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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

A deconvolution framework that uses single-cell sequencing plus a small benchmark data set for accurate analysis of cell type ratios in complex tissue samples

  • Shuai Guo
  • Xiaoqian Liu
  • Xuesen Cheng
  • Yujie Jiang
  • Shuangxi Ji
  • Qingnan Liang Andrew Koval Yumei Li Leah A. Owen Ivana K. Kim Ana Aparicio Sanghoon Lee Anil K. Sood Scott Kopetz John Paul Shen
  • ... [+10 authors] ...,
  • John N. Weinstein
  • Margaret M. DeAngelis
  • Rui Chen
  • Wenyi Wang
  • First Published November 25, 2024
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
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
Method

metaSPAdes: a new versatile metagenomic assembler

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

Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform" > Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

  • Jeffrey S. McLean
  • Mary-Jane Lombardo
  • Michael G. Ziegler
  • Mark Novotny
  • Joyclyn Yee-Greenbaum
  • Jonathan H. Badger Glenn Tesler Sergey Nurk Valery Lesin Daniel Brami Adam P. Hall Anna Edlund Lisa Z. Allen Scott Durkin Sharon Reed Francesca Torriani Kenneth H. Nealson
  • ... [+12 authors] ...,
  • Pavel A. Pevzner
  • Robert Friedman
  • J. Craig Venter
  • Roger S. Lasken
  • First Published April 5, 2013
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