Scientist I, Stem Cell Genomics, CELLxSTATE
About The Position
Biohub is a large-scale initiative that integrates frontier AI models, massive compute, and experimental capabilities to accelerate scientific discovery, with the ultimate goal of curing disease. It operates as a 501(c)(3) biomedical research organization, building technology to help scientists worldwide use AI-powered biology to study cellular operations, organization, and system integration to understand and correct disease. Biohub collaborates with Stanford, UC Berkeley, and UC San Francisco. The CELLxSTATE Program, part of the Imaging Grand Challenge, is dedicated to building next-generation technologies to decode and control how cells make decisions. This involves combining live-cell imaging, multi-omics, and AI at an unprecedented scale. A core component is multiDPS (Multimodal Dynamic Pooled Screening), a high-throughput platform integrating custom microscopy, automation, CRISPR screening, and molecular profiling to map and predict dynamic cell states. The Intracellular Architecture team at CZ Biohub San Francisco focuses on developing scalable technologies to map the molecular architecture of human cells, understand its changes in disease, and explore methods of control. Their approach combines genome engineering, fluorescence microscopy, proteomics, robotics, software engineering, and data science to build large datasets and derive new biological insights, exemplified by their open-source OpenCell project. This Scientist I position is within the CELLxSTATE program, specifically advancing Stem Cell Genomics efforts. The successful candidate will be responsible for developing and implementing single-cell and multi-omics approaches in human stem cell systems, integrating these with CRISPR-based perturbation and high-content imaging platforms. The role emphasizes building scalable, high-throughput experimental workflows for multimodal profiling of cellular states and requires close collaboration with computational teams for data analysis pipeline development. The scientist will contribute to both technology development and biological discovery, aiming to uncover how genetic perturbations influence cell state and function within a highly collaborative, well-resourced, and open-science-driven environment.
Requirements
- 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
- 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
Nice To Haves
- Experience with multi-omics approaches (e.g., RNA-seq + ATAC-seq, or related assays) is strongly preferred
Responsibilities
- 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
Benefits
- 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
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What This Job Offers
Job Type
Full-time
Career Level
Mid Level
Education Level
Ph.D. or professional degree
