Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics
Texas A&M Agrilife Research
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Benefits offered by this job
Job summary
The Associate Research Scientist at Texas A&M AgriLife will lead the lab's bioinformatics and molecular diagnostics program.
The incumbent will develop and validate sequencing and PCR based detection methods for pathogens, parasites, vectors, and antimicrobial resistance determinants; build reproducible pipelines for amplicon, metagenomic, and whole genome data from short read and long read platforms; and translate results into surveillance outputs for research sponsors and agency partners.
Qualifications
- 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 (e.g., 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 for academic, agency, and producer audiences, and the ability to work collaboratively 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 multi-task and work cooperatively with others.
Responsibilities
- Research Leads the development and validation of molecular detection assays (qPCR, digital PCR, and targeted sequencing) for One Health surveillance, including primer and probe design, in silico specificity screening, and determination of limit of detection, analytical sensitivity and specificity, and repeatability.
- Designs and conducts amplicon, metabarcoding, and shotgun metagenomic sequencing studies on Illumina and Oxford Nanopore platforms across animal, food, and environmental sample types.
- Builds, documents, and maintains 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.
- C urates reference sequence databases and benchmarks pipeline performance using mock communities, reference materials, and cross platform comparisons.
- Manages sequencing data, metadata, and analysis code under the laboratory data management policy and FAIR principles, including version control and deposition in public repositories.
- Integrates molecular results with spatial, temporal, and epidemiological surveillance data to provide decision support for research sponsors and agency partners.
- Prepares manuscripts as lead or contributing author and drafts methods, preliminary data, and figures for federal, state, and industry proposals.
- Coordinates sample logistics, data sharing, and joint analyses with federal, national laboratory, and university collaborators.
- Maintains biosafety, contamination control, and sample tracking standards; assists with the preparation, organization, and cleaning of the laboratory worksite.
Skills
Education
Tools
Job description
Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics
Texas A&M AgriLife
Research Department Animal Science
Commensurate
College Station, Texas
Staff
Texas A&M AgriLife is comprised of the following Texas A&M University System members: Texas A&M AgriLife Extension Service Texas A&M AgriLife Research College of Agriculture and Life Sciences at Texas A&M University Texas A&M Forest Service Texas A&M Veterinary Medical Diagnostic Laboratory As the nation’s largest most comprehensive agriculture program, Texas A&M AgriLife brings together a college and four state agencies focused on agriculture and life sciences within The Texas A&M University System. With over 5,000 employees and a presence in every county across the state, Texas A&M AgriLife is uniquely positioned to improve lives, environments and the Texas economy through education, research, extension and service.
Job Summary: The Associate Research Scientist will lead the laboratory's bioinformatics and molecular diagnostics program. The incumbent will develop and validate sequencing and PCR based detection methods for pathogens, parasites, vectors, and antimicrobial resistance determinants; build reproducible pipelines for amplicon, metagenomic, and whole genome data from short read and long read platforms; and translate results into surveillance outputs for research sponsors and agency partners. This is a staff scientist position with defined ownership of the laboratory's diagnostic and computational workflows. The incumbent is expected to lead publications, contribute to grant proposals, and provide technical guidance to students and staff.
- Research Leads the development and validation of molecular detection assays (qPCR, digital PCR, and targeted sequencing) for One Health surveillance, including primer and probe design, in silico specificity screening, and determination of limit of detection, analytical sensitivity and specificity, and repeatability.
- Designs and conducts amplicon, metabarcoding, and shotgun metagenomic sequencing studies on Illumina and Oxford Nanopore platforms across animal, food, and environmental sample types.
- Builds, documents, and maintains 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.
- Curates reference sequence databases and benchmarks pipeline performance using mock communities, reference materials, and cross platform comparisons.
- Manages sequencing data, metadata, and analysis code under the laboratory data management policy and FAIR principles, including version control and deposition in public repositories.
- Integrates molecular results with spatial, temporal, and epidemiological surveillance data to provide decision support for research sponsors and agency partners.
- Prepares manuscripts as lead or contributing author and drafts methods, preliminary data, and figures for federal, state, and industry proposals.
- Coordinates sample logistics, data sharing, and joint analyses with federal, national laboratory, and university collaborators.
- Maintains biosafety, contamination control, and sample tracking standards; assists with the preparation, organization, and cleaning of the laboratory worksite.
Trains graduate students, postdoctoral researchers, undergraduate researchers, and laboratory staff in sequence analysis, assay design and validation, and sequencing library preparation. Reviews student analyses and drafts and helps troubleshoot computational and wet laboratory workflows.
Presents research at laboratory meetings, stakeholder and agency briefings, and scientific conferences. Prepares technical progress reports for federal and industry sponsors.
Performs other duties as assigned.
- 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 (e.g., 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 for academic, agency, and producer audiences, and the ability to work collaboratively 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 multi-task and work cooperatively with others.
- 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 with formal assay validation.
- Experience curating reference databases for DNA based identification of pathogens or host species (e.g., 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.
- Ability to work in a BSL-2 laboratory and handle animal, food, and environmental samples under institutional biosafety protocols.
- This position is funded through grants or contracts.
- Continued employment is dependent upon ongoing funding and satisfactory job performance.
- Occasional travel to field sites, partner institutions, and scientific conferences.
Salary: Compensation is commensurate with the candidate’s qualifications. Position funding is through grants or contracts. Continued employment is dependent upon ongoing funding and satisfactory job performance.
Your employment at Texas A&M AgriLife may require nonimmigrant sponsorship. A Presidential proclamation issued on September 19, 2025, imposes a $100,000 fee on new H-1B petitions filed after September 21, 2025. Texas A&M AgriLife will NOT pay this fee. If the fee is imposed on your petition, this offer of employment will be revoked. If actions taken during your employment result in the imposition of this fee, your employment will be terminated. To the extent that this statement conflicts with any applicable System or member Policy, Regulation, or Rule, this statement will control. We recommend that you consult with your private immigration counsel at your own expense regarding potential implications. In addition, on January 27, 2026, Texas Governor Abbott issued a moratorium on the filing of any new H-1B unless approved by the Texas Workforce Commission. Accordingly, if you will now or in the future require sponsorship for employment visa status this moratorium may affect our ability to employ you should you be selected as the final candidate.
- Health, dental, vision, life and long-term disability insurance (AgriLife contributes to premiums)
- 12–15 annual paid holidays
- Up to 8 hours/month sick leave and at least 8 hours/month 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
Equal Opportunity/Veterans/Disability Employer. The Texas A&M University System is one of the largest systems of higher education in the nation, with a statewide network of twelve universities, eight state agencies, a comprehensive health science center, Texas A&M-Fort Worth and Texas A&M-RELLIS. The A&M System is committed to providing an educational and work environment that is conducive to the personal and professional development of each employee. Each member institution provides equal opportunity and access to all students, employees and prospective employees.
The Texas A&M University System is an Equal Opportunity/ Veterans/ Disability Employer.
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