Engineering Research Associate, 1 Year Fixed Term

Stanford University
Job Location
Stanford, CA 94305-4160
Not Specified
Job Description

Stanford University


Engineering Research Associate, 1 Year Fixed Term


Job Number: 67780


Stanford Center for Genomics and Personalized Medicine (SCGPM), situated in the heart of SF Bay Area, has an excellent opportunity available for a motivated Bioinformatics Research Lead. This is a key position with Center's Informatics Core team that will support Stanford Clinical Genomics Service (SCGS,


Stanford Medicine integrates research, medical education and health care at its three institutions - Stanford University School of Medicine, Stanford Health Care (SHC, formerly Stanford Hospital & Clinics), and Stanford Children's Health (SCH, aka Lucile Packard Children's Hospital). Stanford Medicine has launched SCGS with the goal of using genome sequencing to evaluate SHC & SCH patients with unexplained genetic diseases. The long-term goal is to bring genomics, proteomics and other cutting edge methods into the clinical laboratory to improve patient care. Although other hospitals offer genomic laboratory testing, SUMC has the unique potential to provide a cutting-edge, precision health care by combining clinical, genomics, statistics, and computer science expertise. SCGS is currently in pilot stage and is slated for production in a year. Thousands of patients will go through this service on an annual basis.


During the initial stages of the program, the focus will be on germline mutation and subsequently will incorporate reporting of somatic mutations. Both DNA-Seq and RNA-Seq data will be used. The focus of the service is to use Whole Genome Sequencing data but in specific disease cases, there will be supplemental deep sequencing data.


The development and production environment is Cloud based. The group will use a document based workflow language (typically json/xml) to specify the pipeline. The software backend, developed by the SCGS software team, will take on the complexity of job management and other features necessary for HIPAA. While programming skills are essential to the job, software engineering skills are not critical.


Ideal person for this position is a bioinformatician who is passionate about improving health care. The successful candidate will have deep knowledge of NGS bioinformatics including DNA-Seq, RNA-Seq and tumor-normal analysis. This is a hands-on leadership role involving a small team of bioinformaticians.


This team effort will include:


• Benchmarking oriented development of analysis pipeline. This is expected to evolve on a continuous basis to keep up with the changes in methods and technologies.

• Development of bioinformatics best practices for various scenarios - singletons, pedigree, tumor/normal as well as disease specific scenarios such as developmental delay, cancer or cardiovascular. Incorporate changes in the field including those in references, databases and filtering strategies.

• Periodic benchmarking against existing tools in public and commercial space and making the white papers accessible to the program management and stakeholders.

• Development of deep QC metrics, for a single patient sample and across case-control cohort.

• Quick proof-of-concept of new methods and protocols

• Establishing and refining the process for bioinformatics analysis and validation.

• Presenting the bioinformatics efforts and best practices at Conferences. Peer reviewed publications are encouraged.


Required Qualifications:


• Ph.D. in Computer Science, Computational Physics/Biology, Bioinformatics or related field and one year of related experience.

• Deep understanding of next-generation sequencing data and bioinformatics algorithms. SCGS primarily uses Illumina sequencing and related bioinformatics stack but this is expected to evolve based on best approaches in industry.

• Proven experience in a large scale, high profile or mission critical project.

• Proven experience working in a Linux cluster environment. Development and production environment will be Cloud based.

• Expert programming skills in Python. Familiarity with C++, Java and Perl are useful.

• Strong background in one or more of: machine learning, statistical methods, distributed computing, algorithm development, variant annotation and interpretation, tumor/normal analysis, GWAS

• Excellent verbal and written communication skills


Desired Qualifications:


• Knowledge of general principles for regulatory compliance.

• Experience working in academic environments.

• Mentorship or project management experience.


Contact information:


Please direct all applicants to


Affirmative Action statement

“Stanford University is an equal opportunity employer and is committed to increasing the diversity of its faculty and academic staff. It welcomes nominations of and applications from women and members of minority groups, as well as others who would bring additional dimensions to the University's research, teaching and clinical missions.”


Job: Research


Location: School of Medicine


Schedule: Full-time


Classification Level: R99


To be considered for this position please visit our web site and apply on line at the following link:


Stanford is an equal opportunity employer and all qualified applicants will receive consideration without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, veteran status, or any other characteristic protected by law.


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