Christoph Dotter

Reply to: Reply to: False positives in the study of memory-related gene expression In the Nature paper “Spatial transcriptomics reveal neuron–astrocyte synergy in long-term memory” published on March 14th, 2024, authors Sun et al. claimed to identify cell-type specifi…

I wrote a review of a recent paper on false discovery and multiple testing correction. liorpachter.wordpress.com/2025/06/16/r...

Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...

Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...

ggalign: Bridging the Grammar of Graphics and Biological Multilayered Complexity 🧬🖥️🧪
Paper: https://www.biorxiv.org/content/10.1101/2025.02.06.636847v1
#Rstats Code: https://github.com/Yunuuuu/ggalign
Docs: https://yunuuuu.github.io/ggalign/
Book (Quarto): https://yunuuuu.github.io/ggalign-book/

My deep learning course at the University of Geneva is available on-line. 1000+ slides, ~20h of screen-casts. Full of examples in PyTorch.

fleuret.org/dlc/

And my "Little Book of Deep Learning" is available as a phone-formatted pdf (nearing 700k downloads!)

fleuret.org/lbdl/

I love the idea of having a phone-formatted pdf! Downloaded it and started reading immediately.

Let's build a starter pack for childhood cancer research.
Please send a message to be added! 🎗️
go.bsky.app/Tpd9QnM

Thanks for including me!