Senior Scientist, Bioinformatics

IDEXX; Westbrook (ME); On-site; USD 99,000 - 121,000; Full time

Benefits offered by this job

Bonus opportunity

Benefits starting Day One

401k matching 5%

Job summary

IDEXX's Genomics group in Discovery Tech Futures, R&D, seeks a Senior Scientist, Bioinformatics to lead NGS pipeline development, validation and implementation. You will translate genomic data into insights supporting diagnostic tools for veterinarians and pet owners, collaborating with scientists, data engineers and研发 teams.

The role emphasizes end-to-end NGS analysis, multi-omics integration and publications or patents, with a focus on rigorous, scalable workflows in cloud/HPC environments.

Qualifications

• PhD in Bioinformatics, Computational Biology, Genomics, Biostatistics, CS or related field.
• Hands-on expertise in NGS data analysis, including long-read data.
• Strong programming in Python and/or R; Linux/Unix and shell scripting.
• Solid foundation in statistics, molecular biology, and genomics.
• Track record via publications, patents, or projects.
• Excellent communication and cross‑functional collaboration.
• Experience with Nextflow or Snakemake and cloud/HPC environments.

Responsibilities

• Perform end-to-end analysis of bulk and single-cell NGS data, including QC, analysis and interpretation.
• Develop workflows for long-read data (Oxford Nanopore and/or PacBio).
• Design, build, and maintain scalable pipelines in cloud environments.
• Collaborate with wet-lab scientists on experimental design and sequencing strategy.
• Integrate multi-omics data to generate actionable biological insights.
• Communicate results via reports, visuals, and stakeholder presentations.

Skills

Python

R

Linux

Shell scripting

Statistics

Communication

Git

Nextflow

Education

PhD in Bioinformatics

Computational biology

Tools

AWS

GCP

Azure

Snakemake

HPC

Job description

The Genomics group in Discovery Tech Futures, R&D, is seeking a highly motivated Senior Scientist, Bioinformatics to join a fast-paced discovery team working at the intersection of molecular biology and diagnosis. In this role, you will be responsible for the development, validation, implementation and support of next-generation sequencing (NGS) bioinformatics pipelines and analytical. You will partner closely with laboratory scientists, R&D teams, and data engineers to turn complex genomic and transcriptomic data into actionable insights that advance our products and research programs.

Why this role matters

At IDEXX, developing high-quality biological reagents is foundational to advancing companion animal health diagnostics. The Genomics team is the critical bridge between biomarker discovery and assay development. As a Senior Scientist, you will bring advanced expertise to identifying novel targets from raw sequencing data, shape the technical direction of the NGS pipeline, and contribute directly to new diagnostic tools for the veterinarians and pet owners we serve. We value scientific curiosity, rigor, and ethnical breadth, and this role offers the opportunity to lead complex problems through genomics pipeline development, analytical evaluation, and functional assessment.

In This Role, You Will

• Perform end-to-end analysis of bulk and single-cell NGS data, including experiment design, quality control, secondary/tertiary analysis, and biological interpretation.
• Develop and apply workflows for TGS (long-read) data from Oxford Nanopore and/or PacBio platforms.
• Design, build, and maintain reproducible, scalable pipelines in cloud environments.
• Evaluate and benchmark new 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 (e.g., transcriptomic, genomic, epigenomic) to generate biological insights.
• Communicate results clearly through reports, visualizations, and presentations to technical and non-technical stakeholders.
• Contribute to publications, patents, and external presentations as appropriate.
• Stay current on emerging technologies, tools, methodologies, and industry best practices in genomics and bioinformatics.

What You Need To Succeed

• PhD in Bioinformatics, Computational Biology, Genomics, Biostatistics, Computer Science, or a related field is required.
• Demonstrated hands‑on expertise in NGS data analysis is required.
• Demonstrated hands‑on experience analyzing third generation (long‑read) sequencing data from Oxford Nanopore and/or PacBio is required.
• Strong programming skills in Python and/or R, and proficiency in Linux/Unix and shell scripting is required.
• Solid foundation in statistics, molecular biology, and genomics is required.
• Track record of scientific contribution, demonstrated through peer‑reviewed publications, patents, or delivered projects is required.
• Excellent communication skills and the ability to work collaboratively in a cross‑functional team is required.
• Experience building reproducible pipelines with Nextflow or Snakemake and working in HPC or cloud (AWS, GCP, or Azure) environments is desired.
• Experience with liquid biopsy, MRD, cancer early detection, ctDNA analysis, or related applications is desired.
• Experience with bulk/single cell/spatial transcriptomics for De novo isoform discovery is desired.
• Experience with pathway analysis is desired.
• Experience with metagenomics, microbial genomics, or veterinary and comparative genomics is desired.
• Familiarity with hybrid assembly approaches combining short‑ and long‑read data is desired.
• Experience with AI/machine learning methods applied to genomic data is desired.
• Experience working experience with Canine/Feline genome is strongly desired.
• Experience with version control (Git), CI/CD, and software engineering best practices is desired.

What You Can Expect From Us

• Salary range starting at $110,000 based on experience
• Opportunity for annual cash bonus
• Health / Dental / Vision Benefits Day‑One
• 5% matching 401k
• Additional benefits including but not limited to financial support, pet insurance, mental health resources, volunteer paid days off, employee stock program, foundation donation matching, and much more

Why IDEXX

We’re proud of the work we do, because our work matters. An innovation leader in every industry we serve since 1983, our team members help pet owners worldwide keep their companion animals healthy and happy, ensure safe drinking water for billions, and help farmers protect livestock and poultry from disease.

We have customers in over 175 countries and a collaborative global workforce. Our culture embraces challenges and encourages learning and discovery. At IDEXX, you’ll be supported by competitive compensation, incentives, and benefits while enjoying purposeful work that drives improvement.

If meaningful work and a sense of purpose are at the top of your list, you’ll find it here. Let’s pursue what matters together.

About the job location:

If you’re thinking about relocating for this role, here are a few things to know about living in Maine (often called “Vacationland”). The Westbrook, ME area provides great access to active downtown areas and the outdoors, with the coast and numerous mountains and hiking trails nearby. You’ll also find a number of large companies like ours in the area, creating a vibrant work culture.

You can learn more on the Portland tourism website: https://www.visitportland.com/visit/resources/moving-to-maine/

IDEXX values a diverse workforce and workplace and strongly encourages women, people of color, LGBTQ+ individuals, people with disabilities, members of ethnic minorities, foreign‑born residents, and veterans to apply.

IDEXX is an equal opportunity employer. Applicants will not be discriminated against because of race, color, creed, sex, sexual orientation, gender identity or expression, age, religion, national origin, citizenship status, disability, ancestry, marital status, veteran status, medical condition, or any protected category prohibited by local, state, or federal laws.