Bioinformatics Specialist III

Job Summary

Responsible for leading complex bioinformatics projects and overseeing the design, validation, and operation of reproducible data analysis workflows that support clinical genomics and translational research.

Essential Functions

• Design, develop, and apply computational methods, bioinformatics algorithms, and machine learning models to analyze and interpret genomic, clinical, and imaging data, including short-read and long-read sequencing data.
• Build, maintain, and troubleshoot production-grade analysis pipelines and data architecture using workflow languages and managers (such as WDL, Nextflow, or Snakemake), containerization (such as Docker or Singularity/Apptainer), and version control with CI/CD practices to ensure reproducibility and traceability.
• Deploy and optimize workflows across high-performance computing and cloud environments (such as AWS, GCP, or Azure), with attention to scalability, cost, and data security.
• Apply machine learning and AI methods, including deep learning and large language models where appropriate, to problems such as variant interpretation, quality control, image analysis, and clinical data extraction, with appropriate validation and performance monitoring.
• Develop and execute validation, documentation, and change control for pipelines and tools used in clinical settings, in line with CLIA/CAP and institutional quality requirements.
• Perform advanced statistical analyses and integrate data across multiple datasets and data modalities.
• Collaborate with pathologists, clinicians, laboratory staff, software engineers, and external partners and vendors on large-scale projects, translating clinical and operational needs into technical solutions.
• Contribute to the development of bioinformatics strategies, technology evaluations, and research plans.
• Mentor and train junior analysts and team members, and promote good practices in code review, testing, and documentation.
• Provide technical expertise and support for bioinformatics tools, software, and data resources.

Qualifications

Education: Bachelor's Degree in Bioinformatics or related field of study required. Master's Degree in Bioinformatics preferred. Equivalent experience may be accepted in lieu of a degree.

Experience: 5+ years of related experience in bioinformatics required. Experience building and supporting production NGS analysis workflows preferred. Experience in a clinical or CLIA/CAP-regulated environment preferred.

Knowledge, Skills and Abilities

• Strong programming ability in Python and/or R, plus shell scripting (Perl is a plus).
• Hands-on experience analyzing next-generation sequencing data (for example, germline or somatic variant calling, RNA-seq, or long-read data).
• Experience with workflow languages and managers (such as WDL, Nextflow, or Snakemake) and with containerization (such as Docker or Apptainer).
• Proficiency with Git-based development, code review, and automated testing; familiarity with CI/CD practices.
• Familiarity with HPC and cloud computing environments.
• Working knowledge of machine learning and statistical modeling, with familiarity with frameworks such as scikit-learn, PyTorch, or TensorFlow.
• Experience applying large language models or other AI tools in a research or clinical setting is a plus.
• SQL proficiency using MySQL, PostgreSQL, and/or SQL Server.
• Knowledge of NoSQL and other DBMS (e.g., MongoDB, Apache CouchDB) is a plus.
• Familiarity with SDLC principles and with validation and documentation practices for clinical software.
• Familiarity with clinical data standards (such as HL7 FHIR and common ontologies) is a plus.
• Familiarity with principles of experimental design and modern data analysis paradigms.
• Strong interpersonal and communication skills, including the ability to work effectively with clinicians, scientists, engineers, and external contacts at all levels.
• Effective problem-solving skills and the ability to work independently and lead projects.

Working Model

Hybrid, 4x/month onsite Monday - Friday eastern standard business hours. Remote working hours require a quiet, secure, HIPAA-compliant working area.