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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

Accurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC

  • Byron J. Smith
  • Chunyu Zhao
  • Veronika Dubinkina
  • Xiaofan Jin
  • Liron Zahavi
  • Saar Shoer
  • Jacqueline Moltzau-Anderson
  • Eran Segal
  • Katherine S. Pollard
  • First Published April 10, 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
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

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
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

Sequence determinants of polyadenylation-mediated regulation

  • Ilya Vainberg Slutskin
  • Adina Weinberger
  • Eran Segal
  • First Published September 17, 2019
Research

Systematic interrogation of human promoters

  • Shira Weingarten-Gabbay
  • Ronit Nir
  • Shai Lubliner
  • Eilon Sharon
  • Yael Kalma
  • Adina Weinberger
  • Eran Segal
  • First Published January 8, 2019
Method

metaSPAdes: a new versatile metagenomic assembler

  • Sergey Nurk
  • Dmitry Meleshko
  • Anton Korobeynikov
  • Pavel A. Pevzner
  • First Published March 15, 2017
Corrigendum

Corrigendum: Large-scale mapping of gene regulatory logic reveals context-dependent repression by transcriptional activators

  • David van Dijk
  • Eilon Sharon
  • Maya Lotan-Pompan
  • Adina Weinberger
  • Eran Segal
  • Lucas B. Carey
  • First Published March 1, 2017
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