What was antibiotic resistance like before we ever used antibiotics? How did we change what antibiotic resistance genes looked like over 100 years? Our paper looking at resistance genes from a century of NCTC historical isolates now out in mGen: www.microbiologyresearch.org/content/jour...

This is one of the findings that really motivates my research: yes, antibiotic resistance genes are ancient, but the age of antibiotics has likely contributed to a big change in their mobility and of the landscape of MGEs we see today! Very happy for Arya and to see this published.

This FTP ftp.ebi.ac.uk/pub/database... from EBI www.ebi.ac.uk/gwas/docs/di... seems to have the iconic GWAS diagram

Unwelcome guests: characterizing the ecological niche of insertion sequences within prokaryotic genomes https://www.biorxiv.org/content/10.1101/2025.07.22.666184v1

With the addition of the soil genome catalogue, MGnify now hosts over half a million genomes - exciting milestone for the resource.

This looks phenomenal. Hat tip to ‪@vivekmutalik.bsky.social‬

Here's our new broad review on the extended mobility of plasmids, about all mechanisms driving and limiting their transfer. From conjugation to conduction, phage-plasmids to hitchers, molecular to evolutionary dynamics, ecology to biotech. The state of affairs. 1/9 academic.oup.com/nar/article/...

Today's reading: Nature should be the model for microbial sciences journals.asm.org/doi/10.1128/... by @brettbakker.bsky.social @emilyraehyde.bsky.social and @pedroleao.bsky.social Looks ideal for a talk I am working on on model organisms ...

New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51

GRC insisting on the vote for the next location being in person in the name of democracy

⚠️ New preprint ⚠️: Two new antibiotics are likely coming for gonorrhea 💊. How should we deploy them in the US to minimize drug resistance? @kroster.bsky.social @dhelekal.bsky.social Eva Rumpler @yhgrad.bsky.social [1/10] www.medrxiv.org/content/10.1...

It's 25 yrs to the day since the Human Genome Project & Craig Venter declared joint victory in sequencing the human genome - an ideal time for @wellcometrust.bsky.social to annouce their new project, involving our lab, to begin work towards synthesising human genomes. wellcome.org/news/researc...

FastGA: Fast Genome Alignment www.biorxiv.org/content/10.1... 🧬🖥️🧪 www.github.com/thegenemyers...

Reading a Big Number xkcd.com/3102/

This seems like an awesome course! jshun.csail.mit.edu/6506-s24/! If there were more hours in the day, I'd want to put something like this together at UMD.

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.

Very excited to share our preprint on a new resource: the Encyclopaedia of Viral Anti-Defence Systems (EVADES)! This is the main result of my PhD at ‪EMBL-EBI (@ebi.embl.org)‬ and the University of Cambridge (@cam.ac.uk‬)! 🔗 www.biorxiv.org/content/10.1... 🧵1/n"

Developing thread that will be a great read.

📜 Excited to share insights from our recent paper: "Kaminari: a resource-frugal index for approximate colored k-mer queries". The study aims to efficiently identify documents containing a query string, focusing on DNA strings. www.biorxiv.org/content/10.1... 🧬 🖥️ 1/8

Slides from my talk (with @kamilsjaron.bsky.social) on an history of k-mers in bioinformatics: rayan.chikhi.name/pdf/2025-kme...

Announcing myloasm, a new long-read (ONT R10/PacBio) metagenome assembler that I've been working on during my postdoc in the Heng Li lab (@lh3lh3.bsky.social). myloasm-docs.github.io

I love this video and a video that often goes with it of humans being way slower at doing the same task. I always wonder, why did the ants want that thing so much? If given a physically impossible version of this puzzle would they try forever?

New in 𝘚𝘊𝘐𝘌𝘕𝘊𝘌: Plague Plays the Long Game As plague pandemics decimated rodent populations, 𝘠𝘦𝘳𝘴𝘪𝘯𝘪𝘢 𝘱𝘦𝘴𝘵𝘪𝘴 adapted Virulence gene 𝘱𝘭𝘢 lost late in outbreaks ➡️ strains with reduced lethality ➡️ pathogen can persist, spread across highly fragmented host networks www.science.org/doi/10.1126/...

Genetic analysis of a (small) group of bedbugs showed their history was entwined with the human story, with the blood-sucking parasites spreading & thriving as humans crammed together in large settlements. 🧪🪲🛏️😬 www.theguardian.com/science/2025...

New blog post! In it, I benchmark the new version of Dorado from @nanoporetech.com, which comes with new DNA basecalling models. Short version: big accuracy gains for hac, small improvements for sup. Check it out for the full results: rrwick.github.io/2025/05/27/d...

Harvard today, your institution tomorrow. It's all part of the Project 2025 plan to destroy high education in America. All leading US universities depend on federal funding and tuition dollars from international students. They severely curtailed the former. Now they're eliminating the latter.

New preprint! Autocycler is a tool for long-read consensus assembly of bacterial genomes. It's like Trycycler but can be run fully automated (without any human intervention). www.biorxiv.org/content/10.1... (1/6)

A simple path, followed by an equation. Basic research leads to knowledge, which leads to nonprofitable ideas, which leads to profitable ideas, which leads to commercial products, which leads to jobs, which fuels the economy. Kill research=kill the economy

Happy to share this interview with Weijie Zhao from NSR at #OxfordUniversityPress. It covers questions I’m often asked—why I chose Korea, AlphaFold2, my unconventional journey into academia, and research insights. Thanks again for the fun conversation. 📄 academic.oup.com/nsr/article/...

these cuts are unconscionable and make America LESS healthy, LESS wealthy, and LESS wise careers of so many of our nation’s brightest young minds are being derailed highlighted in the story is the laboratory of Michael Baym, producing some of the most innovative research on antibiotic resistance

Delighted to see this paper from danderson123.bsky.social 's PhD out. We have been building tools for AMR gene detection for over a decade now, but multicopy genes remain challenging. Dan shows that with a gene-space de Bruijn graph and long reads, you can do well www.biorxiv.org/content/10.1...

Lossless Pangenome Indexing Using Tag Arrays www.biorxiv.org/content/10.1... 🧬🖥️🧪 github.com/parsaeskanda...

Apart from Typst, the other new tech I've been playing with recently is jj VCS. It's good; like, really good. The beauty is in the stripping away of unnecessary complexity from git while refining the primitives so as to be more consistent and not lose any power! github.com/jj-vcs/jj

PHast (Piotr Beling & Peter Sanders) looks like a very shiny new MPHF! It has some very nice improvements over PtrHash, most notably by replacing the load factor alpha<1 by a 'bumped' structure, where unplacable buckets go into a 2nd level. 1/ www.arxiv.org/abs/2504.17918

Looking for examples of beautiful, controversial or impactful microbial modelling papers - ideally a mixture of the above! It’s for teaching in the context of microbial eco/evo/epi. The modelling should be relatively easy to understand for a master’s student with a biology background.

@pavelvesely.bsky.social (CSI) on the mother of spss: masked superstrings that help you representing k-mer sets in a very compact way. He actually takes a lot from @brinda.eu since he squeezed 3 papers in a 12 min talk 😳

V interesting paper from Haoyu Cheng, and @lh3lh3.bsky.social . Key step is a new error correction approach

I was waiting two years to see this out!! The genomic location of bacterial genes is not random!!! Congratulation on the authors (Martin Lercher and Team!). www.science.org/doi/10.1126/...

Phylogenetic compression achieves performant and lossless compression of massive collections of microbial genomes, facilitating fast BLAST-like search and versatile alignment tasks. www.nature.com/articles/s41...

We're looking for a PhD student to join us at Vilnius University in Lithuania. We work on RNA virus evolution computationally but we'd like to generate more mosquito RNA virus sequence data. Official ad: www.gmc.vu.lt/en/doctoral-.... Please share & continue reading if interested.

Is the genome just a bag of genes? A new paper in Science now reports that for two thirds of an organisms' genes the position along the chromosome is actually very tightly constrained! Amazing work from my favorite night scientist Martin Lercher and his team! www.science.org/doi/10.1126/...

A decade ago, we had thousands of bacterial genomes. Now, we have millions. How to scale computational methods? Our paper in @naturemethods.bsky.social answers this: use evolutionary history to guide compression and search. rdcu.be/eg4OA w/ @baym.lol, @zaminiqbal.bsky.social et al. 🧵1/

So glad this is finally out. The method has been instrumental in allowing us to compress the AllTheBacteria data - ~2 million bacterial genomes shrink from 3Terabytes (gzipped) to 100Gb using phylogenetic compression. Great work by @brinda.eu

Open question for CS community: What to teach from modern parallel algorithms to 2nd CS undergrads? We teach sorting networks (bitonic sort) and boolean circuits (summation, multiplication), which is fine but does not feel very modern. What else to show about parallelism in, say, 2 lectures?

Fully funded positions + included travels between Simon Puglisi's and our group. Dm/email if you have questions.

New preprint is out! We investigate how well you can call variants directly from genome assemblies compared to traditional read-based variant calling. Read it here: www.biorxiv.org/content/10.1... Data & code: github.com/rrwick/Are-r... (1/8)

Our pangenome graph-based Nanopore Adaptive Sampling (NAS) tool, GNASTy, is available now in Genome Research! genome.cshlp.org/content/earl...

Excited to share our latest, out today in @naturemicrobiol.bsky.social Bacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium www.nature.com/articles/s41... @idpittstop.bsky.social

1/ Transposable elements are often called "jumping genes" because they mobilize within genomes. 🧬 But did you know they can also jump 𝘣𝘦𝘵𝘸𝘦𝘦𝘯 cells? 🤯 Our new study reveals how retrotransposons invade the germline directly from somatic cells. www.biorxiv.org/content/10.1... A short thread 🧵👇

Reading: Predicting antimicrobial resistance phenotypes across 7,000 E. coli genomes research.arcadiascience.com/pub/result-e... from @arcadiascience.com