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Reposted by Franz Baumdicker

John Lees @bacpop.org · 21d

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

EMBL International PhD Programme – Unique in the world and waiting for you!

www.embl.org

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Franz Baumdicker @fbaumdicker.bsky.social · 16d

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!

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Reposted by Franz Baumdicker

James Kitchens @kitchensjn.bsky.social · Aug 19

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

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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...

arxiv.org

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Reposted by Franz Baumdicker

Torsten Günther @trstngnthr.bsky.social · Aug 12

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/...

Bioinformatician - Uppsala University

Bioinformatician, Department of Organismal Biology, Uppsala University

www.uu.se

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Reposted by Franz Baumdicker

Fabienne Benz @fabbenz.bsky.social · May 15

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

Nature Reviews Bioengineering @natrevbioeng.nature.com · May 14

ICYMI: CRISPR–Cas therapies targeting bacteria

CRISPR–Cas therapies targeting bacteria

Nature Reviews Bioengineering, Published online: 13 May 2025; doi:10.1038/s44222-025-00311-8CRISPR–Cas tools can be designed to kill or modify specific bacteria. This Review explores the engineering of CRISPR–Cas tools and corresponding delivery strategies for the treatment of bacterial infections and modification of the microbiome.

www.nature.com

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Reposted by Franz Baumdicker

Dan Schrider @samurscicop.bsky.social · May 14

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)

popgen_benchmark Info Page

lists.uoregon.edu

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Reposted by Franz Baumdicker

Anne Kupczok @annecmg.bsky.social · Apr 24

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

Franz Baumdicker @fbaumdicker.bsky.social · Apr 23

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...

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Franz Baumdicker @fbaumdicker.bsky.social · Apr 23

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...

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Reposted by Franz Baumdicker

Anne Kupczok @annecmg.bsky.social · Apr 10

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...

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Reposted by Franz Baumdicker

Dan Schrider @samurscicop.bsky.social · Mar 24

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...

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...

doi.org

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Reposted by Franz Baumdicker

Honour McCann @honour.bsky.social · Mar 4

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

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Franz Baumdicker @fbaumdicker.bsky.social · Feb 25

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

Alexis Stamatakis @stamatak.bsky.social · Feb 24

The next edition of our LEGEND conference on Machine Learning for Evolutionary Genomics Data will take place in Aussois (French Alps) from Dec 8-12 2025.

All practical information and a list of our keynote speakers are available at: legend2025.sciencesconf.org

We hope to meet you there again!

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Reposted by Franz Baumdicker

Universität Tübingen @unituebingen.bsky.social · Feb 18

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.🔍👩‍🔬

Thesencheck - Über diese 11 Behauptungen zur Klimapolitik lässt sich streiten

YouTube video by Eberhard Karls Universität Tübingen

youtu.be

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Reposted by Franz Baumdicker

PopGen Vienna @popgenviennaphd.bsky.social · Feb 13

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/

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/

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Reposted by Franz Baumdicker

Cluster of Excellence CMFI @cmfi.bsky.social · Feb 17

#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

Folge 2: Paleomycin: Wiederbelebung eines Urantibiotikums

Inside CMFI: Potenziale der Mikrobiomforschung · Episode

open.spotify.com

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Reposted by Franz Baumdicker

Anne Kupczok @annecmg.bsky.social · Feb 11

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)

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Franz Baumdicker @fbaumdicker.bsky.social · Feb 7

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...

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...

dx.plos.org

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Reposted by Franz Baumdicker

DaganLab @daganlab.bsky.social · Feb 4

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.

TransEvo @transevo.bsky.social · Jan 31

7 PhD positions in Translational Evolutionary Research available @uni-kiel.de
Application deadline is March 27, 2025
Please spread the word!
www.kec.uni-kiel.de/news_events/...

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Reposted by Franz Baumdicker

Gavin Douglas @gmdouglas.bsky.social · Jan 21

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

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Franz Baumdicker @fbaumdicker.bsky.social · Jan 21

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.

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Reposted by Franz Baumdicker

Jakob Macke @jakhmack.bsky.social · Jan 20

SBI hackathon is back! Join us in Tübingen for the 4th edition, make the toolbox better, brainstorm new direction, have fun!

sbi - Simulation-based inference @sbi-devs.bsky.social · Jan 14

🚀 Join the 4th SBI Hackathon! 🚀
The last SBI hackathon was a fantastic milestone in forming a collaborative open-source community around SBI. Be part of it this year as we build on that momentum!

📅 March 17–21, 2025
📍 Tübingen, Germany or remote
👉 Details: github.com/sbi-dev/sbi/...

More Info:🧵👇

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Reposted by Franz Baumdicker

Harald Ringbauer @hringbauer.bsky.social · Dec 3

PhD opportunity in computational population genetics at @MPI_EVA_Leipzig:
Join our fully funded project to develop IBD-segment tools, connecting high-quality genomes from 500 Black Death victims to modern Europeans. 🌍💻🧬
Please spread the word! 📢🙌 #aDNA #PopGen

www.eva.mpg.de/de/karriere/...

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Reposted by Franz Baumdicker

Jamie Hall @jpjhall.bsky.social · Dec 3

🆕New in @plosbiology.bsky.social: we show compensatory mutations make plasmids play Rock-Paper-Scissors and turn conjugation into a weapon🛡️💫✂️🦠

w/Rosanna Wright, Jamie Wood, @mbottery.bsky.social, @kmudz.bsky.social, @scottishwormboy.bsky.social, Ellie Harrison & @brockhurstlab.bsky.social #MicroSky

A chromosomal mutation is superior to a plasmid-encoded mutation for plasmid fitness cost compensation

Plasmids spread important traits in microbiomes but impose fitness costs on their hosts. This study of the ecological consequences of plasmid-bacterial compensatory evolution reveals benefits to bacte...

journals.plos.org

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Franz Baumdicker @fbaumdicker.bsky.social · Nov 28

Only a few days left to apply!

Franz Baumdicker @fbaumdicker.bsky.social · Nov 8

Join us as a #PostDoc 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 Böhringer Ingelheim. More info here:
uni-tuebingen.de/forschung/se...

AI & Data Science Fellowship Program

uni-tuebingen.de

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Franz Baumdicker @fbaumdicker.bsky.social · Nov 20

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

GitHub - fbaumdicker/SpacerPlacer: ancestral reconstruction and likelihood analysis for CRISPR spacer arrays

ancestral reconstruction and likelihood analysis for CRISPR spacer arrays - fbaumdicker/SpacerPlacer

buff.ly

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