Owen Hudson

PhD candidate in plant pathology with publications using predictive and comparative genomics for disease resistance breeding. Experience in machine learning and image analysis.

Research Expertise

Plant pathology
bioinformatics
plant breeding
genomics

About

My name is Owen Hudson, I’m currently a PhD candidate in Plant Pathology at the University of Florida and I expect to complete my degree in December 2024. In my current position at the University of Florida, I study Fusarium ear rot of maize, specifically genomic methods to improve disease resistance breeding, identification of disease-related genes, and high throughput plant phenotyping. While my degree will be in plant pathology, my activities have been more focused on plant breeding and bioinformatics, specifically quantitative genetics, comparative genomics, and genomic selection models. I now employ Linux/Bash, R, and Python regularly in my research and analysis, and I have included machine learning and predictive proteomics in my research. In my PhD, I build a machine to image maize ears and developed several machine learning classification models for disease prediction estimates on those images. I've also built machine learning models with the USDA-ARS to identify the most influential protein domains in specific microbial groups to predict their life habit (pathogenic, saprophytic, etc.) and then use the model to predict unknown fungi. I also was able to modify the model for use in my own dataset and improve my comparative genomic methods.

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Publications

Comparative analysis of different molecular and serological methods for detection of Xylella fastidiosa in blueberry
PLOS ONE
2019
First Report of Resistance to Pyraclostrobin, Boscalid, and Thiophanate-methyl in Colletotrichum gloeosporioides from Blueberry in Georgia
Plant Health Progress
2019
Marker Development for Differentiation of Fusarium oxysporum f. sp. Niveum Race 3 from Races 1 and 2
International Journal of Molecular Sciences
2021
Molecular Characterization of Laboratory Mutants of Fusarium oxysporum f. sp. niveum Resistant to Prothioconazole, a Demethylation Inhibitor (DMI) Fungicide
Journal of Fungi
2021
Detection of <em>Phytophthora capsici</em> in Irrigation Water using Loop-Mediated Isothermal Amplification
Journal of Visualized Experiments
2020
Fusarium oxysporum f. sp. niveum Molecular Diagnostics Past, Present and Future
International Journal of Molecular Sciences
2021
Phylogenetic and phenotypic characterization of Fusarium oxysporum f. sp. niveum isolates from Florida-grown watermelon
PLOS ONE
2021
Multilocus phylogeny of Acrospermaceae: New epibiotic species and placement of Gonatophragmium, Pseudovirgaria, and Phaeodactylium anamorphs
Mycologia
2019
Draft Genome Sequences of Three Fusarium oxysporum f. sp. niveum Isolates Used in Designing Markers for Race Differentiation
Microbiology Resource Announcements
2020
Detection of Phytophthora capsici from Irrigation Ponds in South Georgia
Plant Health Progress
2021
Sensitivity of Colletotrichum Isolates Collected from Strawberries in Georgia to Pyraclostrobin, a Quinone Outside Inhibitor (QoI) Fungicide
Plant Health Progress
2020
Next-generation fungal identification using target enrichment and Nanopore sequencing
BMC Genomics
2023
Comparative Genomics of Fusarium circinatum Isolates Used to Screen Southern Pines for Pitch Canker Resistance
Molecular Plant-Microbe Interactions®
2022
First Report of Bacterial Leaf Scorch Disease of American Elm Caused by Xylella fastidiosa in Georgia, U.S.A.
Plant Disease
2020
First Report of Downy Mildew on Blackberry Caused by Peronospora sparsa in Georgia, U.S.A.
Plant Disease
2020
Prediction of resistance, virulence, and host-by-pathogen interactions using dual-genome prediction models
Theoretical and Applied Genetics
2024
Development of Loop-Mediated Isothermal Amplification Assay for Rapid Detection of Cucurbit Leaf Crumple Virus
International Journal of Molecular Sciences
2020
Clade-Specific Biosurveillance of Pseudoperonospora cubensis Using Spore Traps for Precision Disease Management of Cucurbit Downy Mildew
Phytopathology®
2021
Integrated Management of Fusarium Wilt of Watermelon
Grow: Plant Health Exchange
2020
DETECTION OFFUSARIUM OXYSPORUMF. SP. ELAEIDIS CAUSING FUSARIUM WILT OF OIL PALM USING LOOP-MEDIATED ISOTHERMAL AMPLIFICATION (LAMP)
Unknown Venue
2019
The Ear Unwrapper: A Maize Ear Image Acquisition Pipeline for Disease Severity Phenotyping
AgriEngineering
2023

Education

University of Vermont

B.A, Plant biology / May, 2018

Burlington, Vermont, United States of America

University of Georgia

M.S, Plant Pathology / May, 2021

Georgia

University of Florida

PhD, Plant Pathology / December, 2024 (anticipated)

Gainesville, Florida, United States of America
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