Author

Lee S. Katz

Centers for Disease Control and PreventionORCID 0000-0002-2533-9161Unclaimed 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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Assay:whole-genome sequencing· 4 Approach:statistical model· 3 Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Research Focus:software / tool· 2 Approach:benchmark study· 1 Research Focus:database / resource· 1 Approach:experimental assay· 1

Frequent Co-Authors

Andrew J. PageiD· 2 shared Aaron Petkau· 1 shared Adam A. WitneyiD· 1 shared Aleisha R. ReimeriD· 1 shared Alexander Manuele· 1 shared Allison BlackiD· 1 shared Amogelang R. RaphenyaiD· 1 shared Andrew G. McArthuriD· 1 shared

Activity by Year

2017-2024 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 29 mutual co-author links

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2 shared papersBioinformatics

Andrew J. PageORCID

Mutual co-authors in cluster

Author profile →

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

Fasten with Pipes

Lee S. Katz, Henk C. den Bakker

Fasten is a bioinformatics tool suite for handling fastq files, supporting interleaved data and Unix pipes, with Rust implementation and command-line integration.

bioRxiv · Oct 30, 2023 · PreprintBioinformatics

Comparison Of Multi-locus Sequence Typing Software For Next Generation Sequencing Data

Andrew J. Page, Nabil-Fareed Alikhan, Heather A. Carleton, Torsten Seemann, Jacqueline A. Keane, Lee S. Katz

This study compares six MLST software tools using real and simulated data, evaluating their accuracy, performance on outbreak datasets, contamination impact, and computational requirements.

Microbial Genomics · Jun 13, 2017Peer-reviewedBioinformatics

SNVPhyl: A Single Nucleotide Variant Phylogenomics pipeline for microbial genomic epidemiology

Aaron Petkau, Philip Mabon, Cameron Sieffert, Natalie Knox, Jennifer Cabral, Mariam Iskander, Mark Iskander, Kelly A. Weedmark, Rahat Zaheer, Lee S. Katz, Celine A. Nadon, Aleisha R. Reimer, Eduardo Napoleon Taboada, Robert Gerald Beiko, William Hsiao, , Gary Van Domselaar

SNVPhyl is a phylogenomics pipeline that identifies SNVs and constructs whole-genome phylogenies from WGS data, showing high sensitivity and specificity in outbreak detection.

Microbial Genomics · Jun 7, 2017Peer-reviewedBioinformatics