Iain Johnston
@mitomaths.bsky.social
Stochastic Biology Group: using maths, stats, and experiments to learn about biology and disease. We love organelles and oDNA, evolution, noise, and inference.
https://org.uib.no/stochasticbiology/
https://org.uib.no/stochasticbiology/
Understanding evolutionary dynamics lets us form future predictions. We tested these predictions with newly sequenced data from decades of clinical study in Tanzania. Fitted model retrospectively predicted those previously unobserved accumulation dynamics! 4/
September 22, 2025 at 7:56 AM
Understanding evolutionary dynamics lets us form future predictions. We tested these predictions with newly sequenced data from decades of clinical study in Tanzania. Fitted model retrospectively predicted those previously unobserved accumulation dynamics! 4/
Interesting, but very high-dimensional, so we project down to find the principal axes of diversity in evolutionary behaviour -- and what predicts them. They're linked both to public health region and drug use regimens 3/
September 22, 2025 at 7:56 AM
Interesting, but very high-dimensional, so we project down to find the principal axes of diversity in evolutionary behaviour -- and what predicts them. They're linked both to public health region and drug use regimens 3/
Following the ideas in journals.asm.org/doi/full/10.... about applying evol accumulation modelling (EvAM) to AMR, we use genomics data to infer the orderings of character accumulation behind observed Klebsiella AMR profiles across countries (e.g. Romania here), with global average in D 2/
September 22, 2025 at 7:56 AM
Following the ideas in journals.asm.org/doi/full/10.... about applying evol accumulation modelling (EvAM) to AMR, we use genomics data to infer the orderings of character accumulation behind observed Klebsiella AMR profiles across countries (e.g. Romania here), with global average in D 2/
Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/
September 22, 2025 at 7:56 AM
Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/
Celebrating grant award with a mountain run! MitoPhyto, a FRIPRO project, will combine modelling and microscopy to explore mitochondrial and mtDNA maintenance across non-bilaterian multicellular eukaryotes. Opportunities to come to Norway: please see next post
June 17, 2025 at 12:25 PM
Celebrating grant award with a mountain run! MitoPhyto, a FRIPRO project, will combine modelling and microscopy to explore mitochondrial and mtDNA maintenance across non-bilaterian multicellular eukaryotes. Opportunities to come to Norway: please see next post
Gratulerer med dagen alle sammen!
(non-Norway-based folks, happy Norwegian Constitution Day!)
(non-Norway-based folks, happy Norwegian Constitution Day!)
May 17, 2025 at 5:02 PM
Gratulerer med dagen alle sammen!
(non-Norway-based folks, happy Norwegian Constitution Day!)
(non-Norway-based folks, happy Norwegian Constitution Day!)
Had a brilliant time at the 54th Jírovec’s Protozoological Days in Frymburk. Amazing organisms, amazing science, lots of exciting organelle work. Beautiful setting too! Thanks to all www.chromera.org/konference/5...
May 7, 2025 at 11:00 AM
Had a brilliant time at the 54th Jírovec’s Protozoological Days in Frymburk. Amazing organisms, amazing science, lots of exciting organelle work. Beautiful setting too! Thanks to all www.chromera.org/konference/5...
May trails on the way to the final Applied Statistics lecture of the semester!
May 7, 2025 at 10:57 AM
May trails on the way to the final Applied Statistics lecture of the semester!
View from the office as summer approaches
May 2, 2025 at 7:15 PM
View from the office as summer approaches
Projector broke today, so a good old-school blackboard lecture on an intro to GLMs!
March 19, 2025 at 7:33 PM
Projector broke today, so a good old-school blackboard lecture on an intro to GLMs!
Started likelihood-based approaches for model selection in STAT200 today, one of my favourite things (and behind many of our research projects)! Combined with likelihood-free methods, my claim is that this is how we turn modelling (not really falsifiable) into science (testing hypotheses with data)
February 26, 2025 at 5:10 PM
Started likelihood-based approaches for model selection in STAT200 today, one of my favourite things (and behind many of our research projects)! Combined with likelihood-free methods, my claim is that this is how we turn modelling (not really falsifiable) into science (testing hypotheses with data)
Some shots from wintery commutes in 2025!
February 20, 2025 at 8:51 PM
Some shots from wintery commutes in 2025!
Nice group meeting today, celebrating exciting new positions and discussing the diverse ways we do science with data! Thanks all
February 20, 2025 at 8:47 PM
Nice group meeting today, celebrating exciting new positions and discussing the diverse ways we do science with data! Thanks all
And very new indeed, here's HyperLAU, an approach using tools from linear algebra to capture uncertainty in (phylogenetically embedded) accumulation models that supports flexible model structure and data inputs @jessirenz.bsky.social ! arxiv.org/abs/2502.05872 . Would love to chat about these! 3/3
February 20, 2025 at 8:45 PM
And very new indeed, here's HyperLAU, an approach using tools from linear algebra to capture uncertainty in (phylogenetically embedded) accumulation models that supports flexible model structure and data inputs @jessirenz.bsky.social ! arxiv.org/abs/2502.05872 . Would love to chat about these! 3/3
Here's a "picture guide" (led by Ramon) describing approaches for these models and their inference, from cancer to evol bio and other applications arxiv.org/abs/2312.06824 (also see Ramon and colleagues' great repo of software approaches for EvAM github.com/rdiaz02/EvAM...) 2/
February 20, 2025 at 8:45 PM
Here's a "picture guide" (led by Ramon) describing approaches for these models and their inference, from cancer to evol bio and other applications arxiv.org/abs/2312.06824 (also see Ramon and colleagues' great repo of software approaches for EvAM github.com/rdiaz02/EvAM...) 2/
We've been thinking a lot about "accumulation models" lately -- inferring how systems accumulate features over time. May be mutations in a tumor, characters in evol bio, gene losses in oDNA. Here's an instance of the well-known Mk model that captures this picture academic.oup.com/bioinformati... 1/
February 20, 2025 at 8:45 PM
We've been thinking a lot about "accumulation models" lately -- inferring how systems accumulate features over time. May be mutations in a tumor, characters in evol bio, gene losses in oDNA. Here's an instance of the well-known Mk model that captures this picture academic.oup.com/bioinformati... 1/
First skitur of 2025, chasing the sunrise
January 2, 2025 at 11:52 AM
First skitur of 2025, chasing the sunrise
More beautiful commuting on the trails, featuring dramatic mist and Norway's biggest tree, celebrated in typical understated style 🇳🇴🌲
December 11, 2024 at 2:31 PM
More beautiful commuting on the trails, featuring dramatic mist and Norway's biggest tree, celebrated in typical understated style 🇳🇴🌲
Here's a mitochondrial "social network" (tracking encounters) emerging over time from their collective dynamics in a plant cell. This picture helps us understand their capacity to share and exchange biomolecules 🔬🌱🫂
Read more www.sciencedirect.com/science/arti...; pubmed.ncbi.nlm.nih.gov/34015261/
Read more www.sciencedirect.com/science/arti...; pubmed.ncbi.nlm.nih.gov/34015261/
December 11, 2024 at 9:54 AM
Here's a mitochondrial "social network" (tracking encounters) emerging over time from their collective dynamics in a plant cell. This picture helps us understand their capacity to share and exchange biomolecules 🔬🌱🫂
Read more www.sciencedirect.com/science/arti...; pubmed.ncbi.nlm.nih.gov/34015261/
Read more www.sciencedirect.com/science/arti...; pubmed.ncbi.nlm.nih.gov/34015261/
First commute run for a while, following some illness, travel, and language exams. Beautiful wintery vibes throughout over the Bergen mountains!
December 10, 2024 at 1:04 PM
First commute run for a while, following some illness, travel, and language exams. Beautiful wintery vibes throughout over the Bergen mountains!
Have had some good chats recently about pivoting to non-profit and society journals. A point to share/underline is that such options exist across the "prestige" spectrum. Some examples in the image. All heavily subjective of course; would love to hear thoughts from others!
December 9, 2024 at 11:37 AM
Have had some good chats recently about pivoting to non-profit and society journals. A point to share/underline is that such options exist across the "prestige" spectrum. Some examples in the image. All heavily subjective of course; would love to hear thoughts from others!
What's the biggest sofa you can move round a right-angled corridor one metre wide? One of my favourite "easy to ask, hard to answer" maths problems has a [claimed] solution after many, many decades (!) of work arxiv.org/abs/2411.19826
(GIF from blogs.ams.org/visualinsigh...)
(GIF from blogs.ams.org/visualinsigh...)
December 6, 2024 at 8:18 PM
What's the biggest sofa you can move round a right-angled corridor one metre wide? One of my favourite "easy to ask, hard to answer" maths problems has a [claimed] solution after many, many decades (!) of work arxiv.org/abs/2411.19826
(GIF from blogs.ams.org/visualinsigh...)
(GIF from blogs.ams.org/visualinsigh...)
Wonderful time visiting and talking at Oslo Natural History Museum www.nhm.uio.no ! A childhood dream come true to present science in such a cool environment. Looking forward to more exploring today!
November 29, 2024 at 7:06 AM
Wonderful time visiting and talking at Oslo Natural History Museum www.nhm.uio.no ! A childhood dream come true to present science in such a cool environment. Looking forward to more exploring today!
EvAM approaches can learn the ordering of resistance acquisitionsᵇ from dataᵃ -- but also which resistance features influence which othersᵈ, what will likely happen in futureᶜ, likely values of unobserved features, differences in evolution between regionsᵉ, and more. 3/
November 29, 2024 at 7:03 AM
EvAM approaches can learn the ordering of resistance acquisitionsᵇ from dataᵃ -- but also which resistance features influence which othersᵈ, what will likely happen in futureᶜ, likely values of unobserved features, differences in evolution between regionsᵉ, and more. 3/