Andries van Tonder
@andriesvt.bsky.social
Research Associate in Dept of Veterinary Medicine, Cambridge
Reposted by Andries van Tonder
Tuberculosis (TB) that doesn’t respond to standard drugs is called drug-resistant TB and emerges when TB medicines are used inappropriately.
Although the number of people developing drug-resistant TB has declined since 2015, it remains a global public health crisis affecting 390 000 people in 2024.
Although the number of people developing drug-resistant TB has declined since 2015, it remains a global public health crisis affecting 390 000 people in 2024.
November 12, 2025 at 2:53 PM
Tuberculosis (TB) that doesn’t respond to standard drugs is called drug-resistant TB and emerges when TB medicines are used inappropriately.
Although the number of people developing drug-resistant TB has declined since 2015, it remains a global public health crisis affecting 390 000 people in 2024.
Although the number of people developing drug-resistant TB has declined since 2015, it remains a global public health crisis affecting 390 000 people in 2024.
I'm very pleased to be back at Noguchi Memorial Institute for Medical Research helping run our "Working with Bacterial Genomes" course for the first time outside of Cambridge. A big thank you to the funding provided by GIZ, CRIT, my collaborator Dr Prince Asare and the ongoing support from NMIMR.
November 12, 2025 at 1:23 PM
I'm very pleased to be back at Noguchi Memorial Institute for Medical Research helping run our "Working with Bacterial Genomes" course for the first time outside of Cambridge. A big thank you to the funding provided by GIZ, CRIT, my collaborator Dr Prince Asare and the ongoing support from NMIMR.
Thread is worth reading as well...
Do you teach #rstats? Do your students complain about how lame and old-fashioned dplyr is? Don't worry: I have the solution for you: github.com/hadley/genzp....
genzplyr is dplyr, but bussin fr fr no cap.
genzplyr is dplyr, but bussin fr fr no cap.
GitHub - hadley/genzplyr: dplyr but make it bussin fr fr no cap
dplyr but make it bussin fr fr no cap. Contribute to hadley/genzplyr development by creating an account on GitHub.
github.com
November 7, 2025 at 9:44 AM
Thread is worth reading as well...
Reposted by Andries van Tonder
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Genome size estimation from long read overlaps
AbstractMotivation. Accurate genome size estimation is an important component of genomic analyses such as assembly and coverage calculation, though existin
academic.oup.com
November 7, 2025 at 3:19 AM
Our method for genome size estimation from long-read overlaps is now published 🥳
academic.oup.com/bioinformati...
academic.oup.com/bioinformati...
Reposted by Andries van Tonder
Leveraging the subgenus category to address monophyletic genus over-splitting: illustration with recently proposed Mycobacteriales genera. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
![Scatter plots of Rhodococcus inter-subgenus AAI scores. The horizontal dashed line indicates the standard 65% AAI threshold for genus demarcation [17, 18, 20]. The “upper” rhodococcal subgenus demarcation boundary is AAI=73%. The average AAI value for each subgenus is represented by a black horizontal line.](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:mmksquuwyw2qm3qdnslkrodx/bafkreiew2x2iuh2tiray3qsni7ql5i7wab6my4ty7cexmgfrycqwd2sugq@jpeg)
October 30, 2025 at 9:02 AM
Leveraging the subgenus category to address monophyletic genus over-splitting: illustration with recently proposed Mycobacteriales genera. Published Open Access and fee-free in IJSEM using a Publish and Read agreement: doi.org/10.1099/ijse... #IJSEM #PublishAndRead
Reposted by Andries van Tonder
The @crick.ac.uk is recruiting Early Career Group Leaders
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
Early career group leaders
We appoint researchers from across biology and biomedicine to set up their first groups at the Crick.
www.crick.ac.uk
October 10, 2025 at 8:20 AM
The @crick.ac.uk is recruiting Early Career Group Leaders
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
- Lab set-up, research costs, salaries for up to 5 researchers
- Support for up to 12 years
- Access to our core facilities
- Competitive salary
- Fantastic colleagues
- All areas of biology
Deadline 27 Nov
www.crick.ac.uk/careers-stud...
Reposted by Andries van Tonder
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211
Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.
coursesandconferences.wellcomeconnectingscience.org
October 8, 2025 at 2:48 PM
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Reposted by Andries van Tonder
Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1
October 2, 2025 at 1:16 PM
Phylodynamics and genome-wide association studies reveal the expansion of modern Streptococcus canis in Germany https://www.biorxiv.org/content/10.1101/2025.09.29.679251v1
Reposted by Andries van Tonder
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by Andries van Tonder
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
EMBL International PhD Programme – Unique in the world and waiting for you!
www.embl.org
September 17, 2025 at 3:49 PM
The EMBL PhD programme is open until 13th October (entry ~Sep 2026):
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
www.embl.org/about/info/e...
We have three positions in microbial genomics at EMBL-EBI, including one in my group. Please do apply, or if you know anyone that would be interested pass on to them
Reposted by Andries van Tonder
Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/
September 22, 2025 at 7:56 AM
Great to see this out there! We infer the evolutionary pathways behind patterns of AMR in Klebsiella across 102 states, finding globally consistent principles, state-specific deviations (and covariates), and validating evol predictions with new genomes. biorxiv.org/content/10.1... 1/
Reposted by Andries van Tonder
Really excited to announce the v1.9 release of the `rich-click` library 🎉 It's a Python library that uses builds on top of command-line help output from click, giving you beautiful output with only a couple of lines of code 🪄 ✨ 🌈
v1.9 TLDR: We have themes!
v1.9 TLDR: We have themes!
September 17, 2025 at 11:55 AM
Really excited to announce the v1.9 release of the `rich-click` library 🎉 It's a Python library that uses builds on top of command-line help output from click, giving you beautiful output with only a couple of lines of code 🪄 ✨ 🌈
v1.9 TLDR: We have themes!
v1.9 TLDR: We have themes!
Reposted by Andries van Tonder
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
September 17, 2025 at 11:58 AM
Come and join us at @shigellameeting.bsky.social in Paris 2026. Registrations are now open! www.shigella2026.conferences-pasteur.org/home and follow the Shigella starter pack go.bsky.app/6Vbwhjc (message to be added)! 215 days to go!
Reposted by Andries van Tonder
Introducing AMR cartography - work by Andrew Balmer
Antimicrobial Resistance Cartography: A Generalisable Framework for Studying Multivariate Drug Resistance https://www.biorxiv.org/content/10.1101/2025.09.12.675231v1
September 17, 2025 at 8:28 AM
Introducing AMR cartography - work by Andrew Balmer
Reposted by Andries van Tonder
🚨 An excellent opportunity for scientists in Africa, at all career stages, working on maternal & child microbiome research 🚨
📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring.
coursesandconferences.wellcomeconnectingscience.org/event/human-...
📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring.
coursesandconferences.wellcomeconnectingscience.org/event/human-...
Human Gut Microbiome Metagenomics – Africa — 20260412
Build skills in microbiome metagenomics, bioinformatics, and data interpretation to advance maternal and child health research
coursesandconferences.wellcomeconnectingscience.org
September 17, 2025 at 8:41 AM
🚨 An excellent opportunity for scientists in Africa, at all career stages, working on maternal & child microbiome research 🚨
📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring.
coursesandconferences.wellcomeconnectingscience.org/event/human-...
📚 Blended learning (3 months) incl. prep modules, hands-on training (12-17 Apr 2026) & mentoring.
coursesandconferences.wellcomeconnectingscience.org/event/human-...
Reposted by Andries van Tonder
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
September 15, 2025 at 2:32 AM
X-Mapper 🦠🧬🧪 - a sequence aligner developed for microbes, now on Bioconda! 🚀
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
• 11–24× fewer suboptimal alignments (same for human genome)
• 3–579× lower inconsistency
• improves on ~30% of reads aligned to non-target species
github.com/mathjeff/map...
bioconda.github.io/recipes/x-ma...
#microsky
Reposted by Andries van Tonder
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
Efficient sequence alignment against millions of prokaryotic genomes with LexicMap - Nature Biotechnology
LexicMap uses a fixed set of probes to efficiently query gene sequences for fast and low-memory alignment.
www.nature.com
September 10, 2025 at 9:12 AM
Sometimes you meet absolutely incredible bioinfo-magicians.
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
It was a huge privilege when @shenwei356.bsky.social
joined our group for a year on an @embl.org sabbatical.
While here, he developed a new way of aligning to
millions of bacteria, called LexicMap 1/n
www.nature.com/articles/s41...
The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...
Research Informatics - Working with Bacterial Genomes (ONLINE LIVE TRAINING) - Mon 27 Oct 2025
www.training.cam.ac.uk
September 8, 2025 at 2:01 PM
The next online version of our "Working with Bacterial Genomes" course is now open for registration. We aim to provide you with comprehensive training in analysing bacterial genomes covering everything from QC to clustering plasmids. Sign up here: www.training.cam.ac.uk/bioinformati...
Reposted by Andries van Tonder
Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
September 8, 2025 at 10:25 AM
Mathematical models in biology are powerful, but often hard to run, visualise, or reuse without specialist skills.
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Menelmacar is a new platform that makes biological models interactive and easy to explore directly in the browser: biomodels.bacpop.org
🧬💻
Reposted by Andries van Tonder
Reposted by Andries van Tonder
New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes
Background Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is wh...
www.biorxiv.org
August 29, 2025 at 2:05 PM
New preprint reveals bacteria can't just collect all resistance genes like Pokemon cards.
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
We found mutually exclusive evolutionary pathways to multidrug resistance in E. coli & P. aeruginosa - some resistance mechanisms actively prevent others from coexisting www.biorxiv.org/content/10.1...
Reposted by Andries van Tonder
New blog post: Using OpenAI Codex in @posit.co Positron with a demo on developing an #Rstats package using the OpenAI Codex agent doi.org/10.59350/ste...
August 28, 2025 at 10:03 AM
New blog post: Using OpenAI Codex in @posit.co Positron with a demo on developing an #Rstats package using the OpenAI Codex agent doi.org/10.59350/ste...
Reposted by Andries van Tonder
A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species
go.nature.com/4fFfx3F
go.nature.com/4fFfx3F
Mysterious coffee species turns out to be a blend
A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species.
go.nature.com
August 15, 2025 at 9:08 AM
A coffee variety called liberica, which is gaining popularity for the distinctive flavour of its beans, is actually three species
go.nature.com/4fFfx3F
go.nature.com/4fFfx3F
Reposted by Andries van Tonder
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Mathematical modelling for biologists - Modelling concepts in biological research
Mathematical modelling for biologists - Modelling concepts in biological research
www.ebi.ac.uk
August 15, 2025 at 10:39 AM
My PhD student @leonielorenz.bsky.social (with Eva Geissen) has made this nice (free) online course to introduce mathematical modelling for biology:
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
www.ebi.ac.uk/training/onl...
Including both molecular and epidemiological examples
Reposted by Andries van Tonder
A cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1
August 5, 2025 at 3:18 AM
A cross-environment comparison of nontuberculous mycobacterial diversity https://www.biorxiv.org/content/10.1101/2025.08.04.668438v1