Bioinformatics Staff Scientist

1.0 FTE Full time – Day 08 Hour – R2657721 Hybrid  Path Lab Molecular Path Hillview Allied Health PALO ALTO, 3375 Hillview Ave, California

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This is a Stanford Health Care job.

The Bioinformatic Staff Scientist will be responsible for developing and maintaining Next Generation Sequencing data analysis workflows for use in a molecular genetic testing setting. This includes algorithms development as well as pipeline design. They will participate in development and implementation of bioinformatics tools for test development and validation, joining a team that develops leading-edge genomic assays and analysis tools that directly impact patient care.

Stanford Health Care

• 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 Clin Gen, Clin Var, HGMD, cbGap, EVS, 1000 Genomes, gnomAD, and DGV

• None.

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