iiinova — where your digital self keeps evolving

Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 21/09/2026

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...

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🧬 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

📚 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🪄 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🚀 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🆕 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🔬 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🔍 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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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

⚙️ 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

🗨️ 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

📚 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 11/11/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

⚕️ 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🔥 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🔬 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

💪 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🔍 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🐁 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🐭 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🩸 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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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

⚙️ 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 24/09/2025

🧬 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🤝 Great teamwork by: Peter Traxler*, Stephan Reichl*, Lukas Folkman, Lisa Shaw, Victoria Fife, Amelie Nemc, Djurdja Pasajlic, Anna Kusienicka, Daniele Barreca, Nikolaus Fortelny, André Rendeiro, Florian Halbritter, Wolfgang Weninger, Thomas Decker, Matthias Farlik, Christoph Bock (8/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🗺️ In summary, this study provides a blueprint of epigenetic & transcriptional dynamics and regulator functions underlying macrophage immune responses. We found it particularly useful to combine and integrate multi-omics time-series with high-content CRISPR screening. (7/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

💡 Biological detail: EP300-mediated repression of interferon-stimulated genes (ISGs), validated genetically & pharmacologically. Proposed mechanism: The histone acetyltransferase EP300 counteracts HDAC activity required for BRD4 availability for transcription elongation. (6/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🤖 We used machine learning to infer functional similarity maps of transcriptional regulators from the CROP-seq data, establishing a broadly applicable method to dissect transcriptional programs. (5/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

✂️ To disentangle causes and consequences, we performed high-content CRISPR screening (CROP-seq + CITE-seq) to perturb 135 regulators during Listeria infection. Our hits include: PU.1, JAK-STAT proteins, splicing factors (SFPQ, SF3B1) & epigenetic regulators (EP300, SMC1A). (4/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🧬 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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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🦠 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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 12/08/2025

🛡️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)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/07/2025

🔍 While vision language models (VLMs) for digital pathology converse about H&E images as a whole, SpotWhisperer provides fine-grained, spot-level resolution. Consequently, SpotWhisperer outperformed SOTA VLMs (PLIP, CONCH) in the prediction of tumor regions and cell types. (3/6)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/07/2025

⚙️ Our SpotWhisperer method predicts spatial transcriptomes from standard H&E images with DeepSpot, and it uses CellWhisperer transcriptome-text embeddings for natural-language conversations about the cells and their transcriptomes. (2/6)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/07/2025

🔬 Toward histopathology 2.0: spatial transcriptomes inferred from routine diagnostic H&E images + a chat interface for cell-resolution histopathology through English language. (1/6)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/07/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/07/2025

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 02/06/2025

What excites you? What could be a great postdoc project? We are open for your ideas! Detailed job advert: medical-epigenomics.org/files/Job_Po... Application website: cemm.at/join-cemm/op...

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 02/06/2025

POSTDOC OPPPORTUNITY: We are recruiting via the CeMM postdoc program. Looking for 3 types of candidates: 1. Bioinformatics & systems biology (e.g., immunology, neurobiology or cancer) 2. ML/AI methods for biology & precision medicine 3. Technology development & bioengineering Details below (1/3)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 06/05/2025

AI in medicine ready for takeoff 🤖🚁 We flew a drone through the Institute of Artificial Intelligence @MedUniWien. Join us for the trip and watch our team at "work". #AI #biomedicine #innovation #makingof (1/2)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 25/03/2025

CeMM's new Research Report is online - a piece of art as always (link below). Each research group selected a mathematical formula that symbolizes their research and visualized it in a live-staged group picture. We picked Shannon entropy, as biomedicine is all about information (and sometimes messy)

Christoph Bock Lab - Group Picture - CeMM Research Report 2024

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 13/02/2025

Job Posting: Senior NGS Technology & Deputy Head of the Biomedical Sequencing Facility (CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences & Medical University of Vienna)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/12/2024

Examples of our recent research: 1. Immunology: Immune regulation by non-immune cells (nature.com/articles/s41...) 2. Cancer: Epigenetic tumor heterogeneity (nature.com/articles/s41...) (2/4)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/12/2024

HIRING: We offer several PhD student positions in the CeMM PhD Program. Looking for 3 types of candidates: experimental systems biology in cancer & immunity; bioinformatics & biomedical ML/AI; tech-dev & bioengineering. Join an a highly collaborative lab in molecular medicine. Details below (1/4)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 02/12/2024

We are recruiting a Tenure-track Assistant Professor "Machine Learning in the Life Sciences" at the Medical University of Vienna. We will nominate the top candidate for a € 1.8 million starting grant by a Viennese foundation. Deadline: Dec 31st. Details: medical-epigenomics.org/files/Tenure...

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/10/2024

🚀 Outlook: CellWhisperer shows how natural language makes data exploration more fluid & creative. Let's build the future of biomedical data analysis with “AI assistants you can talk to”! How about: Interactions by voice, virtual reality integration, agent-based automation? (9/9)

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Christoph Bock Lab @ CeMM & MedUni Vienna @bocklab.bsky.social · 18/10/2024

📝 Internally, CellWhisperer uses Geneformer for transcriptomes and BioBERT for text, and it integrates their embeddings into a shared space using the CLIP approach. And we finetuned Mistral 7B to chat based on the embeddings, combined with the model’s biological knowledge (6/9)

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