Bioinformatics Staff Scientist Pathology Molecular Lab Full Time, Days (8-HRS)

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• Develop document and deploy novel clinical sequencing analysis approaches meeting CLIA and CAP guidelines for clinical NGS analysis
• Develop document and deploy in-house web-applications and databases for clinical genomics data storage analysis and visualization
• Enhance maintain and support established sequencing pipelines and workflows meeting CLIA and CAP guidelines for clinical NGS analysis
• Develop implement and maintain tools and workflows for system administration and data management
• Collaborate with technical and medical teams in specifying requirements for tools to enhance workflow efficiency turnaround times and robustness
• Summarize results in written or oral reports for computational biologists molecular biologists clinicians and internal researchers
• Contribute to publishing of relevant findings in scientific journals

• Graduate Degree (Ph.D./M.S) in bioinformatics genetics and genomics computer science or other work-related field/discipline from an accredited college or university

• Ph.D. with no experience or M.S. plus 3 years of experience developing pipelines and algorithms for computational biology genomics and/or clinical diagnostics preferred

• Knowledge of algorithmic techniques common to bioinformatics (e.g. dynamic programming and graph algorithms) machine learning and statistical analysis methods (e.g. Bayesian inference Hidden Markov Models Principal Component Analysis)
• Proficient in Python competent in C Java SQL and R
• Demonstrated experience in software development for bioinformatics applications
• Experience with SQL and relational database design
• Comfortable with Bash scripting and working in UNIX/Linux environments
• Ability to produce readable maintainable and well documented code
• Experience with version control and source code management systems (e.g. Git)
• Detail oriented mindset for working on applications that directly impact patient care
• Ability to collaborate and communicate with other bioinformaticians researchers and medical staff
• Excellent problem-solving skills for common problems in bioinformatics
• Familiarity with system administration and IT operations
• Strong team-oriented work ethic with open honest and considerate communication skills

• Molecular Pathology: Expertise in cancer genomics and NGS technologies including somatic variant calling Familiarity with standard genomics/bioinformatics tools (e.g. Samtools BWA IGV) Good understanding of human molecular genetics Experience analyzing genomic sequencing data from Illumina platforms Experience developing web-applications with Python and Django
• Clinical Genomics: Familiarity with NGS data and best practices for germline sequencing Expertise in bioinformatics resources and tools such as BLAST BWA GATK dbGaP NCBI EBI UCSC genome browser etc Experience using public annotation sources such as ClinGen ClinVar HGMD cbGap EVS 1000 Genomes gnomAD and DGV

• None .

• Know Me: Anticipate my needs and status to deliver effective care
• Show Me the Way: Guide and prompt my actions to arrive at better outcomes and better health
• Coordinate for Me: Own the complexity of my care through coordination

Equal Opportunity Employer Stanford Health Care (SHC) strongly values diversity and is committed to equal opportunity and non-discrimination inall ofits policies and practices including the area of employment. Accordingly SHC does not discriminate against any person on the basis of race color sex sexual orientation or gender identity and/or expression religion age national or ethnic origin political beliefs marital status medical condition genetic information veteran status or disability or the perception of any of the above. People of all genders members of all racial and ethnic groups people with disabilities and veterans are encouraged to apply. Qualified applicants with criminal convictions will be considered after an individualized assessment of the conviction and the job requirements.

The salary of the finalist selected for this role will be set based on a variety of factors including but not limited to internal equity experience education specialty and training. This pay scale is not a promise of a particular wage.