Senior Scientist, Bioinformatics

Idexx•Westbrook, ID

About The Position

The Genomics group in Discovery Tech Futures, R&D, is seeking a Senior Scientist, Bioinformatics to join a discovery team working at the intersection of molecular biology and diagnosis. The role is responsible for developing, validating, implementing, and supporting next-generation sequencing (NGS) bioinformatics pipelines and analyses. The scientist will work closely with laboratory scientists, R&D teams, and data engineers to translate genomic and transcriptomic data into actionable insights for products and research programs. The position bridges biomarker discovery and assay development, identifying novel targets from sequencing data and helping shape the technical direction of NGS pipelines. The role includes end-to-end analysis of bulk and single-cell sequencing data, development of workflows for long-read sequencing, and integration of multi-omics datasets. It also involves evaluating sequencing technologies and analytical tools, communicating findings to varied audiences, and contributing to scientific outputs such as publications and patents.

Requirements

PhD in Bioinformatics, Computational Biology, Genomics, Biostatistics, Computer Science, or a related field.
Hands-on expertise in NGS data analysis.
Hands-on experience analyzing third-generation, long-read sequencing data from Oxford Nanopore and/or PacBio.
Strong programming skills in Python and/or R.
Proficiency in Linux/Unix and shell scripting.
A solid foundation in statistics, molecular biology, and genomics.
A track record of scientific contribution demonstrated through peer-reviewed publications, patents, or delivered projects.
Excellent communication skills and ability to work collaboratively in a cross-functional team.

Nice To Haves

Experience building reproducible pipelines with Nextflow or Snakemake and working in HPC or cloud environments such as AWS, GCP, or Azure.
Experience with liquid biopsy, MRD, cancer early detection, ctDNA analysis, or related applications.
Experience with bulk, single-cell, or spatial transcriptomics for de novo isoform discovery.
Experience with pathway analysis.
Experience with metagenomics, microbial genomics, or veterinary and comparative genomics.
Familiarity with hybrid assembly approaches combining short- and long-read data.
Experience applying AI or machine-learning methods to genomic data.
Experience working with canine or feline genomes.
Experience with version control (Git), CI/CD, and software engineering best practices.

Responsibilities

Perform end-to-end analysis of bulk and single-cell NGS data, including experiment design, quality control, secondary and tertiary analysis, and biological interpretation.
Develop and apply workflows for third-generation, long-read sequencing data from Oxford Nanopore and/or PacBio platforms.
Design, build, and maintain reproducible, scalable pipelines in cloud environments.
Evaluate and benchmark sequencing technologies, algorithms, and tools, and recommend best practices for adoption.
Collaborate with wet-lab scientists on experimental design, sequencing strategy, and statistical power considerations.
Integrate multi-omics datasets, including transcriptomic, genomic, and epigenomic data, to generate biological insights.
Communicate results through reports, visualizations, and presentations to technical and non-technical stakeholders.
Contribute to publications, patents, and external presentations as appropriate.
Stay current on emerging genomics and bioinformatics technologies, tools, methodologies, and industry best practices.