Senior Bioinformatics Engineer

Evolutionary Scale; San Francisco, New York (CA, NY); Hybrid; USD 150,000 - 250,000; Full time

Job summary

An innovative firm is seeking a talented Bioinformatics Engineer to join their dynamic team in San Francisco. In this role, you will develop and maintain scalable data processing pipelines that support cutting-edge biological AI models. Your expertise in Python, cloud computing, and bioinformatics will be essential as you collaborate with scientists and engineers to create efficient workflows for analyzing complex biological datasets. This position offers a unique opportunity to contribute to groundbreaking research that aims to revolutionize human health through AI. Join a team that values flexibility and fosters collaboration across disciplines while being part of a mission-driven organization.

Benefits

Comprehensive medical, dental, and vision benefits

Competitive equity package

Flexible work schedules

Collaborative work environment

Qualifications

• 3+ years of experience in bioinformatics or data pipeline development.
• Strong programming skills in Python and experience with cloud platforms.

Responsibilities

• Design and maintain scalable bioinformatics pipelines using Apache Spark.
• Collaborate with research teams to build robust data processing workflows.

Skills

Python

Data Pipeline Development

Collaboration

Bioinformatics Data Formats

Cloud Computing

Containerization (Docker)

Apache Spark

Nextflow

Snakemake

Airflow

Luigi

WDL

Education

Bachelor's degree in Bioinformatics, Computational Biology, or Computer Science

Master's or PhD in relevant field

Tools

Apache Spark

Docker

AWS

GCP

Azure

Job description

EvolutionaryScale's mission is to develop artificial intelligence to understand biology for the benefit of human health and society, through open, safe, and responsible research, and in partnership with the scientific community. Over the next ten years AI will transform biological design, making molecules and entire cells programmable. We will develop the foundation models for biology that enable this.

We are seeking a skilled Bioinformatics Engineer to drive the development of robust, scalable data processing pipelines that support our biological AI models. The ideal candidate has a strong commitment to data—collecting, curating, and ensuring its accessibility to enable advanced biological analysis and discovery. You will collaborate closely with research teams to design and implement robust data pipelines, both by engineering new infrastructure from the ground up and by elevating research prototypes into production-quality systems. We expect all EvolutionaryScale employees to be able to make cross-cutting engineering contributions to our codebase, and have a high technical bar.

The Role

• Design, develop, and maintain scalable bioinformatics pipelines using Apache Spark and other distributed computing frameworks
• Transform one-off research scripts into production-ready, maintainable code with proper testing, documentation, and deployment processes
• Create automated workflows for processing large, complex biological datasets
• Build infrastructure for efficient analysis of genomic, proteomic, and other biological data types
• Collaborate closely with research scientists, AI engineers, and other team members to meet the evolving data needs of model training
• Innovate on pipeline architecture to enhance scalability, performance, and efficiency

Qualifications (Required)

• Bachelor's degree in Bioinformatics, Computational Biology, Computer Science, or related field; Master's or PhD preferred
• 3+ years of experience developing bioinformatics pipelines or building data pipelines
• Strong programming skills in Python.
• Experience with Apache Spark, Nextflow, Snakemake, Airflow, Luigi, and/or WDL
• Solid understanding of containerization (Docker) and infrastructure-as-code tools
• Experience with cloud computing platforms (AWS, GCP, or Azure)
• Demonstrated contributions to the fields of genomics, proteomics, transcriptomics or related as evidenced by publications in top-tier journals.
• Strong collaboration and communication skills
• Expert knowledge of bioinformatics data formats (e.g., FASTA, FASTQ, VCF, BAM, GFF) and biological databases (e.g., Ensembl, NCBI, UniProt), including their structure, applications, and relevance in biological analysis

Qualifications (Preferred)

• Strong baseline technical skills, ability to contribute across our engineering infrastructure as a generalist
• Knowledge of bioinformatics tools such as sequence analysis tools (e.g., BLAST, HMMER), RNA expression tools (Bowtie2, STAR, Kallisto, cellranger/STARsolo, DESeq2), genomic data processing tools (e.g., SAMtools, GATK), and ML-integrated bioinformatics frameworks (e.g., AlphaFold, Biopython).
• Experience working with large genomic datasets, especially NGS data
• Contributions to open-source bioinformatics and data projects

Our Team

The EvolutionaryScale team is based in two locations: San Francisco and New York. We believe in flexibility around work schedules and locations, but expect that our team members will work half of the days or more of most weeks from one of our two offices.

We are building a world-class multi-disciplinary team spanning AI research, engineering, biology research, and business roles, which requires strong communication and collaboration across roles.

The salary range for this position is $150,000 to $250,000 per year, plus a competitive equity package. Compensation package will vary based on job-related skills, experience, and knowledge. The compensation package also includes comprehensive medical, dental, and vision benefits.

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