---
title: 'Director, Software and Data Engineering at Profluent'
canonical: 'https://feeny.ai/job/director-software-and-data-engineering-profluent-emeryville-qxjw00tzjncs'
type: 'job'
last_seen: '2026-09-06'
---

# Director, Software and Data Engineering at Profluent

- **Company:** Profluent
- **Location:** Emeryville, CA
- **Compensation:** $268k–$355k
- **Work type:** hybrid
- **Posted:** 2025-09-04
- **Last confirmed live:** 2026-09-06
- **Apply:** https://job-boards.greenhouse.io/profluent/jobs/4905081008

## Job description

Profluent is the frontier AI lab for biology. Profluent builds powerful foundation models for all of life's molecules, unlocking solutions that transform medicine, agriculture, and beyond. Founded in 2022 and headquartered in Emeryville, CA, Profluent is backed by leading investors including Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, and Convergent Ventures and has raised over $150M to date.

We’re looking for a Director of Software and Data Engineering to lead Profluent’s software engineering function and build the platform connecting AI-driven protein design, high-throughput experimental screening, and quantitative data analysis.

You’ll own the software and data architecture connecting computational designs to the constructs, samples, assays, and measurements generated through automated laboratory workflows. Your team will build the scientist-facing tools, integrations, and data systems needed to manage experimental data at scale, preserve lineage and context, and turn results into reliable inputs for analysis, machine learning, and the next round of design.

The ideal candidate is an experienced engineering leader with a strong technical foundation, sound judgment, and a track record of building scalable data platforms. You’ll manage and mentor a small team while remaining close to architecture, data modeling, and technical decision-making, partnering across science, automation, data, and ML to advance Profluent’s lab-in-the-loop platform.

## Responsibilities

- Lead, mentor, and grow Profluent’s software engineering team, with responsibility for technical direction, hiring, organizational development, and execution
- Own the roadmap for software and data engineering, balancing scientific impact, user needs, delivery speed, scalability, and long-term platform strategy
- Define the software and data architecture, system boundaries, and data flows connecting computational design, high-throughput experimentation, analysis, and machine learning
- Architect and guide delivery of scientist-facing applications and data systems supporting experimental design, sample tracking, laboratory automation, assay data capture, and analysis
- Establish scalable data models and standards for identifiers, provenance, lineage, versioning, interoperability, and access control, ensuring experimental results are reliable, reusable, and model-ready
- Partner across science, automation, bioinformatics, data science, and ML while establishing strong engineering and product practices that drive reliable delivery and adoption

## Qualifications

- 8+ years of software engineering experience, including 3+ years managing or leading engineers
- BS, MS, or PhD in Computer Science, Bioengineering, Computational Biology, or a related field, or equivalent practical experience
- Track record of leading teams that architect and deliver production-quality, data-intensive software platforms
- Strong technical foundation in Python, backend systems, databases, APIs, cloud infrastructure, and modern software development practices
- Experience designing data architectures, schemas, and domain models for complex scientific, experimental, or similarly interconnected workflows
- Demonstrated ability to translate ambiguous user and scientific needs into reliable systems, make sound technical and product tradeoffs, and drive adoption

Preferences

- Experience building scientific data infrastructure, research software, LIMS integrations, or scientist-facing applications
- Experience with Benchling, laboratory automation, instrument integration, sample tracking, or high-throughput experimental platforms
- Experience connecting experimental workflows with downstream analysis and machine learning
- Familiarity with biological data from protein engineering, gene editing, sequencing, screening, or mammalian or bacterial systems
- Frontend development experience and an interest in building intuitive scientist-facing interfaces

## What We Offer

- High-growth opportunity with meaningful impact on the future of protein design
- Competitive compensation package with equity participation
- 401(k) with a strong employer match
- Comprehensive benefits including health/dental/vision insurance
- Generous PTO policy and commitment to work-life balance
- Professional development opportunities in a cutting-edge field at the intersection of AI and biology

Profluent Bio, Inc is an equal opportunity employer promoting diversity and inclusion in the workspace. We do not discriminate on the basis of race, color, religion, marital status, age, national origin, ancestry, physical or mental disability, medical conditions, veteran status, sexual orientation, gender (including gender identity and gender expression), sex (which includes pregnancy, childbirth, and breastfeeding), genetic information, taking or requesting statutorily protected leave, or any other basis protected by law.

Work Authorization Requirement

Applicants must have ongoing work authorization in the United States that does not require employer sponsorship. Sponsorship will not be provided now or at any time in the future for this position.

Employment Eligibility Verification

Legal authorization to work in the United States is required. In compliance with federal law, all persons hired must verify their identity and work eligibility and complete the required employment verification form upon hire.

TO ALL RECRUITMENT AGENCIES: Profluent does not accept agency resumes. Please do not forward resumes to our jobs alias or employees. Profluent is not responsible for any fees related to unsolicited resumes. Hiring Salary Range $268,000—$355,000 USD

## About Profluent

## Company Overview
- **One-liner**: Profluent is an AI-first protein design company that develops deep generative models to design and validate novel, functional proteins for biomedicine, agriculture, and other industries.
- **Entity Type**: Private (Series B; total funding $150M)
- **Headquarters**: Emeryville, California, United States
- **Founded**: 2022
- **Founders**: Ali Madani (CEO), Alexander Meeske

## Core Business
- **Primary industries**: Biotechnology, Artificial Intelligence, Genetic Medicine
- **Target customers**: B2B – pharmaceutical companies, biotech firms, agricultural companies, and research institutions
- **Mission statement**: "Decode the language of life with AI" – using AI to author new biology and create solutions that transform medicine, agriculture, and beyond.

## Products & Services
- **OpenCRISPR**: The world's first AI-designed gene editor, made open-source to accelerate genome editing research. Based on a novel nuclease generated by Profluent's generative AI.
- **AI Protein Design Platform**: A proprietary platform that writes proteins from scratch or by reimagining natural scaffolds, enabling rapid design of proteins for therapeutic, industrial, and agricultural applications.
- **Partnerships (e.g., Eli Lilly)**: Collaborations to develop AI-designed recombinases for genetic medicine, with deal value up to $2.25 billion.

## Market Standing
- **Valuation / Market Cap**: Not publicly available
- **Key Metric (Total Funding)**: $150M raised across multiple rounds (Seed $9M in 2022, Venture Round $35M in 2024, Series B $106M in 2025)
- **Notable Investors**: Altimeter Capital, Bezos Expeditions, Spark Capital, Insight Partners, Air Street Capital, AIX Ventures, Convergent Ventures
- **Growth Signals**: 
  - Headcount grew 78.4% YoY (53 employees as of mid-2026)
  - Published generative AI research in Nature (July 2025)
  - Secured a landmark partnership with Eli Lilly (up to $2.25B in milestones)
  - LinkedIn followers grew 67.8% in the past year (11,906 followers)

## Competitive Advantages
- **Pioneering AI-first protein design**: One of the few companies translating large language models (LLMs) to biology, with demonstrated ability to create functional gene editors from scratch.
- **Open-source gene editing**: OpenCRISPR-1 provides a freely available AI-designed nuclease, establishing thought leadership and potential ecosystem lock-in.
- **Cross-disciplinary team**: Combines top ML talent (from Salesforce, Meta, Amazon) with leading biologists (from CRISPR pioneers, UCSF, Harvard, Arc Institute).
- **Published in top journals**: Nature publication validates the scientific rigor of their approach.

## Strategic Focus
- Advance AI-designed recombinases for in vivo gene editing through the Lilly partnership
- Expand platform to design enzymes, antibodies, and industrial proteins
- Continue open-source releases to drive adoption and attract top research talent
- Scale headcount across ML, biology, and bioinformatics functions

## Why Work Here
- **Culture & Mission**: Opportunity to work at the frontier of AI and biology, authoring new proteins that can transform medicine and agriculture. Team culture emphasizes curiosity, societal impact, and breakthrough science.
- **Work Policy**: Hybrid – most roles require 2-3 days on-site at the Emeryville, CA headquarters. Some lab-based roles (e.g., in vivo pharmacology, LNP formulation) are fully on-site.
- **Team mix**: Diverse backgrounds spanning ML science, structural biology, software engineering, and drug discovery. Flat structure with direct access to founders and top domain experts.
- **Notable perks**: Backed by top-tier investors; highly collaborative environment; opportunities to publish and release open-source work.
- **Growth trajectory**: Fast-growing company (78% headcount increase in last year) with substantial funding runway and a high-profile pharma partnership, offering strong career progression.

## Sources
1. [profluent.bio](https://www.profluent.bio/)
2. [Greenhouse Jobs at Profluent](http://job-boards.greenhouse.io/profluent)
3. [LinkedIn Company Page](https://www.linkedin.com/company/profluent-bio)
4. [CB Insights Profile](https://www.cbinsights.com/company/profluent-bio)

## Other roles at Profluent

- [Software Engineer, Machine Learning Platform](https://feeny.ai/job/software-engineer-machine-learning-platform-profluent-emeryville-hywmbz47mnac) — Emeryville, CA
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- [Controller](https://feeny.ai/job/controller-profluent-emeryville-5cn74bd9x1tp) — Emeryville, CA
- [Executive Director / Vice President, Biology & Translational Pharmacology](https://feeny.ai/job/executive-director-vice-president-biology-translational-pharmacology-profluent-rr9mkm28evx8) — Emeryville California, United States
- [Machine Learning Scientist, BioML](https://feeny.ai/job/machine-learning-scientist-bioml-profluent-emeryville-4q794vqye0e5) — Emeryville, CA
- [Associate Director - Director, In Vivo Pharmacology](https://feeny.ai/job/associate-director-director-in-vivo-pharmacology-profluent-emeryville-california-st6r3q5meyk1) — Emeryville California, United States
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