Author

Jonathan T. Lee

Pfizer (United States)ORCID 0000-0002-9546-5294Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:whole-genome sequencing· 3 Organism:human· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Research Focus:database / resource· 1 Approach:machine learning (classical)· 1

Frequent Co-Authors

Hao LiiD· 3 shared Paul LiberatoriD· 3 shared Annaliesa S. AndersoniD· 2 shared Bradley Scott PerriniD· 2 shared Alexey V. GribenkoiD· 1 shared Craig L HydeiD· 1 shared Daniel Katze· 1 shared Joppe W. HoviusiD· 1 shared

Activity by Year

2022-2023 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 34 mutual co-author links

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3 shared papersGenomics

Hao LiORCID

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Author profile →

3 papers

Recent·Most cited

Development of a sequence-based in silico OspA typing method for Borrelia burgdorferi sensu lato

Jonathan T. Lee, Zheng-Hui Li, Lorna Nuñez, Daniel Katze, Bradley Scott Perrin, Varun Raghuraman, Urvi Rajyaguru, Katrina E. Llamera, Lubomira Andrew, Annaliesa S. Anderson, Joppe W. Hovius, Paul Liberator, Raphael Simon, Hao Li

This paper develops an in silico sequence-based method for OspA typing of Borrelia burgdorferi sensu lato using next-generation sequencing data, identifying new OspA variants and introducing a novel nomenclature system.

bioRxiv · Nov 30, 2023 · PreprintGenomics

PfaSTer: A ML-powered serotype caller for Streptococcus pneumoniae genomes

Jonathan T. Lee, Xingpeng Li, Craig L Hyde, Paul Liberator, Hao Li

PfaSTer predicts serotypes of Streptococcus pneumoniae genomes using machine learning and k-mer analysis, achieving >97% concordance with biochemical and other in-silico methods.

bioRxiv · Nov 30, 2022 · PreprintBioinformatics

Genetic surveillance of SARS-CoV-2 Mpro reveals high sequence and structural conservation prior to the introduction of protease inhibitor Paxlovid

Jonathan T. Lee, Qingyi Yang, Alexey V. Gribenko, Bradley Scott Perrin, Yuao Zhu, Rhonda D. Cardin, Paul Liberator, Annaliesa S. Anderson, Hao Li

This study analyzes SARS-CoV-2 Mpro sequences from 4.89 million genomes to assess mutation patterns and structural conservation before Paxlovid use, finding rare escape mutations and strong purifying selection.

bioRxiv · Mar 29, 2022 · PreprintGenomics