Bioinformatics Engineer

Job description

Bioinformatics Engineer🔍School of Medicine, Stanford, California, United StatesNew📁Information Technology Services📅5 days ago Post Date📅89894 Requisition #The Stanford Center for Genomics and Personalized Medicine (SCGPM) has an exciting opportunity available for a motivated Bioinformatics Engineer to help us create data infrastructure that will automate the process of turning big genomic data into biomedical insights. The ideal person for this position is a keen listener who can interpret biological questions, assess the value and relevance of different technologies and methods, and quickly prototype and deliver actionable technical solutions.

The Department of Veterans Affairs has commissioned the sequencing of 150,000+ whole genomes from participants in the Million Veteran Program [see:]. This data is currently being delivered to Stanford’s cloud computing environment and constitutes one of the largest repositories of whole-genome sequencing data in the world. The scale and richness of this data make it an incredible resource for biomedical research. Our goal is to turn this data lake into a data commons; a dynamic computing environment where researchers bring questions and get answers, all without having to go through the ordeal of manually collecting, cleaning, massaging, waxing, scrubbing, sorting, transforming, and filtering data.

Duties include:

  • Collaborating with researchers to design solutions to relevant biological questions and maximize the value of our whole-genome sequencing dataset to the public.
  • Determining how to implement big data technical solutions to those questions in a cloud environment (Google Cloud Platform).
  • Dockerizing bioinformatics tools and integrating them with our internal data management system to automate workflows.
  • Implementing population-level genomic analyses (GWAS, PCA) using big data technologies.
  • Connecting research data to biological knowledge, using a Neo4j graph database, to streamline the process of answering biological questions.
  • Transforming genomic data from custom file formats into database-native formats.
  • Developing an ontology to describe the relationships between data objects and resources involved in research data management.

Our SCGPM core bioinformatics team is a multi-disciplinary group composed of about a dozen scientists, engineers, and software developers with complementary backgrounds, each contributing their own expertise in managing and analyzing complex biomedical data [see]. Projects supported by this team include the Stanford Genome Sequencing Center, the Stanford Center for Excellence in Stem Cell Genomics (funded by CIRM), the VA’s Million Veteran Project, and the ENCODE Functional Genomics Project. This position will support on-site office accommodations at our Palo Alto office or fully remote work.


  • Four-year degree in Genetics, Computer Science, Computational Physics/Biology, Bioinformatics, or related field.
  • Experience modelling biological/biomedical data and metadata.
  • Knowledge of and experience with biological omics data formats (FASTQ, FASTA, BAM, Proteomics, Metabolomics, et al.).
  • Good programming skills in Python or Java.
  • Experience with cloud computing is a plus.
  • Experience with databases (SQL, Neo4j) or big data technologies (BigQuery, Spark) is a plus.
  • Familiarity with FAIR principles of data management.
  • Ability to rapidly learn new technologies and programming techniques.
  • Excellent verbal and written communication skills.


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


  • Expertise in designing, developing, testing, and deploying applications.
  • Proficiency with application design and data modeling.
  • Ability to define and solve logical problems for highly technical applications.
  • Strong communication skills with both technical and non-technical clients.
  • Ability to lead activities on structured team development projects.
  • Ability to select, adapt, and effectively use a variety of programming methods.
  • Knowledge of application domain.


  • 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.


  • May work extended hours, evening and weekends.


  • Interpersonal Skills: Demonstrates the ability to work well with Stanford colleagues and clients and with external organizations.
  • Promote Culture of Safety: Demonstrates commitment to personal responsibility and value for safety; communicates safety concerns; uses and promotes safe behaviors based on training and lessons learned.
  • Subject to and expected to comply with all applicable University policies and procedures, including but not limited to the personnel policies and other policies found in the University's Administrative Guide,

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Job No:
Posted: 6/10/2021
Application Due: 8/9/2021
Work Type: Full Time