Senior Bioinformatics Engineer

BiomeSense • Chicago, IL

4d • $125,000 - $200,000

About The Position

You’ll help build our MetaBiome platform, a novel software solution for collection, curation and analysis of longitudinal microbiome & health data at scale. This role provides a unique opportunity to be one of the earliest employees at a rapidly growing start-up, contributing across bioinformatics, data engineering, and product development. We’re looking for someone who is excited to build - and someone who has the character and drive to grow into a platform leader over time. You’ll join near the ground floor of development, getting hands-on experience building the infrastructure, pipelines, and novel analytical workflows to turn raw microbiome data into actionable and high-integrity microbiome intelligence.

Requirements

• B.S. /M.S. /PhD in Computational Biology, Bioinformatics, Computer Science or a related field with 3+ yrs industry experience (biotech start-up ideal)
• Strong proficiency in Python and JavaScript, with experience building scalable, reusable, testable, and maintainable software.
• Proficiency with PostgreSQL or other relational SQL database systems.
• Familiarity with clinical ontologies such as SNOMED, ICD-11, ATC, and LOINC.
• Familiarity with Amazon Web Services and best practices in computer security.
• Proficiency with one or more modern frontend web technologies.
• Excellent communication skills for presenting complex scientific concepts to diverse stakeholders.
• Strong ownership mindset and the ability to execute in fast-moving environments.
• Strong fundamentals in bioinformatics pipelines, QC, and reproducibility.

Nice To Haves

• Bioinformatician with experience working with NGS data and bioinformatics pipeline verification and knowledge of microbiome-specific challenges (compositional data, variability, confounders).
• Familiarity with longitudinal / repeated-measures biological datasets.
• Experience integrating external ontologies or standardized vocabularies.
• Exposure to cloud infrastructure, workflow orchestration, or containerization.
• Interest in AI/ML applications built on large biological datasets.

Responsibilities

• Bioinformatics Architecture & Infrastructure - help design, implement, and maintain the robust, auditable backend required for the highest-quality extraction of clean microbiome data from raw shotgun metagenomic sequencing data.
• Data Engineering – contribute to the development and maintenance of cloud-based infrastructure, including databases, distributed computing workflows, and REST endpoints, supporting a data platform that organizes microbial sequence data and associated clinical metadata.
• Statistical Analysis – lead the design, execution, and documentation of reproducible computational experiments from concept to conclusion, including experimental design, data preparation, model selection, and evaluation strategies.
• Methods Development – Develop and implement novel analytical methodologies and algorithms informed by experimental findings and validated through rigorous evaluation.
• Frontend / Backend Development – design, implement, and maintain robust data ingestion interfaces leveraging external APIs and clinical ontologies such as SNOMED, MedDRA, and ICD-10, adhering to software engineering best practices including wireframe design, unit testing, version control, code review, and security and compliance.

What This Job Offers

• Job Type: Full-time
• Career Level: Senior