Ph.D. Graduate Research Assistantship — Plant Pathogen Metagenomics and Bioinformatics

Applications are invited for a Ph.D. Graduate Research Assistantship beginning Spring 2027 at the Institute for Biosecurity and Microbial Forensics (IBMF), Department of Entomology and Plant Pathology, Oklahoma State University.

We are seeking a motivated student interested in plant pathology who is passionate about bioinformatics, computational biology, and fungal and viral plant pathogens. The selected student will focus primarily on developing and applying bioinformatics pipelines for pathogen detection and identification using metagenomic and targeted sequencing data.

Research opportunities include:

• Development, implementation, and optimization of bioinformatics pipelines for sequencing-based pathogen detection
• Application and evaluation of existing pipelines across diverse sequencing datasets
• Assessment of pipeline performance, reproducibility, and diagnostic accuracy
• Bioinformatic analysis of metagenomic, metatranscriptomic, and targeted amplicon sequencing data
• Investigation of fungal and viral diversity through comparative sequence analysis and phylogenetics
• Integration of computational workflows with laboratory-based diagnostic validation

Research will connect computational methods with practical challenges in plant disease diagnosis and agricultural biosecurity.

Applicants should hold an M.S. degree in Plant Pathology, Bioinformatics, Computational Biology, Microbiology, Molecular Biology, Genetics, Genomics, or a related discipline, subject to program admission requirements.

Preference will be given to applicants with demonstrated experience developing and using bioinformatics pipelines, proficiency in Linux environments, and programming skills in Python, R, or other relevant languages. Candidates who have applied these skills to pathogen detection, metagenomics, mycology, virology, or plant pathology are particularly encouraged to apply.

Experience using artificial intelligence tools to support code development, review, debugging, and documentation is also desirable, together with the ability to critically evaluate and validate AI-generated code.

Applicants must also have hands-on experience with molecular laboratory techniques, such as nucleic acid extraction, PCR or RT-PCR, gel electrophoresis, or sequencing library preparation. Experience with every technique listed is not required.

Strong scientific curiosity, initiative, communication skills, and the ability to integrate computational analyses with laboratory research are essential.

The anticipated start date is Spring 2027. Applicants must be able to complete the admission process and begin their appointment in accordance with applicable OSU Graduate College and program deadlines. Early application is strongly encouraged. Please review the OSU Graduate College Final date to receive applicationss and contact us promptly to discuss your anticipated availability.

The student will be advised by Dr. Andres S. Espindola
, Assistant Professor at the Institute for Biosecurity and Microbial Forensics, Department of Entomology and Plant Pathology.

Applications and questions should be directed to andres.espindola.

Review will begin immediately and continue until a suitable candidate is identified, subject to university admission deadlines.