Author

Katherine Do

University of MinnesotaORCID 0000-0002-1230-8577Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Signature Assays, Organisms & Methods

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Assay:metagenomics· 4 Research Focus:benchmarking· 3 Assay:proteomics· 3 Approach:statistical model· 3 Research Focus:database / resource· 2 Approach:experimental assay· 2 Organism:human· 2 Organism:bacteria (other)· 1

Frequent Co-Authors

Pratik Dilip JagtapiD· 5 shared Timothy J. GriffiniD· 5 shared Subina MehtaiD· 4 shared Andrew T. RajczewskiiD· 3 shared James E. JohnsoniD· 3 shared Reid WagneriD· 3 shared Manuel KleineriD· 2 shared Aleksey Y. OgurtsoviD· 1 shared

Activity by Year

2024-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 36 mutual co-author links

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5 shared papersBioinformatics

Pratik Dilip JagtapORCID

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Author profile →

5 papers

Recent·Most cited

Microbiology Galaxy Lab: The first community-driven gateway for reproducible and FAIR analysis of microbial data

Engy Mohamed Taha Nasr, Nikolaos Pechlivanis, Nikolaos Strepis, Pierre Amato, Matthias Bernt, Anshu Bhardwaj, Daniel J Blankenberg, Daniela Brites, Fabio Cumbo, Katherine Do, Emanuele Ferrari, Timothy J. Griffin, Björn Andreas Grüning, Saskia Hiltemann, Cameron J. Hyde, , Bérénice Batut

The paper introduces the Microbiology Galaxy Lab, a community-driven platform for reproducible and FAIR microbial data analysis, offering tools for various omics data types and use cases.

Communications Biology · Oct 29, 2026Peer-reviewedBioinformatics

A modular, immunopeptidogenomic (iPepGen) analysis pipeline for discovery, verification, and prioritization of cancer peptide neoantigen candidates

Subina Mehta, Reid Wagner, Katherine Do, James E. Johnson, Fengchao Yu, Tyler A. Jubenville, Kyle A. Richards, Susan Coleman, Flavia E. Popescu, Alexey I. Nesvizhskii, David A. Largaespada, Pratik Dilip Jagtap, Timothy J. Griffin

The paper introduces a modular pipeline for neoantigen discovery, verification, and prioritization in cancer research using immunopeptidogenomic data.

Genome biology · Feb 25, 2026Peer-reviewedBioinformatics

Comparative Performance of Scribe and Database Search Engines in Metaproteomic Profiling of a Ground-Truth Microbiome Dataset

Andrew T. Rajczewski, Subina Mehta, Reid Wagner, Wassim Gabriel, James E. Johnson, Katherine Do, Simina Vintila, Mathias Wilhelm, Manuel Kleiner, Brian C. Searle, Timothy J. Griffin, Pratik Dilip Jagtap

This study compares Scribe and database search engines in metaproteomic analysis of a ground-truth microbiome dataset, finding Scribe detects more proteins and quantifies microbial composition more accurately.

Journal of Proteomics · Oct 22, 2025Peer-reviewedBioinformatics

Evaluation of Parallel Accumulation-Serial Fragmentation methods for metaproteomics using a model microbiome

Ruben Shreshta, Andrew T. Rajczewski, Aleksey Y. Ogurtsov, Katherine Do, Gelio Alves, Yi-Kuo Yu, Matthew Willets, Manuel Kleiner, Timothy J. Griffin, Pratik Dilip Jagtap

The paper presents a metaproteomic dataset to evaluate the performance of ddaPASEF and diaPASEF in terms of detection, coverage, and strain-level resolution.

bioRxiv · Aug 13, 2025 · PreprintBiochemistry

A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease

Katherine Do, Subina Mehta, Reid Wagner, Dechen Bhuming, Andrew T. Rajczewski, Amy P.N. Skubitz, James E. Johnson, Timothy J. Griffin, Pratik Dilip Jagtap

The paper introduces a clinical metaproteomics workflow that enables analysis of host-microbe dynamics in disease by integrating mass spectrometry and bioinformatics tools.

mSphere · May 23, 2024Peer-reviewedBioinformatics