Bioinformatics Staff Scientist

Bioinformatic Staff Scientist

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.

Locations:
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.

Base Pay Scale:
Generally starting at $52.69 - $69.82 per hour

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.