Constantin Ahlmann-Eltze (@const-ae.bsky.social)
@const_ae
Postdoc at UCL with @JL_Reading. Previously at EMBL working with @wolfgangkhuber. Biostats, R, cancer immunology Find me on 🦋 at http://const-ae.bsky.social
New single-cell analysis framework, LEMUR, disentangles covariates and latent cell states from multi-condition data to predict counterfactual gene expression and identify cell neighborhoods with similar DEGs without clustering. doi.org/10.1038/s41588… @NatureGenet @wolfgangkhuber
For the Monday morning crowds :) Also, take a look at my blog post, in which I compress the full lemur package into 100 lines of code and explain the core algorithm. const-ae.name/post/2025-01-0…
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳 nature.com/articles/s4158… LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space. Some highlights⬇️
Extremely proud to see my PhD project exploring intra-tumor heterogeneity in complex karyotype AML finally out in @NatureGenet ! 🎉👩🏻🔬 They say that 10,000 hours make you an expert, so I guess after more than five years of work I’m half-way there 😅 ⬇️1/5 nature.com/articles/s4158…
The #rstats community on bluesky seems to be really picking up steam, so you can also find me over there: bsky.app/profile/hadley…
🚀Interested in doing a PostDoc in my lab? Consider applying for a🇨🇭SNSF Swiss Postdoctoral Fellowship 2024. If you have any questions, join the information event tomorrow via Zoom (register via shorturl.at/zP93m) or reach out to us via bunnelab.com! 🧬Who…
📢 #Call for SNSF Swiss Postdoctoral Fellowships 2024 This highly competitive call is aimed at researchers who wish to obtain a position in a non-profit research institution in Switzerland for a period of 12 to 24 months. 🗓️Deadline: 2 December 2024 sohub.io/6afa
Great thread by Anshul, one of the pioneers of deep learning for biology, summarizing our preprint!
biorxiv.org/content/10.110… Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction. Long-story short: they can't beat the linear baselines. 1/
Very excited to announce that I started a postdoc in @JL_Reading's lab at UCL working on tumor immunology 🥳 So, if you are in London and want to meet for a coffee, hit me up :)
Great talk from @const_ae this morning beautifully giving the intuition behind LEMUR, a computational tool for the analysis of multi-condition single-cell data! #AsconaSpatial2024 GitHub: github.com/const-ae/lemur
I wrote a new ggplot2 extension to draw Bezier curves github.com/const-ae/ggbez…🎉 The curves are defined by a set of control points and the tangents at those points. This makes each parameter directly interpretable and the curves easy to tweak! #rstats #ggplot2
