Andries van Tonder
@andriesvt.bsky.social
Research Associate in Dept of Veterinary Medicine, Cambridge
Reposted by Andries van Tonder
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...
rrwick.github.io/2026/01/21/p...
P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
rrwick.github.io
January 21, 2026 at 3:38 AM
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...
rrwick.github.io/2026/01/21/p...
Reposted by Andries van Tonder
"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
doi.org
January 20, 2026 at 9:49 AM
"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
Reposted by Andries van Tonder
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!
The Weisberg Lab at Oregon State University is recruiting a postdoctoral scholar in molecular microbiology to study mobile genetic element host range and transmission in microbial communities. Please see the full job description here: files-dev.cqls.oregonstate.edu/Weisberg_Lab...
January 14, 2026 at 11:57 PM
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!
Reposted by Andries van Tonder
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
🔗 doi.org/10.1093/bioinformatics/btag005
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
doi.org
January 14, 2026 at 10:25 PM
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
🔗 doi.org/10.1093/bioinformatics/btag005
Reposted by Andries van Tonder
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...
www.cam.ac.uk
January 15, 2026 at 10:03 AM
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...
Reposted by Andries van Tonder
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/...
January 14, 2026 at 5:10 AM
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/...
Reposted by Andries van Tonder
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
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
January 15, 2026 at 11:19 AM
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
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
Reposted by Andries van Tonder
I didn't even realize how long I had been waiting for a tool like this!
Want to get the data out of a PDF figure? As in, the actual data – not a rough trace-along-the-lines version?
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
I made an app you might like: adamkucharski.github.io/pdf2plot/
It all started a few years ago... 🧵
January 15, 2026 at 7:36 AM
I didn't even realize how long I had been waiting for a tool like this!
Reposted by Andries van Tonder
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
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
January 13, 2026 at 8:27 AM
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
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
Reposted by Andries van Tonder
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
This ongoing practice is the largest delegation of editorial power academia has ever seen.
2/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; ...
direct.mit.edu
January 13, 2026 at 8:27 AM
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
This ongoing practice is the largest delegation of editorial power academia has ever seen.
2/n
Reposted by Andries van Tonder
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
Home - EMBO Workshop Shigella: from biology to prevention
EMBO Workshop Shigella: from biology to prevention
www.shigella2026.conferences-pasteur.org
January 12, 2026 at 9:34 AM
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
Reposted by Andries van Tonder
Academia too often has a ‘passion first, money second’ culture. Overcoming this mindset is crucial for building a happy career
go.nature.com/4bvaCCh
go.nature.com/4bvaCCh
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.
go.nature.com
January 12, 2026 at 10:20 AM
Academia too often has a ‘passion first, money second’ culture. Overcoming this mindset is crucial for building a happy career
go.nature.com/4bvaCCh
go.nature.com/4bvaCCh
Reposted by Andries van Tonder
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...
doi.org/10.64898/202...
January 8, 2026 at 7:36 AM
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change
doi.org/10.64898/202...
doi.org/10.64898/202...
Reposted by Andries van Tonder
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...
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...
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...
edzz.fa.em3.oraclecloud.com
January 7, 2026 at 5:06 PM
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...
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...
Reposted by Andries van Tonder
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
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
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
PhD Carrying a toxic burden: the continuing spread of “Shiga toxin stx2a”-harbouring phage in E. coli (LANGRIDGE_Q26MMB) 2026/27 | UEA
www.tinyurl.com
January 6, 2026 at 2:16 PM
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
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
Reposted by Andries van Tonder
🔊 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...
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...
Job profile
hrwebapp.qub.ac.uk
January 5, 2026 at 10:00 AM
🔊 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...
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...
Reposted by Andries van Tonder
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...
www.nature.com/articles/s41...
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 ...
www.nature.com
December 17, 2025 at 6:53 PM
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...
www.nature.com/articles/s41...
Reposted by Andries van Tonder
New work from my team, identifying drug targets in M. abscessus. Pre-print posted here:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
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...
www.biorxiv.org
December 17, 2025 at 1:15 AM
New work from my team, identifying drug targets in M. abscessus. Pre-print posted here:
www.biorxiv.org/content/10.6...
www.biorxiv.org/content/10.6...
Reposted by Andries van Tonder
💾 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...
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...
Release Heading into the sunset · tseemann/prokka
The future
This is probably the last release of Prokka. I won't be making any code changes except bug fixes. I will update the databases occasionally. I strongly recommend you use Bakta by @oschwen...
github.com
December 15, 2025 at 9:09 PM
💾 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...
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...
Reposted by Andries van Tonder
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...
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...
dx.plos.org
December 16, 2025 at 8:49 PM
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...
Reposted by Andries van Tonder
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
December 12, 2025 at 10:09 AM
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
Reposted by Andries van Tonder
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....
Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero
link.springer.com/protocol/10....
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...
link.springer.com
December 11, 2025 at 9:49 AM
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....
Thanks to co-authors @rikhaagmans.bsky.social @ryancook94.bsky.social & Alise Ponsero
link.springer.com/protocol/10....
Reposted by Andries van Tonder
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-...
academic.oup.com/nar/advance-...
December 2, 2025 at 10:15 AM
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-...
academic.oup.com/nar/advance-...
Reposted by Andries van Tonder
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
November 26, 2025 at 12:02 PM
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
Reposted by Andries van Tonder
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...
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...
High frequency body site translocation of nosocomial Pseudomonas aeruginosa - Nature Communications
Here, the authors report within-host diversity and body site translocation dynamics in hospital samples of Pseudomonas aeruginosa and reveal that body site sharing was likely due to within-patient tra...
www.nature.com
November 25, 2025 at 10:40 AM
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...
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...