Bioinformatics Specialist III

Site: Mass General Brigham Incorporated

Mass General Brigham relies on a wide range of professionals, including doctors, nurses, business people, tech experts, researchers, and systems analysts to advance our mission. As a not-for-profit, we support patient care, research, teaching, and community service, striving to provide exceptional care. We believe that high-performing teams drive groundbreaking medical discoveries and invite all applicants to join us and experience what it means to be part of Mass General Brigham.

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 Bioinformatics or related field of study required
• Master's Degree 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

Additional Job Details (if applicable)

Remote Type

Hybrid

Work Location

75 Francis Street

Scheduled Weekly Hours

40

Employee Type

Regular

Work Shift

Day (United States of America)

Pay Range $93,953.60 - $136,739.20/Annual

Grade 7

At Mass General Brigham, we believe in recognizing and rewarding the unique value each team member brings to our organization. Our approach to determining base pay is comprehensive, and any offer extended will take into account your skills, relevant experience if applicable, education, certifications and other essential factors. The base pay information provided offers an estimate based on the minimum job qualifications; however, it does not encompass all elements contributing to your total compensation package. In addition to competitive base pay, we offer comprehensive benefits, career advancement opportunities, differentials, premiums and bonuses as applicable and recognition programs designed to celebrate your contributions and support your professional growth. We invite you to apply, and our Talent Acquisition team will provide an overview of your potential compensation and benefits package.

EEO Statement:

0100 Mass General Brigham Incorporated is an Equal Opportunity Employer. All qualified applicants will receive consideration for employment without regard to race, color, religious creed, national origin, sex, age, gender identity, disability, sexual orientation, military service, genetic information, and/or other status protected under law. We will ensure that all individuals with a disability are provided a reasonable accommodation to participate in the job application or interview process, to perform essential job functions, and to receive other benefits and privileges of employment. To ensure reasonable accommodation for individuals protected by Section 503 of the Rehabilitation Act of 1973, the Vietnam Veteran’s Readjustment Act of 1974, and Title I of the Americans with Disabilities Act of 1990, applicants who require accommodation in the job application process may contact Human Resources at (857)-282-7642.

Mass General Brigham Competency Framework At Mass General Brigham, our competency framework defines what effective leadership “looks like” by specifying which behaviors are most critical for successful performance at each job level. The framework is comprised of ten competencies (half People-Focused, half Performance-Focused) and are defined by observable and measurable skills and behaviors that contribute to workplace effectiveness and career success. These competencies are used to evaluate performance, make hiring decisions, identify development needs, mobilize employees across our system, and establish a strong talent pipeline.