Author

Justin Y. Kim

Centers for Disease Control and PreventionORCID 0000-0003-0161-1236Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 1 Microbiology· 1

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 2 Research Focus:benchmarking· 2 Approach:statistical model· 2 Assay:whole-genome sequencing· 2 Approach:benchmark study· 1 Approach:deep learning· 1 Organism:human· 1 Assay:long-read sequencing· 1

Frequent Co-Authors

Kaitlin A. TaggiD· 2 shared Anthony Marius SmithiD· 1 shared Arancha Peñil-CelisiD· 1 shared Arti KapiliD· 1 shared Assaf RokneyiD· 1 shared Ayorinde O. AfolayaniD· 1 shared Benjamin P. HowdeniD· 1 shared Chelsey GriffiniD· 1 shared

Activity by Year

2024-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 31 mutual co-author links

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2 shared papersMicrobiology

Kaitlin A. TaggORCID

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2 papers

Recent·Most cited

MicrobiologyGenome MedicinePeer-reviewedOct 24, 2025

✦ In-depth digest

Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Danielle J. Ingle, Jane Hawkey, Martin Hunt…·Kathryn E. Holt

Mykrobe k-mer panel genotypes Salmonella Typhi lineages, antimicrobial resistance (AMR) markers and plasmids from Illumina or nanopore reads, matching mapping-based lineage calls for 99.8% of genomes.

12 citationstop 5%

bacteria (other)human

𝕏 PostBluesky

GenomicsmSystemsPeer-reviewedJul 26, 2024

Harnessing the pangenome for genomic surveillance: Salmonella enterica serotype Typhi as a paradigm

Arancha Peñil-Celis, Kaitlin A. Tagg, Hattie E. Webb…·Fernando de la Cruz

The paper introduces a method to measure pangenome relatedness using Jaccard Index and a novel distance metric to capture both vertical and horizontal gene transfer in Salmonella Typhi, enhancing genomic surveillance.

11 citations

bacteria (other)whole-genome sequencing

𝕏 PostBluesky