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Method

Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs

  • Juri Kuronen
  • Samuel T. Horsfield
  • Anna K. Pöntinen
  • Sudaraka Mallawaarachchi
  • Sergio Arredondo-Alonso
  • Harry Thorpe Rebecca A. Gladstone Rob J.L. Willems Stephen D. Bentley Nicholas J. Croucher
  • ... [+5 authors] ...,
  • Johan Pensar
  • John A. Lees
  • Gerry Tonkin-Hill
  • Jukka Corander
  • First Published August 12, 2024
Method

Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe

  • Gerry Tonkin-Hill
  • Rebecca A. Gladstone
  • Anna K. Pöntinen
  • Sergio Arredondo-Alonso
  • Stephen D. Bentley
  • Jukka Corander
  • First Published January 20, 2023
Research

RET regulatory code is disrupted in Hirschsprung disease" > A multi-enhancer RET regulatory code is disrupted in Hirschsprung disease

  • Sumantra Chatterjee
  • Kameko M. Karasaki
  • Lauren E. Fries
  • Ashish Kapoor
  • Aravinda Chakravarti
  • First Published November 15, 2021
Method

Sequence-based correction of barcode bias in massively parallel reporter assays

  • Dongwon Lee
  • Ashish Kapoor
  • Changhee Lee
  • Michael Mudgett
  • Michael A. Beer
  • Aravinda Chakravarti
  • First Published July 20, 2021
Research

Neisseria meningitidis" > The effect of recombination on the evolution of a population of Neisseria meningitidis

  • Neil MacAlasdair
  • Maiju Pesonen
  • Ola Brynildsrud
  • Vegard Eldholm
  • Paul A. Kristiansen
  • Jukka Corander
  • Dominique A. Caugant
  • Stephen D. Bentley
  • First Published June 9, 2021
Method

Fast and flexible bacterial genomic epidemiology with PopPUNK

  • John A. Lees
  • Simon R. Harris
  • Gerry Tonkin-Hill
  • Rebecca A. Gladstone
  • Stephanie W. Lo
  • Jeffrey N. Weiser
  • Jukka Corander
  • Stephen D. Bentley
  • Nicholas J. Croucher
  • First Published January 24, 2019
Method

cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants" > Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants

  • Dongwon Lee
  • Ashish Kapoor
  • Alexias Safi
  • Lingyun Song
  • Marc K. Halushka
  • Gregory E. Crawford
  • Aravinda Chakravarti
  • First Published August 23, 2018
Resource

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 December 15, 2015
Research

Staphylococcus aureus pandemic" > A genomic portrait of the emergence, evolution, and global spread of a methicillin-resistant Staphylococcus aureus pandemic

  • Matthew T.G. Holden
  • Li-Yang Hsu
  • Kevin Kurt
  • Lucy A. Weinert
  • Alison E. Mather
  • Simon R. Harris Birgit Strommenger Franziska Layer Wolfgang Witte Herminia de Lencastre Robert Skov Henrik Westh Helena Žemličková Geoffrey Coombs Angela M. Kearns Robert L.R. Hill Jonathan Edgeworth Ian Gould Vanya Gant Jonathan Cooke Giles F. Edwards Paul R. McAdam Kate E. Templeton Angela McCann Zhemin Zhou Santiago Castillo-Ramírez Edward J. Feil Lyndsey O. Hudson Mark C. Enright Francois Balloux David M. Aanensen Brian G. Spratt J. Ross Fitzgerald
  • ... [+28 authors] ...,
  • Julian Parkhill
  • Mark Achtman
  • Stephen D. Bentley
  • Ulrich Nübel
  • First Published January 8, 2013
Research

Microevolution of extensively drug-resistant tuberculosis in Russia

  • Nicola Casali
  • Vladyslav Nikolayevskyy
  • Yanina Balabanova
  • Olga Ignatyeva
  • Irina Kontsevaya
  • Simon R. Harris Stephen D. Bentley Julian Parkhill Sergey Nejentsev
  • ... [+4 authors] ...,
  • Sven E. Hoffner
  • Rolf D. Horstmann
  • Timothy Brown
  • Francis Drobniewski
  • First Published January 31, 2012
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