Founding Bioinformatics Engineer

Novaflow (YC S25); San Francisco (CA); On-site; USD 90,000 - 130,000; Full time

Benefits offered by this job

Competitive salary and equity

401(k) with company match

Unlimited PTO

Monthly health and wellness stipend

Meals covered in-office

Team offsites and events

Job summary

An innovative biotech firm in San Francisco is seeking a Founding Bioinformatics Engineer to build and maintain bioinformatics pipelines. The role requires expertise in Python and/or R, plus experience managing cloud infrastructure on AWS or GCP. You will work directly with founding members and be integral in the development processes. Competitive salary, equity, and benefits, including unlimited PTO, are offered, alongside a unique opportunity to gain insights into startup dynamics.

Qualifications

• 2+ years building bioinformatics pipelines or workflows.
• Strong programming in Python and/or R.
• Experience with AWS or GCP for workloads.

Responsibilities

• Build and maintain bioinformatics pipelines.
• Write clean, reproducible analysis code.
• Manage cloud infrastructure for large-scale workloads.
• Integrate bioinformatics tools and databases.
• Validate outputs against real scientific standards.

Skills

Python

R

Bioinformatics pipelines

AWS

GCP

Linux/Unix

Molecular biology

Bioinformatics file formats

Education

Bachelor's or Master's in Computational Biology

PhD in related field

Tools

Nextflow

Snakemake

Docker

Job description

About Novaflow

Novaflow is the AI data analyst for biology labs. Analytics is the bottleneck for scientific discovery. Biologists have to outsource analysis to expensive bioinformaticians or core services and wait weeks or months for results. We're solving this by putting analysis directly back into the hands of researchers, allowing them to go from raw data to publication-ready insights and visualizations in days instead of months. We're well‑funded, growing extremely fast, and backed by leading investors including Y Combinator and BioRender.

About The Role

We're hiring a Founding Bioinformatics Engineer to own the analysis pipelines behind our platform. You'll build the workflows that take raw sequencing data and turn it into something a biologist can actually use, make sure the science is right, and figure out how to do all of it at scale on cloud infrastructure. This is a high‑agency, high‑ownership role. You'll work directly with the founders, have real input on what we build and how we build it, and be expected to drive things forward on your own. This role is in‑person at our San Francisco office. The founding team works side by side every day to make fast decisions and ship.

What You'll Work On

• Build and maintain bioinformatics pipelines for genomics, transcriptomics, and other -omics data
• Write clean, reproducible analysis code in Python and/or R
• Set up and manage cloud infrastructure (AWS or GCP) for large-scale compute workloads
• Integrate existing bioinformatics tools, databases, and data sources into the platform
• Validate pipeline outputs against published methodologies and real scientific standards
• Work with academic labs, tool providers, and data partners to expand what the platform can do
• Help decide what we build next based on what researchers actually need

Requirements

• Bachelor's or Master's in Computational Biology, Bioinformatics, Biomedical Engineering, or a related field (PhD is a plus)
• 2+ years building bioinformatics pipelines or computational biology workflows
• Strong in Python and/or R
• Know your way around bioinformatics file formats (FASTQ, BAM, VCF, HDF5, etc.)
• Experience running workloads on AWS or GCP
• Comfortable in Linux/Unix command-line environments
• Solid understanding of molecular biology (genomics, gene expression, variant calling)
• Good communicator who can work across biology and engineering

Nice to Have

• Experience with Nextflow, Snakemake, or similar workflow managers
• Docker experience
• Familiarity with LLMs or AI/ML tools
• Experience across multiple biomedical domains
• Startup or biotech/pharma background
• Previous startup experience (prior experience either working for or founding a startup)

Why Join Us?

• Competitive salary and meaningful equity as a founding team member
• 401(k) with company match
• Unlimited PTO + federal holidays
• Monthly health and wellness stipend
• Meals covered when you're in the office (lunch daily, dinner when you're working late)
• Team offsites and company events
• If you're curious about being a founder one day, this is your front-row seat. You'll work side by side with the founders and have full visibility into product strategy, customer conversations, and fundraising as we scale.