Senior Software Engineer, Algorithms

Menlo Park, CA
May 13, 2022
Biotech Bay
Required Education
Position Type
Full time

Please be aware that, as a condition of employment, proof of COVID vaccination is required for all U.S.-based employees (subject to limited exceptions).  To ensure the health and safety of all PacBio employees and our prospective candidates, we have instituted a virtual interview and onboarding experience.

Senior Software Engineer, Algorithms

Pacific Biosciences (NASDAQ: PACB) is seeking a highly driven and talented software engineer with a strong background in data modeling, machine learning and bioinformatics to join our Primary Analysis team in the sequencing platform development group.
In this role, you'll work closely with other algorithm developers, software engineers, R&D scientists, and external collaborators to develop ML models and algorithms for improving the accuracy and efficiency of our basecalling software. 


  • Design, develop and evaluate modeling and ML approaches to improve sequence read accuracy at the level of single-pass detection.
  • Investigate algorithms to classify sequencing errors more accurately in the raw data stream. Use these to inform model training strategies and to develop tooling to characterize fundamental system performance. 
  • Work collaboratively with internal and external partners to develop methods for the most effective use of basecalling model outputs in downstream multi-pass consensus algorithms (HiFi).  
  • Understand the engineering constraints of our real-time analysis pipeline. Focus designs to meet future product throughput requirements and explore avenues for performance optimization of ML models, both in terms of model design and implementation.


  • PhD in computer science, bioinformatics, physics or a related quantitative field.
  • 3+ years professional experience developing algorithms for scientific data analysis.
  • Strong background in statistical signal processing and machine learning.
  • Demonstrated expertise in a low-level and high-level programming language (C++, python preferred).

Preferred Qualifications    

  • Experience in Deep Learning approaches used for NLP.
  • Algorithm design and implementation for HPC architectures.

All listed tasks and responsibilities are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional tasks and responsibilities.

All qualified applicants will receive consideration for employment without regard to race, sex, color, religion, national origin, protected veteran status, or on the basis of disability, gender identity, and sexual orientation.