Computational Biologist II, 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 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. 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 the Imaging Grand Challenge, The CELLxSTATE Program builds next‑generation technologies to decode and control how cells make decisions — combining live‑cell imaging, multi‑omics, and AI at unprecedented scale. We also create large reference datasets that can be mined and reused by the entire community for discovery, like our OpenCell project that maps protein localization and interactions ( Our science is fully open‑source and published in journals such as Science, Nature Methods, and Cell ( At the core of our current efforts 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. We are seeking a Computational Biologist to help lead image analysis for our next‑generation Optical Pooled Screening program. This is a great opportunity for candidates with a strong interest in data science, engineering, and cell biology, supported by experts in a highly collaborative and well‑funded scientific environment. What You’ll Do Design, develop, and maintain scalable image analysis pipelines for large‑scale fluorescent microscopy datasets, with an emphasis on image quality robustness and computational efficiency. Integrate emerging multi‑modal data types (e.g., spatial transcriptomics) into unified, AI‑ready datasets that support downstream modeling and discovery. Advance our bio‑image analysis capabilities (e.g., segmentation, tracking, image‑stitching, and image registration). Partner closely with biologists and automation engineers to implement end‑to‑end quality control metrics, ensuring the fidelity of our experimental and computational pipelines. Architect modular and reusable processing frameworks that can flexibly support multiple experiment types within a shared infrastructure. Publish and disseminate impactful findings through preprints, papers, and software repositories (e.g., GitHub). What You’ll Bring PhD in Computational Biology, Biology, or Computer Science, or a MS with relevant job experience. At least 4 years of experience in Python‑based image analysis or scientific computing. Experience with fluorescence microscopy, confocal, or lightsheet is a plus. Fluency with computational tools and infrastructure such as Python, GitHub, and Slurm. Experience with modern biological data formats such as OME‑Zarr and AnnData. Experience designing workflows for large, complex datasets, including scalable storage formats, and reliable metadata and experiment tracking. A proven track record of individual innovation, together with a strong ability to work collaboratively. A passion for research and understanding how cells work. An enthusiasm for team science and open science - this position will be embedded in a large multi‑disciplinary team. Excellent written and oral communication skills. Compensation The San Francisco, CA base pay range for a new hire in this role is $153,000 – $210,100. 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 Biohub's discretionary annual performance bonus program. Bonus eligibility and targets are determined in accordance with Biohub's 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. Relocation support for employees who need assistance moving. We encourage applicants whose previous experience doesn’t perfectly align with each qualification listed in the job description to still apply, as they may be the perfect fit for this or another role. Equal Employment Opportunity As set forth in the organization’s Equal Employment Opportunity policy, we do not discriminate on the basis of any protected group status under any applicable law. If you believe you belong to any of the categories of protected veterans listed below, please indicate by making the appropriate selection. Classification of protected categories is as follows: “disabled veteran,” “recently separated veteran,” “active duty wartime or campaign badge veteran,” “armed forces service medal veteran.” We also maintain voluntary self‑identification for race/ethnicity and other categories as part of our reporting obligations. Participation is entirely voluntary and will not be considered in the hiring process. Reasonable Accommodation Notice: The organization provides (and state and federal law requires) reasonable accommodations to be provided to qualified applicants with disabilities. Your recruiter will work with you during the interview process should you require any such accommodations. Examples of reasonable accommodation include making a change to the application process or work procedures, providing documents in an alternate format, using a sign language interpreter, or using specialized equipment. Background Check Notice: As part of our hiring process, all offers of employment are contingent upon the successful completion of a background check. By submitting your application, you acknowledge that you will be required to undergo a background check prior to employment. Artificial Intelligence Usage Notice: We use artificial intelligence (AI) tools to support parts of the hiring process, such as reviewing applications and analyzing resumes. These tools assist our recruitment team but do not replace human judgment. Hiring decisions are ultimately made by humans. #J-18808-Ljbffr