--- title: 'Senior Bioinformatics Scientist at Cellular Intelligence' canonical: 'https://feeny.ai/job/senior-bioinformatics-scientist-cellular-intelligence-boston-43k367g8n2ar' type: 'job' last_seen: '2026-10-18' --- # Senior Bioinformatics Scientist at Cellular Intelligence - **Company:** Cellular Intelligence - **Location:** Boston, MA - **Compensation:** $160k–$190k - **Employment:** full-time - **Work type:** onsite - **Posted:** 2026-07-16 - **Last confirmed live:** 2026-10-18 - **Apply:** https://jobs.ashbyhq.com/cellular-intelligence/6b80682f-9486-431c-b9a9-7d5c714af294 ## Job description ## About Cellular Intelligence Cellular Intelligence is building a universal foundation model for cell signaling to understand, predict, and ultimately control how cells behave, transforming biology from trial and error into an engineering discipline. A clinical-stage AI company, Cellular Intelligence holds the global rights to STEM-PD, an investigational Phase 2-ready cell therapy for Parkinson's disease with FDA Fast Track designation, acquired from Novo Nordisk. The company's founding team includes repeat AI entrepreneur Micha Breakstone, Ph.D. ([Chorus.ai](http://Chorus.ai), acquired for $575M), the Head of the Fundamental AI Group at MIT, and five professors from Harvard Medical School, the University of Pennsylvania, and the University of Washington, collectively holding five National Academy memberships. Based in Boston, Cellular Intelligence has raised over $70M from Khosla Ventures, the Chan Zuckerberg Initiative, Novo Nordisk, AMD Ventures, and others. Cellular Intelligence’s Core Values - We show up - fully accountable, all-in, doing whatever it takes. - We act with urgency - swift, decisive, proactive. - We support one another - collaborative, helpful, empathetic. Location: Boston, MA Reports to: Director of Bioinformatics About the Role: We seek a Senior Bioinformatics Scientist to own and develop the methods and pipelines that power our proprietary capsule platform and feed our Universal Virtual Cell-Signaling Model. Working across single-cell, spatial, and bulk RNA-seq, you'll build reproducible pipelines, develop new bioinformatics methods, and apply them to our data. You'll collaborate closely with wet lab scientists, software engineers, and machine learning researchers to advance novel sequencing protocols and our therapeutic programs. This is a hands-on role spanning single-cell and spatial omics, ideal for someone who thrives in a fast-paced, interdisciplinary environment and wants to help build our cell-replacement therapy platform from the ground up. Responsibilities: - Develop new bioinformatics methods for single-cell, spatial, and bulk transcriptomics data, and adapt and benchmark existing ones. - Build and maintain reproducible analysis pipelines for single-cell, spatial, and bulk RNA-seq, from QC and normalization through the downstream analysis appropriate to each modality (integration, clustering, annotation, differential expression). - Analyze large-scale single-cell and spatial transcriptomics data, from raw output through to biological interpretation, including visualization of spatial data. - Partner with wet-lab scientists to bring novel multi-omic assays online, developing the analysis methods and pipelines that new experimental modalities require. - Collaborate with wet-lab and computational scientists to design experiments and interpret results. - Provide technical guidance and mentorship across the bioinformatics, ML, and engineering teams, including code and method reviews. Qualifications: - PhD in Bioinformatics, Genomics, Computational Biology, Computer Science, or a related field. Equivalent industry experience is also welcome. - 3+ years of experience developing, adapting, and benchmarking bioinformatics methods and building reproducible pipelines for large-scale single-cell and/or spatial transcriptomic data. - Hands-on experience with single-cell transcriptomics analysis. - Strong Python and/or R programming skills. - Experience building reproducible workflows with a pipeline manager (e.g. Nextflow or Snakemake), containers, and version control. - Experience applying state-of-the-art large language models (LLMs) to bioinformatics projects. - Excellent organizational and documentation habits. Prefered Qualifications: - Experience with spatial transcriptomics data analysis and visualization. - Experience applying and improving automated cell type annotation methods (e.g. marker-based and reference-based methods). - Experience working at the interface of technology development and data analysis, particularly involving novel molecular biology or sequencing techniques. - Strong domain knowledge in developmental biology or stem cell research. - Experience mentoring scientists or reviewing scientific code. - Prior experience in a startup or fast-paced, interdisciplinary environment. Cellular Intelligence is committed to creating a diverse and inclusive workplace. We welcome and encourage applicants from all backgrounds, regardless of race, ethnicity, gender, sexual orientation, religion, disability, or age. We embrace differences and believe that a diverse workforce enhances our creativity, innovation, and overall success. ## About Cellular Intelligence ## Company Overview - **One-liner**: Cellular Intelligence is an AI-native TechBio company building the first universal virtual cell-signaling model to decode and control the complex language of cells. - **Entity Type**: Private (Series A; total funding ~$62M) - **Headquarters**: Boston, Massachusetts, United States - **Founded**: 2023 - **Founders**: Micha Breakstone (CEO & co-founder), Allon Klein (Scientific co-founder), Olivier Pourquié (Scientific co-founder), Jay Shendure (Scientific co-founder), Cliff Tabin (Scientific co-founder) ## Core Business - **Primary industry**: Biotechnology Research / AI-driven drug discovery and regenerative medicine - **Target customers**: B2B – pharmaceutical companies, biotech firms, academic research institutions - **Mission/Purpose**: To transform biology into a predictive engineering discipline, enabling in silico control of cellular behavior for therapeutic discovery and disease modeling. ## Products & Services - **Capsule Data Engine**: Proprietary platform that generates dynamic cellular data at over 1,000x higher efficiency than existing methods. Produces massive, context-rich datasets covering millions of perturbation conditions. - **Universal Virtual Cell-Signaling Model** (in development): A foundation model capable of predicting how any cell state changes in response to external signals. Designed to enable rational protocol design for regenerative medicine, context-specific drug response prediction, and systematic disease modeling. ## Market Standing - **Valuation**: Not publicly disclosed - **Key Metric**: Total funding of over $62 million (conflicting reports: LinkedIn lists $57.3M) - Pre-Seed (April 2024): $10.3M led by TechAviv - Series A (May 2025): $47M led by Khosla Ventures - Venture Round (September 2025): led by AMD Ventures - **Notable Investors**: Khosla Ventures, Chan Zuckerberg Initiative, AMD Ventures, TechAviv - **Growth Signals**: - Headcount: 51 employees (as of mid-2025), +167.7% YoY - 4 active job postings (Chief of Staff, ML Researcher, Senior Research Associate) - Office presence in Boston, Israel, and Canada - Published white paper outlining technical roadmap (January 2026) - Collaboration with OmniaBio Inc. for cell therapy manufacturing (announced September 2024) ## Competitive Advantages - **Unrivaled data scale**: Capsule platform generates millions of perturbation conditions, solving the context-dependence problem that limits competitor approaches. - **Dynamic vs. static**: Uses human stem cells to decode combinatorial signaling logic, turning cell fate engineering into a tractable problem. - **AI-first approach**: Training large-scale transformer models on proprietary high-fidelity datasets to learn the fundamental “grammar” of cellular signaling. - **World-class scientific team**: Co-founders and advisors include members of the National Academy of Sciences, HMS professors, and HHMI investigators. ## Strategic Focus - Scale data generation through the capsule engine to produce increasingly large, context-rich datasets. - Train and refine the Universal Virtual Cell-Signaling Model, moving from discrete predictions to high-resolution continuous-time models. - Validate platform across high-impact applications: regenerative medicine protocol design, drug response prediction, and disease modeling. - Expand partnerships with pharma and biotech for translational collaborations. ## Why Work Here - **Culture**: AI-native TechBio at the intersection of cutting-edge machine learning and developmental biology; fast-paced, research-heavy environment. - **Work mode**: In-office (Boston, MA). All employees work from physical locations. - **Team**: Small but rapidly growing (51 people; +167% YoY); roles span research, ML engineering, computational biology, and strategy. - **Perks**: Not publicly detailed, but the company is well-funded by top-tier venture firms, offering a strong foundation for career growth and impact. - **Engineering focus**: Emphasis on building foundation models and large-scale data infrastructure; opportunities for engineers and scientists to shape the platform from the ground up. ## Sources 1. [cellularintelligence.com](https://www.cellularintelligence.com/) 2. [cellularintelligence.com – Science page](https://www.cellularintelligence.com/science) 3. [LinkedIn – Cellular Intelligence](https://www.linkedin.com/company/cellular-intelligence) 4. [Built In – Cellular Intelligence](https://builtin.com/company/cellular-intelligence) 5. [Ashby Careers](https://jobs.ashbyhq.com/cellular-intelligence) ## Other roles at Cellular Intelligence - [Infrastructure & IT Systems Engineer](https://feeny.ai/job/infrastructure-it-systems-engineer-cellular-intelligence-boston-0ppx9rcx0scq) — Boston, MA - [Director, Marketing Communications](https://feeny.ai/job/director-marketing-communications-cellular-intelligence-boston-x5q1w4ed4rcp) — Boston, MA - [Senior Bioinformatics Scientist](https://feeny.ai/job/senior-bioinformatics-scientist-veracyte-san-diego-28gm8vnx9d0y) — San Diego, CA / South San Francisco, CA