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Optimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm

  • Samuel T. Horsfield
  • Basil C.T. Fok
  • Yuhan Fu
  • Paul Turner
  • John A. Lees
  • Nicholas J. Croucher
  • First Published March 4, 2025

k-mer analysis" > Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis

  • Romain Derelle
  • Johanna von Wachsmann
  • Tommi Mäklin
  • Joel Hellewell
  • Timothy Russell
  • Ajit Lalvani
  • ... [+1 authors] ...,
  • Leonid Chindelevitch
  • Nicholas J. Croucher
  • Simon R. Harris
  • John A. Lees
  • First Published October 15, 2024

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

Accurate and fast graph-based pangenome annotation and clustering with ggCaller

  • Samuel T. Horsfield
  • Gerry Tonkin-Hill
  • Nicholas J. Croucher
  • John A. Lees
  • First Published August 24, 2023

Genealogical inference and more flexible sequence clustering using iterative-PopPUNK

  • Bin Zhao
  • John A. Lees
  • Hongjin Wu
  • Chao Yang
  • Daniel Falush
  • First Published May 30, 2023

C. Thomas Caskey (1938–2022)

  • Richard A. Gibbs
  • Aravinda Chakravarti
  • Evan E. Eichler
  • Eric D. Green
  • Richard M. Myers
  • Anne C. Ferguson-Smith
  • Kateryna D. Makova
  • Hillary E. Sussman
  • First Published February 17, 2022

Deborah A. Nickerson (1954 –2021)

  • Aravinda Chakravarti
  • Evan E. Eichler
  • Richard A. Gibbs
  • Eric D. Green
  • Richard M. Myers
  • Hillary E. Sussman
  • First Published January 24, 2022

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

Enhancers with tissue-specific activity are enriched in intronic regions

  • Beatrice Borsari
  • Pablo Villegas-Mirón
  • Sílvia Pérez-Lluch
  • Isabel Turpin
  • Hafid Laayouni
  • Alba Segarra-Casas
  • Jaume Bertranpetit
  • Roderic Guigó
  • Sandra Acosta
  • First Published July 21, 2021

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
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