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John Spouge, MD, PhD


Research Interests

Presently, I am attempting to understand the genetics of HIV or other retroviruses immediately after infection of a single host. Animal trials using infection as an end-point might not have enough sensitivity to detect subtle reductions in virulence, so my specific practical goal is to develop genetic criteria for detecting when a therapy has reduced virulence. I am also examining applications of exact k-mer matching to taxonomic identification of unknown biological samples.


Martín MP, Daniëls PP, Erickson D, Spouge JL. Figures of merit and statistics for detecting faulty species identification with DNA barcodes: A case study in Ramaria and related fungal genera. PLoS One. 2020;15(8):e0237507. doi: 10.1371/journal.pone.0237507. eCollection 2020. PubMed PMID: 32813726; PubMed Central PMCID: PMC7437900.

Patel V, Spouge JL. Estimating the basic reproduction number of a pathogen in a single host when only a single founder successfully infects. PLoS One. 2020;15(1):e0227127. doi: 10.1371/journal.pone.0227127. eCollection 2020. PubMed PMID: 31923263; PubMed Central PMCID: PMC6953795.

Hoang MTV, Irinyi L, Chen SCA, Sorrell TC, Meyer W. Dual DNA Barcoding for the Molecular Identification of the Agents of Invasive Fungal Infections. Front Microbiol. 2019;10:1647. doi: 10.3389/fmicb.2019.01647. eCollection 2019. PubMed PMID: 31379792; PubMed Central PMCID: PMC6657352.

Manzourolajdad A, Spouge JL. Structural prediction of RNA switches using conditional base-pair probabilities. PLoS One. 2019;14(6):e0217625. doi: 10.1371/journal.pone.0217625. eCollection 2019. PubMed PMID: 31188853; PubMed Central PMCID: PMC6561571.