Plasmid mutation rates scale with copy number
doi.org/10.1073/pnas...

How somatic evolution affects health - Nature Ecology & Evolution As somatic evolution becomes directly measurable, integrating eco-evolutionary principles with high-resolution molecular data creates opportunities to anticipate and prevent disease.

How somatic evolution affects health?
www.nature.com/articles/s41...

Paul Ehrlich has died www.nytimes.com/2026/03/15/b..., some say the coming misery of my generation might have something to do with him.

No need to share near identical receptors, but this would make the jump easier. In some contexts, sharing some molecular features would suffice, e.g, some amino acid motif.

Riboviruses are cool!
A symbiotic origin of the ribosome?
academic.oup.com/pnasnexus/ar...

Chen Ning “Frank” Yang (1922–2025): Profound proponent of symmetry
'Where there is a bang, there is Yang'
www.pnas.org/doi/10.1073/...

Courtesy of @martibartfast.bsky.social , we have a new release of AllTheBacteria which adds another 322,920 assemblies, covering all ENA (illumina, isolate) prokaryotes to May 2025.
allthebacteria.readthedocs.io/en/latest/ov...

Fitness flux and ubiquity of adaptive evolution | PNAS Natural selection favors fitter variants in a population, but actual evolutionary processes may decrease fitness by mutations and genetic drift. Ho...

Finally, got the whole idea, it just took 10+ years to get there.
It seems to connect everything since Fisher and Wright, etc.
www.pnas.org/doi/10.1073/...

A mathematical model from statistical physics can help reveal properties of populations under changing immune selection (changing fitness landscapes/seascapes).
www.biorxiv.org/content/10.1...

朋友们，马年大吉！

A small polymerase ribozyme that can synthesize itself and its complementary strand The emergence of a chemical system capable of self-replication and evolution is a critical event in the origin of life. RNA polymerase ribozymes can replicate RNA, but their large size and structural ...

So understanding origin of life and RNA viruses converges?
www.science.org/doi/10.1126/...

CHAOS AND UNPREDICTABILITY IN EVOLUTION Abstract. The possibility of complicated dynamic behavior driven by nonlinear feedbacks in dynamical systems has revolutionized science in the latter part

Such a nice paper, finally got the time to read it.
academic.oup.com/evolut/artic...

Interesting paper www.nature.com/articles/s41... it seems to be consistent with recent spillover event(s) discovered in a dairy farm in the northern Netherlands, but would be interesting to see how many of those potentially mammal adaptive mutations in this wave of bird migration?

Sec and Tat mediated secretion safeguards Mycobacterium tuberculosis membrane homeostasis
www.biorxiv.org/content/10.1...

"HLA micropolymorphisms confine neoantigen conformational adaptability and guide T cell receptor selectivity"
www.biorxiv.org/content/10.6...

It is odd to me too, first read your post.

Well, that's almost every postdoc's daily life in Oxford or Cambridge. On the positive side, some of the research directions you pursue can be intellectually satisfactory and beneficial to your career even if they did not make it to one of these journals.

Somatic and germline mutational processes across the tree of life
www.researchsquare.com/article/rs-8...

"...progression to colorectal cancer requires traversing a rugged fitness landscape, whereas subsequent CNA evolution is constrained by negative selection."
aacrjournals.org/cancerdiscov...

Bird flu antibodies found in cow in the Netherlands, a first outside of U.S. Dead cat led to discovery, but officials stress no further spread of H5N1 has been detected

This first probable case of highly pathogenic avian influenza in a dairy cow in Europe raises two points. First, it suggests that virus incursion is possible in the Dutch housing system, which differs from that in the southern U.S., where cows were first infectted. www.science.org/content/arti...

Molecular characterization of Ebola virus glycoprotein V75A substitution in the 2018–2020 epidemic An Ebola virus glycoprotein mutant, which emerged early during the 2018–2020 epidemic, enhances viral infectivity through multiple mechanisms and may have contributed to its dominance in the outbreak.

Will there be convergent evolution in the GP RBD for NPC1 for ongoing and future outbreaks assuming they are from different zoonotic reservoirs? www.biorxiv.org/content/10.1...
www.cell.com/cell/fulltex...

Going Founder Mode On Cancer Sid Sijbrandij's extraordinary care journey

Interesting blog about a Dutch software entrepreneur and his approach to fight his own cancer. centuryofbio.com/p/sid

I guess it wont work well is because many genes and their carriers/genomes evolve in a way determined by non-fixed population genetic parameters, and current data do not cover their changing evolutionary landscapes spanning vast biological complexity. www.biorxiv.org/content/10.6...

Prediction in ecology and evolution Abstract. Prediction is frequently asserted to be the sine qua non of science, but prediction means different things to different people in different conte

This is fun: "By the year 2000, the United Kingdom will be simply a small group of impoverished islands, inhabited by some 70 million hungry people. —Ehrlich (1968)"

"Prediction in ecology and evolution"
academic.oup.com/bioscience/a...

Healthcare Infrastructure Shapes Evolutionary Trade-offs and Geographic Dissemination of Multidrug-Resistant Acinetobacter baumannii Antimicrobial-resistant pathogens pose an existential threat to modern medicine, yet the evolutionary forces driving their adaptation in healthcare systems remain largely unexplored. We revealed that ...

Healthcare setting driven evolution:

doi.org/10.64898/202...

Happy New Year with a nice pint of IPA.

EP20: Yann LeCun YouTube video by The Information Bottleneck

One comment I like is that many of the "working" methods are like "cooking recipes", and you also need diversity for future success in this field.
www.youtube.com/watch?v=7u-D...

Gene copy-number features generalize better than SNPs for antimicrobial resistance prediction in Staphylococcus aureus - npj Antimicrobials and Resistance npj Antimicrobials and Resistance - Gene copy-number features generalize better than SNPs for antimicrobial resistance prediction in Staphylococcus aureus

Generally bacteria can have large effective population size, and there are less genetic redundancy due to effective selection, so gene copy number can be very useful in certain context for predictive modelling.
www.nature.com/articles/s44...

Using LLMs responsibly should be taught from primary schools now.

A metabolic atlas of the Klebsiella pneumoniae species complex reveals lineage-specific metabolism and capacity for intra-species co-operation Why are there so many co-circulating Klebsiella pneumoniae clones? Using genomics and large-scale metabolic modelling of >7000 isolates, this study identifies structured, clone-specific metabolic spec...

Absolutely stoked to have this published in @plosbiology.org

We looked at the metabolism of #Klebsiella pneumoniae 🦠🧫. We not only demonstrated lineage-specific #metabolism, but that lineages can cross-feed and support each other.

journals.plos.org/plosbiology/...

#MicroSky #microbiology 🧬 🧪 💊