Tommi Mäklin

Happy to share the latest work from Zunair Khurram, a PhD student in our lab! Zunair has developed a new method, MxSure, to infer within-host substitution rates and transmission thresholds from longitudinal isolate and metagenomic sequencing data. www.biorxiv.org/content/10.6...

🧬 New preprint! We clustered 5.6 million bacterial genomes into genomically cohesive units (GCUs) 500× faster than existing tools. (In just 14 hours, 16.5 GB RAM using 48 CPUs). 🦠🐙Meet gemsparcl 💎✨! www.biorxiv.org/content/10.6...

This is now published in Genome Research (doi.org/10.1101/gr.2...). Thank you everyone for your feedback and also the anonymous reviewers who helped to greatly improve the paper. I hope this becomes a useful resource for the community.

Want to annotate a bacterial genome with structures? @oschwengers.bsky.social bakta and @gbouras13.bsky.social phold got together, and the result is Baktfold: protein annotation across the microbial tree of life using structures www.biorxiv.org/content/10.6... #phagesky #microsky #microbiomesky

someone registered a codeberg account just to make a pull request updating a dependency in a side project that I haven't worked on in nearly a year and nobody uses. respect.

Today, MSF is going public with something we've been fighting behind closed doors for months: Gilead will not sell us their new HIV drug, lenacapavir. The sticking point isn't even price, they just refuse to sell. Open letter linked + explainer 🧵1/ www.doctorswithoutborders.org/latest/gilea...

A quick rant on people vibe-translating our Rust libraries to other languages That's the second time in a week that I see new bioinformatics tools with a vibe-coded translation of our Rust libraries to C/C++. I have two major issues with that:

We created a database compatible with Kaptive3 of 90 distinct capsule (K) loci; 66% represented novel K-loci that did not correspond to the known phenotypic K-antigens. Give it a whirl, and get in touch to have novel K-loci added to the DB github.com/rgladstone/E...

Now published! 'Identification of transporter-dependent capsular loci associated with the invasive potential of Escherichia coli' www.nature.com/articles/s41... insights below.....

Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...

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 - 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

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

📣 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 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

"Ethical standards do not become optional because the participants are African." bktitanji.substack.com/p/how-unethi...

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

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...

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...

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...

#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/...

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/...

Very happy to see this piece out in @plosbiology.org, on the bacterial immune systems and microbial communities. It was a great team effort with Rafael Custodio, @brockhurstlab.bsky.social , @brownlab.bsky.social, and Edze Westra! 🦠🧫 #phagesky #mevosky journals.plos.org/plosbiology/...

@wytamma.bsky.social : so, it took a little bit of extra time (not the flight back from the CZI meeting), but I decided to just f#&$ing do it, and the basic code to build and parse with the auxiliary fastq index is working (github.com/COMBINE-lab/...). 1/2

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

New preprint: we looked into production of the bacterial toxin colibactin and found that MDR E. coli from the global north have co-evolved with endemic colibactin producers, acquiring colibactin resistance genes before undergoing clonal expansions. www.biorxiv.org/content/10.1...

My account's upload and bulk download access were terminated permanently in 2021 without explanation after I published *checksums* of GISAID genomes. GISAID and its SAB have since ignored a dozen emails seeking explanation. 4 yrs on, even Nextstrain has lost access. GISAID has rotted from its core.

The link between the gut #microbiome and autism is not backed by science, researchers say. Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA @wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social

Metagenomics colleagues! I'm looking for studies where both Illumina and ONT sequencing were performed on the same samples from soil, human, ruminent, and other sample types for comparison. Bonus if those studies include PacBio data. Please help and share!