Iain Johnston

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://stochasticbiology.w.uib.no/

944 followers216 following87 posts

Iain Johnston
@mitomaths.bsky.social

... finding striking similarities of evol dynamics across different pathogens, but also notable 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.bsky.social

... across several decades of clinical study. Would love to hear feedback, and on the aligned work on Klebsiella natural histories journals.plos.org/plosbiology/... and on *the perspective of EvAM in AMR evolution journals.asm.org/doi/full/10.... 3/

journals.plos.orgEvolutionary inference reveals global natural histories and predicted pathways of antimicrobial resistance in Klebsiella pneumoniaeAntimicrobial resistance in Klebsiella pneumoniae is a growing global threat, but its evolutionary routes remain hard to predict. This study uses machine learning to explore how resistance evolves acr...
Iain Johnston
@mitomaths.bsky.social

Excited to meet this in its final form, and thanks to all at @plosbiology.org for a very smooth and useful review and editing process!

PLOS Biology@plosbiology.org

How does #AntimicrobialResistance in #Klebsiella pneumoniae arise? @mitomaths.bsky.social &co use machine learning to explore how resistance evolves across different countries, revealing shared & region-specific pathways that may help forecast #AMR evolution @plosbiology.org 🧪 plos.io/4vc5v19

Iain Johnston
@mitomaths.bsky.social

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/

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Iain Johnston
@mitomaths.bsky.social

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/

Iain Johnston
@mitomaths.bsky.social

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/

Iain Johnston
@mitomaths.bsky.social

If features influence each other (resistance to drug X makes resistance to drug Y more likely), that's a complication. If features can be lost as well as gained, that's another. If there are lots of them, or missing data, that's another. Few methods can handle all that. 2/

Iain Johnston
@mitomaths.bsky.social

One can -- the classic Mk model in evol bio. But it struggles with many interacting features, because the possible state space becomes huge. But, though possible, many of these states are unlikely. So, basically, we prune them in a rational way. 3/

Iain Johnston reposted

The Sainsbury Laboratory
@thesainsburylab.bsky.social

📽️ "Medicine can save your life one day. Plants save your life every day." 🌱 @kamounlab.bsky.social shares his personal journey, his passion for science and his vision for the future in an inspiring talk at TEDx Pasha Street, now freely available online 🌾 www.youtube.com/watch?v=kiqt...

youtube.comGenetics, Climate & the Future of Food | Sophien Kamoun | TEDxPasha StreetIn this thought-provoking talk, Sophien Kamoun explores the urgent connection between climate change, food security, and the future of agriculture. Drawing from his scientific research and personal…

Iain Johnston reposted

Payam Gammage
@mito-oncogene.bsky.social

🚨Excited to announce a new preprint from our lab, where we describe an ancient metabolic axis that controls mitochondrial genome copy number; a mechanism we uncovered in human cells that stretches through evolution to control mtDNA in flies, yeast and even plants!

biorxiv.orgbiorxiv.org

Iain Johnston reposted

Carl T. Bergstrom
@carlbergstrom.com

"The increasing involvement of technology companies in mathematical research raises the risk that research questions may come to be prioritized because of their amenability to automated mathematics, rather than expert judgment of their deeper significance."

leidendeclaration.aiLeiden Declaration on Artificial Intelligence and MathematicsThis declaration calls for action to address the challenges posed by the use of artificial intelligence within mathematics research.

Iain Johnston reposted

Admirable Women
@admirablewomen.bsky.social

Chemist/physician Dr. Maud Menten co-authored the seminal paper 𝘋𝘪𝘦 𝘒𝘪𝘯𝘦𝘵𝘪𝘬 𝘥𝘦𝘳 𝘐𝘯𝘷𝘦𝘳𝘵𝘪𝘯𝘸𝘪𝘳𝘬𝘶𝘯𝘨, 1931. This intro'd the Michaelis–Menten equation (image). It remains a cornerstone of #biochemistry, used in drug design, metabolic studies & enzyme engineering. She was born #OTD in 1879. #WomenInSTEM

Iain Johnston reposted

Kin Pan Chung
@kinpanchung.bsky.social

Mitochondria can indeed be inherited from the father! 🍀 In this new study, we uncovered the molecular mechanisms underlying mitochondrial inheritance in Nicotiana tabacum. @natplants.nature.com doi.org/10.1038/s414...

doi.orgHigh-frequency biparental inheritance of plant mitochondria upon chilling stress and loss of a genome-degrading nuclease - Nature PlantsMaternal inheritance of mitochondria breaks down in the cold when a mitochondrial DNA degrading nuclease is defective, resulting in biparental inheritance that can rescue mitochondrial mutations and g...

Iain Johnston reposted

Carl T. Bergstrom
@carlbergstrom.com

1. The thing about science that these jokers don't understand is that science cannot be vibe-coded. Whatever its flaws, the point with vibe coding is that you're trying to quickly make something that sorta works, where you can immediately sorta see if it sorta works and then sorta use it.

Carl T. Bergstrom@carlbergstrom.com

“The idea is to put ChatGPT front and center inside software that scientists use to write up their work in much the same way that chatbots are now embedded into popular programming editors. It’s vibe coding, but for science.”

technologyreview.comOpenAI’s latest product lets you vibe code sciencePrism is a ChatGPT-powered text editor that automates much of the work involved in writing scientific papers.

Iain Johnston reposted

Osman Lab
@osman-lab.bsky.social

How do cells assess mtDNA quality? Local ATP and membrane-potential gradients reflect mtDNA integrity and drive intracellular purifying selection. We introduce FAST, a scalable mtDNA QC assay in S. cerevisiae. Great collaboration with the Schmoller Lab. journals.plos.org/plosgenetics... 🧬⚡

journals.plos.orgLocal mitochondrial physiology defined by mtDNA quality guides purifying selectionAuthor summary Mitochondria are essential organelles in our cells that convert nutrients into usable cellular energy. They contain their own DNA, and mutations in this DNA can compromise mitochondrial...

Iain Johnston reposted

Sandy Hetherington
@sandyheth.bsky.social

Looking for a new 📕 to read about plants?? I highly recommend the brilliant book ‘Ferns, Lessons in survival from Earth’s most adaptable plants’ Written by @fernway.bsky.social and Jacob Suissa with amazing illustrations by Laura Silburn 🌿 #FernFriday 🌿

Iain Johnston
@mitomaths.bsky.social

1. Apply for one of the positions below (lab or theory) by Jan 18th 2. Learn interdisc skills and discover cool new things about how mitochondria move and socialise 3. Explore some of Norway's beautiful nature (both the below, Rundemanen and Gullfjellet, <10km from work)

Iain Johnston@mitomaths.bsky.social

‼️Two new PhD positions open! One experimental, one modelling, exploring these beautiful collective dynamics in mitochondria across species. 🇳🇴, good pay, full staff benefits. [Shares much appreciated] Lab: www.jobbnorge.no/en/available... Modelling: www.jobbnorge.no/en/available...

Iain Johnston
@mitomaths.bsky.social

‼️Two new PhD positions open! One experimental, one modelling, exploring these beautiful collective dynamics in mitochondria across species. 🇳🇴, good pay, full staff benefits. [Shares much appreciated] Lab: www.jobbnorge.no/en/available... Modelling: www.jobbnorge.no/en/available...

Iain Johnston@mitomaths.bsky.social

Excited to share our new review looking at how mitochondrial dynamics help resolve conflicting priorities that the cell faces! We extend the "social network" mito picture to a "societal network": trade networks, infrastructure, comms, pollution... www.sciencedirect.com/science/arti...

Iain Johnston reposted

Pawel Burkhardt
@pawelburkhardt.bsky.social

Thrilled to see our review article "The evolutionary origins of synaptic proteins" highlighted on the cover of Nature Reviews Neuroscience 🤩. www.nature.com/articles/s41... @msarscentre.bsky.social 🧠✨🧬🌊🪼🧽

Pawel Burkhardt@pawelburkhardt.bsky.social

First neurons didn’t appear overnight. We trace their roots to ancient secretory cells - showing how lifestyle & behavior shaped the evolution of first synapses.🧠🌊 #Evolution #Neuroscience Our latest in @natrevneuro.nature.com Link: rdcu.be/eMX3E @jeffcolgren.bsky.social @msarscentre.bsky.social

rdcu.beThe evolutionary origins of synaptic proteins and their changing roles in different organisms across evolutionNature Reviews Neuroscience - Recent studies have shed further light on the evolutionary origins of chemical synapses, In this Review, Colgren and Burkhardt explore how ancient proteins were...

Iain Johnston reposted

Buzz Baum
@buzzbaum.bsky.social

Replying to @tbharat-lab.bsky.social

We have wondered what a complex archaeal cell might look like ever since 2014. It’s been a long road (and the journey is far from over), but it’s a good time to pause for breath and look. These Asgard archaeal cells are a surprise! And that is the joy of being a cell biologist.

Iain Johnston reposted

Journal of Evolutionary Biology
@jevbio.bsky.social

In some species, #mitochondria have lost functions: from specific complexes to the ability to produce #ATP (and more!). We examine the evolutionary pathways of this reduction, from yeast and mistletoe to parasite "MROs": doi.org/10.1093/jeb/... @mitomaths.bsky.social et al. 2025

doi.orgConvergent pathways of reductive mitochondrial evolution characterized with hypercubic inferenceAbstract. For a striking example of mitochondrial behaviour beyond adenosine triphosphate (ATP) generation, consider mitochondrion-related organelles (MROs
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Iain Johnston
@mitomaths.bsky.social

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/

Iain Johnston
@mitomaths.bsky.social

Would love to hear any feedback; we continue to believe that EvAM applied to AMR (learning evolutionary history) can be a powerful complement to genomic surveys (focussing on the present). Thanks for reading! www.biorxiv.org/content/10.1... 5/5

biorxiv.orgGlobal diversity, predictors, and predictions of AMR evolutionary pathways in Klebsiella pneumoniaeAntimicrobial resistance (AMR) is a substantial and growing global health burden. Understanding, and predicting, its evolution in specific pathogens will help responses across scales from individual p...
Iain Johnston
@mitomaths.bsky.social

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/

Iain Johnston
@mitomaths.bsky.social

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

Iain Johnston
@mitomaths.bsky.social

There'll be 2 PhD positions (math / microscopy) on MitoPhyto. But the Norwegian research council is also offering opportunities for non-European postdocs to come to Norway for 3 years associated with FRIPRO projects. Please DM me if interested! www.forskningsradet.no/en/call-for-...

forskningsradet.noRecruitment of Talented Researchers to NorwayThe Research Council supports the recruitment of talented international researchers to the Research Council's centre calls and for projects funded ...

Iain Johnston reposted

Kin Pan Chung
@kinpanchung.bsky.social

Glad to share this review, which takes a narrative approach to explore mechanisms governing cytoplasmic inheritance. It highlights exciting advances in the field, while also pointing to the many open questions that remain. Have a read here: doi.org/10.1093/plph...

doi.orgCytoplasmic Inheritance: The Transmission of Plastid and Mitochondrial Genomes Across Cells and GenerationsAbstract. In photosynthetic organisms, genetic material is stored in the nucleus and the two cytoplasmic organelles: plastids and mitochondria. While both

Iain Johnston reposted

Dr. Hilary Rose Dawson
@hilaryrosed.bsky.social

Exciting permanent(!) #JobAlert for a #botanist to work in Bergen, Norway 🧪 PhD required, language proficiency required within two years. Apply by 25 April. #Ecology #Restoration #Botany

Norwegian Institute for Nature Research (NINA)@ninanatureresearch.bsky.social

NINA is expanding its expertise in vegetation ecology and restoration and is seeking a skilled and dedicated researcher to strengthen our team in Bergen. nina-english.attract.reachmee.com/jobs/70-rese...