Senior Genomics Software Engineer - Scalable Bioinformatics

Simons Foundation; 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 join a growing team building HumanBase, a web-based platform enabling thousands of biomedical researchers to explore molecular mechanisms of disease. This hands-on backend role focuses on large-scale data, pipelines, and ML workflows.

Based in New York City, you will translate cutting-edge computational biology into scalable production systems, maintain data pipelines, and collaborate with

Qualifications

• BS in CS/SE/Bioinformatics or related field.
• Experience with production systems and data-intensive applications.
• Collaborate with interdisciplinary teams.
• Strong Python data pipelines experience.
• Experience with large biological datasets (HDF5, Parquet, PyArrow).
• Experience with distributed compute workflows (Celery, Dask, SLURM, Nextflow, Snakemake).
• Strong relational DB experience (PostgreSQL/MySQL).
• Containerization and cloud-native infra (Docker/Kubernetes).
• Familiarity with ML frameworks like scikit-learn, PyTorch.
• SDLC, testing, CI/CD, version control, deployment.

Responsibilities

• Design and implement new HumanBase features and infrastructure improvements.
• Translate research methods into robust production software and data pipelines.
• Develop scalable genomics and biomedical data processing pipelines.
• Integrate machine learning methods into production workflows.
• Apply software engineering best practices and CI/CD processes.
• Collaborate with researchers to align engineering with scientific goals.
• Evaluate new technologies to improve platform capabilities.

Skills

Python

Data pipelines

Bioinformatics

Distributed compute

AWS

Docker

Kubernetes

SQL databases

PyTorch

SDLC/CI-CD

Education

B.S. in CS/SE/Bioinformatics or related

Advanced degree in CS/Engineering/Bioinformatics

Tools

Celery

Dask

SLURM

Nextflow

Snakemake

PostgreSQL/MySQL

Docker

Kubernetes

Job description

The Center for Computational Biology (CCB) at the Simons Foundation seeks a senior software engineer to join a growing team building HumanBase, a web-based platform enabling thousands of biomedical researchers to explore molecular mechanisms of disease. This hands-on backend role focuses on large-scale data, pipelines, and ML workflows.

Based in New York City, you will translate cutting-edge computational biology into scalable production systems, maintain data pipelines, and collaborate with