Christoph Bock Lab @ CeMM & MedUni Vienna
Technology-driven biomedical research at CeMM Research Center for Molecular Medicine & MedUni Vienna #cancer #immunology #bioinformatics #AI #singlecell #CRISPR
- 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)
- 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...) 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...)
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View full threadFurther details & application portal: apply.cemm.at Additional information about our research: cemm.at/research/gro... | bocklab.org | med-ai.org
- Reposted by Christoph Bock Lab @ CeMM & MedUni ViennaA 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 🧬 🧪
- Reposted by Christoph Bock Lab @ CeMM & MedUni ViennaMultimodal 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)
- ⚙️ 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)
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View full thread🤝 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)
- Reposted by Christoph Bock Lab @ CeMM & MedUni Vienna🗨️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. ➡️ bit.ly/3JQqe87 📄 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)
- ⚙️ 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)
- 🩸 Using CELLFIE, we conducted 58 genome-wide CRISPR screens, with readouts for CAR T cell proliferation, target cell recognition, activation, apoptosis & fratricide, and exhaustion. The screens identified known genes (PD-1, CTLA4, TIM3, TIGIT etc.) and promising new hits. (3/13)
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View full thread📑 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)
- Reposted by Christoph Bock Lab @ CeMM & MedUni ViennaWe’re thrilled to announce that the "High-Content CRISPR Screening" conference will take place on March 18–19, 2026, in Vienna, Austria. The registration is now open via the conference website: lnkd.in/d8KACZy5 Meet the Speaker: Christoph Bock @bocklab.bsky.social
- 🛡️How do macrophages tailor their defenses to different pathogens? Our new paper in @cp-cellsystems.bsky.social combines dense multi-omics time series with high‐content CRISPR screens (CROP-seq) to map the regulatory landscape underlying macrophage immune responses: www.cell.com/cell-systems... (1/9)
- 🦠 Pathogens & cytokines trigger macrophage receptors and induce immune gene expression. We challenged mouse macrophages (BMDMs) with 6 immune stimuli (Listeria, LCMV, Candida, LPS, IFN-β, IFN-γ) and profiled genes (RNA-seq) and chromatin (ATAC-seq) over six time points. (2/9)
- 🧬 Integrative analysis revealed strong differences between interferon-driven (IFN-β/γ) and pathogen-driven (Listeria/LPS) trajectories. Many immune genes showed "epigenetic potential": pre-established open chromatin ready for rapid expression upon stimulation. #Epigenetics (3/9)
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View full thread🚀 Check out the paper, dataset, and computational methods (open access | open data | open source): 📑 Paper: www.cell.com/cell-systems... 🧬 Dataset: macrophage-regulation.bocklab.org 💻 Code: github.com/epigen/macro... Feedback & suggestions are very welcome. (9/9)
- Reposted by Christoph Bock Lab @ CeMM & MedUni Vienna🧬How do #macrophages respond so quickly to pathogens? A new study by CeMM & @meduniwien.ac.at researchers, led by @bocklab.bsky.social & @mfarlik.bsky.social, reveals key regulators of immune responses using gene editing & machine learning. ➡️ More info: bit.ly/40p5ABe 🔗 Study: bit.ly/4lwEAIm
