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

The American Phytopathological Society (APS); Stillwater (OK); Sur place; USD 24 000 - 32 000; Plein temps

Résumé du poste

Oklahoma State University invites applications for a Ph.D. Graduate Research Assistantship in Plant Pathogen Metagenomics and Bioinformatics. The position focuses on developing and applying bioinformatics pipelines for pathogen detection in metagenomic and targeted sequencing data.

The work spans computational analysis and laboratory validation, with emphasis on fungal and viral plant pathogens, starting Spring 2027 at IBMF, OSU.

Qualifications

• MS degree in a related field per OSU admissions rules.
• Experience developing and using bioinformatics pipelines.
• Proficiency in Linux environments; programming in Python, R.
• Experience with pathogen detection, metagenomics, mycology, virology, or plant pathology is a plus.

Responsabilités

• Develop and optimize bioinformatics pipelines for sequencing-based pathogen detection.
• Apply pipelines across diverse sequencing datasets to evaluate performance.
• Assess reproducibility and diagnostic accuracy of pipelines.
• Analyze metagenomic, metatranscriptomic, and targeted amplicon data.
• Integrate computational workflows with lab-based validation.

Connaissances

Python

R

Linux

Bioinformatics pipelines

AI tools

Formation

MS degree in Plant Pathology, Bioinformatics, Computational Biology, Microbiology, Molecular Biology, Genetics, Genomics

Outils

PCR

RT-PCR

Sequencing

Gel electrophoresis

Description du poste

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 Focus

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.

Qualifications

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.

Start Date and Application Timeline

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 application deadlines 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 [e-mail].

Application Review:

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