📣 The much-revised manuscript of LIANA+, our all-in-one solution to study cell-cell communication from single-cell, spatial, and multi-omics technologies, is now published in Nature Cell Biology nature.com/articles/s4155…

Check out NiCo for integrative analysis of single-cell resolution spatial transcriptomics and scRNA-seq reference data. NiCo detects cell state covariation between niche neighbours, infers underlying gene programs and signalling mediators. biorxiv.org/content/10.110…

NetID for scalable identification of lineage-specific gene regulatory networks from metacells is now online! We demonstrate superior performance for GRN inference at lineage resolution in large single-cell RNA-seq datasets. biorxiv.org/content/10.110…

NetID for scalable inference of lineage-specific gene regulatory networks from large scRNA-seq datasets now published. Amazing work by @KenWang89437252 from an internship (!) in my lab. genomebiology.biomedcentral.com/articles/10.11…

Best and shortest chapter ever

I normally don’t tweet politics… but I could not resist…

Hiring! I'm looking for a postdoc in machine learning of spatial single-cell data. Exciting project to develop methods for modelling cellular circuits in disease and regeneration of heart, liver and bone marrow using Xenium data from our lab. tinyurl.com/ymkvk7vn

The success of AI applied to drug discovery is being decided by a number of clinical trials. So far, the results are lackluster. Why? For AI to have a transformational effect in drug discovery, training data must come from living mammals. (🧵1/9)

.ankit agrawal Dominic Grün introduce #NiCo to predict the downstream effect of cell-cell interactions on cellular states in tissue niches from spatial transcriptomics data #BiotechNatureComms nature.com/articles/s4146…

NiCo is out! Our new algorithm for spatial transcriptome data analysis predicts the crosstalk of cell types co-localized in tissue niches and sheds light on the downstream effects of cell-cell interactions by inferring covarying gene programs. nature.com/articles/s4146…

A few days left to apply if you would like to work on spatial multi-omics modeling in an interdisciplinary team!

Our new lab coffee machine. What a beauty…

Check out this nice "Tools of the Trade" piece in Nature Reviews Genetics by Ankit Agrawal on our NiCo algorithm for the analysis of single-cell spatial transcriptomics data from platforms like Xenium, MERSCOPE, seqFISH etc. Feel free to reach out for advice. nature.com/articles/s4157…

Seeing is believing! Few spots left for Imaging the Immune System—the 6th edition of this world-class meeting. Don’t miss the amazing speakers, wine, and science 🍷🧬 📅 June 11–13 📍 Historic Juliuspital Winery, Würzburg, Germany 👉 imaging-immune-system.wuesi.com

We have an attractive opening for a tenure-track professorship in Single-Cell Systems Biology. Excellent package and infrastructure at the Institute of Systems Immunology WüSI - Systems Immunology Würzburg. Great place to live and work in the heart of the franconian wine region! jobs.sciencecareers.org/job/673667/jun…

New preprint from the lab! Using multiplexed spatial analysis and single-cell multiomics, we resolved the portal liver immune niche and identified crosstalk between cholangiocytes, dendritic cells and gdT cells controlling fibrosis in a cholangitis model. biorxiv.org/content/10.110…

Join our "Advances in Single-Cell Technologies" meeting in December in Freiburg, co-organised with Marco Prinz and Katrin Kierdorf. Excellent line-up of speakers covering spatial technologies, lineage tracing, computational methods, and more. uniklinik-freiburg.de/single-cell-te…

Registration for our "Advances in Single-Cell Technologies" meeting is still open and we invite abstract submissions until October 30th. Join us in beautiful Freiburg together with an excellent line-up of single-cell technology experts! uniklinik-freiburg.de/single-cell-te…