Author

Daniel Fornika

BC Centre for Disease ControlORCID 0000-0002-6178-3585Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 4

Signature Assays, Organisms & Methods

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Research Focus:database / resource· 3 Approach:statistical model· 3 Assay:whole-genome sequencing· 3 Research Focus:benchmarking· 2 Approach:experimental assay· 2 Research Focus:software / tool· 2 Organism:bacteria (other)· 1 Approach:benchmark study· 1

Frequent Co-Authors

Leonid ChindelevitchiD· 3 shared Andrew G. McArthuriD· 2 shared Cédric ChauveiD· 2 shared Emma GriffithsiD· 2 shared Jennifer L. GardyiD· 2 shared Pedro Feijão· 2 shared William HsiaoiD· 2 shared A. Roudgar· 1 shared

Activity by Year

2018-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 39 mutual co-author links

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3 shared papersBioinformatics

Leonid ChindelevitchORCID

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4 papers

Recent·Most cited

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

Expanding the Galaxy's reference data

VIJAY NAGAMPALLI, Jayadev Joshi, Nate Coraor, Jennifer Hillman‐Jackson, Dave Bouvier, Marius van den Beek, Ignacio Eguinoa, Frederik Coppens, John Davis, Michał Stolarczyk, Nathan C. Sheffield, Simon L. Gladman, Gianmauro Cuccuru, Björn Andreas Grüning, Nicola Soranzo, , Daniel J Blankenberg

The paper describes integrating refgenie into Galaxy to manage and share reference datasets, with tools for retrieval and a global repository for easy access.

Bioinformatics Advances · Jan 1, 2022Peer-reviewedBioinformatics

The Integrated Rapid Infectious Disease Analysis (IRIDA) Platform

Thomas C Matthews, Franklin Bristow, Emma Griffiths, Aaron Petkau, Josh Adam, Damion Dooley, Peter Kruczkiewicz, John Curatcha, Jennifer Cabral, Daniel Fornika, Geoffrey L. Winsor, Mélanie Courtot, Claire Bertelli, A. Roudgar, Pedro Feijão, , Gary Van Domselaar

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

bioRxiv · Jul 31, 2018 · PreprintBioinformatics

MentaLiST - A fast MLST caller for large MLST schemes

Pedro Feijão, Hua-Ting Yao, Daniel Fornika, Jennifer L. Gardy, William Hsiao, Cédric Chauve, Leonid Chindelevitch

MentaLiST is a fast and accurate MLST caller designed for large MLST schemes, outperforming existing tools in speed while maintaining or improving accuracy.

Microbial Genomics · Jan 10, 2018Peer-reviewedBioinformatics