Stochastic Biology Group: using maths, stats, and experiments to learn about biology and disease. We love organelles and oDNA, evolution, noise, and inference.
University of Bergen, Norway
Joined January 2013
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How does AMR evolution vary across pathogens? Regions? Patients? We used EvAM* to take a look. biorxiv.org/content/10.64898…
Inferring evol pathways to multi-drug resistance as transition networks, we use the amazing CABBAGE dataset to learn AMR "roadmaps" across global ESKAPEEs... 1/
... finding striking similarities of evol dynamics across different pathogens, but also diffs predicted by geography and patient demographics. The networks (grey) are predictive, and perform well forecasting new resistome phenotypes (coloured dots) from sub-Saharan Africa... 2/
... across several decades of clinical study. Would love to hear feedback, and on the aligned work on Klebsiella natural histories journals.plos.org/plosbiolog… and on *the perspective of EvAM in AMR evolution journals.asm.org/doi/full/10… 3/
... finding remarkable consistency across pathogen evolutionary "roadmaps", but some notable diffs which covary with region and patient demography. The inferred roadmaps also predict unseen and future resistance states, which we test with new data from sub-Saharan Africa... 2/
... finding that the trained models do well at predicting multi-drug resistance states over several decades of clinical sampling. Related: Klebsiella-focussed natural history journals.plos.org/plosbiolog… and *EvAM-AMR perspective journals.asm.org/doi/full/10…
Mitochondria and chloroplasts are inherited through a "bottleneck". Smaller bottleneck ➡️ more powerful segregation of DNA damage. So why don't organisms just always use a bottleneck of size 1? And what's up with paternal leakage, DUI, etc? Take a look!
doi.org/10.1093/gbe/evag161
Super grateful to @RCG_Heretic (and maker @NeuroWoodworks) for this beautiful art celebrating Robert's successful PhD defence! Featuring Eqn. 15 journals.plos.org/ploscompbi… linking physical behaviour of mitochondria and genetic behaviour of mtDNA :-)
Iain Johnston retweeted
Tupper’s formula is a formula that represents itself when one plots all the points in the plane that satisfy it.
Iain Johnston retweeted
Today in cursed code: a computer program that plays pong by modifying its own source code. (Each frame is a new compilation). github.com/uellenberg/Insert
Iain Johnston retweeted
The majority of axonal mitochondria in mammalian neurons lack mitochondrial DNA and do not produce ATP biorxiv.org/content/10.1101/…
Excited to share a new preprint!
Lots of evolutionary processes, from AMR to cancer, involve biology acquiring features (drug resistances, mutations, etc). These are sometimes called "accumulation pathways", an instance of discrete character evolution. 1/
This sets up for a version of the Mk model that scales linearly in observations instead of exponentially in features, and can handle interactions, reversibility, coupling, missing data, and more. We think this could be quite a generally useful advance! 4/
We apply it to the evolution of drug resistance in TB and Klebsiella, and show its interoperability with other problems. The link is
biorxiv.org/content/10.64898…
... would love to hear thoughts!
It's 17th May and Norway is beautiful. Gratulerer med dagen! 🇳🇴
(lots going on in arXiv and other science news, but that's for later)
Iain Johnston retweeted
David Attenborough, 'the voice for nature,' turns 100 reut.rs/48EFrlX reut.rs/48EFrlX
The dish occupies a cubic metre and the bacteria are generating 10kW of heat. They can clearly access nutrients beyond currently understood biochem (and physics). The wobbly, hot mass has noticeably expanded while I've been typing. An alarm sounds. The sky darkens
#bionumbers
