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Method

OMKar automates genome karyotyping using optical maps to identify constitutional abnormalities

  • Siavash Raeisi Dehkordi
  • Zhaoyang Jia
  • Joey Estabrook
  • Jen Hauenstein
  • Neil Miller
  • Naz Güleray-Lafci Jürgen Neesen Alex Hastie
  • ... [+3 authors] ...,
  • Alka Chaubey
  • Andy Wing Chun Pang
  • Paul Dremsek
  • Vineet Bafna
  • First Published November 14, 2025
Method

CoRAL accurately resolves extrachromosomal DNA genome structures with long-read sequencing

  • Kaiyuan Zhu
  • Matthew G. Jones
  • Jens Luebeck
  • Xinxin Bu
  • Hyerim Yi
  • King L. Hung Ivy Tsz-Lo Wong
  • ... [+2 authors] ...,
  • Shu Zhang
  • Paul S. Mischel
  • Howard Y. Chang
  • Vineet Bafna
  • First Published July 9, 2024
Method

Ancestry-agnostic estimation of DNA sample contamination from sequence reads

  • Fan Zhang
  • Matthew Flickinger
  • Sarah A. Gagliano Taliun
  • Gonçalo R. Abecasis
  • Laura J. Scott
  • Steven A. McCaroll
  • Carlos N. Pato
  • Michael Boehnke
  • Hyun Min Kang
  • First Published January 24, 2020
Research

Detection of vancomycin-resistant Enterococcus faecium hospital-adapted lineages in municipal wastewater treatment plants indicates widespread distribution and release into the environment

  • Theodore Gouliouris
  • Kathy E. Raven
  • Danesh Moradigaravand
  • Catherine Ludden
  • Francesc Coll
  • Beth Blane Plamena Naydenova Carolyne Horner Nicholas M. Brown
  • ... [+4 authors] ...,
  • Jukka Corander
  • Direk Limmathurotsakul
  • Julian Parkhill
  • Sharon J. Peacock
  • First Published March 21, 2019
Method

Targeted genotyping of variable number tandem repeats with adVNTR

  • Mehrdad Bakhtiari
  • Sharona Shleizer-Burko
  • Melissa Gymrek
  • Vikas Bansal
  • Vineet Bafna
  • First Published October 23, 2018
Corrigendum

Corrigendum: Building a genomic framework for prospective MRSA surveillance in the United Kingdom and the Republic of Ireland

  • Sandra Reuter
  • M. Estée Török
  • Matthew T.G. Holden
  • Rosy Reynolds
  • Kathy E. Raven
  • Beth Blane Tjibbe Donker Stephen D. Bentley David M. Aanensen Hajo Grundmann
  • ... [+5 authors] ...,
  • Edward J. Feil
  • Brian G. Spratt
  • Julian Parkhill
  • Sharon J. Peacock
  • First Published September 1, 2017
Research

Systematic longitudinal survey of invasive Escherichia coli in England demonstrates a stable population structure only transiently disturbed by the emergence of ST131

  • Teemu Kallonen
  • Hayley J. Brodrick
  • Simon R. Harris
  • Jukka Corander
  • Nicholas M. Brown
  • Veronique Martin
  • Sharon J. Peacock
  • Julian Parkhill
  • First Published July 18, 2017
Research

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

  • James Hadfield
  • Simon R. Harris
  • Helena M.B. Seth-Smith
  • Surendra Parmar
  • Patiyan Andersson
  • Philip M. Giffard Julius Schachter Jeanne Moncada Louise Ellison María Lucía Gallo Vaulet Marcelo Rodríguez Fermepin Frans Radebe Suyapa Mendoza Sander Ouburg Servaas A. Morré Konrad Sachse Mirja Puolakkainen Suvi J. Korhonen Chris Sonnex Rebecca Wiggins Hamid Jalal Tamara Brunelli Patrizia Casprini Rachel Pitt Cathy Ison Alevtina Savicheva Elena Shipitsyna Ronza Hadad Laszlo Kari Matthew J. Burton David Mabey Anthony W. Solomon David Lewis Peter Marsh
  • ... [+29 authors] ...,
  • Magnus Unemo
  • Ian N. Clarke
  • Julian Parkhill
  • Nicholas R. Thomson
  • First Published June 6, 2017
Method

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

  • Peter Edge
  • Vineet Bafna
  • Vikas Bansal
  • First Published December 9, 2016
Research

Multiple major disease-associated clones of Legionella pneumophila have emerged recently and independently

  • Sophia David
  • Christophe Rusniok
  • Massimo Mentasti
  • Laura Gomez-Valero
  • Simon R. Harris
  • Pierre Lechat John Lees Christophe Ginevra Philippe Glaser Laurence Ma Christiane Bouchier Anthony Underwood
  • ... [+7 authors] ...,
  • Sophie Jarraud
  • Timothy G. Harrison
  • Julian Parkhill
  • Carmen Buchrieser
  • First Published September 23, 2016
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