Franz Baumdicker
@fbaumdicker.bsky.social
Mathematical and Computational Population Genetics
Microbial Evolution | Machine Learning in PopGen | CRISPR-Cas | Pangenomes | HGT
🦠 ➔ 🧬 ➔ 💻 ➔ 🤔
www.baumdickergroup.de
Microbial Evolution | Machine Learning in PopGen | CRISPR-Cas | Pangenomes | HGT
🦠 ➔ 🧬 ➔ 💻 ➔ 🤔
www.baumdickergroup.de
Reposted by Franz Baumdicker
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!
Grateful to have collaborated with researchers across many institutions to consolidate what we've learned about making these methods work in practice!
Simulation-based inference (SBI) has transformed parameter inference across a wide range of domains. To help practitioners get started and make the most of these methods, we joined forces with researchers from many institutions and wrote a practical guide to SBI.
📄 Paper: arxiv.org/abs/2508.12939
📄 Paper: arxiv.org/abs/2508.12939
Simulation-Based Inference: A Practical Guide
A central challenge in many areas of science and engineering is to identify model parameters that are consistent with prior knowledge and empirical data. Bayesian inference offers a principled framewo...
arxiv.org
November 21, 2025 at 4:04 PM
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!
Grateful to have collaborated with researchers across many institutions to consolidate what we've learned about making these methods work in practice!
Reposted by Franz Baumdicker
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
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...
rdcu.be
November 18, 2025 at 9:01 PM
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
Reposted by Franz Baumdicker
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...
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...
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.
www.ebi.ac.uk
November 5, 2025 at 4:33 PM
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...
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...
Reposted by Franz Baumdicker
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...
doi.org/10.5281/zeno...
Pursuit of Knowledge: A Charter for Academic Renewal
This paper identifies systemic problems in how academic research is structured, evaluated, and supported. It argues for a realignment of incentives and institutional cultures to restore trust, enable ...
doi.org
October 30, 2025 at 10:18 PM
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...
doi.org/10.5281/zeno...
Reposted by Franz Baumdicker
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.
October 28, 2025 at 9:31 PM
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.
Reposted by Franz Baumdicker
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...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
October 27, 2025 at 5:53 PM
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...
Complexity welcome: Pangenome graphs for comprehensive population genomics
#pangenomes #plantscience #genomegraphs
www.cambridge.org/core/journal...
Reposted by Franz Baumdicker
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
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
September 17, 2025 at 3:49 PM
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
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!
September 22, 2025 at 2:46 PM
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!
Reposted by Franz Baumdicker
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
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
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
August 19, 2025 at 2:12 PM
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
@yanwong.bsky.social and I have been developing a method to programmatically drawing these graphs.
🔗 arxiv.org/abs/2508.03958
1/6
Reposted by Franz Baumdicker
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/...
www.uu.se/en/about-uu/...
Bioinformatician - Uppsala University
Bioinformatician, Department of Organismal Biology, Uppsala University
www.uu.se
August 12, 2025 at 7:10 AM
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/...
www.uu.se/en/about-uu/...
Reposted by Franz Baumdicker
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
May 15, 2025 at 6:53 AM
Reposted by Franz Baumdicker
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
May 14, 2025 at 1:04 AM
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)
Reposted by Franz Baumdicker
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...
Only two days left to submit your abstract!
eseb2025.com/call-for-abs...
April 24, 2025 at 8:31 AM
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...
Only two days left to submit your abstract!
eseb2025.com/call-for-abs...
April 23, 2025 at 7:05 AM
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...
Only two days left to submit your abstract!
eseb2025.com/call-for-abs...
Reposted by Franz Baumdicker
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...
April 10, 2025 at 4:10 PM
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...
Reposted by Franz Baumdicker
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
March 24, 2025 at 6:29 PM
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...
Reposted by Franz Baumdicker
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
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
March 4, 2025 at 5:31 PM
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
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!
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!
All practical information and a list of our keynote speakers are available at: legend2025.sciencesconf.org
We hope to meet you there again!
February 25, 2025 at 1:11 PM
Save the date for the second conference on Machine Learning for Evolutionary Genomics Data!
Reposted by Franz Baumdicker
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.🔍👩🔬
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
February 18, 2025 at 3:53 PM
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.🔍👩🔬
Damit ist sie die 5. Tübinger Forscherin, die im "Thesencheck" in der Öffentlichkeit herumwabernde Aussagen mit ihrer Expertise betrachtet.🔍👩🔬
Reposted by Franz Baumdicker
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/
February 13, 2025 at 3:01 PM
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/
Reposted by Franz Baumdicker
#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
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
February 17, 2025 at 10:21 AM
#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
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
Reposted by Franz Baumdicker
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)
February 11, 2025 at 5:16 PM
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)
Reposted by Franz Baumdicker
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.
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/...
Application deadline is March 27, 2025
Please spread the word!
www.kec.uni-kiel.de/news_events/...
February 4, 2025 at 7:57 AM
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.
Reposted by Franz Baumdicker
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
January 21, 2025 at 2:00 PM
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
Reposted by Franz Baumdicker
SBI hackathon is back! Join us in Tübingen for the 4th edition, make the toolbox better, brainstorm new direction, have fun!
🚀 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:🧵👇
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:🧵👇
January 20, 2025 at 4:45 PM
SBI hackathon is back! Join us in Tübingen for the 4th edition, make the toolbox better, brainstorm new direction, have fun!