@aldertzomer
Associate Professor at Utrecht University, Infectious Diseases & Immunology. (meta)genomes, AMR, zoonotic pathogens. Cookie and cake connoisseur. publications: https://scholar.google.com/citations?hl=nl&user=VHHhpoAAAAAJ&view_op=list_works&sortby=pubdate
Our faculty has a particularly interesting PhD position open on antimicrobial resistance, effects of antibiotics treatment on the microbiome and resistome, restoration of the equine microbiome using FMT.
www.uu.nl/en/organisat...
Please contact Mathijs Theelen, email address in the link below.
Congratulations!
Announcing a new tool for "denoising" long-read amplicon sequences: savont.
Savont enables amplicon sequence variants (ASVs) directly from nanopore (or HiFi) long reads. Tested on 16S nanopore amplicons -- seems to work okay.
1/4
github.com/bluenote-157...
Only if Iβm being paid. That sounds like one workday a week.
Vacancy graphic showing a microbial microscopy image on a computer. The text reads "Bursting Bugs Summer Internship. To generate microscopy videos of bacteria bursting in response to administering antibiotics. Salary: Β£3,270 total. Contract length: 5 weeks. Apply by 5 January 2026."
Weβre looking for a Summer Intern to generate microscopy videos of bacteria bursting in response to administering antibiotics as part of a public education video on the uses of antibiotics and risks of misuse π¬
ποΈ Apply by 5 January
β‘οΈ buff.ly/YlUQUho
I did exactly the same thing. Why bother poor editors and reviewers over Christmas.
πΎ Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
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...
8/
Authored by Aldert Zomer, Sam Nooij, Cailean Carter, and Alison Mather (@alisonmather.bsky.social).
Supported by the JPIAMR MEGAISurv project: jpiamr.eu/projects/meg...
Thanks to all contributing to strengthening mutation-focused AMR surveillance in metagenomic data.
7/
The code is open-source, with both a web-based interface and the full repository available:
Web tool: klif.uu.nl/metapointfin...
GitHub: github.com/aldertzomer/...
Feedback on extending reference sets and integrating the approach into surveillance pipelines is welcome.
6/
We applied the tool to public datasets on fluoroquinolone, Ξ²-lactam, and rifamycin resistance, showing how mutation-level profiling resolves discrepancies between phenotypes and gene-only predictions.
5/
In benchmarks using simulated reads (100β5000 bp), MetaPointFinder outperformed existing mutation mappers and showed strong recovery of mutation-positive reads, particularly from long-read metagenomes.
4/
The outputs enable calculation of both relative abundance of mutation-driven AMR and the proportion of resistant reads among all reads mapping to a locus (WT + R). Metrics can be summarised at read, gene, or antibiotic-class level, extending metagenomic resistome profiling beyond gene presence.
3/
MetaPointFinder performs read-level protein and DNA alignment (DIAMOND + KMA) against curated AMRFinder mutation references. A custom scoring engine evaluates each substitution, enabling accurate detection across both long- and short-read datasets.
2/
In metagenomic data, most AMR tools detect only acquired genes, while point mutations in gyrA, parC, folA, rpoB, 23S rRNA and others are major drivers of resistance. These variants are rarely quantified because they require precise alignment and position-specific evaluation.
1/
Our preprint on MetaPointFinder is online:
www.biorxiv.org/content/10.6...
Current resistome profiling has a major gap: it misses mutation-driven AMR, even though chromosomal mutations underpin resistance to key antimicrobials. MetaPointFinder addresses this at the read level in metagenomes.
MetaPointFinder:
A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads.
Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss.
github.com/aldertzomer/...
πΎ ABRicate 1.2.0 has been released!
This 'oversight' lasted 6 years, but with help from @finlaym.bsky.social we got CI working and updated all the databases. #bioconda #conda #bioinformatics #microbiology #genomics
github.com/tseemann/abr...
It's the last few days to apply for this #PhDposition starting in Oct 2026 with us @quadraminstitute.bsky.social.
Do you like bacteria, genomics & puzzles?π¦ π§¬π§©
Do you wanna work in a cutting edge of science, with some awesome people? π
Please apply or share by 2 Dec ποΈ
Find out more β¬
All good things come in threes. This paper wasnβt.
Nice. 23 thousand pound for a 5 week internship.
I am increasingly of the opinion that people who change menus and look and feel of computer software just so that you know it's a new version should be personally forced to play tech support to my mother for five months.
Found it! No Netherlands map but UK is still good
Cool! Where did you get that device?
Amazon announced 14,000 layoffs. Its CEO made over $40M last year.
UPS announced 48,000 layoffs. Its CEO made over $24M last year.
Intel announced 20,000 layoffs. Its new CEO's pay package is valued at nearly $69M.
This is what I mean when I say the system is rigged.
![4-panel vertical comic. (1) 100 Years Ago [two people standing next to bicycle with small car nearby] PERSON 1: Itβs too dangerous riding a bike with these cars around. I should get a car, too. (2) 50 Years Ago [two people between smaller car and bigger car] PERSON 2 with short hair: Small cars are less safe in collisions with larger vehicles, so I should get a bigger one. (3) Today [two people between big car and even bigger car] PERSON 1: Everyone has huge SUVs now. If I donβt get the biggest one, Iβm putting my family at risk. (4) Soon [two people next to large armored car with spiked clubs attached] PERSON 2: If I donβt install more whirling spike clubs, Iβll be destroyed by all the other drivers who...](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:cz73r7iyiqn26upot4jtjdhk/bafkreiby6can6k76yzfmv2czxs4pu2l7zie7bqbrpswi7h3ifmiadkuqvu)
4-panel vertical comic. (1) 100 Years Ago [two people standing next to bicycle with small car nearby] PERSON 1: Itβs too dangerous riding a bike with these cars around. I should get a car, too. (2) 50 Years Ago [two people between smaller car and bigger car] PERSON 2 with short hair: Small cars are less safe in collisions with larger vehicles, so I should get a bigger one. (3) Today [two people between big car and even bigger car] PERSON 1: Everyone has huge SUVs now. If I donβt get the biggest one, Iβm putting my family at risk. (4) Soon [two people next to large armored car with spiked clubs attached] PERSON 2: If I donβt install more whirling spike clubs, Iβll be destroyed by all the other drivers who...
Car Size
xkcd.com/3167/
I find the small peaks at +/-4 interesting as well
A digital illustration of DNA with the text "Funded PhD, Out of order: investigating genetic and environmental drivers of genome rearrangement, with Dr Gemma Langridge, Apply by 2 December 2025"
π #PhDPosition !
𧬠Out of order: investigating genetic and environmental drivers of genome rearrangement with Dr Gemma Langridge @langridgelab.bsky.social
π
Apply by 2 December
β‘οΈhttps://buff.ly/k31MNuV
October 2025 batch of Kraken 2 indexes, including core_nt and many others, available: benlangmead.github.io/aws-indexes/k2
Coming soon to K2: a feature for querying many K2 indexes as though they're a single index. Highly useful if the index you want to query is too big to build and/or fit in RAM.
Are there plans to build a kraken2 database of the LLNL cleaned up nt db?
