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Reposted by Leonie Lorenz

Wolfgang Huber @wkhuber.bsky.social · 10d

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 · 20d

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 · 19d

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

#MathematicalModelling
#BacterialGenomics
#Bioinformatics

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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Reposted by Leonie Lorenz

EMBL-EBI @ebi.embl.org · Sep 8

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 · Sep 3

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!)

Leonie Lorenz @leonielorenz.bsky.social · Sep 3

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! 🤓

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Leonie Lorenz @leonielorenz.bsky.social · Sep 3

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...

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

doi.org

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Reposted by Leonie Lorenz

EMBL-EBI Training @training.ebi.embl.org · Aug 19

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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Reposted by Leonie Lorenz

John Lees @bacpop.org · Aug 15

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

Mathematical modelling for biologists - Modelling concepts in biological research

www.ebi.ac.uk

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Reposted by Leonie Lorenz

Ewan Birney @ewanbirney.bsky.social · Jun 20

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

Nature Reviews Nephrology @natrevneph.nature.com · Jun 19

Leveraging data as a patient–scientist: frustrations and opportunities

Nature Reviews Nephrology, Published online: 19 June 2025; doi:10.1038/s41581-025-00968-9The transition from data scientist to patient–scientist has given me new perspectives into clinical research and strengthened my commitment to open science. Although limitations on data availability have led to frustration, collaboration bodes well for a future in which patients will have access to more personalized information.

www.nature.com

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Reposted by Leonie Lorenz

bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · May 19

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

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Reposted by Leonie Lorenz

EMBL-EBI Training @training.ebi.embl.org · May 8

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 · May 7

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

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...

arxiv.org

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Reposted by Leonie Lorenz

Max Delbrück Center @mdc-berlin.bsky.social · Mar 7

"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

Celebrating our #WomenInSTEM: Jana Wolf

YouTube video by Max Delbrück Center

youtu.be

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Leonie Lorenz @leonielorenz.bsky.social · Jan 9

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!

EMBL-EBI Training @training.ebi.embl.org · Jan 9

We're bringing you a brand new course for 2025! This EMBO practical course will introduce concepts, methods and tools for carrying out infectious disease modelling, as well as for developing models further using the power of genomics.

Register your interest: www.ebi.ac.uk/training/eve...

💻🧬🧪🦠🧫

EMBO practical course
Infectious disease modelling using genomics
14 - 19 September 2025
Hinxton, United Kingdom

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Reposted by Leonie Lorenz

John Lees @bacpop.org · Aug 8

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...

www.embl.org

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Leonie Lorenz @leonielorenz.bsky.social · Apr 8

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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