repeat separation" > Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation

  • Sergey Koren
  • Brian P. Walenz
  • Konstantin Berlin
  • Jason R. Miller
  • Nicholas H. Bergman
  • Adam M. Phillippy
  • First Published March 15, 2017
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