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Out now – our preprint "A live attenuated vaccine confers superior mucosal and systemic immunity to SARS-CoV-2 variants", comparing live attenuated/mRNA/Adeno vaccines using histopathology, serology, scRNA-seq in hamsters. biorxiv.org/content/10.110… – summary in the thread … (1/8)

Was a lot of fun to write this! Shocking to see so much variation in signal-to-noise ratios across datasets tbh...

Everything #CRISPR & #singlecell for #machinelearning all in one place - scperturb.org Favourite takeaway figures attached: compare data size & quality before benchmarking - PLUS - how everything ties together! CC Nils Blüthgen CompCancer Chris Sander aka cscbio Debora Marks

Open reviews are such a great thing, honored to have received one. Made our work a lot easier, greatly appreciate it.

* ~200 German institutions negotiate with Elsevier * Negotiation fails, Elsevier restricts journal access * Affected researchers started publishing in Elsevier journals less * & citing Elsevier papers a little less direct.mit.edu/qss/article/do…

(1/6) Very excited to share our work on Nature Medicine using #AI to predict #cancer with disease history only (no CT scan!). Glad to co-lead the work with Davide Placido Jessica Hjaltelin Chunlei Zheng Chris Sander aka cscbio Brunak Lab and many more great colleagues nature.com/articles/s4159… .

Cell-cell communication analyses are the most overinterpreted analyses in single-cell genomics

Cluster analysis is the first thing most PhD students do when working with scRNAseq data because it's simple and part of scanpy/seurat's tutorials. But often enough data does not actually allow clustering because it is too homogeneous (e.g. cell lines)!

The US is notorious for it's mass shootings, but its immigration policies (or lack thereof) set a new standard for the art of shooting yourself in the foot with a bazooka. Advice to graduate students from countries the US doesn't like: just go to Europe.

For our 3rd competition for #NeurIPS2023, we’re asking: can you predict a new algorithm for how cells respond to a drug treatment?​ Learning how #singlecells respond to perturbations will help support more efficient drug design. See more on Kaggle: kaggle.com/competitions/o…

Very unique data with mutliple doses and time points after infection. We had lots of opportunity for data analysis. And go check out the amazing diffusion map we got for the endothelials!

✨#ImmuneDictionary✨is out today in nature! Paper nature.com/articles/s4158… Software immune-dictionary.org We created scRNA-seq dictionary of 17+ immune cell types responding to 86 cytokines in vivo, discovered the immune system is far more complex than previously known 1/

Congratulations to CompCancer graduate @Speidli for the publication in Cell Reports, covered by German newspaper Tagesspiegel: Warum Covid-19 mal schwer und mal mild verläuft: Immunzellen, die sich nicht deaktivieren lassen tagesspiegel.de/gesundheit/war…

Out now: "Single-cell-resolved interspecies comparison shows a shared inflammatory axis and a dominant neutrophil-endothelial program in severe COVID-19" cell.com/cell-reports/f… (Graphics: Polygraph Design) (1/7)

Check out datavzrd, super useful tool for making tables pretty for showing on the web. I used it to make a simple metadata table for a database, see here: projects.sanderlab.org/scperturb/data…

I'm stoked to announce our new end-to-end framework for perturbation analysis! Our scverse advisory committee highlighted that a maintained and well-documented framework for perturbation analysis is missing. Pertpy is our attempt to satisfy this request biorxiv.org/content/10.110…

🧵 Excited to share our latest work: scPCA — a flexible factorization model for single-cell data that integrates both cellular heterogeneity and experimental condition effects! 🚀 Let's dive in! (1/9)