Publications by authors named "Jeff Knaggs"

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Characterizing the performance of an antibiotic resistance prediction tool, gnomonicus, using a diverse test set of 2,663 samples.
Jeremy Westhead, Catriona S Baker, Marc Brouard, Matthew Colpus, Bede Constantinides, Jeff Knaggs

Microb Genom· December 2025

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Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny.
Martin Hunt, Angie S Hinrichs, Daniel Anderson, Lily Karim, Bethany L Dearlove, Jeff Knaggs

bioRxiv· November 2024

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MmpR5 protein truncation and bedaquiline resistance in Mycobacterium tuberculosis isolates from South Africa: a genomic analysis.
Leah W Roberts, Kerri M Malone, Martin Hunt, Lavania Joseph, Penelope Wintringer, Jeff Knaggs

Lancet Microbe· August 2024

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Mobilisation and analyses of publicly available SARS-CoV-2 data for pandemic responses.
Nadim Rahman, Colman O'Cathail, Ahmad Zyoud, Alexey Sokolov, Bas Oude Munnink, Jeff Knaggs

Microb Genom· February 2024

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The 2021 WHO catalogue of complex mutations associated with drug resistance: A genotypic analysis.
Timothy M Walker, Paolo Miotto, Claudio U Köser, Philip W Fowler, Jeff Knaggs

Lancet Microbe· April 2022

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Performance comparison of next generation sequencing analysis pipelines for HIV-1 drug resistance testing.
Emma R Lee, Neil Parkin, Cheryl Jennings, Chanson J Brumme, Eric Enns, Jeff Knaggs

Sci Rep· January 2020

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Formalin fixation increases deamination mutation signature but should not lead to false positive mutations in clinical practice.
Leah M Prentice, Ruth R Miller, Jeff Knaggs, Alborz Mazloomian, Rosalia Aguirre Hernandez

PLoS One· August 2018

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