Andries van Tonder

A tour de force in
1) genomic epidemiology,
2) global equity of access and representation, and
3) phylogenetic wizardry.

Congrats Zam and Viridian team on this tremendous resource!

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...

New blog post: ONT read QC strategies for assembly
rrwick.github.io/2026/02/05/r...

Mini-study comparing a few QC/subsampling approaches, plus practical notes from my experience.

We're Hiring! We're looking for a postdoc with bioinformatics/modelling skills to join us in an exciting microbiome ecology project in Manchester (deadline 1st March) www.jobs.manchester.ac.uk/Job/JobDetai...

EMBL-EBI Training. Sustainable computing in science: an introduction to the environmental impacts of computational research. This course has been developed in collaboration with the Cambridge Sustainable Computing Lab at the University of Cambridge. It was supported by funding from the Wellcome Trust Foundation and the University of Cambridge.

Have you ever paused and wondered about the many different ways in which computing infrastructure and activities impact the environment?

@loiclnlg.bsky.social and our own Flaminia Zane have created a free guide dedicated to sustainable computing in science: www.ebi.ac.uk/training/onl...

🧬🖥️📊🌱

Research Group Leader Do you want to lead groundbreaking research in computational biology? Join us at EMBL-EBI! EMBL's European Bioinformatics Institute (EMBL-EBI) is seeking talented and highly-motivated scientists to jo...

We are hiring for group leaders again — EBI is a great place to start your research group!

embl.wd103.myworkdayjobs.com/EMBL/job/Hin...

New blog post with some thoughts on @nanoporetech.com and their recent announcement that the P2 Solo will be discontinued:
rrwick.github.io/2026/01/21/p...

"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

This position is still open. The Weisberg lab is recruiting a postdoc or Ph.D. student to study horizontal gene transfer in plant-associated microbial communities. Please see the job ad for more information and feel free to contact me if you have any questions!

PanForest: predicting genes in genomes using random forests AbstractMotivation. The presence or absence of some genes in a genome can influence whether other genes are likely to be present or absent. Understanding t

New paper out in Bioinformatics! PanForest uses random forests to predict gene presence/absence in bacterial genomes based on other genes present. Joint work with Alan Beavan & Maria Rosa Domingo-Sananes.
🔗 doi.org/10.1093/bioinformatics/btag005

We are looking for a new lab administrator (0.5 FTE) - come and join in pushing forward our research and impact in infectious disease! www.cam.ac.uk/jobs/researc...

Phold's manuscript is now available @narjournal.bsky.social thanks to @susiegriggo.bsky.social @npbhavya.bsky.social @vijinim.bsky.social @linsalrob.bsky.social @martinsteinegger.bsky.social @milot.bsky.social @eunbelivable.bsky.social & others not on bsky #phagesky academic.oup.com/nar/article/...

My team at @cbitoulouse.bsky.social is recruiting a postdoc #bioinformatics with solid experience in metagenomic analyses.
Interest in evolution, ecology & MGEs is important.
The offer stands until the perfect candidate is found, and it could be you 🫵

🔁 🙏

#microSky #phagesky #UTIsky
@cnrs.fr

I didn't even realize how long I had been waiting for a tool like this!

We've got ISSUES. Literally.

We scraped >100k special issues & over 1 million articles to bring you a PISS-poor paper. We quantify just how many excess papers are published by guest editors abusing special issues to boost their CVs. How bad is it & what can we do?

arxiv.org/abs/2601.07563

A 🧵 1/n

The strain on scientific publishing Abstract. Scientists are increasingly overwhelmed by the volume of articles being published. The total number of articles indexed in Scopus and Web of Science has grown exponentially in recent years; ...

In the strain on scientific publishing, we showed that total publications have grown out of control. A huge part of that was guest edited special issues by groups like #MDPI and #Frontiers.

This ongoing practice is the largest delegation of editorial power academia has ever seen.

2/n

Home - EMBO Workshop Shigella: from biology to prevention EMBO Workshop Shigella: from biology to prevention

Just two more days to submit your abstracts to the @shigellameeting.bsky.social - can't wait to see everyone there! www.shigella2026.conferences-pasteur.org/home

We need to talk about salaries in science Academia too often has a ‘passion first, money second’ culture. Overcoming this mindset is crucial for building a happy career.

Academia too often has a ‘passion first, money second’ culture. Overcoming this mindset is crucial for building a happy career

go.nature.com/4bvaCCh

Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...

Research Fellow - Department of Microbes, Infection and Microbiomes - 106849 - Grade 7 To create and contribute to the creation of knowledge by undertaking a specified range of activities as part of an Investigator project funded by Wellcome, focusing on understanding microbial and diet...

Happy New Year – new role! 🎉

We’re looking for a PostDoc to join us in @halllab.bsky.social @unibirmingham.bsky.social.

Full-time, fixed-term to March 2028. Note tight closing date: 11 Jan 2026. CV + cover letter (submit via portal).

Further details 👇

edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Just a few hours left to apply for this #PhD!!

Do you like phages, genomes & public health impact?🦠🧬🏥

Wanna work in a cutting edge of science, with some awesome people @quadraminstitute.bsky.social?

🤔this could be just the project for you!!🧑‍🔬😎

Apply NOW before midnight

#PhDposition #academicsky

🔊 Job Opportunity: Postdoctoral Research Fellow in Bacterial Evolution.

Looking to recruit a postdoc to join a UKRI FLF-funded project on antibiotic resistance evolution in the microbiome 🦠

3 years funding, deadline 26th Jan, please share!
hrwebapp.qub.ac.uk/tlive_webrec...

Gene-specific selective sweeps are pervasive across human gut microbiomes - Nature Development and application of the integrated linkage disequilibrium score (iLDS) reveals both selective pressures impacting the human gut microbiome and the mechanisms by which gut bacteria adapt to ...

Grateful to share our paper on gene-specific selective sweeps in human gut microbiomes, now out in Nature! It has been a joy to work with @rwolff.bsky.social, whose insights and hard work made this possible.
www.nature.com/articles/s41...

Chemoproteomic elucidation of β-lactam drug targets in Mycobacterium abscessus The pathogen Mycobacterium abscessus ( Mab ) can cause severe and difficult to treat chronic lung infections. Despite the rising incidence and clinical concern of Mab infections, treatment options are...

New work from my team, identifying drug targets in M. abscessus. Pre-print posted here:
www.biorxiv.org/content/10.6...

💾 Prokka 1.15.6 is released!

This is the last major release of Prokka. But don't be sad, because @oschwengers.bsky.social already has an excellent replacement called Bakta you can migrate to.
#bioinformatics #microbiology #genomics

github.com/tseemann/pro...

Biased sampling driven by bacterial population structure confounds machine learning prediction of antimicrobial resistance Machine learning methods have emerged as promising tools to predict antimicrobial resistance (AMR) and uncover resistance determinants from genomic data. This study shows that sampling biases driven b...

Our new paper from my PhD work is online. It shows how bacterial population structure can trick machine learning—sampling matters! Many thanks to @lbarquist.bsky.social for the support and guidance! dx.plos.org/10.1371/jour...

Which LLM writes the best R code? posit.co/blog/r-llm-e... Interestingly, GPT-5.2 underperformed OpenAI’s own older/legacy GPT-5, as well as Gemini 3 and all the Claude models. #Rstats

Virome Analysis Viruses are omnipresent and the most abundant biological entities on the planet. They play a critical role in shaping the ecology and evolution of all life forms. This chapter provides methods to perf...

I'm proud to share the latest methods work from my group. Led by @revathykri.bsky.social we wrote a book chapter on how we process and analyse viromes.

Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero

link.springer.com/protocol/10....

proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes. #ProkaryoticGenomes #AnnotatedGenomes #Bioinformatics #Genomics #NAR @narjournal.bsky.social 🧪🧬 🖥️
academic.oup.com/nar/advance-...

Geographical distribution of ETEC cases in England based on available patient postcodes (n=438/557). Note: seven cases had Welsh residential postcodes, but their samples were referred to laboratories in England for testing.

Surveillance of genomic diversity and antimicrobial resistance in enterotoxigenic Escherichia coli in England, 2015–2023. Published Open Access and fee-free in JMM using a Publish and read agreement: doi.org/10.1099/jmm.... #JMM #PublishAndRead