Tommi Mäklin

the assignment operator is a function and you can overwrite it in the global scope with '<<-' if you need to brick a session:

> unlockBinding('<-', baseenv())
> '<-' <<- function(x) 5
> a = '<-'()
> a
[1] 5

didn't apply this year so I have no personal point of comparison but always "fun" watching the collapse in real time

wow this really looks like a mountain of LLM generated reviews and/or proposals

(this is a joke but the funding system is rapidly becoming a net negative on the time/money spent vs. funding available axis)

maybe phd programs should skip the research training part and train people to write applications, instead, since that's all you'll have time to do anyway

With a +64% increase in MSCA 2025 scholarship applications, funding cut-offs reached absurd levels. (e.g. a score of 96/100 remained unfunded, got news today from a candidate I sponsored). When rating is this compressed, a lottery among top-rated proposals deserves serious consideration I think.

At long last, my final PhD chapter is out: we developed a novel evolutionary simulator of bacterial pangenomes, Pansim, fitting it to data from >600K genomes using a likelihood-free framework, PopPUNK-mod, to explore neutral and adaptive pangenome dynamics www.biorxiv.org/content/10.6...

Bioinformatics Orphanage A place for bioinformatics software that has been abandoned - Bioinformatics Orphanage

Bioinformatics orphanage - repository of bioinformatics packages that are no longer maintained upstream but still have users, or is a dependency for other more frequently used packages.

I think this is a fun idea, and potentially an important one for the future...💻🧬

github.com/bioinformati...

Very excited about this latest work led by @jermp.bsky.social! Since it's initial release, SSHash has served as the basis for several other tools (Fulgor, piscem, etc.). It was already very fast. It is now *substantially* faster!

www.biorxiv.org/content/10.6...

"Machine learning-based lineage prediction from antimicrobial susceptibility testing phenotypes for Escherichia coli sequence type 131 clade C surveillance across infection types" Spoiler: the MDR ST131-C is pervasive in UTIs, underlying BSI trends. doi.org/10.1099/mgen... @microbiologysociety.org

Fluorescence increases over time in mother cells due to aggregates.

How does E. coli age? According to this #mBio study, the the decisive factor driving growth decline in E. coli is not the presence of protein aggregates, but the fraction of the intracellular space they occupy. Learn more: asm.social/2KZ

Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes d...

📣 preprint alert!
We sampled #klebsiella isolates from💩 patients when they entered the hospital & 🩸 after development of infection.

🎯 We tracked phenotypic changes & correlate them w genotypic changes.
@klebclub.bsky.social
-in collab with Clermont-Ferrand lab
#microsky
🧵
doi.org/10.64898/202...

The changing roles of Escherichia coli - Nature Microbiology Richard Lenski traces the legacy of Escherichia coli and how science is evolving to use this model organism in new ways.

The changing roles of Escherichia coli www.nature.com/articles/s41... #jcampubs

"..based on a common wavefront design that can be adapted to support a variety of dynamic programming algorithms: local, global, and semi-global alignment of genomic and protein sequences with a variety of commonly used scoring schemes" from
@martinsteinegger.bsky.social andco

How Unethical Research Seeds Medical Mistrust The absence of equipoise can turn research into harm

"Ethical standards do not become optional because the participants are African."

bktitanji.substack.com/p/how-unethi...

Context Widows or, of GPUs, LPUs, and Goal Displacement

I wrote a piece on LLMs, citation metrics, and the institution of science. It's been up for a couple of days, but it is officially "out" now.

Preprint Alert!
With @tmthrz.bsky.social and @rayanchikhi.bsky.social we aim to tackle practical unitigs compression!
A thread:

If you ever need to fuzzy search some DNA, sassy is your tool.

Please spread the word; I think many people just outside my own circle could benefit from this :)

cc @rickbitloo.bsky.social

github.com/RagnarGrootK...

Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage https://www.biorxiv.org/content/10.64898/2025.12.08.692488v1

The Ice is Alive: Uncovering the Vanishing World of Glacial Microbes Glaciers are flush with microbial life. But, as climate change speeds glacial melting, scientists rush to establish microbial biobanks to preserve them.

Lovely to feature alongside the brilliant Birgit Sattler & Tom Battin in this story about life in Earth's dying ice.

www.the-scientist.com/the-ice-is-a...

Amazing dataset describing the metabolic profiles of 66 E. coli transporter knockouts by @sulheim.bsky.social with Peter Doubleday and @nzamboni.bsky.social. The tool, set up by @lambdapp.bsky.social and Eric Ulrich allows you to explore for yourself. Enjoy! Pre-print here: doi.org/10.1101/2025...

The specificity and structure of DNA cross-linking by the gut bacterial genotoxin colibactin Accumulating evidence has connected the chemically unstable, DNA-damaging gut bacterial natural product colibactin to colorectal cancer, including the identification of mutational signatures that are ...

Colibactin-DNA interstrand crosslinks structure reveals DNA-damaging acitivity of colibactin that is linked to colorectal cancer #MicroSky www.science.org/doi/10.1126/...

1/9 Just out:

k-mer indexes are the backbone of fast search in genomic data, but many degrade under small k, subsampling, or high diversity.

With Ondřej Sladký and @pavelvesely.bsky.social we asked: can we build one that works efficiently for any k-mer set?

Preprint out! Check out our new long-read metagenomic SNP-caller, SNooPy 😀. Work with Chris Quince. Thread 🧵
👉 www.biorxiv.org/content/10.6...

🧬🛡️How are new immune mechanisms created?

We show how Lamassu antiphage system, originated from a DNA-repair complex and evolved into a compact and modular immune machine, wt Dinshaw Patel lab in @pnas.org.
👏 @matthieu-haudiquet.bsky.social, Arpita Chakravarti & all authors!

doi.org/10.1073/pnas...

Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1

If you're about to push these last manuscripts before wrapping up 2025, remider that our MGen Eukaryotic collection @microbiologysociety.org is open & growing; #Protists #Parasites #Fungi; friend or foe; all welcome 😊
#MicroSky #IDSky #Protistsonsky 🧬💻
www.microbiologyresearch.org/content/micr...

High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...

Really pleased to share the first paper to come out of the lab.
We found that hospital patients were frequently colonised with P. aeruginosa and that the same clone was shared between the gut and the lung.
The phylogenies indicate that the clones moved from lung->gut

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

Chromosomal Curing Drives an Arms Race Between Bacterial Transformation and Prophage Abstract. Transformation occurs when bacteria import exogenous DNA via the competence machinery and integrate it into their genome through homologous recom

#microsky #phagesky #phage

Anyone who’s tried deleting prophages in the lab by HR knows the difficulties of the task. Here we have an example of how HR-mediated natural transformation might hit the same hurdle in a more native context.

academic.oup.com/mbe/article/...

Intracellular competition shapes plasmid population dynamics From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...

Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/
www.science.org/doi/10.1126/...