Job:Scientific Applications Programmer at UCSF Clinical Cancer Genomics Lab
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7.1 years ago
Eric T. ★ 2.8k

The University of California, San Francisco is seeking a person to serve as an Scientific Applications Programmer for the Cancer Genomics Laboratory (CCGL) tasked with supporting the development of molecular assays and integrating genomic information into the oncology clinical care.

CCGL's flagship product is the UCSF500 Cancer Gene Panel, a targeted sequencing assay and genome analysis suite providing information on somatic and germline alterations in roughly 500 cancer-associated genes. Some technical details about this service have been written up in this blog post.


In this role, you will be part of a team responsible for design, construction and maintenance of a genomic analysis pipeline for clinical cancer samples.

Under the general direction of the Associate Director of Informatics for the CCGL, you will plan and specify needs for implementation of in-house and vendor-provided software and assist in integration tasks. Working with the bioinformaticians on the team, you will develop software to support integration of our internally developed cloud-based sequence analysis pipeline, laboratory information management system (LIMS), and clinical reporting software. You will gain familiarity and practical experience with genomic data analysis, high-throughput sequencing technology, and precision medicine.

Required qualifications:

  • Bachelor's degree in related area and/or equivalent experience/training; Master's preferred
  • Computer programming skills:
    • Good software engineering principles, including version control, automated testing, and development processes
    • Basic security
    • Unix/Linux operating systems, bash, and associated system utilities
    • Programming languages: Python, and preferably some R, or demonstrated ability to pick up either language quickly
    • Relational database management
    • Basic statistics and data visualization techniques
  • Strong communication skills (verbal and written) to communicate effectively with clinical laboratory technicians, bioinformaticians, software vendors, and clinicians
  • Desire to learn about next generation sequencing and cancer genomics

How to apply:

Search for job requisition number 47165 at:

Submit your resume and a cover letter explaining why you're interested in this job specifically. Include a link to some of your code on GitHub or Bitbucket, if you can, or be ready to send code samples by some other means. Short samples are OK, for example, your solutions to a couple of Rosalind problems.

* The internal HR title is Application Programmer I/II/III, with the level based on experience. The working title can be different, e.g. Scientific Programmer or Bioinformatics Engineer, and this is negotiable.

cancer sequencing python cloud • 3.0k views
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Can anyone with a PhD also apply for it being an non-US applicant and based in EU?

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You can apply from outside the US, I believe. The job itself is based in San Francisco (UCSF's Mission Bay campus) and requires being on site at least most of the week.

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Yes, I agree to your point but am interested to know if it is strictly for US citizens or there is a possibility for J1 or H1B if its open for people outside of US. Obviously, I am interested at working onsite but if it is restricted for only US citizens I will not apply for it then. Some times it is really hard to figure out disclaimers like "applicable to people allowed to work in US" , this can either mean only US citizens or non-US citizens in the US with a valid work permit or even people who can avail one being a non-US. I will check the post. Thanks a lot.


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