Scientist I, Stem Cell Genomics, CELLxSTATE

Biohub is the first large-scale initiative bringing frontier AI models, massive compute, and frontier experimental capabilities under one roof. We're building a general-purpose system to accelerate scientific discovery, integrating frontier AI models, biological foundation models, and lab capabilities, with the ultimate goal of curing disease. Our technology powers scientists around the world, translating AI capabilities into tools that accelerate research everywhere.

The Team

Biohub is a 501(c)(3) biomedical research organization building the first large-scale scientific initiative combining frontier AI with frontier biology to solve disease. We build the technology to help scientists around the world use AI-powered biology to study how cells operate, organize, and work as part of systems to understand why disease happens and how to correct it. With our compute capacity, AI research and engineering, and state-of-the-art technology for measuring, imaging, and programming biology, we are enabling scientists worldwide to use AI-powered biology to advance our understanding of human health. 

Through our multi-dimensional imaging program, we build imaging tools that capture life across scales — from single proteins to whole organisms — revealing how proteins and cells function, communicate, and assemble into living systems. These observations are laying the groundwork for a new generation of AI models that can predict cellular behavior and guide the development of better treatments for widespread diseases. You can learn more about our work here. 

Our work brings together three powerhouse universities - Stanford, UC Berkeley, and UC San Francisco - into a single collaborative technology and discovery engine. 

Our Vision

• Pursue large scientific challenges that cannot be pursued in conventional environments
• Enable individual investigators to pursue their riskiest and most innovative ideas
• Facilitate research by scientists and clinicians at our home institutions and beyond

We are a team of passionate individuals powered by technology, guided by scientific research, and driven by collaboration, working toward a mission to cure or prevent all disease.

The Opportunity

Part of Imaging Grand Challenge, the CELLxSTATE Program is building next-generation technologies to decode and control how cells make decisions, combining live-cell imaging, multi-omics, and AI at unprecedented scale. At the core of our current effort is multiDPS (Multimodal Dynamic Pooled Screening), a high-throughput platform that integrates custom microscopy, automation, CRISPR screening and molecular profiling to map and predict dynamic cell states. As part of this effort, the Intracellular Architecture team at the CZ Biohub San Francisco is building scalable technologies to map the molecular architecture of human cells, how it changes in disease, and how we can control it. 

For this we combine genome engineering, fluorescence microscopy, proteomics, robotics, software engineering and data science. We build large datasets and use them to draw new biological insights. For example, our OpenCell project provides a large reference of protein localization and interactions that can be mined and re-used by the entire community for discovery. Our science is fully open-source and published in journals like Science, Nature Methods, and Cell.

We are seeking a Scientist I to advance our Stem Cell Genomics efforts within the CELLxSTATE program. The successful candidate will develop and implement single-cell and multi-omics approaches in human stem cell systems, and integrate these with CRISPR-based perturbation and high-content imaging platforms. This role focuses on building scalable, high-throughput experimental workflows to enable multimodal profiling of cellular states, and involves close collaboration with computational teams to develop robust data analysis pipelines. The candidate will contribute to both technology development and biological discovery, helping to uncover how genetic perturbations influence cell state and function. This is an excellent opportunity to contribute to cutting-edge platform development in a highly collaborative, well-resourced, and open-science-driven environment.

What You'll Do

• Develop and implement multi-omics assays (e.g., scRNA-seq, scATAC-seq) for transcriptomic and epigenetic profiling; 
• Lead whole-genome sequencing (WGS) assays for genomic characterization of engineered cell lines;
• Contribute to high-throughput cell engineering pipelines (e.g. CRISPR-Cas9 based genome editing), including culture of human stem cells and iPSCs, as part of a collaborative effort;
• Contribute to image-based pooled barcoded screens;
• Collaborate with genomics and computational biologist experts to develop data analysis pipelines;
• Present results internally and externally to multidisciplinary teams, author publications, and mentor junior colleagues.

What You'll Bring

• PhD in Molecular Biology, Cell Biology, Systems Biology, or a related discipline
• At least 4 years of experience with single-cell genomic workflows, including sample and library preparation, sequencing, and data analysis
• Experience with multi-omics approaches (e.g., RNA-seq + ATAC-seq, or related assays) is strongly preferred
• At least 2 years of experience with stem cells or iPSCs culture
• At least 2 years of experience in CRISPR-based genome engineering, including CRISPR screening or generation of gene-edited cell libraries
• At least 2 years of single-cell data analysis in Python or R
• Demonstrated ability or strong interest in high-throughput and/or automated experimental pipelines
• Strong interest in cell biology and understanding cellular function and state transitions
• Enthusiasm for team science and open science, working within a highly collaborative, multidisciplinary environment
• Excellent written and oral communication skills

Compensation

The San Francisco, CA base pay range for a new hire in this role is $120,000-$150,000. New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. Actual placement in range is based on job-related skills and experience, as evaluated throughout the interview process. 

This position may be eligible to participate in our discretionary annual performance bonus program. Bonus eligibility and targets are determined in accordance with our total rewards philosophy and may vary by role.

Better Together

As we grow, we’re excited to strengthen in-person connections and cultivate a collaborative, team-oriented environment. This role is a hybrid position requiring you to be onsite for at least 60% of the working month, approximately 3 days a week, with specific in-office days determined by the team’s manager. The exact schedule will be at the hiring manager's discretion and communicated during the interview process.

Benefits for the Whole You 

We’re thankful to have an incredible team behind our work. To honor their commitment, we offer a wide range of benefits to support the people who make all we do possible. 

• Provides a generous employer match on employee 401(k) contributions to support planning for the future.
• Paid time off to volunteer at an organization of your choice. 
• Funding for select family-forming benefits. 
• Relocation support for employees who need assistance moving

If you’re interested in a role but your previous experience doesn’t perfectly align with each qualification in the job description, we still encourage you to apply as you may be the perfect fit for this or another role.

#LI-Hybrid #LI-Onsite