The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

Nature Methods · Feb 9, 2026Peer-reviewedBioinformatics

Characterising the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse testset of 2,663 Mycobacterium tuberculosis samples

Jeremy Westhead, Catriona S. Baker, Marc J. Brouard, Matthew Colpus, Bede Constantinides, Alexandra Hall, Jeff Knaggs, Marcela Lopes Alves, Ruan Spies, Hieu Thai, Sarah Surrell, Kumeren N. Govender, Tim Peto, Derrick W. Crook, Shaheed Vally Omar, , Philip William Fowler

This paper evaluates the performance of the gnomonicus tool for predicting antibiotic resistance in Mycobacterium tuberculosis using a diverse testset of 2,663 samples and compares it to TB-Profiler.

Microbial Genomics · Dec 15, 2025Peer-reviewedMicrobiology

An improved catalogue for whole-genome sequencing prediction of bedaquiline resistance in M. tuberculosis using a reproduciblealgorithmic approach.

Dylan Adlard, Lavania Joseph, Hermione J. Webster, Ailva O’Reilly, Jeff Knaggs, Tim Peto, Derrick W. Crook, Shaheed Vally Omar, Philip William Fowler

The paper develops an automated method to predict bedaquiline resistance in M. tuberculosis using a reproducible algorithmic approach, achieving high sensitivity and specificity in variant classification.

Microbial Genomics · Jun 18, 2025Peer-reviewedMicrobiology

Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses

Nadim Rahman, Colman O’Cathail, Ahmad Zyoud, Alexey Sokolov, Bas B. Oude Munnink, Björn Andreas Grüning, Carla A. Cummins, Clara Amid, David F. Nieuwenhuijse, Dávid Visontai, David Yu Yuan, Dipayan Gupta, Divyae K. Prasad, Gábor Máté Gulyás, Gabriele Rinck, , Guy Cochrane

The paper describes open data sharing, analysis tools, and lessons learned from the European COVID-19 Data Platform's SARS-CoV-2 data collection and analysis efforts.

Microbial Genomics · Feb 15, 2024Peer-reviewedBioinformatics

Quantitative measurement of antibiotic resistance in Mycobacterium tuberculosis reveals genetic determinants of resistance and susceptibility in a target gene approach

Ivan Barilar, Simone Battaglia, Emanuele Borroni, Angela Pires Brandão, Alice E. Brankin, Andrea Maurizio Cabibbe, Joshua J. Carter, Darren Chetty, Daniela María Cirillo, Pauline Claxton, David A. Clifton, Ted Cohen, Jorge Coronel, Derrick W. Crook, Viola Dreyer, , Guy Edward Thwaites

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

Nature Communications · Jan 12, 2024Peer-reviewedGenomics

GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes

Daniel J. Wilson, Derrick W. Crook, Tim Peto, Ann Sarah Walker, Sarah Hoosdally, Ana Lúıza Gibertoni Cruz, Joshua J. Carter, Clara Grazian, Sarah G. Earle, Samaneh Kouchaki, Alexander S. Lachapelle, Yang Yang, David A. Clifton, Philip William Fowler, Zamin Iqbal, , Dick van Soolingen

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

Molecular Biology and Evolution · Mar 10, 2020Peer-reviewedGenomics