Author

Johnathan B. Shih

Georgia Institute of TechnologyORCID 0009-0007-8442-794XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Microbiology· 2 Bioinformatics· 1

Signature Assays, Organisms & Methods

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Organism:human· 3 Research Focus:cell type annotation· 2 Assay:metagenomics· 2 Research Focus:variant calling· 2 Research Focus:benchmarking· 1 Research Focus:clustering· 1 Research Focus:deconvolution· 1 Approach:deep learning· 1

Frequent Co-Authors

Abigail LindiD· 2 shared Caroline M. MitchelliD· 1 shared Chunyu ZhaoiD· 1 shared Douglas S. KwoniD· 1 shared Fredrick LeoniD· 1 shared Gabriela A. NineiD· 1 shared Jiawu XuiD· 1 shared Joseph ElsherbiniiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 15 mutual co-author links

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2 shared papersMicrobiology

Abigail LindORCID

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3 papers

Recent·Most cited

MicrobiologybioRxivPreprintOct 21, 2026

A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence

Fredrick Leon, Johnathan B. Shih, lydia keller…·Abigail Lind

This study develops a new cultivation method for Blastocystis, revealing that multiple strains can coexist within a single host.

DOI 10.64898/2026.10.19.760120

humannon-human primate

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MicrobiologybioRxivPreprintJun 25, 2026

Quantitative detection of gut microbial eukaryotes with EukDetect2 reveals global distribution of commensal protists and association with distinct microbial community structure

Johnathan B. Shih, Chunyu Zhao, Katherine S. Pollard, Abigail Lind

EukDetect2 improves eukaryote detection in metagenomes with a larger database and quantitative metrics, revealing Blastocystis and Dientamoeba as prevalent gut eukaryotes.

DOI 10.64898/2026.06.24.734308

humanmetagenomics

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BioinformaticsbioRxivPreprintAug 15, 2025

StrainFacts accurately quantifies both endogenous and live biotherapeutic product strain abundances in simulated and clinical vaginal microbiota samples

Johnathan B. Shih, Seth M. Bloom, Jiawu Xu…·Douglas S. Kwon

1 citation

humanmetagenomics

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