Senior Bioinformatics Scientist/Engineer

Position Title: Senior Bioinformatics Scientist/Engineer Location: Carmel, IN (preferred) / Boston, MA / U.S. Remote available 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, microbiomics, 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 clinical-grade pipelines across pharmacogenomics (PGx), polygenic risk scoring (PRS), and other WGS applications. You will be expected to produce production-grade tools capable of deriving clinical utility from raw genomic data. You'll work hand-in-hand with software engineers, medical subject matter experts, and regulatory leaders to deliver clinical grade interpretations directly in the hands of physicians. What You'll Own Pipeline Design & Validation Architect and optimize clinical genomics pipelines in your area of expertise: - PGx track: Star-allele calling pipelines (e.g., CYP2D6, CYP2C19, DPYD, TPMT) handling complex structural variation, gene duplications, and hybrid alleles. - PRS track: Polygenic risk scoring pipelines with integrated multi-ancestry PRS models and clinical calibration utilizing traditional WGS SNV/INDEL variant calling plus phenotypic data. Extend existing 30X WGS infrastructure to support robust feature extraction and clinical annotation. Annotation & Interpretation Curate and maintain annotation stacks integrating domain-specific databases (PharmGKB, CPIC, PharmVar, PGS Catalog) and proprietary AI-derived knowledge graphs. Build automated cadenced updates of clinical-grade knowledge sources to feed the AI engine. Data Quality & Compliance Implement validation, reproducibility, and audit trails; pipeline change-control logs; briefing decks. Collaboration & Mentorship Partner with software and AI engineers to integrate genomic features into AI models. Participate in cross-team design reviews and internal workshops on clinical curation and validation. Minimum Qualifications - PhD (or MS with 5+ yrs experience) in Genetics, Genomics, Bioinformatics, Computational Biology, or related field. - 4+ yrs deep expertise in one of the following: - Pharmacogenomics: star-allele calling, diplotype assignment, phenotype prediction, complex locus resolution - Polygenic risk scoring: PRS development (PRS-CS, LDpred, etc.), multi-ancestry methods, clinical calibration, integrated scoring with phenotypic+monogenic data - 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 statistical analysis, and visualizations; AWS database resource 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 services (Lambda, Fargate, Step Functions, Glue, Athena). - Highly comfortable with AI-based development tools (Claude Code, Cursor, OpenAI Agents). Preferred Qualifications - Exposure and familiary with other 'omics' (proteomics, epigenomics, transcriptomics) - Strong communication skills—able to translate genomic insights into plain language for physicians, regulators, and engineers. - Experience contributing to or curating clinical-grade databases in your domain. - Prior authorship of clinical validation studies published in peer-reviewed journals. - Experience integrating multi-omics datasets or developing multi-modal AI features. Success Metrics - First 12 Months - Production pipeline in your domain validated and integrated into the clinical decision-support platform by month 3. - Expanded clinical coverage—additional genes, conditions, or ancestry groups validated by month 6. - Active maintenance and iteration of your module with exploration of adjacent omics integrations by month 9. - Contribute significant improvements and optimizations across the broader genomics platform and bioinformatics infrastructure by month 12. Tech & Tool Stack Python · Jupyter · REST APIs · AWS Batch/EKS/Lambda/ECS · AWS S3 · AWS Glue/Athena · PostgreSQL · Nextflow · DRAGEN · GATK · Stargazer/Cyrius · PharmCAT · PGS Catalog · PRS-CS · GitHub Actions · Docker

Benefits

Remote/Hybrid flexibility · Comprehensive health/dental/vision plans · 401k Plan · Annual company wide meet-ups Apply tot his job Apply To this Job