A thread by Michael Love on best practices for QC before DGE analyses -- prompted by a recent paper claiming that edgeR, DESeq2 etc have spurious false positives (but only if you omit QC as he shows)

Just started using Nils Trost's R package for plotting 3D scatter points (and more). It's very convenient, powerful and useful.

The current system of journals and peer review is not serving science. I have therefore resigned from all editorial roles and will no longer do pre-publication peer review. I explain why in this article and in the thread below. Please consider joining me. neural-reckoning.org/reviewing.html

cellpypes - cell type pipes for R. Annotate scRNAseq data manually with simple rules:

Proud to present this work by Lukas PM Kremer, Santiago Cerrizuela et al. from Martin-Villalba Lab and our group:

Lukas PM Kremer presenting our latest study on epigenetic features of adult neural stem cells at #TCESRC22 on Sicily 🌅, organized by Brunet Lab and @giacomo_cavalli.

Life science postdoc positions in Heidelberg: health-life-sciences.de/postdocs

PhD and postdoc postions for computational biologists, in the labs of Simon Anders (me) and Martin-Villalba Lab (A. Martin-Villalba): Single-cell omics methods in neurobiology. dkfz.de/en/neurobiolog…

Thanks chromatin community! We’ve been digging around in your repetitive DNA (>40,000 ChIP-seq samples) and have discovered a totally unexpected role for BRD4 and JQ1 at centromeres. Very happy to share our preprint. biorxiv.org/content/10.110…

“Is Science Self-Correcting? Evidence from 5 Recent Papers on the Effect of Replications on Citations.” replicationnetwork.com/2023/04/05/ree…

Physicist Suvrat Raju shared this letter he sent to an editor of Nature Communications, declining to referee for them.

We're so excited to share our latest work “Identification of astrocyte-driven pseudolineages reveals clinical stratification and therapeutic targets in #Glioblastoma” spearheaded by Oğuzhan Kaya on the wet & @LCForst on the dry lab as a preprint @Biorxiv biorxiv.org/content/10.110…

.Lukas PM Kremer, Martin-Villalba Lab, Simon Anders and colleagues introduce a data processing approach along with an easy-to-use software tool MethSCAn for scBS-seq data analysis. nature.com/articles/s4159…

And read the Research Briefing here: nature.com/articles/s4159…

🎉 Excited to share our latest study in @nature, showing that DNA🧬 #methylation is key to stemness in the adult #brain: nature.com/articles/s4158… A collaboration with Simon Anders, driven by Lukas PM Kremer and Santiago Cerrizuela. #epigenetics #neuroscience #singlecell. Pre-print summary 🧵👇

There's a lot of excitement about foundation models and their ability to learn biology 🧬💻 But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress. biorxiv.org/content/10.110…

This is the result of my brief postdoc with Simon Anders in the last 6 months and grew out of an intriguing reviewer comment for the LEMUR paper with @wolfgangkhuber.

Great thread by Anshul, one of the pioneers of deep learning for biology, summarizing our preprint!

New preprint from our group: