Bioinformatics Software Engineer, AI Applications - Keplogic

Keplogic develops enterprise-grade AI agents for the life sciences. Our flagship product, Kepler AI, is a bioinformatics agent designed to accelerate scientific discovery. As biology becomes increasingly data-driven, wet-lab teams generate data faster than bioinformatics groups can analyze it, with week-long turnarounds throttling iteration and delaying key scientific decisions. Kepler AI bridges this gap by enabling scientists to conduct bioinformatics analyses on terabyte scale, multi-modal, messy data in natural language and receive rigorous answers in minutes, not weeks.

Today we’re powering research at several well-known biotech, pharma companies and top academic labs, accelerating decisions that drive new medicines. Join us as we solve challenging problems and revolutionize life sciences research!

As a founding Senior Software Engineer, Bioinformatics, you’ll closely work with leading biotech/pharma customers and research labs, learning about their workflows and needs, and integrating Kepler AI into their organization. This role is similar to that of a forward deployed software engineer. You will also gather crucial feedback and requirements from wet lab scientists and bioinformaticians, and translate them into product ideas and implementation plans for the core Kepler AI platform. This is a role with a high degree of autonomy, end-to-end ownership, and potential for leadership – you will wear many hats from bioinformatics scientist to software engineer to product manager, and shape the culture of our fast‑growing, mission‑driven startup.

• Translate customer needs into product requirements – You will be the main point of contact for one or more life science customers – you will partner directly with bench scientists & bioinformaticians, and think deeply about how to integrate the customer’s systems and Kepler AI

• Develop, test, and verify bioinformatics workflows – You will be the main person developing the bioinformatics workflows that are running at the customer’s organization – you will need to learn the science and intuition behind each workflow, measure and evaluate its effectiveness, and rapidly make improvements.

• Design and implement delightful software that fulfills customer needs and augments the Kepler AI platform. Whether a new data connector or pioneering an analysis workflow, you will be writing crucial code that unlocks the core value of Kepler for customers.

• Build an AI native company: help us design an agent-friendly product development cycle and infrastructure, and shape a constantly self-improving company. You will be living and breathing AI, and help shape the future of work.

• Bachelor’s degree or above in Computer Science, Computational Biology, Bioinformatics, or equivalent professional experience.

• 3+ years professional experience with Python for backend software development

• 3+ years professional experience with Python/R for data science – pandas, matplotlib, numpy, scikit-learn, etc.

• 3+ years professional experience with one or more common bioinformatics analysis modalities – bulk and single-cell RNAseq, genomics, proteomics analysis. Familiarity with statistical methods.

• Hands-on experience with common bioinformatics tools (e.g. GATK, STAR, DESeq2), data sources (Ensembl, GEO, ENCODE, etc), and pipelining languages (e.g. Nextflow, Snakemake). Specific items not required here, just for illustrative purposes.

• Fluency with Git workflows, automated CI/CD pipelines, and test-driven development

• Proven ability to communicate scientific and technical concepts to different audiences

• Familiarity with LLM concepts and APIs (OpenAI completion/responses APIs, function calls, etc.)

• Background in biological and bioinformatics research.

• Hands‑on experience with cloud infrastructure AWS, Docker, Kubernetes, and Infrastructure as Code (Terraform preferred)

• Highly autonomous and take ownership and responsibility for outcomes: drives and keeps track of work to 100% completion without the need for reminders.

• High standard of quality: you hold work to a high bar even when no one is looking—it is in your personality. You make forward-thinking improvements to infrastructure and process.

• Customer obsessed: care deeply about delivering clean, intuitive user experiences and deeply curious about how customers are using the product.

• Are energized by ambiguity and rapid iteration: you prototype, measure, refactor, repeat.

• AI native: eagerly evaluate, prototype, and adopt AI tools intelligently for every aspect of your work. You have a taste about where AI can do better/worse than humans and adjust quickly to maximize the leverage.

• Deeply motivated by mission: you want your code to accelerate life‑saving discoveries, not just move pixels.

• Meaningful equity & competitive salary—own a slice of a category‑defining company.

• Hybrid work from SF Mission Bay office.

• Reimbursement for healthcare and transportation costs.

• Budget to adopt any work-related tool and software you need.

• Autonomy & fast growth—you’ll influence architecture, culture and product direction from day one.