Bioinformatics Programmer

Feb 28, 2017
Institution Type
Four-Year Institution

Stanford University

Bioinformatics Programmer

Job Number:

Stanford University, located between San Francisco and San Jose in the heart of California's Silicon Valley, is one of the world's leading teaching and research universities. Since its opening in 1891, Stanford has been dedicated to finding solutions to big challenges and to preparing students for leadership in a complex world.

Supporting that mission is a staff of more than 10,000, which is rooted in a culture of excellence and values innovation, collaboration, and life-long learning. To foster the talents and aspirations of our staff, Stanford offers career development programs, competitive pay that reflects market trends and benefits that increase financial stability and promote healthy, fulfilling lives. An award- winning employer, Stanford offers an exceptional setting for professionals looking to advance their careers”

The Genome Sequencing Service Center at the Stanford Center for Genomics and Personalized Medicine, has an excellent opportunity available for a motivated Bioinformatics Programmer. You will be part of a dynamic team and responsible for the sequencing data processing and delivery.

The successful candidate will have knowledge of high-throughput sequencing technologies and experience with genomic data and analysis. Excellent communication skills are critical. A significant part of your work will involve interacting with customers, creating documentation, and contributing to wiki, FAQs, video tutorials, and publications.

Experience with web development, particularly using Ruby on Rails, will be very valuable for maintaining the in-house Laboratory Informatics Management System (LIMS), as well as expanding the Stanford Sequencing Center web presence.

Computational fluency in a Linux/Cloud environment is essential as analysis is done on the DNAnexus cloud bioinformatics platform ( The successful candidate must be able to learn to work independently and collaborate effectively with co-workers. Previous experience working in an academic environment is a plus. The work will take place in a dynamic environment where the workload often changes rapidly in response to user demand, so the candidate needs to be good at multi-tasking and managing the expectations of multiple stakeholders. The successful candidate will comply with University and government health and safety regulations and policies.

Duties include but are not limited to:
  • Regularly update the LIMS Ruby on Rails application.
  • Create new websites to enhance sequencing center operations.
  • Implement systems for tracking, analyzing, and reporting on sequencing center operations.
  • Design, develop, and manage bioinformatics pipelines for Next-Generation Sequencing data from various platforms and propose methods to streamline data analysis.
  • Make code changes following software development best practices such as source control, regression testing, and code reviews.
  • Be responsible for data processing from Center's high throughput sequencing lab (Illumina and PacBio platforms).
  • Communicate the data processing results to researchers in a helpful and timely fashion, and provide answers to technical questions through 1-on-1 communication and written documentation.
  • Work with other internal and external groups to streamline processes related to sample submission, processing, billing, and data management.
  • Troubleshoot poor quality data arising from biological issues or analysis artifacts.
  • Write scripts for liquid handling robotic devices.
  • Work with colleagues in the lab to analyze the whole genome, exome, RNA seq data and assess data quality
* - Other duties may also be assigned
  • Advanced degree in Biology, Computational Biology, Bioinformatics or related field is preferred
  • Technical expertise in genetics, molecular biology, or bioinformatics.
  • Experience with genomics laboratory techniques.
  • Experience with relational databases.
  • Experience working in academic environments.
  • Experience with user support.

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.


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,

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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