German single-cell nerd
Heidelberg
Joined October 2019
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Check out scPerturb, out now in Nature Methods!
Among other things: new datasets in our database, and a lot more information per dataset (e.g. mean No. of counts, cells per perturbation) in the interactive data table. You can find it on our website, link in thread!
Stefan Peidli retweeted
My lab at MSKCC in New York is hiring for two positions. Join us at the frontier of functional genomics, studying fibroblast state transitions, combinatorial genetics, and ECM in disease. Please share with anyone who might be a good fit! (Mustache not required.)
Stefan Peidli retweeted
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/10.1101/…
Are you developing or benchmarking methods for single-cell perturbation data?
I've written a very simple example pipeline in snakemake that auto downloads all (/selected) datasets from scperturb and applies your custom script to each of them in parallel: github.com/stefanpeidli/scpe…
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/scper…
#datavzrd, our tool for rendering modern interactive, visual, server-free, tabular scientific HTML reports with zero/low-code (datavzrd.github.io), now has a tutorial (1-2h): datavzrd.github.io/docs/tuto….
Stefan Peidli retweeted
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/fullte…
(Graphics: Polygraph Design)
(1/7)
Stefan Peidli retweeted
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/w…
Stefan Peidli retweeted
✨#ImmuneDictionary✨is out today in @Nature!
Paper nature.com/articles/s41586-0…
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/
ALT The Immune Dictionary is a large-scale compendium of single-cell transcriptomic profiles of more than 17 immune cell types in response to each of 86 cytokines in vivo, a reference for understanding the complex immune system. The image lists the 86 cytokines, representing almost all major cytokines in the immune system, studied in the dictionary. For more information, see our Nature (2023) publication "Dictionary of immune responses to cytokines at single-cell resolution": https://www.nature.com/articles/s41586-023-06816-9
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!
What drives severe COVID-19? In our new preprint, we explore this question using and interspecies comparison of lung single-cell RNA-seq data – summary in the thread below, lead by @SPeidli and Samantha Praktiknjo! … (1/7)
Stefan Peidli retweeted
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/open…
Stefan Peidli retweeted
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.
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)!
Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s41592-0…
Stefan Peidli retweeted
Cell-cell communication analyses are the most overinterpreted analyses in single-cell genomics
Stefan Peidli retweeted
(1/6) Very excited to share our work on @NatureMedicine using #AI to predict #cancer with disease history only (no CT scan!). Glad to co-lead the work with @davplacido @jessicaxhu Chunlei Zheng @sandercbio @TheBrunakLab and many more great colleagues nature.com/articles/s41591-0… .
Stefan Peidli retweeted
* ~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/d…
Open reviews are such a great thing, honored to have received one. Made our work a lot easier, greatly appreciate it.
Big news from scPerturb: our preprint received an open review by @ArcadiaScience. Me, @stefanpeidli, and team incorporated their feedback into a new version of scPerturb, now on bioRxiv. The biggest change: in-depth benchmarking of E-statistics. doi.org/10.1101/2022.08.20.5… 1/7
Stefan Peidli retweeted
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 @molsysbio @CompCancerRTG @sandercbio @deboramarks
Introducing scPerturb, a collection of 44 single cell perturbation datasets with unified annotations available at scperturb.org (1/5)
Was a lot of fun to write this! Shocking to see so much variation in signal-to-noise ratios across datasets tbh...
Introducing scPerturb, a collection of 44 single cell perturbation datasets with unified annotations available at scperturb.org (1/5)