Christoph Bock Lab @ CeMM &amp; MedUni Vienna

21 Sept

We are recruiting PhD students in ML/AI methods & biomedical applications via the @ellis.eu PhD Program (ellis.eu/news/ellis-p...). Keywords: Perturbation modeling, generative AI, synthetic biology, cancer immunotherapy, precision medicine. Details: medical-epigenomics.org/files/PhD_St...

nature.comMultimodal learning enables chat-based exploration of single-cell data - Nature BiotechnologyCellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

8 Mar

CellWhisperer can now run on your laptop. Talk to your cells! And check out our paper: www.nature.com/articles/s41...

Moritz Schaefer@moritzbaio.bsky.social

Want to analyze your single-cell data, but don't like to deal with code? 🧬 Good news: CellWhisperer now runs on your MacBook! 💻 Get your single-cell AI assistant running in under 5 minutes. ⏱️ Made with ❤️ @bocklab.bsky.social Code and docs at cellwhisperer.bocklab.org

cemm.atPostDoc ProgramCeMM Pre-ERC Postdoc Program

HIRING: We recruit postdocs via the CeMM Pre-ERC Postdoc Program (cemm.at/postdoc-prog...). Seeking 3 types of candidates: (1) experimental systems biology in immunity or cancer; (2) bioinformatics & biomedical ML/AI; (3) tech-dev & bioengineering (CRISPR, single-cell, spatial, cell programming).

Maybe get some inspiration from our recent papers and consider proposing a project idea or research direction (as part of your application's cover letter) that connects your and our research expertise. Be ambitious & creative!

bocklab.orgMedical Epigenomics | Bock Lab at CeMM & MedUni ViennaLed by Christoph Bock, the Medical Epigenomics Lab pursues technology-driven biomedical research for cancer, immunology, and precision medicine.

Additional information about our research: cemm.at/research/gro... | bocklab.org | med-ai.org Full job posting: cemm.at/fileadmin/im... Further details & application portal: cemm.at/postdoc-prog... & cemm.onlyfy.jobs/job/7k2624z5

cemm.atPostDoc ProgramCeMM Pre-ERC Postdoc Program

3. Cancer: Epigenetic tumor heterogeneity (nature.com/articles/s41...) 4. Technology: High-content CRISPR screening for causality at scale (nature.com/articles/s43...) 5. Biomedical ML/AI: Chat-based single-cell data analysis with natural language (nature.com/articles/s41...)

What excites you? What expertise do you bring from your PhD? What do you envision your future independent research group to focus on (or the start-up company you will found)? What could be a truly exciting & impactful postdoc project?

cemm.atPostDoc ProgramCeMM Pre-ERC Postdoc Program

We are open to purely wet-lab candidates (including organoids & mouse models), purely computational candidates (including ML/AI), and those who want to pursue a mix of wet-lab & computational work. We are a highly interdisciplinary & collaborative research group with ambitions in molecular medicine.

nature.comStructural cells are key regulators of organ-specific immune responses - NatureStructural cells implement a broad range of immune-regulatory functions beyond their roles as barriers and connective tissues, and they utilize an epigenetically encoded potential for immune gene acti...

Examples of our recent research: 1. Immunology: Immune regulation by non-immune cells (nature.com/articles/s41...) 2. Cell engineering: CRISPR-optimized CAR T cell immunotherapy (www.nature.com/articles/s41...)

cemm.atCeMM PhD Program – Molecular Medicine Research in ViennaJoin the CeMM PhD Program in Vienna and pursue cutting-edge research in cancer, immunology, aging, and precision medicine. Applications open in 2025!

HIRING: We recruit PhD students via the AITHYRA-CeMM PhD Program (cemm.at/phd-program). Seeking 3 types of candidates: (1) experimental systems biology in immunity or cancer; (2) bioinformatics & biomedical ML/AI; (3) tech-dev & bioengineering (CRISPR, single-cell, spatial, cell programming) (1/5)

What excites you? What could be a great PhD project? Please have a look at our recent publications and consider proposing an idea or research direction (as part of your application's cover letter) that you might want to pursue in our PhD. (4/5)

Further details & application portal: apply.cemm.at Additional information about our research: cemm.at/research/gro... | bocklab.org | med-ai.org

nature.comSystematic discovery of CRISPR-boosted CAR T cell immunotherapies - NatureCELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.

@natureportfolio.nature.com

4. Technology: High-content CRISPR screening for causality at scale (nature.com/articles/s43...) 5. Biomedical ML/AI: Chat-based single-cell data analysis with natural language (nature.com/articles/s41...)

Christoph Bock Lab @ CeMM & MedUni Vienna reposted

Nature Portfolio

15 Nov 2025

A paper in Nature Biotechnology presents CellWhisperer, which uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data. go.nature.com/3XqzItR 🧬 🧪

Christoph Bock Lab @ CeMM & MedUni Vienna reposted

Nature Biotechnology

@natbiotech.nature.com

go.nature.comMultimodal learning enables chat-based exploration of single-cell data - Nature BiotechnologyCellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

Multimodal learning enables chat-based exploration of single-cell data - @bocklab.bsky.social @cemm.oeaw.ac.at @meduniwien.ac.at go.nature.com/3WPGJnW

🗨️ Just published in Nature Biotechnology: Our CellWhisperer AI enables chat-based analysis of single-cell sequencing data. You can talk to your cells & figure out the biology without writing any computer code. Paper here: www.nature.com/articles/s41.... Annotated walkthrough in a thread below (1/11)

🧬 CellWhisperer introduces a chat-based way to explore scRNA-seq data. By enabling natural language analysis, it bridges biologists and bioinformaticians—paving the way for AI-driven bioinformatics assistants. (10/11)

🤝 Huge thanks to the team! Moritz Schaefer & Peter Peneder with Daniel Malzl, Salvo Lombardo, Mihaela Peycheva, Jake Burton, Anna Hakobyan, Varun Sharma, Thomas Krausgruber, Celine Sin, Jörg Menche, Eleni Tomazou, Christoph Bock. @cemm.oeaw.ac.at, @meduniwien.ac.at, @stanna-ccri.bsky.social (11/11)

📚 We trained on >1 million bulk & pseudo-bulk transcriptomes with textual annotations that we AI-curated from GEO & @CELLxGENE Census. Our training data is open source and useful for developing multimodal biomedical AI models and future bioinformatics research assistants. (8/11)

doi.orgMultimodal learning enables chat-based exploration of single-cell data - Nature BiotechnologyCellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.

Ready to talk to cells? 📖 Read the paper: doi.org/10.1038/s415... 🧬 Try the web app with public datasets: cellwhisperer.bocklab.org 🖥️ Analyze your own datasets: github.com/epigen/cellw... (9/11)

🚀 We also validated CellWhisperer’s chat-based analysis with conventional bioinformatics. CellWhisperer was >4x faster (and 10x cooler 😊). Our recommendation: Use CellWhisperer for dataset exploration – but statistics is still important to ensure rigor & reproducibility (6/11)

🪄 How does CellWhisperer work behind the scenes? We trained a multimodal AI that links transcriptomes and text, enabling free-text search and annotation of RNA profiles. And we connected this model to an LLM that we fine-tuned into a chat assistant for transcriptome data (7/11)

🔬 You can easily query large transcriptome datasets for your favorite biological process using CellWhisperer. Just open Tabula Sapiens (cellwhisperer.cemm.at/tabulasapiens/) or GEO (cellwhisperer.cemm.at/geo/) in CellWhisperer & type your query into the chat box – for example “infection” (4/11)

🆕 The CellWhisperer paper (doi.org/10.1038/s415...) includes several new analyses beyond our 2024 bioRxiv preprint (biorxiv.org/content/10.1...). For example, we used CellWhisperer for an AI-guided analysis of human organ development (5/11)

⚙️ To get started, let’s find cells by typing into the CellWhisperer chat box. For example ‘Show me structural cells with immune functions’. CellWhisperer scores each transcriptome by how well it matches this textual query and colors by query match (red: high, blue: low) (2/11)

🔍 We investigate one of the identified cell clusters by selecting the cells & prompting CellWhisperer with ‘Describe these cells in detail’. This interactive workflow is enabled by seamless integration of the CellWhisperer AI chat box into a version of CELLxGENE Explorer (3/11)

Christoph Bock Lab @ CeMM & MedUni Vienna reposted

CeMM

@cemm.oeaw.ac.at

🗨️Chat with your cells, explore #CellWhisperer! CeMM PI Christoph Bock (@bocklab.bsky.social) together with @meduniwien.ac.at & @stanna-ccri.bsky.social have developed a new #AI tool that lets scientists explore single-cell data using plain English. ➡️ https://bit.ly/3JQqe87 📄 https://bit.ly/3WJCxGi

🧬 CAR T cells demonstrate the power of engineered cells as therapeutics. But they fail for most patients. Can CRISPR help here? Our new paper in Nature (www.nature.com/articles/s41...) presents a screening platform to optimize immunotherapies & discover boosters of CAR T cell function. (1/13)

🤝 This was a large project & great teamwork by: P. Datlinger*, E.V. Pankevich*, C.D. Arnold*, N. Pranckevicius, J. Lin, D. Romanovskaia, M. Schäfer, F. Piras, A.-C. Orts, A. Nemc, P. Biesaga, M. Chan, T. Neuwirth, A. Artemov, W. Li, S. Ladstätter, T. Krausgruber, C. Bock (12/13)

📑 Check out our paper titled “Systematic discovery of CRISPR-boosted CAR T cell immunotherapies” at @Nature (open access): www.nature.com/articles/s41.... Feedback & suggestions are very welcome. (13/13)

🔥 What’s next? Our discovery of strong combined effects for RHOG & FAS knockout underlines the potential of synergistic gene edits for boosting CAR T cell function. We thus integrated combinatorial screening into CELLFIE, using the Blainey lab’s CROPseq-multi method. (10/13)

⚕️ Our CELLFIE platform supports clinical translation of CRISPR-boosted CAR T cells. For example, to avoid the DNA double-strand breaks introduced by CRISPR knockout, we performed a tiling base-editing screen across RHOG and identified promising gRNA for clinical testing. (11/13)

💪 We also observed prolonged survival for FAS knockout CAR T cells, likely because these cells are less effective at killing each other (“fratricide”). Combining RHOG & FAS knockout, we obtained more & better CAR T cells, which further improved survival in leukemic mice. (8/13)

🔬 From a technical perspective, we are excited how our new in vivo CROP-seq method improves gRNA detection (reading from an mRNA transcript as in nature.com/articles/nme...) and reduces experimental noise (by using UMIs), which enables larger screens with fewer mice. (9/13)

🐁 We performed extensive in vivo validations and found that RHOG knockout CAR T cells achieve strong reductions in cancer cell numbers and prolonged survival in an aggressive mouse model of human leukemia, with consistent results across different CARs and T cell donors. (6/13)

🔍 RHOG is a small GTPase involved in cell signaling. How does it influence CAR T cells ? We found that RHOG knockout increases the proliferative capacity of CAR T cells and helps them retain a highly functional state with reduced exhaustion and enhanced memory phenotype. (7/13)

💡 Conceptually, our CRISPR screens create a form of “artificial evolution” by which we optimize CAR T cells for their tasks as cancer therapeutics. This is important because CAR T cells are products of cell engineering and lack task-specific evolutionary optimization. (4/13)

🐭 But not everything that makes CAR T cells proliferate or kill better in vitro translates into more effective therapies. For scalable validation in mice, we conducted pooled in vivo CRISPR screening and observed strong positive effects of RHOG, PRDM1, and FAS knockouts. (5/13)

⚙️ We developed CELLFIE (“cell engineering for immunotherapy enhancement”), a CRISPR platform to make & test gene-edited CAR T cells at scale. CELLFIE supports in vitro & in vivo screens with various clinically relevant readouts, plus combinatorial & base-editing screens. (2/13)