Senior/Staff Software Engineer, Bioinformatics

San Diego, California

Company Description

Quantum-Si is pioneering a new generation of technology to create the market of Next Generation Protein Sequencing (NGPS). Similar to Next Generation DNA Sequencing (NGS), which gave us a blueprint of what could happen by studying our DNA, NGPS enables an unbiased view of the proteome through improved scale, resolution, and sensitivity leading to better understanding of disease and improved general health. 

We operate at the intersection of biochemistry, chemistry, hardware, molecular biology, photonics, semiconductor chips, and software with a goal to drive a digital transformation of a $44 billion dollar proteomics market.

Join us on the journey to transform healthcare, motivated by the idea that the products you work on will change the lives of millions of people around the world.

Job Description

The R&D team at Quantum-Si is responsible for bringing our technology to life. For more than a decade, next-generation DNA sequencing has transformed every aspect of the life sciences. However, genetics is only one component of human disease. New tools are required to understand how genes interact with the environment to improve how we develop drugs, diagnose patients, and combat outbreaks. The R&D team plays a critical role in developing products that will be used all around the world. Come work alongside a world-class team of scientists and engineers to define a new frontier for next generation sequencing.

As Senior/Staff Software Engineer, Bioinformatics, you will contribute to assay development efforts for a major initiative related to our core single-molecule technology platform. You will contribute scientific leadership and skills to a multi-disciplinary team of scientists (including biologists, chemists, and computer scientists) who will develop highly innovative assay options for commercial application while meeting project timelines. You possess a strong working knowledge of bioinformatics, algorithm development, statistical modelling and familiarity with machine learning. You are also familiar with basic laboratory techniques, such as DNA sequencing or single-molecule based assays. The key requirements of the role are to provide strong technical skills across a breadth of bioinformatics tools, exceptional scientific achievement and intuition, and passion for basic and applied research.

As part of our team, your core responsibilities will be: 

  • Help setup, organize and design a new R&D site for single-molecule biochemistry and product development.
  • Contribute to software development that generates and processes a variety of single-molecule signal data.
  • Help develop tools related to signal processing, detection calling, demultiplexing barcoded information, and QC tools to measure data quality, accuracy, and assay performance.
  • Optimize and integrate analysis/informatics tools with on-instrument control software and existing cloud infrastructure.
  • Analyze and benchmark data to keep track of performance, and quantitative regressions.
  • Explore next-generation software through close collaborations with established leaders and newcomers in the field. 
  • Produce high quality documentation.


Baseline skills/experiences/attributes:

  • Degree(s) in Computer Science, Bioinformatics, Statistics, Machine Learning or related field.
  • Modern C++ design and programming skills
  • Bioinformatics algorithms expertise
  • Design and work experience with high-level abstractions that map efficiently to different hardware architectures.
  • Daily experience with version control, git.
  • Experience with statistical models and machine learning is considered a plus.
  • Excellent verbal, written, and interpersonal communication skills.


You deeply identify with core Quantum-Si values:

  • Efficient & Speedy - you get work done in a fraction of the time as industry peers 
  • Intellectually Curious - you are thoughtful & inquisitive; people enjoy working with you because they learn from you
  • Mission-Driven & Committed - you are passionate about the company's purpose and are immensely productive
  • Team Oriented - you celebrate and take joy in the success of others on the team

Additional Information

We offer great perks: 

  • Fully covered medical insurance plan, and dental & vision coverage - as a health-tech company, we place great worth on our teams’ well-being
  • Competitive salaried compensation - we value our employees and show it 
  • Equity - we want every employee to be a stakeholder
  • Pre-tax commuter benefits - we make your commute more reasonable 
  • Kitchen stocked with snacks
  • 401k plan - we facilitate your retirement goals
  • Beautiful office in Sorrento Mesa area of San Diego
  • The opportunity to build a revolutionary healthcare product and save millions of lives! 

For this role, we provide visa assistance for qualified candidates. 

Applicants, please answer the following in your cover letter:

Describe an exciting scientific problem that you have worked on and what you found most appealing.

What aspects of Quantum-Si most interest you?

Please describe yourself in one word.

Quantum-Si does not accept agency resumes.

Quantum-Si is an E-Verify and equal opportunity employer regardless of race, color, ancestry, religion, gender, national origin, sexual orientation, age, citizenship, marital status, disability, or Veteran status. All your information will be kept confidential according to EEO guidelines.