Author

David Dooley

University of Tennessee at Knoxville

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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Systems Biology· 3

Signature Assays, Organisms & Methods

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Organism:bacteria (other)· 2 Approach:experimental assay· 2 Research Focus:gene regulatory network inference· 2 Assay:proteomics· 2 Assay:bulk RNA-seq· 1 Research Focus:differential expression· 1 Approach:statistical model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Cong T. TrinhiD· 3 shared Richard J. GiannoneiD· 2 shared Seunghyun RyuiD· 2 shared Brian J. Mendoza· 1 shared Bruce S. DieniD· 1 shared Caleb Walker· 1 shared Dana L. CarperiD· 1 shared Jackson Edwards· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 26 mutual co-author links

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3 shared papersSystems Biology

Cong T. TrinhORCID

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3 papers

Recent·Most cited

Proteome Reallocation Reveals Dynamics and Mechanisms of Phage Infection and Defense in Staphylococcus aureus

David Dooley, Dana L. Carper, Richard J. Giannone, Cong T. Trinh

This study uses longitudinal proteomics to analyze how Staphylococcus aureus reallocates resources during phage infection, revealing mechanisms of host defense and phage evasion.

bioRxiv · Oct 23, 2025 · PreprintSystems Biology

Expanded Genome and Proteome Reallocation in a Novel, Robust Bacillus coagulans Capable of Utilizing Pentose and Hexose Sugars

David Dooley, Seunghyun Ryu, Richard J. Giannone, Jackson Edwards, Bruce S. Dien, Patricia J. Slininger, Cong T. Trinh

This study characterizes a novel robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars, revealing proteome reallocation and metabolic strategies for biomass hydrolysate utilization.

bioRxiv · Jul 15, 2024 · PreprintSystems Biology

Gene Co-expression Connectivity Predicts Gene Targets Underlying High Ionic Liquid Tolerance in Yarrowia lipolytica

Caleb Walker, Seunghyun Ryu, Sergio Garcia, David Dooley, Brian J. Mendoza, Cong T. Trinh

The paper introduces GeCCo to identify gene targets for high ionic liquid tolerance in Y. lipolytica and finds that GeCCo-selected genes, BRN1 and OYE2, enhance tolerance when overexpressed.

bioRxiv · Mar 17, 2022 · PreprintSystems Biology