Biomedical Research Engineer

Mar 16, 2017
Institution Type
Four-Year Institution

Stanford University

Biomedical Research Engineer

Job Number:

At the Stanford Center for Genomics and Personalized Medicine (SCGPM), we are applying our expertise on the science and ethics of genomics to build a new collaborative model of science focused on transforming the practice of medicine. This creates a new paradigm of patient-centered medicine that can monitor the entire genome of individuals to vastly improve disease prediction, prevention, and treatment of conditions such as cancer, diabetes, heart disease, asthma, schizophrenia, and many others. Stanford is uniquely positioned to drive such an endeavor. We have extraordinary talent in science, engineering and medicine; our location in Silicon Valley provides unique opportunities for technological collaborations; our faculty are highly successful at obtaining competitive funding for their research; and we are leaders in the ethics of personalized medicine and in training physicians to help patients understand their genetic information. Genomics, in particular, requires technologically advanced facilities, and computational infrastructure and benefits from an economy of scale that can only be achieved in center settings like the SCGPM. Our Center offers an omics driven biomedical platform composed of state-of-the-art laboratory and computational facilities to an interdisciplinary research community.
Our computational facility is built on the principles of NIH Data Commons - a platform where researchers have access to secure, scalable, affordable and flexible computing environment, software tools, reference data and specialized bioinformatics consulting. Our bioinformatics core team works on multiple high value projects and in the process develops this Commons. The Commons in turn is available to all Stanford researchers, our affiliates (e.g. Stanford Hospitals, VA) and collaborators at other institutions. Core team is interdisciplinary, have a wide range of expertise, and diversity of experience. What is common is that they are all exceptionally talented individuals with a passion to make a difference.
We are seeking a Biomedical Research Engineer to join our core bioinformatics team. Our team works closely with faculty members, researchers, and technologists to build data science research infrastructure solutions. Suitable candidate will have fundamental understanding of Big Data scale programming, including distributed programming, Cloud programming, coarse and fine grained parallelism. Experience with programming methodologies like Spark, and Hadoop are preferred. Data Science skills are preferred - you will be expected to dogfood the solutions you build.
All our solutions, while technologically broad, support biomedical research. It is critical to be able to communicate effortlessly with the biomedical community who are working with data types such as Next Generation Sequencing (DNA-Seq, RNA-Seq), Imaging (e.g. MRI), biosensors (e.g. wearable devices) and methods such as Genome Wide Association Studies (GWAS), Machine Learning (e.g. Clustering), and algorithms (e.g. Decision Tree, Bayesian Classifiers). You are expected to be comfortable with complex algorithmic concepts of alignment, variant calling, and gene expression analysis.
Our systems support bleeding edge academic research. We build for real time data analysis at affordable prices for Big Data. We build for reproducible science. We build for community adoption. These requirements are challenging. We do not expect anyone to know everything at the get go - Stanford is a learning environment. But we do expect everyone in the team to be fast learners. We have a lean team; this means that you own your project from conception to user support. For you to be effective, you need to be analytically strong, be an exceptionally strong individual contributor, a trusted collaborator with strong work ethics, and be a strong communicator.
Duties include:
  • Conceptualize design, implement, and develop solutions for complex system/programs independently.
  • The team typically develops novel biomedical applications based on open source or commonly accessible technologies.
  • But these applications are complex involving very massive datasets (Terabyte to Petabyte scale), thousands to millions of experiments, multiple researchers (1-100s), institutions (1-20), and support various regulatory requirements.
  • Work with a variety of users to gain information, and develop intra-system tradeoffs between different users, as necessary; interact with a diverse client base and outside vendor contacts.
  • At any time, the team routinely works with dozens of clients including Stanford faculty, collaborators, graduate students and postdoctoral scholars, startups and mature companies.
  • Document system builds and application configurations; maintain and update documentation as needed. These applications are used in innovative and cutting edge research and related publications and reproducibility and traceability are integral to deliverables.
  • Provide technical analysis, design, development, conversion, and implementation work. We expect our team members to own the project in its entirety.
  • Work as a project leader, as needed, for projects of moderate complexity. Nearly all projects involve multiple stakeholders, timelines are often tight and it is important to keep the stakeholders in the loop.
  • Serve as a technical resource for applications that are developed and used by the team. These systems are used by 10-100s of researchers. Training and user support is integral part of the job.
  • Compare, evaluate, and implement new features and technologies, and integrate them into the computing environment. Our team uses a diversity of programming languages (Python, R, Java, Ruby-on-Rails), compute environments (HPC, Cloud IaaS, Cloud PaaS), and technologies (Linux, Hadoop).
  • Follow team software development methodology. This includes best practices is software design and coding, use of Github/BitBucket, Dockerhub, issue tracker, ReadTheDocs, wikis etc.
  • Mentor lower level software developers. This may include other members in the core team, researchers who may wish to learn, interns etc.
  • You will be expected to routinely put together documents containing results, or present at conferences. For some projects you may be expected to write peer reviewed publications or even grant applications (NIH/NSF).
* - Other duties may also be assigned DESIRED QUALIFICATIONS:
  • Experience with Big Data Science research and technologies is needed.
  • Experience with biomedical applications is preferred.

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.

Job: Information Technology Services

Location: School of Medicine
Schedule: Full-time
Classification Level:

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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