Bioinformatics Software Engineer

ArkeaBio is a pioneer in developing technology to reduce greenhouse gas (GHG) emissions from the agricultural sector. Backed by Breakthrough Energy Ventures, ArkeaBio is using innovative vaccine technologies to create solutions to reduce the on-farm methane emissions responsible for 6% of global GHG emissions. ArkeaBio technology will be integrated into proven delivery systems and farming practices to safely reduce global methane emissions from multiple ruminant species across a variety of geographies and agronomic systems.

Job Summary

The Bioinformatics Software Engineer is responsible for designing, developing, and deploying in-house bioinformatics tools to support the analysis of genomic and metagenomic data generated from ArkeaBio’s research and development programs. They will play a critical role in scaling ArkeaBio’s computational capabilities as the company grows. The Bioinformatics Software Engineer will collaborate across experimental and computational teams to develop robust, scalable software solutions that advance our mission.

Key Responsibilities

Role

Reporting to the Head of Computational Biology, the Bioinformatics Software Engineer role requires a passionate, learning-focused individual who can work collaboratively within a team to contribute to overall R&D strategy as well as develop and deliver on software engineering solutions in support of Arkea’s vaccine development pipeline. A successful Bioinformatics Software Engineer will perform the following:

• Implement user-driven software solutions leveraging containerization (e.g., Docker) and cloud platforms (e.g., AWS).
• Integrate and optimize bioinformatics tools and algorithms, such as BLAST, AlphaFold, etc., for internal use.
• Contribute to the development and maintenance of bioinformatics pipelines for genomic and metagenomic data analysis, including sequence alignment, assembly, and annotation.
• Ensure reproducibility and quality of software through version control, testing, and thorough documentation.
• Collaborate with scientists to translate research needs into functional software and web applications.
• Contribute to the publication of patents and journal articles as a member of the Research team.

Minimum Qualifications / Skills

• Advanced degree in Computer Science, Bioinformatics, Computational Biology, or a related field.
• Strong programming skills in Python; experience with other languages like R is a plus.
• Proficiency in bioinformatics tools and databases (e.g., BLAST, NCBI).
• Experience with containerization software (Docker) and cloud platforms (AWS preferred).
• SQL (PostgreSQL, MySQL, SQLite) expertise
• Knowledge of software development best practices, including git/version control, code review, and documentation.
• Curiosity with a passion for learning.
• Exhibit flexibility and willingness to work closely with members of the scientific team.

Preferred Qualifications / Skills

• Experience with large-scale genomic or metagenomic datasets.
• Familiarity with bioinformatics workflow managers (e.g., Nextflow, Snakemake).
• Experience with Benchling or other ELN/LIMS platforms
• Knowledge of statistical analysis and machine learning techniques.
• Experience with developing applications using Infrastructure as Code (IaC) best practices

ArkeaBio is deeply committed to diversity, equity, and inclusion in all of its practices, especially when it comes to growing our team. Our culture promotes inclusion and embraces the personal and organizational benefits of working with people from all walks of life.

ArkeaBio offers 100% paid health, vision, dental and life insurance, up to a 4% matching contribution to a 401(K) retirement account and unlimited paid time off.

It is the policy of ArkeaBio to provide equal employment opportunities to all employees and employment applicants.

ArkeaBio has a 13,000 square foot lab in Charlestown, MA. We are open to setting up offices and lab space according to the geographical needs of our hires and offer a flexible work environment.