Senior Bioinformatics Scientist/Engineer

Position Title: Senior Bioinformatics Scientist/Engineer Location: Remote-first (U.S. time-zone overlap preferred) Employment Type: Full-time Role Overview Join the AI-first team that is transforming precision medicine into everyday clinical practice. Our platform integrates whole-genome sequencing, microbiome metagenomics, electronic medical records, and AI reasoning to generate mechanism-based guidance for physicians. As a Senior Bioinformatics Scientist/Engineer, you will play a major role in designing, validating, and continuously improving end-to-end analysis pipelines and knowledge frameworks that power these insights. You will be expected to produce production-grade tools capable of deriving clinical utility from raw biological data. You’ll work hand-in-hand with software engineers, medical subject matter experts, and regulatory leaders to deliver clinical grade interpretations delivered directly in the hands of physicians. What You’ll Own Pipeline Design & Validation Architect and optimize a post-sequencing microbiome metagenomic analysis pipeline (e.g., QC → alignment → variant calling → taxonomic profiling → clinical analysis). Build workflows, ingestion, and annotation pipelines for 30X WGS Structural and Copy Number Variant Calling. Annotation & Interpretation Curate and maintain annotation stacks integrating microbiome functional databases, and proprietary AI-derived knowledge graphs. Assist in building out automated cadenced updates of clinical-grade knowledge sources (ClinVar, gnomAD, ClinPgx, HGMD) to provide automated variant-to-mechanism mapping modules feeding the AI engine. Data Quality & Compliance Implement validation, reproducibility, and audit trails required for CLIA + CAP and prepare evidence packages for FDA SaMD / LDT submissions.IQ/OQ/PQ documents; pipeline change-control logs; regulatory briefing decks. Collaboration & Mentorship Partner with software and AI engineers to integrate multi-omics features into AI models; coach junior programmers on best practices. Participate in cross-team design reviews; internal workshops on variant curation or microbiome stats. Minimum Qualifications • PhD (or MS with 5+ yrs experience) in Genetics, Microbiomics, Genomics, Bioinformatics, Computational Biology, or related field. • 4+ yrs working knowledge of microbiome metagenomics bioinformatics pipelines, analytics, and databases. • 4+ yrs hands-on pipeline development for NGS (WGS, targeted panels) using Nextflow, Snakemake, WDL, or similar on cloud or HPC. • Solid grasp of variant calling (DRAGEN, GATK), structural variant/copy number variant detection, and functional annotation methods. • Proficiency in Python for production-grade code, full unit-test coverage, REST API usage, reproducible statistic analysis, and visualizations; SQL and noSQL database familiarity. • Experience working in an agile based software organization, clearly documenting ticketed work, and modifying code in git-tracked production code bases. • Comfort with AWS genomics services (Fargate, Step Functions, Glue, Athena). • Strong communication skills—able to translate genomic insights into plain language for physicians, regulators, and engineers. Preferred Qualifications • Highly comfortable with AI-based development tools (Claude code, Cursor, OpenAI Agents) • Prior authorship of clinical validation studies published in peer-reviewed journals (e.g., JAMA Netw Open, Nature Medicine). • Experience integrating multi**-omics** datasets (metabolomics, proteomics) or developing multi-modal AI features. • Knowledge of FDA SaMD guidance, LDT regulation, and evidence generation for 510(k)/De Novo submissions. Success Metrics First 12 Months • Integrate microbiome insights into the clinical decision-support platform delivering AI-curated genomic + microbiome results by month 3. • CLIA-ready Structural Variant and Copy Number Variant pipeline validated and integrated within 6 months. • Design and integrate novel features regarding the existing bioinformatic infrastructure that expand the clinical utility of the Bioscope platform by month 9 • Onboard and train at least 2 junior level bioinformatic scientists/programmers to extend company bandwidth by month 12 Tech & Tool Stack (Indicative) Python · Jupyter · REST APIs · AWS Batch/EKS/Lambda/ECS · AWS S3 · AWS Glue/Athena · PostgreSQL · Nextflow · DRAGEN · GATK · Kraken2/Bracken · HUMAnN · GitHub Actions · Docker Compensation & Benefits Competitive salary + meaningful early-stage equity · Fully remote flexibility · Comprehensive health/dental/vision plans · Annual conference & training budget · Option to contribute to open-source genomics projects on company time. Job Type: Full-time Pay: $125,000.00 - $200,000.00 per year Benefits: • Health insurance Work Location: Remote Apply tot his job Apply To this Job