Iain Johnston

Stochastic Biology Group: using maths, stats, and experiments to learn about biology and disease. We love organelles and oDNA, evolution, noise, and inference.

[Iain Johnston @mitomaths]

How does AMR evolution vary across pathogens? Regions? Patients? We used EvAM* to take a look. https://t.co/0MlhKAbP13
Inferring evol pathways to multi-drug resistance as transition networks, we use the amazing CABBAGE dataset to learn AMR "roadmaps" across global ESKAPEEs... 1/

[Iain Johnston @mitomaths]

@anshulkundaje ... positive/negative bias, isn't that kind of worse in an orthogonal direction? How would one even push back against that?

[Iain Johnston @mitomaths]

@anshulkundaje But don't you worry, for example, that the AI's bias will itself bias the human reading it, in a way that has never involved an accountable party? I appreciate current LLMs are good at *spotting errors*, but if opaque cues give them (and thereby us) an opaque...

[Iain Johnston @mitomaths]

@lzz334 @NikonSmallWorld Here's our current guess about what part of that logic is! https://t.co/H1y00PQalk

[Iain Johnston @mitomaths]

@HelixMind_ 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!

[Iain Johnston @mitomaths]

@HelixMind_ 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 https://t.co/zv93Ne3afL

[Iain Johnston @mitomaths]

... across several decades of clinical study. Would love to hear feedback, and on the aligned work on Klebsiella natural histories https://t.co/5daVwr8IBw and on *the perspective of EvAM in AMR evolution https://t.co/7AW5Jn1lTN 3/

[Iain Johnston @mitomaths]

How does AMR evolution vary across pathogens? Regions? Patients? We used EvAM* to take a look. https://t.co/0MlhKAbP13
Inferring evol pathways to multi-drug resistance as transition networks, we use the amazing CABBAGE dataset to learn AMR "roadmaps" across global ESKAPEEs... 1/

[Iain Johnston @mitomaths]

... 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/

[Iain Johnston @mitomaths]

... finding that the trained models do well at predicting multi-drug resistance states over several decades of clinical sampling. Related: Klebsiella-focussed natural history https://t.co/5daVwr8IBw and *EvAM-AMR perspective https://t.co/7AW5Jn1lTN

[Iain Johnston @mitomaths]

... 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/

[Iain Johnston @mitomaths]

Some recent science venues during 🇳🇴🇩🇰🇩🇪🇳🇱🇬🇧 adventure!

[Iain Johnston @mitomaths]

@e_cdalton

[Iain Johnston @mitomaths]

A collection of summer mitochondria and chloroplasts, along with their environments 🇳🇴

[Iain Johnston @mitomaths]

@Madam_Mito This *is* the same as our picture in https://t.co/KT8yLNxc1K! How odd

[Iain Johnston @mitomaths]

@Madam_Mito @DocLarus Wait, isn't this the same as our picture in https://t.co/KT8yLNxc1K ?

[Iain Johnston @mitomaths]

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!
https://t.co/BGrWIqrDnL

[Iain Johnston @mitomaths]

Super grateful to @RCG_Heretic (and maker @NeuroWoodworks) for this beautiful art celebrating Robert's successful PhD defence! Featuring Eqn. 15 https://t.co/lKjq7fI6UO linking physical behaviour of mitochondria and genetic behaviour of mtDNA :-)

[Math Files @Math_files]

Tupper’s formula is a formula that represents itself when one plots all the points in the plane that satisfy it.

[Tim McNamara @timClicks]

Today in cursed code: a computer program that plays pong by modifying its own source code. (Each frame is a new compilation). https://t.co/kS2ACZ7r79