Bioinformatics Engineer II - Metagenomics

We are seeking a motivated individual with a background in biology, metagenomics, and programming to support Metagenomi’s proprietary metagenomics-based discovery platform. Reporting to the metagenomics lead, this position will play a crucial role in designing methods to expand our metagenomics platform, including algorithm development, pipeline optimization and big data analytics. This role will be based in Emeryville, California.

• Develop algorithms and computational infrastructure for processing, curating, and extracting value from metagenomic datasets
• Automate methods for high throughput discovery of novel enzymes and systems from metagenomic data 
• Integrate diverse data sources for improved candidate protein discovery and predicted activity ranking
• Apply software engineering best practices to optimize new and existing bioinformatics algorithms to run at scale and cost-effectively
• Coordinate and encourage standardized coding best practices, lead and collaborate with team members on code reviews
• Develop pipelines through their complete lifecycle, including testing, deployment, maintenance

• PhD in Biology, Computer Science, Statistics, or closely related discipline or equivalent relevant experience working in biotechnology
• Experience working with common tools for metagenomics data analysis (assemblers, de novo protein prediction, functional annotation methods, hidden markov models, phylogenetic tree construction, protein clustering)
• Extensive knowledge of NGS platforms, including their mechanisms and technical limitations
• Experience designing, troubleshooting, and optimizing complex metagenomics algorithms (gene neighborhood analysis, assemblers, binning)
• Experience with Nextflow, SQL, NoSQL, graph-based database design
• Experience generating and processing proprietary metagenomics datasets
• AWS Well-Architected Framework, severless development
• Experience with machine learning applications for complex biological problems (e.g. protein engineering, functional annotation) 
• Experience building front-end dashboards with Plotly Dash
• Experience creating data mesh architecture solutions for research 
• Experience with full lifecycle development of software and pipelines
• Advanced proficiency in Python and experience or a strong interest in working with cloud computing systems 
• Experience with Docker and building containerized data workflows to handle large scale data streams
• Familiarity with software development practices such as unit testing, code reviews, and version control

The anticipated base salary range for this position will be $100,000 - $130,000 depending on the exact level of the role. As this role is open to candidates with a wide range of skills and experience, the exact salary will be dependent on the specific level of the position. We value transparency and will make every effort to provide you with a succinct explanation for how the final salary within this range is determined.

Please note, all candidates must be authorized to work in the United States.