Senior Bioinformatics Data Scientist

The Infectious Disease Laboratory Division (IDLD) is currently seeking a highly motivated Senior Bioinformatics Data Scientist to join the Genomics Center group and serve as a technical lead for bioinformatics data science this role you will lead and coordinate the development implementation maintenance and improvement of Next-Generation Sequencing (NGS) computational workflows that support the surveillance diagnostics outbreak response and research efforts of the California Department of Public Health. The position will collaborate with multidisciplinary CDPH teams and other internal and external partners provide technical direction and review for complex genomic analyses mentor staff and support data systems that enable infectious disease research and surveillance. The ideal candidate should have advanced computational experience a strong understanding of molecular and cellular biology demonstrated leadership in sequencing workflow development and expertise with sequencing platforms such as Illumina and Oxford Nanopore. The position is in Richmond CA.

Must submit a resume with application.

Must be able to work flexible hours that may include weekends and holidays.

The salary range for the position is $99924 - $129348 annually depending on experience and qualifications.

If hired for this position applicant will be required to provide proof of full vaccinated for COVID-19 prior to the start date; or have a valid religious or medical reason qualifying the applicant for an exemption (that may or may not require accommodation). The applicant will need to have the qualifying exemption.

ESSENTIAL FUNCTIONS

• Serve as a lead bioinformatics data scientist for the design implementation modernization quality oversight and maintenance of NGS workflows used for infectious disease research and surveillance.
• Lead the development management maintenance and governance of large-scale genomic databases and workflow tracking systems used by the Genomics Center group.
• Review interpret and troubleshoot complex genomic data analyses that support public health surveillance and infectious disease outbreak investigations and provide technical recommendations to supervisors and leadership.
• Establish and promote standards for reproducible code workflow validation version control documentation quality assurance security deployment and future maintainability.
• Coordinate technical priorities with internal and external collaborators including local public health laboratories collaborating sequencing laboratories CDC academic partners and other public health entities.
• Lead the development of innovative solutions for interoperability of data systems among federal state and local health departments commercial and governmental laboratories hospitals and medical providers academic partners and other public health entities.
• Collaborate with CDPH response teams surveillance/epidemiology outbreak investigations policy makers information technology and leadership to define needs evaluate tools and implement systems for storing analyzing reporting and sharing related data.
• Lead the conceptualization coordination production and review of internal reports and public-facing materials (e.g. tables and visualizations) that describe/interpret epidemiologic analysis and may influence prevention policy.
• Mentor and train Bioinformatics Data Scientist I/II staff support onboarding review technical work products and promote consistent team practices.
• Represent the program at meetings and scientific conferences and lead or facilitate conference calls with key stakeholders at CDPH local health jurisdictions (LHJs) CDC and academic partners if applicable.
• Perform other duties as directed by CDPH Leadership and maintain flexibility to work onsite as needed to meet IDLD demands and team collaboration requirements.

NON-ESSENTIAL FUNCTIONS

• Perform other duties as assigned.

JOB QUALIFICATIONS

• Advanced experience with Next-Generation Sequencing technologies microbial genomics and sequence analysis tools used for surveillance and outbreak response.
• Demonstrated ability to design validate maintain improve and document reproducible bioinformatics workflows databases and data products.
• Advanced ability to code in Python R SQL or similar programming languages with a focus on clarity security deployment scalability and future maintainability.
• Advanced familiarity with shell scripting command line usage in Linux environments workflow or pipeline management and cloud or high-performance computing concepts.
• Ability to lead technical projects coordinate priorities review analytical methods and results and provide sound recommendations to supervisors leadership and multidisciplinary teams.
• Strong knowledge of fundamentals and principles of epidemiology biostatistics public health surveillance infectious disease genomics and outbreak response.
• High-level analytical and problem-solving skills including the ability to evaluate uncertainty identify data quality concerns and guide resolution of complex technical issues.
• Demonstrated ability to communicate complex methods results limitations and recommendations orally and in writing to computational audiences non-computational audiences leadership and external partners.
• Advanced knowledge and application of security confidentiality data governance and public health information protection requirements.
• Ability to mentor staff build consensus manage multiple high-priority deliverables and work independently under general direction.
• Demonstrate reliability integrity attention to detail and fluency in spoken and written English.

Education/Experience

• B.S. or higher degree in Bioinformatics or a related field such as Data Science statistics or computer science; M.S. or Ph.D. preferred.
• B.S. or higher degree in Biology/Virology or a related field with significant advanced bioinformatics experience.
• Substantial experience in Bioinformatics and Next Generation Sequencing analysis including production public health clinical academic or surveillance-oriented workflows.
• Demonstrated experience developing validating maintaining and improving genomic analysis pipelines databases and data products.
• Advanced expertise in a programming language such as R Python SQL or a similar language is required; experience with workflow tools and version control is preferred.
• Experience with cloud computing high-performance computing containers or secure data infrastructure is highly desirable.
• Experience mentoring training or leading technical staff and coordinating technical work across multidisciplinary teams.
• Excellent written and oral communication skills including technical reports stakeholder briefings and scientific presentations.

Certificates/Licenses

• None

Other Skills Knowledge and Abilities

• Experience with cloud computing high-performance computing containers workflow orchestration and maintenance of secure infrastructure is preferred.
• Advanced knowledge and/or experience in microbiology virology molecular biology or public health genomics is preferred.
• Extensive familiarity with public genomic databases and resources (NCBI GISAID Ensembl etc.).
• Strong knowledge and understanding of data governance data quality access controls security and public health data-sharing considerations.
• Knowledge of and skilled in the use of Microsoft Office products data visualization/reporting tools and project coordination tools.

PHYSICAL DEMANDS

• Stand: Occasionally
• Walk: Occasionally
• Sit: Frequently
• Handling / Fingering: Frequently
• Reach Outward: Occasionally
• Reach Above Shoulder: Occasionally
• Climb Crawl Kneel Bend: Occasionally
• Lift / Carry: Occasionally - Up to 30 lbs
• Push/Pull: Occasionally - Up to 50 lbs
• See: Constantly
• Taste/ Smell: Not Applicable

KEY

• Not Applicable Not required for essential functions
• Occasionally (0 - 2 hrs/day)
• Frequently (2 - 5 hrs/day)
• Constantly (5 hrs/day)

WORK ENVIRONMENT

General office and laboratory setting indoors temperature controlled.

EEOC STATEMENT

It is the policy of Heluna Health to provide equal employment opportunities to all employees and applicants without regard to age (40 and over) national origin or ancestry race color religion sex gender sexual orientation pregnancy or perceived pregnancy reproductive health decision making physical or mental disability medical condition (including cancer or a record or history of cancer) AIDS or HIV genetic information or characteristics veteran status or military service.

Required Experience:

Senior IC