Author

Brian P. Alcock

Michael G. DeGroote Institute for Infectious Disease ResearchORCID 0000-0002-5129-4673Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 3 Genomics· 3 Microbiology· 1

Signature Assays, Organisms & Methods

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Approach:statistical model· 7 Research Focus:benchmarking· 4 Assay:whole-genome sequencing· 4 Research Focus:database / resource· 3 Research Focus:gene regulatory network inference· 3 Assay:metagenomics· 3 Organism:human· 2 Research Focus:variant calling· 2

Frequent Co-Authors

Amogelang R. RaphenyaiD· 7 shared Andrew G. McArthuriD· 6 shared Finlay MaguireiD· 4 shared Robert Gerald BeikoiD· 3 shared Alexander Manuele· 2 shared Fiona S. L. BrinkmaniD· 2 shared Abigail Leigh GlascockiD· 1 shared Adam A. WitneyiD· 1 shared

Activity by Year

2022-2026 · peak 3/yr

Co-Author Collaboration Network

10 top collaborators · 32 mutual co-author links

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7 shared papersGenomics

Amogelang R. RaphenyaORCID

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Author profile →

7 papers

Recent·Most cited

Analysing antimicrobial resistance mobility patterns using a diverse dataset of over 8000 bacterial species

Baofeng Jia, Brian P. Alcock, Amogelang R. Raphenya, Jason Spence, Finlay Maguire, Robert Gerald Beiko, Andrew G. McArthur, Claire Bertelli, Fiona S. L. Brinkman

The paper analyzes antimicrobial resistance gene mobility across 8000 bacterial species, finding that certain resistance mechanisms are more associated with mobile elements than others.

bioRxiv · Mar 5, 2026 · PreprintGenomics

Increasing the predictive accuracy of the Resistance Gene Identifier by evaluating antimicrobial resistance gene over- and underprediction

Karyn M Mukiri, Brian P. Alcock, Amogelang R. Raphenya, Andrew G. McArthur

This study evaluates the accuracy of antimicrobial resistance gene prediction by analyzing bit-score cutoff values in CARD models and identifies sources of over- and underprediction in the RGI tool.

bioRxiv · Dec 15, 2025 · PreprintBioinformatics

CARD k-mers: Unmasking the pathogen hosts and genomic contexts of antimicrobial resistance genes in metagenomic sequences

Mateusz A. Wlodarski, Tammy Lau, Brian P. Alcock, Amogelang R. Raphenya, Tiffany E. Ta, Finlay Maguire, Robert Gerald Beiko, Andrew G. McArthur

CARD k-mers classifies antimicrobial resistance genes in metagenomic data by predicting taxonomy and genomic context, outperforming existing tools in accuracy and speed.

bioRxiv · Sep 15, 2025 · PreprintBioinformatics

CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment

Dirk Hackenberger, Hamna Imtiaz, Amogelang R. Raphenya, Brian P. Alcock, Hendrik N. Poinar, Gerard D. Wright, Andrew G. McArthur

CARPDM enables cost-effective antibiotic resistome profiling in metagenomic samples through targeted enrichment and in-house probe synthesis.

Applied and Environmental Microbiology · Feb 28, 2025Peer-reviewedGenomics

Simultaneous detection of pathogens and antimicrobial resistance genes with the open source, cloud-based, CZ ID pipeline

Dan Lu, Katrina Kalantar, Victoria T. Chu, Abigail Leigh Glascock, Estella Sanchez Guerrero, Nina Bernick, Xochitl Butcher, Kirsty Ewing, Elizabeth Fahsbender, Olivia Holmes, Erin Hoops, Ann E. Jones, Ryan Lim, Suzette McCanny, Lucia Reynoso, , Charles Langelier

The paper develops an open-source, cloud-based tool for detecting pathogens and antimicrobial resistance genes in metagenomic and whole-genome sequencing data, demonstrating its application across clinical and environmental studies.

bioRxiv · Apr 12, 2024 · PreprintMicrobiology

hAMRonization: Enhancing antimicrobial resistance prediction using the PHA4GE AMR detection specification and tooling

Catarina Inês Mendes, Emma Griffiths, Alexander Manuele, Daniel Fornika, Simon H. Tausch, Thanh Le-Viet, Jody Emile Phelan, Conor Joseph Meehan, Amogelang R. Raphenya, Brian P. Alcock, Elizabeth J. Culp, Federico Lorenzo, María Sol Haim, Adam A. Witney, Allison Black, , Finlay Maguire

hAMRonization standardizes AMR gene detection outputs from multiple tools into a unified format for easier analysis and integration.

bioRxiv · Mar 7, 2024 · PreprintBioinformatics

Exploring the mobilome and resistome of Enterococcus faecium in a One Health context across two continents

Haley Sanderson, Kristen L. Gray, Alexander Manuele, Finlay Maguire, Amjad Khan, Chaoyue Liu, Chandana Navanekere Rudrappa, John J. Nash, James A. Robertson, Kyrylo Bessonov, Martins Oloni, Brian P. Alcock, Amogelang R. Raphenya, Tim Angus McAllister, Sharon J. Peacock, , Robert Gerald Beiko

This study profiles resistance determinants, virulence factors, and mobile genetic elements in 1273 Enterococcus faecium genomes from UK and Canada, showing habitat-associated gene and MGE patterns and a workflow for AMR surveillance.

Microbial Genomics · Sep 21, 2022Peer-reviewedGenomics