Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics

Texas A&M University System; College Station (TX); On-site; USD 90,000 - 130,000; Full time

Job summary

Texas A&M Agrilife Research in College Station, Texas, seeks an Associate Research Scientist to lead bioinformatics and molecular diagnostics efforts for One Health. The role focuses on developing qPCR, sequencing-based detection methods, and reproducible pipelines across short and long-read platforms.

The incumbent will guide students and staff, publish results, and contribute to grant proposals while coordinating with federal and state partners on data sharing and surveillance initiatives.

Qualifications

• PhD 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

Responsibilities

• Leads development and validation of molecular detection assays for One Health surveillance.
• Designs sequencing studies across diverse sample types on Illumina and Oxford Nanopore platforms.
• Builds reproducible bioinformatics pipelines for read processing, taxonomy, genome assembly, and resistance gene detection.
• Maintains reference databases and benchmarks pipeline performance.
• Manages sequencing data, metadata, and analysis code under lab policies.
• Integrates molecular results with epidemiological data to support sponsors and partners.
• Prepares manuscripts and drafts methods for proposals.
• Coordinates sample logistics and data sharing with collaborators.
• Maintains biosafety, contamination control, and lab housekeeping.

Skills

PhD in Bioinformatics

Research experience

R and Bash on Linux/HPC

Python

Workflow managers

Git

QIIME 2

DADA2

Dorado

minimap2

Education

PhD in Bioinformatics or related field

Tools

SLURM

Nextflow

Snakemake

IQ-TREE

DADA2 tooling

minimap2

Kraken2

BLAST+

Job description

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 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.

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