Franz Baumdicker

Work from my amazing undergrad @leyan-wang.bsky.social is just preprinted! TL;DR: If you worry that ARG methods might fail on unphased data due to phasing errors, you may not need to.

Check it out & consider reposting to support a great young scientist!

Thanks! You should also contact @fabbenz.bsky.social when you are in Europe. Considering silencing VS cleaving was her idea.

This is awesome!
Welcome to Europe, Fernando.

Cool work!
But the best strategy to win a contest between plasmids can also be to silence the opponent instead of direct elimination.
At least that's what we found in a recent theoretical study.
academic.oup.com/genetics/art...
One might argue though that silencing is just subtile elimination.

After years of working on SBI methods and the sbi toolbox, we finally wrote the practical guide we wished had existed when we started.

Grateful to have collaborated with researchers across many institutions to consolidate what we've learned about making these methods work in practice!

Introgression impacts the evolution of bacteria, but species borders are rarely fuzzy Nature Communications - It is commonly thought that bacterial species borders tend to be fuzzy, due to frequent exchange of DNA. Here, Diop et al. quantify the patterns of gene flow between core...

Our latest paper is out with @adiop.bsky.social and @gmdouglas.bsky.social. We analyzed the extent of homologous recombination between bacterial species (introgression) and how it affects species borders (it can vary a lot depending on the approach used to classify species!). rdcu.be/eQAMf

SPRTA: a smarter way to measure evolution uncertainty A new method from EMBL-EBI and collaborators offers fast, easy-to-interpret confidence scores for phylogenetic trees for pandemic preparedness.

During the COVID-19 pandemic, the millions of viral genomes coming in overwhelmed traditional methods for data analysis.

Find out how SPRTA, a new tool, provides a fast, scalable way to measure confidence of phylogenetic trees, helping scientists track outbreaks.

www.ebi.ac.uk/about/news/t...

Many are painfully aware that the environment within which we function -- as scientists -- needs fixing. We've come up with a proposal for academic renewal. It's not perfect, but its a start. Input, comments, suggestions are welcome. Making a difference matters 👇

doi.org/10.5281/zeno...

The Johri Lab has an open postdoc position. Please send me an email, if interested. Start date is flexible. Please do share! Thank you in advance.

1/2 Want to become up to date with pangenomes and genome graphs and their history? Check out this fantastic review by @zbao.bsky.social!

Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...

The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...

We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them

Only a few hours left to submit your abstract for a talk at the Machine Learning in Evolutionary Genomics conference in December in Aussois in the French alps!

tskit_arg_visualizer: interactive plotting of ancestral recombination graphs Summary: Ancestral recombination graphs (ARGs) are a complete representation of the genetic relationships between recombining lineages and are of central importance in population genetics. Recent brea...

Excited to share our new preprint for the tskit_arg_visualizer Python package! ARGs can sometimes feel like a black box, so
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.

🔗 arxiv.org/abs/2508.03958

1/6

Bioinformatician - Uppsala University Bioinformatician, Department of Organismal Biology, Uppsala University

The @scilifelab.se ancient DNA unit is looking for an bioinformatician placed at Uppsala University. This is a great way to be part of diverse #aDNA research projects as a staff scientist with permanent (!!) employment:

www.uu.se/en/about-uu/...

1/6 Excited to share our review 🚀
🧬 CRISPR–Cas therapies targeting bacteria!
#MicroSky

The PopSim Consortium wants you! Please join us on zoom on May 27 at noon Eastern Time (1600 UTC) to tell us you would like to see in the next version of stdpopsim! DM me for meeting link, or just sign up for our email list: lists.uoregon.edu/mailman/list... (1/3)

Abstract deadline for @eseb2025.bsky.social extended to 5 May! Still time to submit your abstract for the evolution of microbial pangenomes ⬇️

If you are interested in microbial #pangenomes, join us at @eseb2025.bsky.social in Barcelona with @bjesseshapiro.bsky.social and @annadewar.bsky.social
Only two days left to submit your abstract!
eseb2025.com/call-for-abs...

Join our symposium The evolution of microbial pangenomes at @eseb2025.bsky.social with @bjesseshapiro.bsky.social and @annadewar.bsky.social (co-organized with @fbaumdicker.bsky.social and Jaime Iranzo) eseb2025.com/call-for-abs...

Accessible, realistic genome simulation with selection using stdpopsim Selection is a fundamental evolutionary force that shapes patterns of genetic variation across species. However, simulations incorporating realistic selection along heterogeneous genomes in complex de...

stdpopsim v0.3.0 is out! You can now mix and match your simulations of different demographic histories with published distributions of fitness effects along with gene annotations, and you can even throw in sweeps for good measure. Check out the new manuscript for more info: doi.org/10.1101/2025...

Using genomics to explore the ecology and evolution of plant-associated microbial populations and communities? 🌿

Submit an abstract by March 11 and join us in Cologne this July for #ISMPMI2025! We serve cool science + cold German beer 🍻 Join the party: buff.ly/uqEfN6O

Save the date for the second conference on Machine Learning for Evolutionary Genomics Data!

YouTube video by Eberhard Karls Universität Tübingen Thesencheck - Über diese 11 Behauptungen zur Klimapolitik lässt sich streiten

In unserer neuen "Thesencheck" Episode diskutiert Politikwissenschaftlerin Dr. Melanie Nagel 11 populäre Thesen zur Klimapolitik.💦🌞🌬️💻 youtu.be/xcjqTgDsfC0

Damit ist sie die 5. Tübinger Forscherin, die im "Thesencheck" in der Öffentlichkeit herumwabernde Aussagen mit ihrer Expertise betrachtet.🔍👩‍🔬

PopGen Seminar Series Summer Term 2025 04.03.25 – Lutz Becks (Univ. of Konstanz, DE)
The evolutionary dynamics of novel endosymbiosis. 11.03.25 – Ilkka Kronholm (Univ. of Jyväskylä, FI)
How chromatin structure influences genetic and epigenetic variation. 18.03.25 – Katja Hoedjes (Vrije Univ. Amsterdam, NL)
Understanding functional impact of genetic variation on complex traits at a single nucleotide resolution. 25.03.25 – Sophie Armitage (Freie Univ. of Berlin, DE)
Evolutionary ecology of host-pathogen interactions. 01.04.25 – Matthew Rockman (New York Univ., US)
Developmental evolution is a population-genetics problem. 08.04.25 – Wen-Juan Ma (Vrije Univ. Brussels, BE)
The evolution of sex chromosomes and sex determination in frogs. 15.04.25 – Almorò Scarpa (Vetmeduni, AT)
Two centuries of transposable element invasions in Drosophila melanogaster 22.04.25 – Julia Kreiner (Univ. of Chicago, US)
The mode and tempo of genomic adaptation to contemporary agriculture. 29.04.25 – Martin Kaltenpoth (Max Planck Inst. for Chemical Ecology, DE)
Microbial symbionts as sources of evolutionary innovations in beetles. 06.05.25 – Luisa Pallares (Friedrich Miescher Laboratory, DE)
Phenotypic robustness across the genotype-phenotype map, from genes to environment and back. 13.05.25 – Diana Rennison (Univ. of Calif., San Diego, US)
Understanding the predictability of evolutionary trajectories using threespine stickleback.

20.05.25 – Filipa Sousa (Univ. of Vienna, AT)
Bioenergetics Evolution: The link between Earth’s and Life’s history. 27.05.25 – Yun Song (Univ. of California, Berkeley, US)
Learning and applying complex probability distributions over biological sequences. 03.06.25 – April Wei (Cornell Univ., US)
Enabling efficient analysis of biobank-scale data with genotype representation graphs. ALT TEXT OUT OF SPACE, GO TO https://www.popgen-vienna.at/news/seminars/

The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/

Folge 2: Paleomycin: Wiederbelebung eines Urantibiotikums Inside CMFI: Potenziale der Mikrobiomforschung · Episode

#Podcast Release!

🎙️Folge 2: 𝗣𝗮𝗹𝗲𝗼𝗺𝘆𝗰𝗶𝗻: 𝗪𝗶𝗲𝗱𝗲𝗿𝗯𝗲𝗹𝗲𝗯𝘂𝗻𝗴 𝗲𝗶𝗻𝗲𝘀 𝗨𝗿𝗮𝗻𝘁𝗶𝗯𝗶𝗼𝘁𝗶𝗸𝘂𝗺𝘀

Kommt mit uns auf eine Schatzsuche nach einem Millionen Jahre alten #Urantibiotikum – dringend benötigt angesichts ansteigender #Antibiotikaresistenzen.

tinyurl.com/yc7vv58j

@nadineziemert.bsky.social & Evi Stegmann

Join our symposium The evolution of microbial pangenomes at @eseb2025.bsky.social with @bjesseshapiro.bsky.social @annadewar.bsky.social (co-organized with @fbaumdicker.bsky.social and Jaime Iranzo)

Neural networks for self-adjusting mutation rate estimation when the recombination rate is unknown Author summary single-layer feedforward neural networks learn the established model-based linear estimators for high and low recombination rates neural networks learn good estimators for intermedi...

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/jour...

We have an open position PhD position in a project aiming to develop novel methodologies for phylogenomic reconstruction of plasmid evolution. See details and how to apply in the Ad. Candidates who will review the relevant literature (see Ad) have a higher chance to write a successful application.

I am looking for graduate students interested in investigating bacterial genome evolution, esp. pangenomes and intergenic regions, and the relative importance of genetic drift! https://buff.ly/3UPVcQ9

I recently used chatGPT to create a list of people working on a certain concept. The list was quite good, but the tool refused to provide their emails (which is probably a good thing) and I did not try to provide an abstract.