Molecular Epidemiologist/Bioinformatician

Seneca Federal Health, LLC (SFH) provides solutions to federal health agencies that enable better health outcomes to those our federal customers serve. SFH is part of the Seneca Nation Group (SNG) portfolio of companies. SNG is Seneca Holdings’ federal government contracting business that meets mission-critical needs of federal civilian, defense, and intelligence community customers. Our portfolio comprises multiple subsidiaries that participate in the Small Business Administration 8(a) program. To learn more about SNG, visit the website and follow us on LinkedIn.

Our team of talented individuals is what makes us successful. To support our team, we provide a balanced mix of benefits and programs. Your total rewards package includes competitive pay, benefits, and perks, flexible work-life balance, professional development opportunities, and performance and recognition programs. We offer a comprehensive benefits package that includes medical, dental, vision, life, and disability, voluntary benefit programs (critical illness, hospital, and accident), health savings and flexible spending accounts, and retirement 401K plan. One of our fundamental principles is to offer competitive health and welfare benefits to our team members, providing coverage and care for you and your family. Full-time employees working at least 30 hours a week on a regular basis are eligible to participate in our benefits and paid leave programs. We pride ourselves on our collaborative work environment and culture, which embraces our mission of providing financial and non-financial benefits back to the members of the Seneca Nation.

Seneca Federal Health is seeking a Molecular Epidemiologist/Bioinformatician in Atlanta, GA.

Responsibilities include, but are not limited to:

• Molecular Network Generation: Execute and maintain high-throughput transmission network mapping via HIV-TRACE, operating precise genetic distance thresholds (0.015 for Subtype B, 0.045 for non-B strains) against the national sequence database.
• Phylodynamic & Evolutionary Analysis: Orchestrate complex evolutionary tracking models using BEAST and TimeTree to isolate priority molecular cluster growth vectors, ancestral lineages, and patterns of drug resistance mutation scoring via Stanford Sierra.
• Cluster Notification Routing: Enforce strict execution of the cluster notification workflow. Package and deliver priority molecular cluster identification sets to the Senior Epidemiologist (SE) within 1 business day of detection threshold violations.
• Geospatial Clusters Scans: Develop and execute automated SaTScan Bernoulli spatial scans and ArcGIS Pro workflows, linking eHARS surveillance case records with sequence network tables to visualize localized geographic outcroppings.
• Prioritization Log Enforcement: Maintain a detailed, audit-ready Cluster Prioritization Log tracking unique IDs, detection times, regional concentrations, growth indices, SE review completions, and subsequent COR transmission windows.
• Modernized Pipeline Ingestion: Design and implement automated sequence ingestion pipelines within the CDC EDAV Databricks cloud platform, embedding explicit schema enforcement, data constraints, and Delta Lake tracking structures.
• Parallel-Run Model Validation: Lead technical execution of parallel-run code validations, ensuring newly migrated cloud Python/pySpark pipelines achieve identical reproducibility when evaluated against historical legacy codebases.
• Git Version Repository Control: Enforce strict version control across all bioinformatics scripts using GitHub/GitLab, establishing standard code annotations, README metadata files, and comprehensive peer-review checks before trunk merges.
• Assurance of Confidentiality Mapping: Apply mandatory Section 308(d) spatial suppression guidelines to all molecular cluster visualizations and geographic maps, ensuring low-density data grids remain protected against identity extraction risks.

Basic Qualifications:

• Master's degree in Bioinformatics, Computational Biology, Molecular Epidemiology, or a heavily computational quantitative discipline required; Ph.D. preferred.
• Ability to obtain and/or maintain an active favorable Tier I background check
• Minimum of five (5) years of applied molecular epidemiology or public health bioinformatics pipeline experience within clinical, academic, or federal research networks.
• Minimum of three (3) years of hands-on production experience analyzing viral sequence data using advanced phylogenetic and transmission network methodologies.
• Expert level proficiency operating specialized bioinformatics utilities including HIV-TRACE, BEAST (v1.10/v2.7), Stanford Sierra, COMET, and TimeTree.
• Demonstrated experience engineering automated Python and R pipelines within secure cloud architectures (Azure Government, Databricks, AWS GovCloud).
• AWS Certified Data Analytics or AWS Certified Solutions Architect preferred.
• Microsoft Azure Data Scientist Associate or Azure Data Engineer Associate Certification preferred.
• Active International Society for Computational Biology (ISCB) or ASM Membership with an established peer-reviewed publication record preferred.