Senior Bioinformatics Engineer at Phylagen, Inc.
San Francisco, CA, US
Phylagen is building a microbial map of the world with unlimited applications ranging from supply chain transparency to public health. The Phylagen team is a diverse, hard-working, and fun-loving group who values teamwork, transparency, and well-being, and we are committed to developing cutting-edge technology together that advances human welfare.

We’re seeking a motivated and experienced Senior Bioinformatics Engineer to oversee and develop advanced data analytics tools and bioinformatics pipelines, translate and optimize research algorithms into industry products, and create reference databases that can be efficiently deployed for machine learning applications. Competitive candidates will possess deep knowledge of next-gen sequence data analysis and manipulation, object-oriented programming (e.g. Python, R, Ruby), database management (e.g. SQL), and scalable algorithm development and optimization. Experience working with large NGS datasets is required, and experience with microbiome data in particular is highly desirable. You will be joining a diverse technology team that includes molecular biologists, data scientists, and ecologists. You will be a key player in a cutting-edge venture-backed microbiome startup with significant professional growth potential, and report to Phylagen’s CTO.

- Develop scalable bioinformatics algorithms, pipelines, and tools to enable advanced microbiome data analysis and discovery
- Build and manage growing NGS databases for efficient routine query
- Provide technical oversight and support in scientific computing, statistics, and data analysis to research and product development teams

- We offer a competitive salary, equity, and benefits package

- M.S. or Ph.D. in bioinformatics, computational biology, computer science, statistics or a related field
- 5+ years of post-masters (or 3+ years post-doctorate) experience working in a production environment with large scientific datasets
- Proficiency in one or more high-level programming languages (e.g. Python, R, Ruby)
- Experience with NGS data analysis and manipulation, including assembly and annotation of genomic and/or shotgun metagenomic sequence data
- Familiarity with Unix-based operating systems and shell scripting
- Familiarity with database (e.g. SQL) design, management, and implementation
- Working knowledge of molecular biology and/or (micro)biology concepts relevant for solving bioinformatics challenges
- Demonstrated ability to implement and prioritize quality work across multiple projects under tight time constraints

- Experience with advanced metagenomics and/or population genomics techniques (e.g. metagenomic binning, metagenomics linkage groups, oligotyping)
- Familiarity with cloud-based computing resources (e.g. Amazon Web Services)
- Experience analyzing NGS data from a variety of platforms, including Illumina, PacBio, and Oxford Nanopore
- Experience with advanced machine learning and feature selection strategies
- Experience analyzing large phylogenetic and/or phylogenomic datasets