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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Here's our current guess about what part of that logic is! biorxiv.org/content/10.64898…
Yup, phenotype profiles paired with accessions for genome data (we exploit the genomes for phylogenetic relatedness, but the phenotypes for the resistomes). Not all bug/drug combinations measured together of course, but definitely a powerful resource!
Yes, we've seen the same. One nice thing about the CABBAGE dataset is its explicitly phenotypic resistome profiles -- so each observation can be traced back to a lab result, which CABBAGE has curated and attempted to systematise biorxiv.org/content/10.1101/…
... 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 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/
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 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…
... 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/
This *is* the same as our picture in journals.plos.org/ploscompbi…! How odd
Wait, isn't this the same as our picture in journals.plos.org/ploscompbi… ?
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
Jeremy and I discuss this a fair bit. A direct, individual-level fitness influence isn't necessary for a population of nuclear encoders to emerge; e.g. this from the SI of pubmed.ncbi.nlm.nih.gov/3910…. We still think there's a link to environmental challenge pubmed.ncbi.nlm.nih.gov/3688…
Iain Johnston retweeted
The majority of axonal mitochondria in mammalian neurons lack mitochondrial DNA and do not produce ATP biorxiv.org/content/10.1101/…