Associate Research Scientist (One Health Bioinformatics and Molecular Diagnostics)

Location: College Station, Texas, United States; onsite laboratory role with occasional travel to field sites, partner institutions, and scientific conferences.

Company

Texas A&M AgriLife Research is part of the Texas A&M University System and conducts agriculture and life sciences research, education, extension, and service.

What you will do

• Lead the development and validation of qPCR, digital PCR, and targeted sequencing assays for One Health surveillance of pathogens, parasites, vectors, and antimicrobial resistance determinants.
• Design and conduct amplicon, metabarcoding, and shotgun metagenomic studies using Illumina and Oxford Nanopore platforms across animal, food, and environmental samples.
• Build, document, maintain, and benchmark reproducible bioinformatics pipelines for read processing, taxonomic classification, genome assembly and annotation, antimicrobial resistance detection, and phylogenetic analysis on Linux HPC systems.
• Manage sequencing data, metadata, analysis code, reference databases, version control, and public repository deposition under laboratory data management and FAIR principles.
• Integrate molecular, spatial, temporal, and epidemiological surveillance data and communicate results through sponsor reports, agency briefings, presentations, publications, and grant proposals.
• Coordinate sample logistics and collaborations, maintain biosafety and contamination-control standards, and train and guide students, postdoctoral researchers, and laboratory staff.

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, plus working knowledge of Python; experience with workflow managers such as Nextflow or Snakemake and Git.
• Familiarity with QIIME 2, DADA2, Dorado, minimap2, Kraken2, BLAST+, SPAdes or Flye, AMRFinderPlus, and IQ-TREE.
• 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.
• Ability to plan and execute independent research, manage concurrent projects, meet publication and reporting deadlines, multitask, and work cooperatively across disciplines.
• Strong scientific writing and oral communication for academic, agency, and producer audiences, including a record of first-author, peer-reviewed publications.
• Ability to work in a BSL-2 laboratory and handle animal, food, and environmental samples under institutional biosafety protocols.

Nice to have

• 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, including DNA barcoding or metabarcoding.
• Experience with livestock, wildlife, companion animal, aquatic animal, food, or environmental samples.
• Teaching or mentoring experience in a laboratory or instructional setting.

Culture & Benefits

• Staff scientist position with defined ownership of diagnostic and computational workflows.
• Health, dental, vision, life, and long-term disability insurance with employer contributions.
• 12–15 paid holidays, up to 8 hours of sick leave per month, and at least 8 hours of vacation per month.
• Automatic enrollment in the Teacher Retirement System of Texas and access to an employee wellness initiative.
• Ongoing professional development and training through Aspire, LinkedIn Learning, and internal programs.
• Position funding is through grants or contracts; continued employment depends on ongoing funding and satisfactory performance.

Hiring process

• Submit a complete application with a CV or resume, cover letter, and list of references.
• Employment is contingent on credential verification, required institutional checks, and a criminal history investigation.
• H-1B sponsorship may be affected by applicable fees and Texas filing restrictions; Texas A&M AgriLife will not pay the stated $100,000 fee.