Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics

Agrilife; College Station (TX); On-site; USD 85,000 - 120,000; Full time

Benefits offered by this job

Health insurance

12–15 annual holidays

Sick leave & vacation

Retirement plan

Professional development

Job summary

Texas A&M AgriLife invites applications for an Associate Research Scientist in College Station to lead the lab’s bioinformatics and molecular diagnostics program. You will develop sequencing and PCR-based methods for detection of pathogens, parasites, vectors, and resistance determinants, and build reproducible pipelines for amplicon, metagenomic, and whole-genome data.

The role requires a PhD and strong collaboration skills to translate results into surveillance outputs for sponsors, with

Qualifications

• PhD required with strong publishing record and grant experience.
• Experience in One Health pathogen surveillance and antimicrobial resistance is preferred.
• Proficiency with Linux/HPC, SLURM, and scripting in R, Bash, and Python.

Responsibilities

• Lead development and validation of molecular detection assays and pipelines.
• Design sequencing studies (amplicon, metagenomic, WGS) on Illumina and Nanopore platforms.
• Maintain reproducible bioinformatics workflows and data governance.

Skills

Bioinformatics knowledge

Molecular biology basics

Team collaboration

Scientific writing

Project management

Education

PhD in Bioinformatics, Microbiology, Molecular Biology, Biomedical or Veterinary Sciences, Animal Science, or related field

Tools

Nextflow

Snakemake

R

Python

Git

QIIME 2

DADA2

Minimap2

Kraken2

AMRFinderPlus

IQ-TREE

SPAdes/Flye

Job description

Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics# Improving lives through science and technology## Associate Research Scientist: One Health Bioinformatics and Molecular DiagnosticsApply: College Station, TX: Full time: Posted 3 Days Ago: R-098277**Job Title**Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics**Agency**Texas A&M Agrilife Research**Department**Animal Science**Proposed Minimum Salary**Commensurate**Job Location**College Station, Texas**Job Type**Staff**Job Description**# **About Texas A&M AgriLife**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 LaboratoryAs 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.Click **here** to learn more about joining AgriLife!# **Position Information****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. **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.* 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. **Mentoring*** 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. **Presentations and Reporting*** Presents research at laboratory meetings, stakeholder and agency briefings, and scientific conferences.* Prepares technical progress reports for federal and industry sponsors. **Other Duties*** Performs other duties as assigned. **Qualifications:****Required 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. **Preferred Qualifications:*** 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. **Other Requirements:*** 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. # **What You Need to Know****Salary:** Compensation is commensurate with the candidate’s qualifications.**Position Funding:** This position is funded through grants or contracts. Continued employment is dependent upon ongoing funding and satisfactory job performance.**Important Notice Regarding H1-B Sponsorship:** 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.**Benefits and Leave:*** 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# **How to Apply**Applications must include all job application data or a complete resume. Incomplete applications may be rejected. Applicants are encouraged to upload a resume or use LinkedIn to prepopulate application fields. **Required Documents:*** CV / Resume* Cover Letter* List of ReferencesAll 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.