Christoph Bock Lab @ CeMM & MedUni Vienna
@bocklab.bsky.social
Technology-driven biomedical research at CeMM Research Center for Molecular Medicine & MedUni Vienna #cancer #immunology #bioinformatics #AI #singlecell #CRISPR
Nice example of "garbage-in, garbage out" behavior of CellWhisperer. We could probably add checks to mark meaningless queries. But for now we rely on cooperative users, and CellWhisperer has a clear warning: "Please keep in mind that CellWhisperer is an AI system and may produce misleading results."
November 16, 2025 at 12:55 PM
Nice example of "garbage-in, garbage out" behavior of CellWhisperer. We could probably add checks to mark meaningless queries. But for now we rely on cooperative users, and CellWhisperer has a clear warning: "Please keep in mind that CellWhisperer is an AI system and may produce misleading results."
🤝 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)
November 11, 2025 at 12:52 PM
🤝 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)
🧬 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)
November 11, 2025 at 12:52 PM
🧬 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)
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)
📖 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)
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
doi.org
November 11, 2025 at 12:52 PM
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)
📖 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 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)
November 11, 2025 at 12:52 PM
📚 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)
🪄 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)
November 11, 2025 at 12:52 PM
🪄 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)
🚀 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)
November 11, 2025 at 12:52 PM
🚀 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)
🆕 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)
November 11, 2025 at 12:52 PM
🆕 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)
🔬 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)
November 11, 2025 at 12:52 PM
🔬 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)
🔍 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)
November 11, 2025 at 12:52 PM
🔍 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)
⚙️ 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)
November 11, 2025 at 12:52 PM
⚙️ 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)
Ready to talk to cells?
📖 Read the paper: www.nature.com/articles/s41...
🧬 Try the web app with public datasets: cellwhisperer.bocklab.org
🖥️ Analyze your own datasets: github.com/epigen/cellw...
(9/11)
📖 Read the paper: www.nature.com/articles/s41...
🧬 Try the web app with public datasets: cellwhisperer.bocklab.org
🖥️ Analyze your own datasets: github.com/epigen/cellw...
(9/11)
Multimodal learning enables chat-based exploration of single-cell data - Nature Biotechnology
CellWhisperer uses multimodal learning of transcriptomes and text to answer questions about single-cell RNA-sequencing data.
www.nature.com
November 11, 2025 at 12:41 PM
Ready to talk to cells?
📖 Read the paper: www.nature.com/articles/s41...
🧬 Try the web app with public datasets: cellwhisperer.bocklab.org
🖥️ Analyze your own datasets: github.com/epigen/cellw...
(9/11)
📖 Read the paper: www.nature.com/articles/s41...
🧬 Try the web app with public datasets: cellwhisperer.bocklab.org
🖥️ Analyze your own datasets: github.com/epigen/cellw...
(9/11)
📚 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)
November 11, 2025 at 12:41 PM
📚 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)
🪄 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)
November 11, 2025 at 12:41 PM
🪄 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)
🚀 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)
November 11, 2025 at 12:41 PM
🚀 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)
🆕 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)
November 11, 2025 at 12:41 PM
🆕 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)
🔬 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)
November 11, 2025 at 12:41 PM
🔬 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)
🔍 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)
November 11, 2025 at 12:41 PM
🔍 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)
⚙️ 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)
November 11, 2025 at 12:41 PM
⚙️ 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)
📑 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)
Systematic discovery of CRISPR-boosted CAR T cell immunotherapies - Nature
CELLFIE, a CRISPR platform for optimizing cell-based immunotherapies, identifies gene knockouts that enhance CAR T cell efficacy using in vitro and in vivo screens.
www.nature.com
September 24, 2025 at 6:42 PM
📑 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)
🤝 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)
September 24, 2025 at 6:42 PM
🤝 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)