Research Associate at Department of Veterinary Medicine, University of Cambridge
Cambridge, England
Joined May 2012
- Tweets1.1K
- Following573
- Followers376
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Andries van Tonder retweeted
We have a new preprint examining the mutational signatures of hantaviruses: biorxiv.org/content/10.64898…
We find that mutagens and host antiviral proteins are key factors shaping hantavirus mutagenesis
With @AndresFloto and @JulianParkhill
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, Dr Prince Asare and the ongoing support from NMIMR
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: training.cam.ac.uk/bioinform…
Andries van Tonder retweeted
Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis genome.cshlp.org/content/34/… 🧬🖥️ github.com/bacpop/ska.rust 🦀
We will be running the next in person iteration of our bacterial genomics course in Cambridge at the beginning of July. Please let anyone who may be interested know.
training.cam.ac.uk/bioinform…
Andries van Tonder retweeted
🚨 Out now!🚨 Our #OneHealth study on multidrug-resistant #Shigella spread between humans & primates in Albuquerque is live @NatureComms 👉 nature.com/articles/s41467-0… Massive thanks to @NMDOH , @UNMHSC , @LosAlamosNatLab , @abqbiopark , @cabq & lead author @rovinsarahtonin ! 🔬🦠
Andries van Tonder retweeted
Ever wondered what a snapshot of single cell/spatial dataset can reveal?
scCellFie - a scalable tool that goes beyond gene expression, making metabolic analysis possible
3-2-1 Say GENES🤳
BioRxiv doi.org/10.1101/2025.05.09.6…
TRY NOW sccellfie.readthedocs.io
#DataScience #Bioinformatics
I’m happy to share that our scCellFie manuscript is finally on bioRxiv — a project that was an amazing opportunity to return to my roots in metabolism!
We infer metabolic activity from single-cell & spatial transcriptomics 🧬
Read the pre-print here👇
📄 doi.org/10.1101/2025.05.09.6…
Andries van Tonder retweeted
Don't forget to apply to work with @OxfordBiology @IneosOxford on #Mtb #Bioinformatics and Microbiology.
Deadline soon !
@UniofOxford
#Mtuberculosis #Jobs #PostDoc #Biology #Microbiology #UkJobs
TWO postdoc positions in Computational Microbiology and/or biochemistry. Join our interdisciplinary group in the new Life and Mind Building @OxfordBiology, @UniofOxford, @IneosOxford
Please apply and share this post:
jobs.ac.uk/job/DMP641/postdo…
Andries van Tonder retweeted
We happily present: “Bakta Web – rapid and standardized genome annotation on scalable infrastructures” @OxUniPress NAR’s Web Server issue
doi.org/10.1093/nar/gkaf335
Easy to use, no registration, fast, various visualizations, in sync with Bakta CLI:
bakta.computational.bio
(1/5)
Andries van Tonder retweeted
Tuberculosis in found dead badgers at the edge of the expanding bovine tuberculosis epidemic. Published: 27 March 2025 nature.com/articles/s41598-0…
Another week and more pipeline updates, this time my two assembly pipelines:
Illumina:
github.com/avantonder/assemb…
ONT:
github.com/avantonder/assemb…
Have a try and let me know what you think
Andries van Tonder retweeted
Just updated seqkit, csvtk, taxonkit, and rush.
Click to see changes:
- github.com/shenwei356/seqkit…
- github.com/shenwei356/taxonk…
- github.com/shenwei356/csvtk/…
- github.com/shenwei356/rush/r…
Andries van Tonder retweeted
If you have experience in sc/spatial transcriptomics with an interest in microbes....come and join our team as a computational postdoc:
sanger.wd103.myworkdayjobs.c…...
Incredibly exciting datasets on host-microbe interactions in the lung.
Pls RT and reach out if you are interested
Andries van Tonder retweeted
Super happy to see the new @nextflowio training videos up online.
This is a brand new course for beginners, called #Hello #Nextflow - we've run it a few times and the feedback has been great!
Material is at training.nextflow.io and videos on YouTube:
youtube.com/watch?v=G3CV-FcV…
I've spent some time updating my two Nextflow-based bacterial QC pipelines (bacQC and bacQC-ONT). It'd be great to get some feedback.
github.com/avantonder/bacQC
github.com/avantonder/bacQC-…
Andries van Tonder retweeted
🦠🧬🖥️ New Bakta DB v6.0 released!
After a year, it was time for a Bakta database update - and it's a huge one:
- IPS: 330.9M
- PSC: 135.3M
- PSCC: 37M
doi.org/10.5281/zenodo.14916…
👇 1/6
Andries van Tonder retweeted
Inference of multiple mergers while dating a pathogen phylogeny academic.oup.com/sysbio/arti…
Andries van Tonder retweeted
A metagenomic perspective on the microbial prokaryotic genome census | Science Advances science.org/doi/10.1126/scia…
Andries van Tonder retweeted
CompàreGenome: a command-line tool for genomic diversity estimation in prokaryotes and eukaryotes bmcbioinformatics.biomedcent… 🧬🖥️🧪 #Rstats github.com/gmoro-bioecopest/…
Andries van Tonder retweeted
Need to visualize multi-dimensional categorical data in R? ggalluvial, an extension of ggplot2, makes it easy to create alluvial diagrams and Sankey plots, helping you uncover patterns and flows across categories.
✔️ Plot alluvial diagrams to represent relationships between categorical variables.
✔️ Create Sankey plots to visualize flows and transitions.
✔️ Customize aesthetics, including colors, labels, and node arrangements.
✔️ Handle both wide and long-format data sets with ease.
Whether you're analyzing survey responses, tracking user behavior, or exploring categorical trends, ggalluvial simplifies the creation of clear and informative visualizations.
The visualization shown here is taken from the package website: corybrunson.github.io/ggallu…
Learn more about ggplot2 and its extensions in my online course "Data Visualization in R Using ggplot2 & Friends."
Click this link for detailed information: statisticsglobe.com/online-c…
#VisualAnalytics #ggplot2 #Rpackage #DataVisualization #datascienceeducation #database #rstudioglobal #RStats #DataAnalytics #tidyverse
