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Research Focus
You will lead the field pathology and pathogen genomics: design and run field and greenhouse pathogen experiments, drive the isolate-to-assembly-to-diagnostic-assay pipeline, and lead population-ecology and disease publications built on that genomic work.

Responsibilities:

• Design and execute field and controlled-environment pathology experiments, including inoculum-density gradient studies; direct undergraduate research interns during field-sampling campaigns.
• Lead hybrid (Oxford Nanopore + Illumina) sequencing, assembly, and annotation of pathogen genomes; conduct comparative and population genomics to characterize spatial/temporal structure, virulence, and effector variation, and to identify diagnostic target regions.
• Translate genomic targets into field-deployable molecular diagnostics (LAMP), with quantitative cross-validation by droplet digital and real-time PCR.
• Contribute to the host-microbiome analyses (GWAS/mGWAS, metagenomics) and the integrative modeling led by the graduate student.
• Apply machine-learning and AI-assisted tools in genome analysis, population and disease-ecology work, and pipeline development, with attention to reproducibility and validation of results.
• Develop reproducible bioinformatic pipelines on Texas A&M HPRC resources; prepare data, figures, and first- and co-authored manuscripts.
• Maintain accurate lab records in both digital and hardcopy form, and ensure up-to-date lab safety documentation.
• Lead and co-author manuscripts in scientific journals; assistance may also be sought in drafting extension documents.
• Mentor the graduate students and interns.
• Collaborate with USDA-ARS scientists.

Required Qualifications:

• Ph.D. (in hand by start date) in plant pathology, microbiology, microbial/molecular genomics, agronomy/crop science with a pathology focus, or a related field.

Preferred Qualifications:

• Demonstrated field and/or greenhouse experimental experience in plant pathology or a closely related discipline.
• Demonstrated bioinformatics capability: microbial/fungal genome assembly and annotation, comparative or population genomics, command-line work in a Linux/HPC environment, and scripting in at least one of Python, R, or Bash.
• Hands-on molecular biology (DNA extraction, library preparation, PCR/qPCR).
• Experience handling Oxford Nanopore (ONT) sequence data.
• A record of scientific productivity appropriate to career stage and strong written and oral communication.
• As a field-demanding position, a current driver's license is required. The laboratory works with machine-learning and AI-assisted tools as part of routine research practice. Prior formal experience is not required, but candidates are expected to use these tools in their work and to develop fluency with them on the job, with a strong emphasis on reproducibility and validation.
• Experience with soil-borne pathogens of cotton or other row crops (fungal and nematodes).
• Population genomics, microbiome analysis, or diagnostic assay (LAMP/qPCR/ddPCR) development.
• Field-trial design and prior mentoring or supervisory experience.

Additional Requirements:

• Ability to obtain a valid US driver's license.
• Initial one-year appointment, renewable up to four years contingent on performance and funding.

Knowledge, Skills, and Abilities:

• Aseptic microbiology: both conceptual and demonstrable technical knowledge.
• Microbial culture of bacteria and fungi; ability to grow microorganisms in pure culture and in interaction studies, including the soil-borne pathogens central to this project.
• A deep understanding of the microbial species concept is mandatory, and is expected to inform the pathogen population-genomics and diagnostic work.
• Ability to collect phenotypic data from plants (healthy, infected, and infested) in field and greenhouse settings.
• Fast learner and self-starter, able to work independently.
• Meticulous record-keeping and a detail-oriented approach.
• Knowledge of laboratory maintenance and equipment.
• Ability to multi-task and to work cooperatively with others across internal and external collaborations.
• Experience in handling ONT data is required, and hands-on experience in running the Oxford Nanopore sequencer is desirable.
• Experience in high-throughput culturomics is desirable.
• Experience in, or interest in, laboratory automation will be an advantage.

Equipment used to perform the essential duties of this position:

Computer - 5 to10 hours/week

PCR machine - 5 to 10 hours/week

Sequencer - 5 to 10 hours/week

All positions are security-sensitive. Applicants are subject to a criminal history investigation, and employment is contingent upon the institution's verification of credentials and/or other information required by the institution's procedures, including the completion of the criminal history check.

Equal Opportunity/Veterans/Disability Employer.