Malva out in Nature! 🚀 RNA sequences make cells different from each other. Single-cell data captures much of this, but most stays in the dark because we reduce it to gene counts. We introduce Malva to make the world's single-cell data searchable. What took days is now one query in seconds.

I'm very excited to announce that my PhD work is out on biorxiv! pyTrance is a computational method to predict and quantify subcellular RNA co-localization from spatial transcriptomics data. www.biorxiv.org/content/10.6...

🚀 We're looking for people to join Malva! 🧬 @danilexn.bsky.social Malva is the first search engine for single-cell genomics: we process massive amounts of sequencing data to enable ultrafast analysis of millions of cells. (1/4)

We’re happy to share our new preprint form @N_Rajewsky, with @tmpentimalli.bsky.social i.bsky.social @Ilan Theurillat lab! 🎉 🧬 Spatiotemporal atlas of tumor–stroma crosstalk in a new TNBC model. Spatial transcriptomics (Open-ST), snRNA-seq, and functional validation. 🔗 biorxiv.org/content/10.1...

Spatiotemporal dynamics of tumor microenvironment remodeling

During tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ...

biorxiv.org

Our 3D study of the tumor microenvironment is finally out! Play around with the data yourself at lung-3d-browser.mdc-berlin.de (Kudos to @danilexn.bsky.social👏 ) Many thanks to Nikolaus Rajewsky lab at @mdc-bimsb.bsky.social and everyone involved, it takes a village to raise a multimodal paper!

🧬 Want to implement Open-ST in your lab? We've published a detailed guide that takes you from tissue sections to 3D molecular maps star-protocols.cell.com/protocols/3922

#SpatialTranscriptomics is revolutionizing gene expression profiling at subcellular resolution! 🔬These 'molecular microscopes' can unlock disease mechanisms & guide therapies... But how to bring ST to the clinic? Our thoughts with T. Pentimalli and N. Rajewsky out @annualreviews.bsky.social 🧵👇