Author

John Koomen

Moffitt Cancer Center

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2 Immunology· 1

Signature Assays, Organisms & Methods

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Assay:metabolomics· 2 Approach:statistical model· 2 Research Focus:differential expression· 1 Research Focus:dimensionality reduction· 1 Approach:experimental assay· 1 Research Focus:host-pathogen & immune response· 1 Organism:human· 1 Organism:mouse· 1

Frequent Co-Authors

Elsa Renee FloresiD· 2 shared Hayley D. AckermaniD· 2 shared Paul A. StewartiD· 2 shared Yonatan Ayalew MekonneniD· 2 shared Alex Soupir· 1 shared Ashley LuiiD· 1 shared Augustine Takyi· 1 shared Brooke L. FridleyiD· 1 shared

Activity by Year

2025-2026 · peak 2/yr

Co-Author Collaboration Network

10 top collaborators · 25 mutual co-author links

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2 shared papersBioinformatics

Elsa Renee FloresORCID

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3 papers

Recent·Most cited

spatialMET: an open and scalable framework for spatial metabolomics analysis

Yonatan Ayalew Mekonnen, Oscar Ospina, Vanessa Rubio, Eric Welsh, Reaz Uddin, Hayley D. Ackerman, Alex Soupir, James E. Cox, Brooke L. Fridley, Elsa Renee Flores, John Koomen, Paul A. Stewart

spatialMET provides a scalable, open-source framework for end-to-end spatial metabolomics analysis, identifying spatial domains and differential metabolites in mouse cancer data.

bioRxiv · Sep 3, 2026 · PreprintBioinformatics

C-terminus CD28 phosphorylation (Y218) modulates IL-2 secretion and antitumor effect of CAR-T cells

Elena Martinez Planes, Maria Cecilia Ramello, Miguel Gomez Fontela, Mohammad-Reza Shokri, Lancia N. F. Darville, John Koomen, Youngchul Kim, Daniel Abate‐Daga

This study identifies Y218 phosphorylation in CD28 as critical for IL-2 secretion and antitumor efficacy of CAR-T cells, showing that enhancing ITK recruitment improves therapeutic outcomes.

bioRxiv · Feb 1, 2026 · PreprintImmunology

EnrichMET: R Package for Integrated Pathway and Network Analysis for Metabolomics

Yonatan Ayalew Mekonnen, Neha Dhake, Vanessa Y. Rubio, Shreya Jaiswal, Isis Yanina Narvaez-Bandera, Ashley Lui, Augustine Takyi, Hayley D. Ackerman, John Koomen, Elsa Renee Flores, Paul A. Stewart

EnrichMET provides an R package for fast and reproducible pathway enrichment analysis in metabolomics, supporting multiple methods and offering both command-line and Shiny interfaces.

bioRxiv · Aug 28, 2025 · PreprintBioinformatics