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Single-cell template strand sequencing reveals culture-induced chromosomal instability in a gibbon cell line

Alessia Daponte
Gerardina Chirico
Annalisa Paparella
Annalaura Montanari
Caterina Manzari
Martina Macino Oliver Dionisi Dyck Francesco De Leonardis Flavia Angela Maria Maggiolini Alberto L'Abbate Francesco Montinaro Sandra Louzada
... [+7 authors] ...,
Mario Ventura
Ashley D. Sanders
Francesca Antonacci
Claudia Rita Catacchio

First Published May 4, 2026

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

A high-resolution map of small-scale inversions in the gibbon genome

Ludovica Mercuri
Donato Palmisano
Alberto L'Abbate
Pietro D'Addabbo
Francesco Montinaro
Claudia Rita Catacchio Patrick Hasenfeld Mario Ventura
... [+3 authors] ...,
Jan O. Korbel
Ashley D. Sanders
Flavia Angela Maria Maggiolini
Francesca Antonacci

First Published September 30, 2022

Single-cell strand sequencing of a macaque genome reveals multiple nested inversions and breakpoint reuse during primate evolution

Flavia Angela Maria Maggiolini
Ashley D. Sanders
Colin James Shew
Arvis Sulovari
Yafei Mao
Marta Puig Claudia Rita Catacchio Maria Dellino Donato Palmisano Ludovica Mercuri Miriana Bitonto David Porubský Mario Cáceres Evan E. Eichler
... [+9 authors] ...,
Mario Ventura
Megan Y. Dennis
Jan O. Korbel
Francesca Antonacci

First Published October 22, 2020

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

Inversion variants in human and primate genomes

Claudia Rita Catacchio
Flavia Angela Maria Maggiolini
Pietro D'Addabbo
Miriana Bitonto
Oronzo Capozzi
Martina Lepore Signorile Mattia Miroballo
... [+2 authors] ...,
Nicoletta Archidiacono
Evan E. Eichler
Mario Ventura
Francesca Antonacci

First Published May 18, 2018

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