Franz Baumdicker

Mathematical and Computational Population Genetics
Microbial Evolution | Machine Learning in PopGen | CRISPR-Cas | Pan-genomes | HGT
🦠 ➔ 🧬 ➔ 💻 ➔ 🤔

[Franz Baumdicker @fbaumdicker]

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: https://t.co/aPWRf6cA6t

[Franz Baumdicker @fbaumdicker]

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!
https://t.co/8csIeisXMo

[Franz Baumdicker @fbaumdicker]

@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 https://t.co/ITbuzQ5OeI

[Daniel Weissman @dbweissman]

please spread the word about this theoretical population biology workshop in chicago in june! should be really fun https://t.co/wgrvA3IFay

[Nora Pyenson @norapyenson]

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🧵 https://t.co/3qQNKT0LVd

[Tanja Stadler @TanjaStadler_CH]

The life of cells, recorded https://t.co/sPv0y0BpIW. We dive into the opportunities of DNA recording for understanding single cell dynamics. Fantastic collaboration with the @JShendure, @ElowitzLab, Gagnon, and Schier labs.

[Keren Carss @kerencarss]

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.
https://t.co/sJoM9GVaOk

[Franz Baumdicker @fbaumdicker]

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: https://t.co/xKaiZPbC2T

[Franz Baumdicker @fbaumdicker]

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... 🧵
https://t.co/0pHz1MR412

[Franz Baumdicker @fbaumdicker]

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.

[Randall Munroe @xkcd]

Geometriphylogenetics https://t.co/9h9Z65RmSK

[Franz Baumdicker @fbaumdicker]

@adamauton This might be an option for some
https://t.co/OsS2QmirEa

[Franz Baumdicker @fbaumdicker]

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: https://t.co/aPWRf6cA6t

[tskit-dev @tskit_dev]

🎉 tskit 0.6.0 is released! 🎉
Thanks to our wonderful contributors, this is a bumper release. Read all about it at:
https://t.co/NaTr9gHSMV