Reposted by Leon StrengerDani León-Periñán @danilexn.bsky.social · 26/08/2026Malva 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. 1207
Leon Strenger @lstrngr.bsky.social · 19/05/2026Check out the python package and documentation: github.com/rajewsky-lab... rajewsky-lab.github.io/pytrance/github.comGitHub - rajewsky-lab/pytranceContribute to rajewsky-lab/pytrance development by creating an account on GitHub. 021
Leon Strenger @lstrngr.bsky.social · 19/05/2026Big thanks to @cledicj.bsky.social , @nukappa.bsky.social , Nikolaus Rajewsky and the whole Rajewsky lab for the support throughout the project! 130
Leon Strenger @lstrngr.bsky.social · 19/05/2026Going one step further, we performed RNA-protein co-staining for Gad1, which showed a strong signal overlap, suggesting it is translated locally. 110
Leon Strenger @lstrngr.bsky.social · 19/05/2026Whats most exciting: In a Xenium mouse brain dataset we predicted four GABAergic markers (Gad1, Gad2, Hapln1, Kcnmb2) to co-localize in neuronal projections. Experimental validation confirmed our predictions. (Col19a1 is used as negative control bellow) 131
Leon Strenger @lstrngr.bsky.social · 19/05/2026We validated and benchmarked pyTrance on simulated data, where it reliably clustered RNAs by their simulated subcellular localization patterns and identified further subclusters with different localization strength. 110
Leon Strenger @lstrngr.bsky.social · 19/05/2026Using a GNN trained on transcript neighborhood graphs, pyTrance computes embeddings that encode spatial RNA localization. RNAs with similar embeddings are likely to co-localize. 110
Leon Strenger @lstrngr.bsky.social · 19/05/2026I'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...biorxiv.org 1115
Reposted by Leon StrengerIvano Legnini @ilegnini.bsky.social · 24/11/2025PhD position in my lab in #AI #RNA, in co-supervision with superstar @florianjug.bsky.social www.polimi.it/dottorato/fu...polimi.itBandi Dottorato Polimi 2025–2026 | Scadenze e Regolamenti - polimiConsulta i bandi di dottorato di ricerca del Politecnico di Milano: scadenze aggiornate, regolamenti, borse INPS e opportunità PNRR. 1128
Reposted by Leon StrengerIvano Legnini @ilegnini.bsky.social · 24/11/2025And in addition to the postdoc position (1 week left to apply!), just opened a PhD position in AI and RNA biology 🤩 032
Reposted by Leon StrengerIvano Legnini @ilegnini.bsky.social · 06/11/20251/6 We are hiring!!! 🐣🐣🐣 Fully funded postdoc position in my group! humantechnopole.it/en/research-...humantechnopole.itLegnini Group - Human TechnopoleLaboratory for Molecular and Systems Biology of RNA The Legnini Group at Human Technopole combines molecular and systems biology approaches to study gene regulation. We use synthetic biology and opt... 1107
Reposted by Leon StrengerKamil Lisek @klisek.bsky.social · 22/07/2025We’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...biorxiv.orgSpatiotemporal dynamics of tumor microenvironment remodelingDuring tumorigenesis, interactions between tumor and stromal cells progressively remodel the tumor microenvironment (TME) towards pro-tumoral functions. Understanding early TME remodeling dynamics is ... 1137