Senior Bioinformatics Scientist​/Engineer

Position Title: Senior Bioinformatics Scientist/Engineer

Location: Carmel, IN (preferred) / Boston, MA / U.S. Remote available

Employment Type: Full-time

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.

• 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.

Curate and maintain annotation stacks integrating domain-specific databases (Pharm

GKB, CPIC, Pharm Var, PGS Catalog) and proprietary AI-derived knowledge graphs. Build automated cadenced updates of clinical-grade knowledge sources to feed the AI engine.

Implement validation, reproducibility, and audit trails; pipeline change-control logs; briefing decks.

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.

• 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).

• Exposure and familiarity 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.

• 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.

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
· Git Hub Actions
· Docker

Remote/Hybrid flexibility
· Comprehensive health/dental/vision plans
· 401k Plan
· Annual company wide meet‑ups