Senior Software Engineer, Genomics

The Transmitter; New York (NY); On-site; USD 160,000 - 200,000; Full time

Benefits offered by this job

Benefits package

Job summary

The Center for Computational Biology (CCB) at the Simons Foundation seeks a senior software engineer to help build HumanBase, a web-based platform used by thousands of biomedical researchers. This backend role focuses on scalable data pipelines, genomics, and production systems in a collaborative environment.

You will translate cutting-edge research into robust software, implement ML workflows, and maintain production infrastructure with CI/CD and cloud-native tools to advance scientific

Qualifications

• 8+ years of professional software engineering experience.
• Experience with Python and data-intensive applications.
• Background in computational biology, bioinformatics, or related field.

Responsibilities

• Contribute to design, architecture, and implementation of new HumanBase features and infrastructure improvements.
• Translate research methods into robust production software and data pipelines.
• Design and optimize scalable genomics and biomedical data processing pipelines.
• Integrate machine learning and statistical methods into production workflows.
• Apply software engineering best practices, including CI/CD, testing, and documentation.

Skills

Python

Data pipelines

Distributed compute

Machine learning

CI/CD

Cloud infrastructure

Collaboration

Genomics

Bioinformatics

SDLC

HPC

Education

B.S. in Computer Science

Advanced degree preferred in CS/Bioinformatics

Tools

Docker

Kubernetes

Celery

Dask

Nextflow

Snakemake

PostgreSQL

MySQL

HDF5

Parquet

PyArrow

xarray

AWS

Job description

POSITION SUMMARY

TheCenter for Computational Biology(CCB)is seeking an experienced senior software engineer to join a growing team of developers within CCB and the other centers across the Flatiron Institute who help build andmaintainHumanBase.HumanBaseis 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 engineer with bioinformatics experience who thrives on solving complex problems at the intersection of large-scale data, pipeline building, 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 collaborate closely with researchers at the Center for Computational Biology to translatecutting-edgecomputational biology research into scalable production systems and data pipelines that powerHumanBase. This is a hands-onbackendrole for an experienced engineer withexpertisein biological data, genomics, and -omics technologies. They will also have experience processing large-scale -omics datasets,maintainingproduction software systems,designingandoptimizingdata-intensive pipelines, and supporting machine learning workflows in scientific computing environments.

This is a full-time position based in the Simons Foundation offices in New York City. Visit the Simons Foundationcareer page to learn more.

ESSENTIAL FUNCTIONS/RESPONSIBILITIES

• Contribute to the design, architecture, and implementation of newHumanBasefeatures and major infrastructure improvements
• Translate research-stage computational methods into robust, maintainable, and reproducible production software and data pipelines
• Design, develop, andoptimizescalable genomics and biomedical data processing pipelines that ingest, normalize, and transform heterogeneous datasets
• Integrate machine learning and statistical methods into production workflows for analysis of complex biological datasets
• Apply software engineering best practices, including code review, testing, version control, documentation, CI/CD, and deployment automation
• Collaborate closely with computational biologists, data scientists, and external partners to align engineering efforts with scientific and platform goals
• Evaluate and adopt emerging technologies in bioinformatics, cloud infrastructure, and scientific computing whereappropriate to improve platform capabilities and performance
• Contribute to operational support, maintenance, and continuous improvement of production systems supportingHumanBase
• Perform other duties or tasks as assigned orrequired

MINIMUM QUALIFICATIONS

Education

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

Experience

• At least 8 years of professional software engineering experience, including work on production systems and data-intensive applications
• Demonstrated ability to collaborate effectively with interdisciplinary teams of different technical and scientific backgrounds
• Extensive experience with Python, including development of complex data pipelines and use of applicable software libraries
• Experience working with large, heterogeneous biological datasets in Python (HDF5, Parquet,PyArrow,xarray) —ideally in genomics or biomedical contexts
• Experience building andoperatingdistributed compute workflows and orchestration systems (e.g., Celery,Dask, SLURM,Nextflow,Snakemake) for large-scale genomic or biomedical data processing
• Strong experience with relational databases such as PostgreSQL or MySQL, including schema design and query optimization
• Experience with containerization and cloud-native infrastructure technologies such as Docker and Kubernetes
• Familiarity with machine learning frameworks and tools, including scikit-learn andPyTorch
• Demonstrated experience with the full software development lifecycle (SDLC), including testing, CI/CD, version control, and deployment
• Background working in computational biology, bioinformatics, or a related field, with experience developing software that supports biological research

Related Skills & Other Requirements

• Excellent communication skills, with the ability to engage technical and non-technical audiences, including senior leadership.
• Strong cross-functional collaboration skills, witha track recordof working effectively with non-engineering stakeholders to translate needs into software solutions.
• Deep curiosity about science and a passion for building tools that empower scientific discovery.

PREFERRED QUALIFICATIONS

• Advanced degree in Computer Science, Engineering, Bioinformatics, or a related field.
• Expertisein bioinformatics, including experience with genomic data processing, analysis pipelines, and related computational methods.
• Familiarity with AWS or other major cloud platforms.
• Experience with high-performance computing (HPC) environments.

REQUIRED APPLICATION MATERIALS

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

COMPENSATION AND BENEFITS

• The full-time annual compensation range for this position is$160,000-$200,000depending on experience.
• In addition to competitive salaries, the Simons Foundation provides employees with an outstanding benefits package.

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 toscienceand mathematicscareers.

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.