Person standing outside next to a building wearing a red jacket
Meet Leonie Johanna Lorenz 🇩🇪, a Predoctoral Fellow at EMBL-EBI who is bringing mathematical modelling to microbes.
Find out more about how Leonie’s passion for modelling patterns extends from bacterial evolution to sewing 🧵
www.ebi.ac.uk/about/news/p...
We are hiring for group leaders again — EBI is a great place to start your research group!
embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
We also published the model as an R package - it's called Stubentiger, which is a German word for cat and stands for STUdying Balancing Evolution (Nfds) To Investigate GEnome Replacement. It's available on GitHub github.com/bacpop/Stube...
Very happy to share our preprint on a mathematical model for Streptococcus pneumoniae population dynamics after vaccine introductions. It's a reusable model that describes vaccine replacement dynamics and can help to determine strategies for genomic surveillance: doi.org/10.64898/2025.12.18.695090
Happy to share our new AMR resource which has phenotypic AMR (usually MIC data) collected from publications and databases. This is paired with assemblies and annotations
We're excited for users who might train new models, find phenotype/genotype mismatches, or any other use
Do you like theoretical biology, mathematical&conceptual modelling and want to apply yourself to cutting-edge research at all levels of biology, from molecules to ecosystems?
Come to EMBL! Scope includes physics-based models, emergence, statistics, ML/AI
embl.wd103.myworkdayjobs.com/en-US/EMBL/j...
Thank you to everyone who joined us this week for the @embo.org Practical Course 'Methods for infectious disease modelling using genomics'.
Join us for 2026's EMBO Practical Course. Sign up for 'Causality in biomedicine' alerts and hear as this new course develops: www.ebi.ac.uk/training/eve...
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Open PhD position in our lab for starting roughly in September 2026. Cannot recommend this lab enough!!! 🦠🖥️
#MathematicalModelling
#BacterialGenomics
#Bioinformatics
Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
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And if you want to dive deeper, we also developed the R package SBMLtoOdin that translates ordinary differential equation models from @biomodels.bsky.social into executable odin code, which should make these models easier to reuse. (More details in the paper of course!)
You can find our web-application Menelmacar ("Making Execution of (Nearly) Every Life-science Model ACcessible to All Researchers"!!!) here: biomodels.bacpop.org
Just try it out, I promise it's fun! 🤓
Very happy to announce that my first first-author paper just got published in Bioinformatics! We developed the web-application Menelmacar that displays differential equation models from @biomodels.bsky.social in the browser - it's beautiful and interactive!
doi.org/10.1093/bioi...
We're so proud of this new on-demand tutorial from Eva-Maria Geissen, @leonielorenz.bsky.social, our recent intern Harry Roussos, third year PhD student at @pdncambridge.bsky.social.
Read Harry's blog all about the tutorial creation: www.embl.org/about/info/c...
Image credit: Juanita Riveros
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My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Powerful stuff from @juliosaezrod.bsky.social who found himself on the other end of the process - as a patient not a computational biology researcher - giving him insight into both research and patient perspectives. Huge credit to Julio for talking about his experiences here
Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads https://www.biorxiv.org/content/10.1101/2025.05.16.654303v1
EMBO Practical Course Methods for infectious disease modelling using genomics 14 - 19 September 2025 Hinxton, United Kingdom
You have until 25 May to apply for this @embo.org Practical Course introducing concepts, methods and tools for carrying out infectious disease modelling using genomics www.ebi.ac.uk/training/eve...
There is some financial assistance provided by EMBO - please see the course website for info
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Very happy and proud to announce that the first preprint of my PhD is out: arxiv.org/abs/2504.20710
We developed an R package to translate mathematical models in SBML format into executable odin models and visualise models from @biomodels.bsky.social on our website Menelmacar biomodels.bacpop.org
"If you find something that you love, just follow it. Keep your eyes open, connect to others, and trust yourself," says Jana Wolf, head of the "Mathematical Modelling of Cellular Processes" lab at #mdcBerlin.
👇 Watch the video & share to inspire others! 👇 #mdcDiversity #WomenInSTEM #WomenInScience
Very excited to be co-organising the new EMBL-EBI and EMBO practical course "Methods for Infectious disease modelling using genomics".
Have a look at the programme and register your interest now if you like!
Josie Bryant and I have a 3yr joint postdoc project at Sanger & EBI (ESPOD)
Topic: Developing new bioinformatic and modelling approaches for exciting new longitudinal microbiome datasets
Project details: www.embl.org/editorhub/wp...
To apply: www.ebi.ac.uk/research/pos...
Excited to be at my first annual conference of the microbiology society #microbio24! Come by my poster (B082) on Wednesday if you want to talk about mathematical modelling and/or the population genetics of Streptococcus pneumoniae.
