Bioinformatician / Software Developer

Stanford University
Job Location
Stanford, CA
Job Description

The Department of Pediatrics at Stanford University School of Medicine seeks a full time computational biologist with expertise in analysis of next-generation sequencing data of cancer to participate in a large clinical cancer genomics effort. The successful applicant will conduct computational and statistical analysis to facilitate biomedical research that uses high-throughput techniques to identify mutations and other alterations in pediatric cancers. Technologies to be employed include whole genome sequencing (WGS), exome sequencing, RNAseq and similar related sequencing approaches. The focus of our studies is the comparison of germline and tumor genomes in order to define individualized therapies for pediatric cancer patients. Opportunities to interact with the wider scientific and computational biology community at Stanford will be available. 

Duties include:

• Assess user needs and requirements. 
• Design and develop applications that may involve sophisticated data manipulation. 
• Maintain and update existing programs.
• Troubleshoot and solve technical problems.
• Create programs to meet reporting and analysis needs.
• Design and implement user and operations training programs. 
• Document changes in software for end users.
• Follow team software development methodology. 
• Serve as technical resource with respect to applications.

* - Other duties may also be assigned



• Ph.D. degree in bioinformatics, computational biology, molecular biology, genetics, biostatistics, or related field with at least three years of relevant experience. While PhD is preferred, applicants with Master’s degree and significant (>2 years) experience will be considered.
• Strong background in bioinformatics with technical expertise in genetics and molecular biology
• Strong knowledge of at least one general programming language (such as Java, Python)
• Experience within a UNIX/Linux high-performance computing or Cloud environment
• Deep knowledge in scientific software development and large scale data analysis
• Prior experience with analysis of next-generation sequencing data (DNA and RNA), file formats, and data quality
• Demonstrated ability to work with biologists to apply computational approaches to their experiments as well as the ability to help them develop their own bioinformatics skills
• Good communication and team skills and fluency in both spoken and written English
• Ability to multitask
• Laboratory experience with genomics laboratory techniques, next-generation sequencing instruments and protocols
• Experience with relational databases and web application development
• Experience in next-generation sequencing analysis of cancer genomes (somatic variant detection, copy number analysis, purity determination, clonal subsets, etc…)
• Experience with statistical modeling and visualization in R
• Experience with novel algorithm development
• Experience with system administration of UNIX/Linux systems
• Experience developing automated data analysis pipelines
• Basic knowledge of software engineering best-practices
• Willingness to work in a fast paced environment that includes rapid turnaround of clinical samples


Bachelor's degree and three years of relevant experience or a combination of education and relevant experience.

• Current knowledge of latest software and design standards. 
• Ability to define and solve logical problems for technical applications.
• Knowledge of and ability to select, adapt, and effectively use a variety of programming methods.
• Ability to recognize and recommend needed changes in user and/or operations procedures.
• Basic knowledge of software engineering principles.
• Strong knowledge of at least one programming language.




• Constantly perform desk-based computer tasks. 
• Frequently sit, grasp lightly/fine manipulation.
• Occasionally stand/walk, writing by hand. 
• Rarely use a telephone, lift/carry/push/pull objects that weigh up to 10 pounds

* - Consistent with its obligations under the law, the University will provide reasonable accommodation to any employee with a disability who requires accommodation to perform the essential functions of his or her job.
Additional PHYSICAL REQUIREMENTS: (remove if none)

May work extended hours, evening and weekends.

How to Apply

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