Senior Software Engineer, Bioinformatics (F#)

Pacific Biosciences
Job Location: 
Menlo Park, CA
Job Description: 

This position can be based in our Menlo Park, California headquarters, or our San Francisco office (with regular travel to Headquarters).

Are you a talented software engineer who wants to use his/her skills to solve problems of real scientific and medical importance? Do you have the analytical chops to build machine learning tools to make sense of DNA sequence reads for our customers worldwide? Do you want to work at a company that uses robots and lasers and nanotechnology to see a single (very important) molecule do its thing in real-time? Pacific Biosciences is seeking a talented software engineer to build tools that use SMRT (single-molecule, real-time) sequencing data to address diverse sequencing applications areas. The candidate will develop robust, reliable and performant software components, documentation and tests that enable our customers and collaborators to rapidly get the insights they need from SMRT sequencing data.


• Work in an exciting multi-disciplinary organization of software and hardware engineers, bioinformaticians, chemists, and molecular biologists developing state-of-the-art, single-molecule, genomic analysis systems.

• Quickly identify solutions to complex data processing and automation problems for use in production instrument software and internal tools; provide methods or prototypes for concept evaluation.

• Design, develop, integrate and test analysis pipeline components for deployment in production software; develop optimized implementations to maximize performance and throughput on available hardware.

• Develop bioinformatics tools for applying SMRT sequence data to a variety of applications, e.g.:
o Epigenetic base modification
o Haplotype Phasing
o Transcript characterization
o De-novo Genome Assembly

• Contribute to analysis pipelines in SMRT Analysis suite


• Minimum M.S. degree, Ph.D. preferred in a field like: bioinformatics, physics, machine learning, or computer science

• Experience implementing sequence analysis algorithms e.g. alignment, consensus, variant calling, graph analysis, or experience using HMM/CRFs/graphical models in other domains (speech recognition, etc.)

• Experience building production quality tools in F#, Haskell, C#, C/C++, or Python

• Experience maintaining software projects under source control with git, svn, p4, or similar

• Understanding of software optimization: algorithm, code quality, and machine architecture considerations

• Experience in the life-sciences tools domain, especially DNA sequencing, is preferred but not required.

• Preference is shown to candidates with strong analytical and development skills who demonstrate the capability to bring solutions beyond the prototype stage for deployment in performance-critical production software.

About Our Organization: 

Pacific Biosciences’ mission is to transform the way humankind acquires, processes and interprets data from living systems through the design, development and commercialization of innovative tools for biological research. The company has developed a novel approach to studying the synthesis and regulation of DNA, RNA and protein. Combining recent advances in nanofabrication, biochemistry, molecular biology, surface chemistry and optics, Pacific Biosciences has created a powerful technology platform called single molecule, real-time, or SMRT™, technology. SMRT technology enables real-time analysis of biomolecules with single molecule resolution, which has the potential to transform the understanding of biological systems by providing a window into these systems that has not previously been open for scientific study.