Author

Kathryn M. Kauffman

University at Buffalo, State University of New YorkORCID 0000-0002-1997-947XUnclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Microbiology· 5

Signature Assays, Organisms & Methods

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Research Focus:cell type annotation· 3 Organism:human· 3 Assay:metagenomics· 3 Approach:statistical model· 3 Approach:experimental assay· 2 Assay:proteomics· 2 Organism:bacteria (other)· 1 Research Focus:benchmarking· 1

Frequent Co-Authors

Ashley K. MilesiD· 2 shared Floyd E. DewhirstiD· 2 shared Jessica L. Mark WelchiD· 2 shared Yinyin YeiD· 2 shared Alexandra Z. WordeniD· 1 shared Amy ZimmermaniD· 1 shared Brady R. CunninghamiD· 1 shared Charmaine C. M. YungiD· 1 shared

Activity by Year

2025-2026 · peak 4/yr

Co-Author Collaboration Network

10 top collaborators · 17 mutual co-author links

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2 shared papersMicrobiology

Ashley K. MilesORCID

Mutual co-authors in cluster

Author profile →

5 papers

Recent·Most cited

maniFasta and the AllOralsDB: simplifying construction of comprehensive reference databases for metaproteomics

Christopher R. Handelmann, Ashley K. Miles, Yinyin Ye, Marcelo Freire, Floyd E. Dewhirst, Tsute Chen, Jessica L. Mark Welch, Kathryn M. Kauffman

maniFasta and AllOralsDB provide a tool and resource for creating standardized, comprehensive protein reference databases for metaproteomics.

bioRxiv · Aug 10, 2026 · PreprintMicrobiology

Pervasive integrative and conjugative elements shape Porphyromonas gingivalis gene repertoires

Cole B. Matrishin, Elaine M. Haase, Ashley K. Miles, Stephanie Steimer, Dam Soh, Matthew Smardz, Patricia I. Diaz, Kathryn M. Kauffman

This paper identifies pervasive integrative and conjugative elements (ICEs) in Porphyromonas gingivalis genomes, showing they contribute to strain-level gene diversity and virulence.

bioRxiv · Aug 5, 2026 · PreprintMicrobiology

Solvent accessibility of chlorine-reactive amino acid residues in icosahedral virus structures: A meta-analysis

Chonglin Zhu, Kerry Prinsen, Leah Ward, Mira Chaplin, Meng Shen, S. TORII, Kathryn M. Kauffman, Yinyin Ye

The paper analyzes the relationship between solvent accessibility of methionine residues and chlorine inactivation rates in icosahedral viruses using a curated dataset of viral structures.

bioRxiv · Jun 18, 2026 · PreprintMicrobiology

Site-specialization of human oral Porphyromonas species

Julian Torres‐Morales, Floyd E. Dewhirst, Kathryn M. Kauffman, Jessica L. Mark Welch, Gary G. Borisy

The paper analyzes oral microbiome metagenomes to identify site-specific distribution and metabolic specialization of Porphyromonas species across health and disease.

bioRxiv · Jun 3, 2026 · PreprintMicrobiology

Iron limitation differentially affects viral replication in key marine microbes

Charmaine C. M. Yung, Rachel L. Kelly, Kathryn M. Kauffman, Brady R. Cunningham, Amy Zimmerman, Alexandra Z. Worden, Seth G. John

This study examines how iron limitation affects viral replication in three marine microbes, finding varied impacts across species and strains.

Proceedings of the National Academy of Sciences · Oct 15, 2025Peer-reviewedMicrobiology