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

Debugging @Nature: Nature’s Reporting Summary PDF has a technical problem: You can’t disable the “Plants” section. Lots of papers have this empty section – not only in Nature, but also in other NPG journals. Turns out this is a bug in the journal's PDF template that can be fixed.

HIRING: We recruit PhD students via the AITHYRA-CeMM 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 etc) (1/5)

🧬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)

📚 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)

🚀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/s41587-025-0…) includes several new analyses beyond our 2024 bioRxiv preprint (biorxiv.org/content/10.1101/…). 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/tabula…) 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)