Postdoctoral Research Associate - Field Pathology

Join the Antony-Babu laboratory as a Postdoctoral Research Associate to lead field pathology and pathogen genomics for a project developing predictive tools for cotton soil-borne disease management. This role is supported through a cooperative agreement with USDA-ARS and conducted in collaboration with the USDA-ARS Southern Plains Agricultural Research Center (Insect Control and Cotton Disease Research Unit).

About the Role

This is a field scientist's role with full ownership of the genomics pipeline. You will take major cotton soil-borne pathogens from field and greenhouse experimentation through isolate sequencing, hybrid genome assembly, comparative and population genomics, and diagnostic-tool development. The position involves close collaboration with a Ph.D. student across the entire project. We seek an independent researcher who integrates field-based research and molecular bioinformatics, viewing genome data and disease ecology as interconnected disciplines.

Research Focus

You will lead field pathology and pathogen genomics by designing and executing experiments, driving the isolate-to-assembly-to-diagnostic-assay pipeline, and publishing population-ecology and disease biology findings.

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 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 host–microbiome analyses (GWAS/mGWAS, metagenomics) and 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, emphasizing reproducibility and validation.
• 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; assist in drafting extension documents.
• Mentor graduate students and interns.
• Collaborate with USDA-ARS scientists.

Requirements

• 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.
• 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.
• Record of scientific productivity appropriate to career stage and strong written and oral communication.
• Current driver's license.

Preferred Qualifications

• 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.
• Hands-on experience running the Oxford Nanopore sequencer.
• Experience in high-throughput culturomics.
• Interest in laboratory automation.

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.

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 soil-borne pathogens central to this project.
• Deep understanding of the microbial species concept to inform 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 work cooperatively across internal and external collaborations.

Equipment Used

• Computer: 5 to 10 hours/week
• PCR machine: 5 to 10 hours/week
• Sequencer: 5 to 10 hours/week

Benefits

• Health, dental, vision, life, and long-term disability insurance with Texas A&M AgriLife contributing to employee health and basic life premiums.
• 12-15 days of annual paid holidays.
• Up to eight hours of paid sick leave and at least eight hours of paid vacation each month.
• Automatic enrollment in the Teacher Retirement System of Texas.
• Employee Wellness Initiative for Texas A&M AgriLife.