Author

Sandeep J. Joseph

Centers for Disease Control and PreventionORCID 0000-0003-0697-2487Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Genomics· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Approach:experimental assay· 3 Research Focus:variant calling· 3 Assay:whole-genome sequencing· 3 Organism:human· 2 Research Focus:gene regulatory network inference· 1 Research Focus:phylogenetics / evolution· 1

Frequent Co-Authors

Damien C. Danavall· 2 shared John C. CarteeiD· 2 shared Allan PillayiD· 1 shared Alyssa Debra· 1 shared Apurva ShrivastavaiD· 1 shared Brian H. RaphaeliD· 1 shared Charles M. ThurlowiD· 1 shared Cheng Chen· 1 shared

Activity by Year

2021-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 22 mutual co-author links

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2 shared papersGenomics

Damien C. Danavall

Mutual co-authors in cluster

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3 papers

Recent·Most cited

BioinformaticsbioRxivPreprintJul 23, 2026

neissflow: Streamlining Genomic Epidemiology of Neisseria gonorrhoeae with Nextflow

Kathryn Morin, Ethan E. Hetrick, Apurva Shrivastava…·Sandeep J. Joseph

neissflow is a Nextflow pipeline for analyzing Neisseria gonorrhoeae genomes, achieving high accuracy in species identification, AMR profiling, and phylogenetic analysis.

DOI 10.64898/2026.07.22.740120

humanwhole-genome sequencing

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GenomicsmSpherePeer-reviewedMay 2, 2022

Selective whole genome amplification as a tool to enrich specimens with low Treponema pallidum genomic DNA copies for whole genome sequencing

Charles M. Thurlow, Sandeep J. Joseph, Lilia Milkova Ganova-Raeva…·Allan Pillay

This paper develops a selective whole genome amplification method to enrich low T. pallidum DNA samples for whole genome sequencing, achieving high coverage and identifying azithromycin resistance mutations.

28 citationstop 4%

humanwhole-genome sequencing

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GenomicsmSpherePeer-reviewedMar 5, 2021

Whole-Genome Enrichment and Sequencing of Chlamydia trachomatis Directly from Patient Clinical Vaginal and Rectal Swabs

Katherine E. Bowden, Sandeep J. Joseph, John C. Cartee…·Deborah Dean

The paper improves whole-genome sequencing of Chlamydia trachomatis from clinical samples by redesigning an RNA bait library, achieving 100% efficiency and identifying genomic recombination in paired specimens.

26 citations

whole-genome sequencingexperimental assay

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