iiinova — where your digital self keeps evolving

Leonie Lorenz @leonielorenz.bsky.social · 09/09/2026

I am excited to share that my main PhD work on developing a Wright-Fisher model for replacement dynamics in Streptococcus pneumoniae populations following vaccine introductions has been published in Genome Medicine! We used it to investigate optimal surveillance strategies. rdcu.be/UGjFZJBhKVba

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Reposted by Leonie Lorenz

Johanna von Wachsmann @johannavw.bsky.social · 16/06/2026

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

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Reposted by Leonie Lorenz

Society for Molecular Biology and Evolution @official-smbe.bsky.social · 09/06/2026

#SMBE2026 S14: Evolution of Host-Pathogen Interactions in the Genomic Age 🗓️ Mon Jun 29, 3:50pm 🔗 smbe2026.org/programme Talks:

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Reposted by Leonie Lorenz

Anna Dornhaus @dornhaus.bsky.social · 16/04/2026

Preprint: What good is modeling? Introducing biology students to theory - arxiv.org/abs/2604.13344 - how to teach and think about what modeling contributes to science. How does it fit into the scientific method? This is often misunderstood.

arxiv.org

What good is modeling? Introducing biology students to theory

Theory and empirical science should be in constant dialogue, but often find it hard to understand one another. Here we describe a graduate-level university course we developed to improve matters. The ...

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Reposted by Leonie Lorenz

John Lees @johnlees.bacpop.org · 27/03/2026

We have two paid internships available in our group starting this summer, suitable for master's / pre-PhD students: - Protein structure search - Promoter variation For full details and how to apply see: www.bacpop.org/jobs/

Reposted by Leonie Lorenz

EMBL-EBI @ebi.embl.org · 02/02/2026

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...

Person standing outside next to a building wearing a red jacket

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Leonie Lorenz @leonielorenz.bsky.social · 22/12/2025

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

doi.org

A reusable model of pangenome selection informs optimal surveillance strategies over vaccine introductions

The human pathogen Streptococcus pneumoniae is a major cause of disease, including pneumonia and meningitis. The introduction of Pneumococcal Conjugate Vaccines (PCVs) initially reduced the burden of ...

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Reposted by Leonie Lorenz

John Lees @johnlees.bacpop.org · 19/11/2025

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

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Reposted by Leonie Lorenz

Wolfgang Huber @wkhuber.bsky.social · 29/09/2025

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...

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Reposted by Leonie Lorenz

EMBL-EBI Training @training.ebi.embl.org · 19/09/2025

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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Leonie Lorenz @leonielorenz.bsky.social · 19/09/2025

Open PhD position in our lab for starting roughly in September 2026. Cannot recommend this lab enough!!! 🦠🖥️ #MathematicalModelling #BacterialGenomics #Bioinformatics

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Reposted by Leonie Lorenz

EMBL-EBI @ebi.embl.org · 08/09/2025

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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Leonie Lorenz @leonielorenz.bsky.social · 03/09/2025

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...

doi.org

SBMLtoOdin and menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences

AbstractSummary. Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predi

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Reposted by Leonie Lorenz

EMBL-EBI Training @training.ebi.embl.org · 19/08/2025

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 🧬📊🖥️🎓

embl.org

From intern to on-demand course author – Course and Conference Office

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Reposted by Leonie Lorenz

John Lees @johnlees.bacpop.org · 15/08/2025

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

ebi.ac.uk

Mathematical modelling for biologists - Modelling concepts in biological research

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Reposted by Leonie Lorenz

Ewan Birney @ewanbirney.bsky.social · 20/06/2025

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

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Reposted by Leonie Lorenz

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 19/05/2025

Amira: gene-space de Bruijn graphs to improve the detection of AMR genes from bacterial long reads www.biorxiv.org/content/10.1101/202…

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Reposted by Leonie Lorenz

EMBL-EBI Training @training.ebi.embl.org · 08/05/2025

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 🧪🧬🖥️🦠🧫

EMBO Practical Course
Methods for infectious disease modelling using genomics
14 - 19 September 2025
Hinxton, United Kingdom

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Leonie Lorenz @leonielorenz.bsky.social · 07/05/2025

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

arxiv.org

SBMLtoOdin and Menelmacar: Interactive visualisation of systems biology models for expert and non-expert audiences

Motivation: Computational models in biology can increase our understanding of biological systems, be used to answer research questions, and make predictions. Accessibility and reusability of computati...

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Reposted by Leonie Lorenz

Max Delbrück Center @mdc-berlin.bsky.social · 07/03/2025

"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

youtu.be

Celebrating our #WomenInSTEM: Jana Wolf

YouTube video by Max Delbrück Center

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Leonie Lorenz @leonielorenz.bsky.social · 09/01/2025

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!

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Reposted by Leonie Lorenz

John Lees @johnlees.bacpop.org · 08/08/2024

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...

embl.org

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Leonie Lorenz @leonielorenz.bsky.social · 08/04/2024

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.

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