One Health Bioinformatics & Molecular Diagnostics Scientist

Texas A&M Agrilife Research; College Station (TX); In loco; USD 90.000 - 140.000; Tempo pieno

Vantaggi offerti da questo lavoro

Health insurance

Paid holidays

Sick leave

Vacation

Retirement plan

Professional development

Descrizione del lavoro

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.

Competenze

• 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.

Mansioni

• 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.

Conoscenze

R

Bash

Python

Nextflow/Snakemake

Git

Statistical analysis

Sequencing data analysis

Formazione

Ph.D. in Bioinformatics, Microbiology, Molecular Biology, Biomedical or Veterinary Sciences, Animal Science

Strumenti

QIIME 2

DADA2

Dorado

minimap2

Kraken2

BLAST+

SPAdes

Flye

AMRFinderPlus

IQ-TREE

Descrizione del lavoro

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.