Senior Software Engineer & Project Lead, Biology

POSITION SUMMARY

The Center for Computational Biology is seeking an experienced software engineer  to be the Project Lead for HumanBase (hb.flatironinstitute.org), a dynamic and interactive web-based platform that supports thousands of biomedical researchers in exploring the molecular mechanisms of human disease. This position is ideal for an experienced engineering leader with bioinformatics experience who thrives on solving complex problems at the intersection of large-scale data, advanced analytics, and scientific discovery. This is a high-impact role that directly advances the study of human genomics and disease.

The successful candidate will lead technical direction and execution, guide other software engineers, and collaborate closely with researchers at the Center for Computational Biology to translate cutting-edge computational biology into robust software tools. The Project Lead will be a hands-on engineering leader with experience in biological data and -omics technology, as well as a complementary skillset that includes both writing high-quality code and managing a small team of software engineers. Success in this role depends on the ability to translate biological questions into computational solutions, collaborate closely with internal scientific stakeholders, and drive technically rigorous projects that advance our understanding of human biology.

ESSENTIAL FUNCTIONS/RESPONSIBILITIES 

• Serve as technical lead for HumanBase, guiding the design, architecture, and implementation of new features and major infrastructure upgrades

• Lead and mentor a team of full stack software engineers, ensuring high-quality code, efficient workflows, and continuous professional development

• Plan, develop, and optimize scalable genomics data processing pipelines

• Integrate machine learning methods into production pipelines to analyze heterogeneous biological datasets

• Establish and enforce software engineering best practices, including coding standards, version control, documentation, testing, and deployment workflows

• Collaborate cross-functionally with computational biologists, data scientists, and external partners to align engineering efforts with scientific goals

• Stay current with emerging technologies in cloud infrastructure, bioinformatics, and scientific computing and assess their relevance for HumanBase

• Perform additional duties or projects as assigned

MINIMUM QUALIFICATIONS

Education

• B.S. in Computer Science, Software Engineering, or a related technical field 

Experience

• At least 10 years of professional software experience in software engineering, including leading teams and direct involvement in the planning, design, and development of software 

• Experience collaborating daily with other key team members of different technical and scientific backgrounds

• Proficiency in full stack software development

• Extensive experience in Python, including developing data pipelines and software libraries

• Demonstrated experience with the full software development lifecycle (SDLC), including testing, CI/CD, version control, and deployment

• Experience building and maintaining web-based interfaces and applications

• Background in computational biology, bioinformatics, or a related field, with experience developing software in support of biological research

• Experience working with large, heterogeneous biological datasets—ideally in genomics or biomedical contexts

Related Skills & Other Requirements 

• Effective technical leadership and mentorship abilities

• Excellent communication skills, especially when working across disciplinary boundaries

• Deep curiosity about science and a passion for building tools that empower scientific discovery

• Strong sense of ownership and drive for continuous improvement 

COMPENSATION

• The range for full-time annual compensation for this position is $190,000-$235,000 based on experience.

• In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.

REQUIRED APPLICATION MATERIALS 

• Please submit a résumé and cover letter stating your interest in the position.

Our Commitment to Expanding Pathways to Science & Opportunities for All:

Many of the greatest ideas and discoveries come from a diverse mix of minds, backgrounds, and experiences. The Simons Foundation is committed to advancing basic science and mathematics to benefit humankind and expand our collective understanding of our world. As part of our mission, we support partners, programs, and initiatives that seek to broaden the scientific community and open pathways to science and mathematics careers.

The Simons Foundation provides equal opportunities to all applicants without regard to race, religion, color, age, sex, pregnancy, national origin, sexual orientation, gender identity, genetic disposition, neurodiversity, disability, veteran status, or any other protected category under federal, state, and local law.