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...

MxSure: a mixture model for inferring within-host substitution rates and transmission SNP thresholds

Quantifying short-term evolutionary rates of microbial genomes is essential for understanding the processes that shape within-host evolution and for establishing thresholds needed to track transmissio...

biorxiv.org

🧬 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.

1/4 Hash functions in genomic sequence analysis (tinyurl.com/4kk9ccmt) : a new survey written together with Ke Chen, Xiang Li, Qian Shi, and Mingfu Shao. Before submitting it, we are posting it online to get feedback from 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...

Gilead refuses to sell groundbreaking HIV prevention drug to MSF

Blocking humanitarian organizations from accessing a medical breakthrough puts vulnerable people across the world in danger.

doctorswithoutborders.org

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...

Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis

Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…

sciencedirect.com

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

Natalie Schaworonkow@nschawor.bsky.social · 6mo ago

the cutoff scores for #MSCA postdoc fellowships are very high this year. has the score distribution shifted compared to previous years? I made a plot with scores from past years. if scores are at ceiling level, the process becomes essentially a lottery, because minor issues can lead to deductions.

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

Alessandro Gozzi@gozziale.bsky.social · 6mo ago

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.

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...

Bioinformatics Orphanage

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

github.com

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...

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...

doi.org

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

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.

nature.com

"..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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 8mo ago

Accelign: a GPU-based Library for Accelerating Pairwise Sequence Alignment https://www.biorxiv.org/content/10.64898/2025.12.17.694868v1

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

How Unethical Research Seeds Medical Mistrust

The absence of equipoise can turn research into harm

bktitanji.substack.com

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.

Context Widows

or, of GPUs, LPUs, and Goal Displacement

artificialbureaucracy.substack.com

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

bioRxiv Bioinfo@biorxiv-bioinfo.bsky.social · 8mo ago

Inverted colored de Bruijn Graph for practical kmer sets storage https://www.biorxiv.org/content/10.64898/2025.12.08.692073v1

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...

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.

the-scientist.com

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...

Snorre Sulheim@sulheim.bsky.social · 9mo ago

Do you think transporters in E. coli contribute to metabolite release? No? Explore the effect of 66 different transporter knockout mutations on the exometabolome dynamics of ~300 metabolites yourself: keio.unil.ch Teaser: Increased proline in ΔputP #microsky #MEvoSky

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

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 ...

science.org

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?

Bioinformatics Advances@bioinfoadv.bsky.social · 9mo ago

🧮 Just out in Bioinformatics Advances: “FroM Superstring to Indexing: A space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT)”  Full article available: https://doi.org/10.1093/bioadv/vbaf290  Authors include: @pavelvesely.bsky.social, @brinda.eu