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Texas A&M University System

Texas public university system

Associate Research Scientist: One Health Bioinformatics and Molecular Diagnostics

Translational Research & Bench Biology +1Confirmed live in the last 24 hours
Full-timeCollege Station, TX, USANo salary listed

About the Job

Requirements

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

Responsibilities

  • Lead the development and validation of molecular detection assays, including 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.
  • Design and conduct amplicon, metabarcoding, and shotgun metagenomic sequencing studies on 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 the 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 provide decision support for 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 the 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.

Desired 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 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.

About the Company

Texas A&M University System

Texas public university system

Texas A&M University System is a statewide public university system combining higher education, research, and public-service agencies. The system coordinates universities and state agencies that deliver teaching, research, extension, engineering, health, and community programs. It serves students, faculty, researchers, public agencies, industries, and communities throughout Texas. Its operating model centers on autonomous member institutions connected through system governance, shared services, public funding, and statewide missions. Teams work across instruction, research, healthcare, extension, engineering, technology, administration, facilities, and public service. Teams support coordinated daily delivery.

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