Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics

Texas A&M University System • College Station, TX

1d • Onsite

About The Position

The Associate Research Scientist will lead Texas A&M AgriLife Research’s laboratory bioinformatics and molecular diagnostics program. The position develops and validates sequencing- and PCR-based detection methods for pathogens, parasites, vectors, and antimicrobial resistance determinants; builds reproducible pipelines for amplicon, metagenomic, and whole-genome data from short- and long-read platforms; and translates findings into surveillance outputs for research sponsors and agency partners. This staff scientist has defined ownership of diagnostic and computational workflows and is expected to lead publications, contribute to grant proposals, and provide technical guidance to students and staff.

The role includes research across animal, food, and environmental samples; mentoring researchers and laboratory staff; presenting findings to scientific and stakeholder audiences; and preparing sponsor progress reports. The position is based in College Station, Texas, and requires occasional travel to field sites, partner institutions, and scientific conferences. It is grant- or contract-funded, and continued employment depends on ongoing funding and satisfactory performance.

Requirements

• Ph.D. in Bioinformatics, Microbiology, Molecular Biology, Biomedical or Veterinary Sciences, Animal Science, or a closely related field.
• Three years of research experience beyond the doctoral degree in bioinformatics, molecular diagnostics, or pathogen genomics.
• Knowledge of microbial ecology, infectious disease surveillance, and antimicrobial resistance within a One Health framework.
• Proficiency in R and Bash on Linux/HPC systems, including SLURM, and working knowledge of Python.
• Experience with workflow managers such as Nextflow or Snakemake and Git.
• Familiarity with tools such as QIIME 2, DADA2, Dorado, minimap2, Kraken2, BLAST+, SPAdes or Flye, AMRFinderPlus, and IQ-TREE.
• Ability to plan and execute independent research, manage concurrent projects, and meet publication and reporting deadlines.
• Strong scientific writing and oral communication skills for academic, agency, and producer audiences, and ability to collaborate across disciplines.
• Demonstrated experience analyzing high-throughput sequencing data from raw reads through statistical interpretation.
• Laboratory experience with nucleic acid extraction, PCR or qPCR, and sequencing library preparation.
• Record of first-author, peer-reviewed publications.
• Ability to multitask and work cooperatively with others.
• Ability to work in a BSL-2 laboratory and handle animal, food, and environmental samples under institutional biosafety protocols.

Nice To Haves

• Experience with Oxford Nanopore sequencing, including benchmarking long-read results against short-read data and mock communities.
• Experience developing or validating diagnostic assays in a veterinary diagnostic, public health, or federal research laboratory.
• Experience with digital PCR and formal assay validation.
• Experience curating reference databases for DNA-based identification of pathogens or host species, such as DNA barcoding or metabarcoding.
• Experience with samples from livestock, wildlife, companion animal, or aquatic animal systems, or from food and environmental sources.
• Teaching or mentoring experience in a laboratory or instructional setting.

Responsibilities

• Lead development and validation of qPCR, digital PCR, and targeted sequencing assays for One Health surveillance, including primer and probe design, in silico specificity screening, and evaluation of detection limits, analytical sensitivity and specificity, and repeatability.
• Design and conduct amplicon, metabarcoding, and shotgun metagenomic sequencing studies using Illumina and Oxford Nanopore platforms across animal, food, and environmental sample types.
• Build, document, and maintain reproducible bioinformatics pipelines for read processing, taxonomic classification, genome assembly and annotation, antimicrobial resistance gene detection, and phylogenetic analysis on Linux high-performance computing systems.
• Curate reference sequence databases and benchmark pipeline performance using mock communities, reference materials, and cross-platform comparisons.
• Manage sequencing data, metadata, and analysis code under laboratory data-management policy and FAIR principles, including version control and deposition in public repositories.
• Integrate molecular results with spatial, temporal, and epidemiological surveillance data to support research sponsors and agency partners.
• Prepare manuscripts as lead or contributing author and draft methods, preliminary data, and figures for federal, state, and industry proposals.
• Coordinate sample logistics, data sharing, and joint analyses with federal, national laboratory, and university collaborators.
• Maintain biosafety, contamination-control, and sample-tracking standards; assist with preparation, organization, and cleaning of the laboratory worksite.
• Train graduate students, postdoctoral researchers, undergraduate researchers, and laboratory staff in sequence analysis, assay design and validation, and sequencing library preparation.
• Review student analyses and drafts and help troubleshoot computational and wet-laboratory workflows.
• Present research at laboratory meetings, stakeholder and agency briefings, and scientific conferences.
• Prepare technical progress reports for federal and industry sponsors.
• Perform other duties as assigned.

Benefits

• Health, dental, vision, life, and long-term disability insurance, with AgriLife contributing to premiums.
• 12–15 annual paid holidays.
• Up to 8 hours per month of sick leave and at least 8 hours per month of vacation.
• Automatic enrollment in the Teacher Retirement System of Texas.
• Employee Wellness Initiative.
• Access to ongoing professional development and training through Aspire, LinkedIn Learning, and internally developed programs.

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: Ph.D. or professional degree