Franz Baumdicker

Join us as a #PostDoc @uni_tue for 2 years! Work on large-scale genealogical data, develop #machinelearning methods, make an impact by decoding local ancestries (ARGs), and improve #popgen and medical studies in collab. with @Boehringer. More info here: uni-tuebingen.de/en/university/…

If you are interested in microbial #pangenomes, join us @eseb2025 in Barcelona with Jesse Shapiro and Anna Dewar. Only two days left to submit an abstract! eseb2025.com/call-for-abstr…

@3rdreviewer @smishra677 Cool! This relates to our site frequency spectrum based neural network to estimate mutation rates. We always assumed that our network implicitly learned the underlying recombination rate based on the smoothness of the SFS but did not check it in detail dx.plos.org/10.1371/journa…

New paper with @smishra677 ! Maybe it will bring you some joy given all this (waves arms around). "Estimating recombination using only the allele frequency spectrum" 1/2 biorxiv.org/content/10.110…

please spread the word about this theoretical population biology workshop in chicago in june! should be really fun nitmb.org/modeling-and-t…

Is it “winner-takes all” when the simplest living things compete? Check out my fresh publication on phage coexistence in Science and a thread below🧵 science.org/doi/10.1126/sc…

The life of cells, recorded nature.com/articles/s4157…. We dive into the opportunities of DNA recording for understanding single cell dynamics. Fantastic collaboration with the @JShendure, @ElowitzLab, Gagnon, and Schier labs.

AstraZeneca's Centre for Genomics Research is hiring! Check it out if you are interested in leading an exceptional team of scientists who apply innovative machine learning approaches to large scale genomic and multi-omic data for drug discovery. lnkd.in/d54cpyvf

It is crucial to use reconstructed arrays to see these deletion patterns, as the position of spacers shifts toward the trailer end over time. I will post more details about our reconstruction tool SpacerPlacer later. But you can find the tool here: buff.ly/40QdDId

Finally, across multiple CRISPR-Cas types and genera, we found no significant difference in deletion rates or lengths, suggesting that spacer deletions are likely not modulated by Cas proteins.

CRISPR arrays store "immune memories" of past invaders as spacers. But these memories aren’t permanent— frequent spacer deletions reshape the array. We investigated the spacer deletion dynamics with our new reconstruction tool and learned a lot... 🧵 buff.ly/4fS4Iu3

Geometriphylogenetics xkcd.com/3010

@adamauton This might be an option for some x.com/fbaumdicker/st…

Yesterday was a hard day at 23andMe, and we said goodbye to a number of tremendously talented colleagues. If people have job openings in the genetics space that they'd like me to share with the impacted folks, please do post here.

🎉 tskit 0.6.0 is released! 🎉 Thanks to our wonderful contributors, this is a bumper release. Read all about it at: tskit.dev/news/20241106-…