Remote Principal Java Software Engineer Jobs in San Francisco, CA

Job Title: Principal Software Engineer

Location: South San Francisco, CA preferred; Remote optional

Job Type: Full-time

We're seeking a Principal Software Engineer to join Natera's R&D team. We build the cloud infrastructure, workflow platforms, and data platforms that R&D uses to do its science - including a Kubernetes-based workflow execution platform, a custom R&D LIMS system, and a set of supporting tools that routinely handle production-scale workloads.

This is a senior technical role. You'll own the full architecture, implementation, and delivery of large projects across our platform. You'll partner with the team lead on roadmap and tough technical calls, mentor mid-level engineers, and help the team find the right solution for the problem - not the most elaborate one. We're a small team (4 engineers + lead) with broad scope, and we're heavily AI-augmented: every engineer uses Claude Code / Cursor as a daily tool, and we build our own AI tooling (custom plugins, MCP servers, agents) to multiply ourselves.

• Architecture & Delivery: Own the design, implementation, and delivery of major initiatives across our platform. Take fuzzy problems through to shipped, working software used in production.
• Technical Leadership: Lead architecture and design reviews. Help the team find the right solution for the problem and avoid unnecessary complexity. Influence technical decisions across the team.
• Mentorship: Mentor mid-level engineers through code review, design docs, and pairing. Raise the engineering bar by example.
• AI-Native Development: Build and improve our AI-coding tooling alongside the rest of the team. Help us push the frontier of agent-driven software development inside the company.
• Cross-Functional Partnership: Work with bioinformaticians, scientists, and other R&D engineers to understand their needs and translate them into platform capabilities. Partner with the team lead on roadmap, prioritization, and tough technical calls.

• Years of Experience: 10+ years of professional software engineering experience across a range of systems and problem types.
• Cloud Infrastructure: Production experience with a major cloud platform (AWS preferred; GCP or Azure equivalent). You've designed for a cloud, not just deployed to one.
• Container Orchestration: Production experience with Kubernetes (or equivalent). Comfortable reasoning about cluster design, scheduling, networking, and workload patterns.
• Infrastructure as Code: Production experience with Terraform (or equivalent). Comfortable owning shared modules and multi-environment deployments.
• Programming: Strong proficiency in at least one general-purpose language (Python, Go, Java, or similar). Comfortable picking up new languages as needed - and comfortable using AI tooling to accelerate that.
• End-User Software: You've shipped software to end users (internal or external). You understand the realities of running a product - incongruent user feedback, competing priorities, the gap between requirements and what users actually need.
• Team Leadership: You've led an engineering team before and have mentored junior engineers. You're comfortable being the technical owner of multi-quarter initiatives.
• Startup Background: You've worked in fast-moving environments where results need to be delivered quickly. Scrappy, MVP-first, comfortable shipping in days rather than weeks.
• Familiarity with our tech stack: AWS, Kubernetes, Python, Go, Groovy, Terraform, Helm, Nextflow, WDL, Django, React.

• Product-Minded: You think in terms of business and user problems, not tickets. You ask "should we build this?" before "how do I build this?"
• Calibrated Judgement: You know when to move fast and break things, and when to slow down and double-check. The ability to dial this in based on context is something we hire specifically for.
• AI-Native Development: Actively excited about AI-native development. Not just willing to use Claude / Cursor, but actively interested in building tooling that makes your colleagues 10x faster.

• Domain-Adjacent Experience: Prior work in any of the following helps you ramp faster, but is not required: scientific or bioinformatics computing, LIMS or laboratory data systems, workflow orchestration engines (Nextflow, WDL, Airflow, Argo, Temporal, Dagster, etc.), large-scale ETL or data pipeline systems, or HPC/batch-compute platforms.

• Work on the software that powers Natera's R&D - a small, high-leverage team where individual contribution is highly visible.
• Operate at the frontier of AI-augmented software engineering. We don't just talk about AI tooling - we build it, and use it daily.
• Significant autonomy and influence over the team's technical direction.
• Competitive salary and benefits.
  

We value diversity and are committed to creating an inclusive environment for all employees. We encourage applicants of all backgrounds to apply.