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Iain Johnston @mitomaths.bsky.social · 16d

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...
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Global diversity, predictors, and predictions of AMR evolutionary pathways in Klebsiella pneumoniae

Antimicrobial 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...

www.biorxiv.org

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Iain Johnston @mitomaths.bsky.social · 16d

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/

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Iain Johnston @mitomaths.bsky.social · 16d

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/

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Iain Johnston @mitomaths.bsky.social · 16d

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/

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Iain Johnston @mitomaths.bsky.social · 16d

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/

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Iain Johnston @mitomaths.bsky.social · Jun 17

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-...

Recruitment of Talented Researchers to Norway

The Research Council supports the recruitment of talented international researchers to the Research Council's centre calls and for projects funded ...

www.forskningsradet.no

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Iain Johnston @mitomaths.bsky.social · Jun 17

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

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Iain Johnston @mitomaths.bsky.social · May 17

Gratulerer med dagen alle sammen!
(non-Norway-based folks, happy Norwegian Constitution Day!)

Reposted by Iain Johnston

Kin Pan Chung @kinpanchung.bsky.social · May 5

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...

Cytoplasmic Inheritance: The Transmission of Plastid and Mitochondrial Genomes Across Cells and Generations

Abstract. In photosynthetic organisms, genetic material is stored in the nucleus and the two cytoplasmic organelles: plastids and mitochondria. While both

doi.org

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Iain Johnston @mitomaths.bsky.social · May 7

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...

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Iain Johnston @mitomaths.bsky.social · May 7

May trails on the way to the final Applied Statistics lecture of the semester!

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Iain Johnston @mitomaths.bsky.social · May 2

View from the office as summer approaches

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Reposted by Iain Johnston

Dr. Hilary Rose Dawson @hilaryrosed.bsky.social · Apr 1

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 · Mar 31

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...

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Reposted by Iain Johnston

Eva Nowack @evanowack.bsky.social · Mar 19

Out today: Exciting intermediate between endosymbiont and organelle identified! Endosymbionts in Angomonas deanei lost nearly all bacterial cell division genes. Instead, we identified a host-encoded protein, ETP9, that became specialized for endosymbiont division. 1/2
www.science.org/doi/10.1126/...

Angomonas deanei with flourescent-labeled nucleus and endosymbiont. ETP9 localizes at the endosymbiont division site.

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Iain Johnston @mitomaths.bsky.social · Mar 19

Projector broke today, so a good old-school blackboard lecture on an intro to GLMs!

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Reposted by Iain Johnston

Kat Holt @katholt.bsky.social · Mar 17

Watching the US take a wrecking ball to science 💔 🤯

Reminder of the importance of doing science in the open. Put data, software, resources in public domain, where no single govt can erase them. This is our collective knowledge. Distributed data systems are essential.

www.nature.com/articles/s41...

Genomic data sharing: you don’t know what you’ve got (till it’s gone) - Nature Reviews Genetics

Reflecting on the core values of early data sharing agreements, the Bermuda Principles and the Fort Lauderdale Agreement, Kathryn E. Holt and Michael Inouye emphasize the need to reaffirm our commitme...

www.nature.com

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Iain Johnston @mitomaths.bsky.social · Mar 7

Great to see this out in final form! www.nature.com/articles/s41...
Continuous buildup of single-cell-specific mtDNA mutations throughout ageing, and their links with health. Mitos, scRNA, scATAC, models, ER, neuro... a smorgasbord of science! Congrats all! @syssig.bsky.social

Cryptic mitochondrial DNA mutations coincide with mid-late life and are pathophysiologically informative in single cells across tissues and species - Nature Communications

Mitochondrial dysfunction is implicated in ageing. Here the authors report that across tissues and species, somatic mitochondrial DNA mutations in single cells (termed cryptic mutations) accumulate wi...

www.nature.com

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Iain Johnston @mitomaths.bsky.social · Feb 26

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)

Iain Johnston @mitomaths.bsky.social · Feb 24

A classic to celebrate this evening's proposal submission. If you haven't heard this before, I recommend sticking with it, it's somewhat unlikely you've heard a song like this before!
www.youtube.com/watch?v=rxjE...
Lyrics www.metalkingdom.net/lyrics-song/...

Grace

YouTube video by Devin Townsend Project - Topic

www.youtube.com

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Iain Johnston @mitomaths.bsky.social · Feb 20

Some shots from wintery commutes in 2025!

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Iain Johnston @mitomaths.bsky.social · Feb 20

Nice group meeting today, celebrating exciting new positions and discussing the diverse ways we do science with data! Thanks all

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Iain Johnston @mitomaths.bsky.social · Feb 20

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

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Iain Johnston @mitomaths.bsky.social · Feb 20

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/

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Iain Johnston @mitomaths.bsky.social · Feb 20

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/

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Reposted by Iain Johnston

Cordian Riener @cordianriener.bsky.social · Jan 25

This year’s Mørketidens Mattemøte once again brought mathematicians from across Norway and the Nordic countries to @uitnorgesarktiske.bsky.social for two inspiring days of idea exchange and new connections.
Thanks to Tromsø Forskningsstiftelse and Trond Mohn forskningsstiftelse for the support !

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