Senior Bioinformatics Scientist/Engineer

Bioscope AI•Boston, MA

26d•Remote

About The Position

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.

Requirements

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).

Nice To Haves

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.

Responsibilities

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.