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Andries van Tonder

@andriesvt.bsky.social
593 followers 809 following 7 posts

Senior Teaching Associate/Research Associate in Genetics & Veterinary Medicine @ University of Cambridge

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Reposted by Andries van Tonder
Jim Shaw @jimshaw.bsky.social · 15/09/2026
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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Julian Parkhill @julianparkhill.bsky.social · 08/09/2026
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate. www.cam.ac.uk/jobs/researc...
cam.ac.uk
Research Professor in the field of Bacteriology
Strengthening Cambridge's leadership in bacteriology research Bacterial infection and antimicrobial resistance remain among the most pressing global health challenges of our time. At Cambridge, the De...
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Microbiology Society @microbiologysociety.org · 17/08/2026
Stabilizing features of cefotaximase harbouring plasmids enable persistence in UK livestock. Published Open Access and fee-free in MGen using a Publish and Read agreement: doi.org/10.1099/mgen.0.001775 #MGen #PublishAndRead
(a) A co-occurrence heatmap, showing the prevalence of cefotaximases among plasmid Inc types. (b) A boxplot showing the median number of AMR genes among plasmid Inc type/cefotaximase combinations. (c) A heatmap displaying the co-resistances harboured by different plasmid Inc types. Metadata pertaining to the isolate from which the plasmid was derived is encoded by colours in the key (right).
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Alexis Stamatakis @stamatak.bsky.social · 17/07/2026
Applications for the 2027 summer school on Computational Molecular Evolution on Crete are now open at: meetings.embo.org/event/27-com...
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Martin Steinegger 🇺🇦 @martinsteinegger.bsky.social · 01/08/2026
Riboseek is a fast RNA/DNA search. More sensitive than nhmmer at 250x speed. Structure-aware realignment produces MSAs approaching rMSA quality. Plus 1.7M precomputed RNA MSAs, and an API to search your own 📄 www.biorxiv.org/content/10.6... 💾 github.com/steineggerla... 🌐 search.foldseek.com/riboseek
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Rod Page @rdmpage.bsky.social · 27/05/2026
Interesting new tool to extract phylogenies from images (Tremble). It is crazy that this is still something we have to do. doi.org/10.1093/bioi...
doi.org
Treemble: a graphical tool to generate Newick strings from phylogenetic tree images
AbstractSummary. Phylogenetic trees are ubiquitous and central to biology, but most published trees are available only as visual diagrams and not in the ma
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Ben J Woodcroft @benjwoodcroft.bsky.social · 26/05/2026
Sandpiper 2 is up. 913,000 metagenomic community profiles w @ace-gtdb.bsky.social R232, 200k more than 1.0. sandpiper.qut.edu.au GlobDB coming. Thanks to @aroneys.bsky.social @thepatientwait.bsky.social @iambrettb.bsky.social and especially the new kid @nhstefan.bsky.social
sandpiper.qut.edu.au
sandpiper
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Francesc Coll @fcic.bsky.social · 21/05/2026
Happy to share our recent work on genetic factors and clinical impact of S. aureus adhesion, published in natcomms.nature.com doi.org/10.1038/s414...
doi.org
Genetic determinants of Staphylococcus aureus adhesion shape virulence trade-offs in bacteremia - Nature Communications
To uncover how Staphylococcus aureus strain variation influences adhesion and thus disease outcomes, the authors profile 236 bacteremia isolates, showing that high-adhesion, low-toxicity isolates may ...
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Willem van Schaik @wvschaik.bsky.social · 13/05/2026
This is an incredibly relevant preprint. Your favourite pipeline and/or AMR gene database cannot be considered authoritative, but neither can others.
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Fiona J Whelan @whelanfj.bsky.social · 11/05/2026
📣 Whelan lab is hiring 📣 We are looking for an entry level technician to help us with our culturing and DNA sequencing prep of cystic fibrosis lung microbiome samples. Applications close 20 May 2026. www.jobs.manchester.ac.uk/Job/JobDetai...
jobs.manchester.ac.uk
Research Technician in Microbiology and Molecular Biology:Oxford Road
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Em Stevens @emstevens93.bsky.social · 12/05/2026
I'm currently advertising a PhD position in my lab, to study the transition from commensal to pathogen in Staphylococcus aureus. Details available here, please share! www.keele.ac.uk/research/pos...
keele.ac.uk
FacultystudentshipinSchoolofLifeSciences
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Stephen Turner @stephenturner.us · 03/05/2026
Free and open-source images, icons, and tools for creating scientific illustrations doi.org/10.59350/5zt... 🧪
doi.org
Free and open-source images, icons, and tools for creating scientific illustrations
Phylopic, NIH Bioart, Bioicons, Scidraw, Open Science Art, Health Icons, Servier Medical Art, Biodiversity Heritage Library, the Noun Project, Segment Anything, Excalidraw, draw.io, Biographics
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Charles Wei @rositea.bsky.social · 06/05/2026
It took years after my masters to publish BaGPipe, now it's out! It's a Nextflow pipeline to run end-to-end bacterial GWAS, heavily tested and benchmarked on different datasets, and now in good hands of the Sanger's Pathogen Informatics Team. link.springer.com/article/10.1...
link.springer.com
BaGPipe: an automated, reproducible, and flexible pipeline for bacterial genome-wide association studies - BMC Microbiology
BMC Microbiology - Microbial genome-wide association studies (GWAS) are crucial for linking genetic variation to phenotypic traits in bacteria. However, current tools often involve complex manual...
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Sam Horsfield @samuelhorsfield.bsky.social · 05/05/2026
Our new preprint is out! We train a transformer on gene order and gene content of bacterial pathogens, applying it to a range of epidemiological and evolutionary analyses (1/8) www.biorxiv.org/content/10.6...
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Prof Jenny Rohn @jennyrohn.bsky.social · 05/05/2026
😱 Take-home message: hospital sinks are perfectly safe if you don’t run the taps! #IDSky
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Nature @nature.com · 05/05/2026
Nature research paper: Demography and life histories across the Roman frontier in Germany 400–700 ce go.nature.com/4cHRUb6
go.nature.com
Demography and life histories across the Roman frontier in Germany 400–700 ce - Nature
Analysis of 258 ancient genomes from southern Germany reveals a major demographic shift during the late fifth century, yet family structures persisted from Late Roman times, demonstrating cultural continuity despite profound demographic reorganization.
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Francesc Coll @fcic.bsky.social · 01/05/2026
Happy to share our latest work on “In Host Mutational Adaptation of Mycobacterium Tuberculosis Complex Strains During Tuberculosis Infection” published in @jidjournal.bsky.social doi.org/10.1093/infd...
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Asher Leeks @asherleeks.bsky.social · 28/04/2026
We're recruiting! We're looking for two graduate students to join us at UBC in Vancouver. Fully funded and open to global applicants, with flexible start-date. Topics include theory, bioinformatics, and microbiology. More details: asherleeks.com/apply #socialviruses #evosky #virosky 🧪
Leeks Lab is recruiting. We study social evolution in viruses. We're recruiting for two fully funded PhD or MSc positions, starting from September 2026. Evolutionary theory / experimental microbiology / viral bioinformatics. Experience optional / enthusiasm essential. asherleeks.com/apply
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Ben Vezina @bananabenana.bsky.social · 21/04/2026
This preprint on #Shigella flexneri covers a new genotyping scheme + tool, #AMR and analysis of 13k genomes from ~1925-current day 🦠 #MicroSky #microbiology 🧪 www.biorxiv.org/content/10.6...
biorxiv.org
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Ryan Cook @ryancook94.bsky.social · 14/04/2026
Really happy to have played a small part in this cool piece of work led by @guido-valverde.bsky.social and @msabrysarhan.bsky.social. We characterised S. pyogenes in a pre-Columbian Bolivian mummy (suggesting circulation before European contact) #VivaBolivianMummies www.nature.com/articles/s41...
nature.com
An ancient genome of Streptococcus pyogenes from a pre-Columbian Bolivian mummy - Nature Communications
Streptococcus pyogenes is a human pathogen responsible for a range of diseases. Here, the authors reconstruct an ancient S. pyogenes genome from a pre-Columbian Bolivian mummy, supporting that the pat...
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Carl Zimmer @carlzimmer.com · 15/04/2026
Until now, scientists have identified only a few dozen variants that went through natural selection in humans in the past 10,000 years. A new study claims to find hundreds--maybe thousands. Here's my story on the provocative research, and the mixed reception it's getting. Gift link: nyti.ms/4tSJH9G
A scientist drills a skull in search of ancient human DNA
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Colin Carlson @colincarlson.bsky.social · 09/04/2026
New in @science.org ‼️ In the most comprehensive study to date, we show that wildlife trade is driving animal-to-human zoonotic spillover at a planetary scale, with +1 spillover per host every 10 years. Live animal markets and illegal trade pose even greater risks. 🔓 www.science.org/doi/10.1126/...
Wildlife trade drives animal-to-human pathogen transmission over 40 years
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Jim Shaw @jimshaw.bsky.social · 27/03/2026
Myloasm, our long-read metagenome assembler, is now published! w/ @mgmarin.bsky.social and @lh3lh3.bsky.social Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers who gave very helpful feedback. rdcu.be/famFj
rdcu.be
High-resolution metagenome assembly for modern long reads with myloasm
Nature Biotechnology - A long-read metagenome assembly method recovers circular and complete genomes better than existing tools.
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Jessica Blair @jessicamablair.bsky.social · 19/03/2026
PhD available with @overtonlab.bsky.social Sara Jabbari and me associated with our BBSRC sLoLa project! www.findaphd.com/phds/project... (UK students only)
findaphd.com
Improving the solvent tolerance of E. coli by understanding the rules of accumulation at University of Birmingham on FindAPhD.com
PhD Project - Improving the solvent tolerance of E. coli by understanding the rules of accumulation at University of Birmingham, listed on FindAPhD.com
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Alan McNally @alanmcn1.bsky.social · 19/03/2026
Am stoked and thrilled that our latest paper is now out. A longitudinal study of invasive E. coli from children in the Netherlands over 50 years www.sciencedirect.com/science/arti...
sciencedirect.com
Lineage dynamics of invasive Escherichia coli isolates in the Netherlands from 1975 to 2021: a retrospective longitudinal genomic analysis
Escherichia coli is a common cause of invasive infections such as bloodstream and cerebrospinal fluid infections in neonates. Strains positive for the…
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ARTIC network @artic.network · 12/03/2026
ARTIC are hiring! Postdoctoral opportunity in metagenomics at the University of Birmingham edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
edzz.fa.em3.oraclecloud.com
Research Fellow (Postdoctoral) - School of Biosciences - 107071 - Grade 7
This post-doctoral position will contribute to both complementary programmes, developing ‘broadband’ metagenomic sequencing capabilities for rapid detection and characterisation of emerging and unknow...
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Ross Fitzgerald @jrossfitz.bsky.social · 18/02/2026
Great work by Jamie Gorzynski and Josh-Harling-Lee from the group providing insights into the evolutionary origins of bacterial lineages. A collaboration with @jrpenades.bsky.social @wfigueroac3.bsky.social. #Staph Cell Reports www.cell.com/cell-reports...
cell.com
Bacterial defense systems and host ecology drive the evolution of intra-species lineages
Staphylococcus aureus lineages vary widely in the frequency of gene exchange and the diversity of genome content. Gorzynski and Harling-Lee et al. show that both host ecology and the horizontal acquis...
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Nandita Garud @nanditagarud.bsky.social · 12/02/2026
I am seeking a postdoc to join my group at UCLA -- ideally the candidate would have some experience in either population genetics or microbes/microbiome (computational background needed). We have a range of projects and are happy to tailer to your interests. Please dm/email me if interested.
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Vaughn Cooper @vscooper.micropopbio.org · 09/02/2026
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!
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Sam Horsfield @samuelhorsfield.bsky.social · 07/02/2026
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...
biorxiv.org
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Ryan Wick @rrwick.bsky.social · 05/02/2026
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.
rrwick.github.io
ONT read QC strategies for assembly
a blog for miscellaneous bioinformatics stuff
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Chris Knight @knightjar.bsky.social · 02/02/2026
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...
jobs.manchester.ac.uk
'Research Associate in Microbiome Ecology:Manchester
We wish to appoint a PostDoctoral Research Associate to an exciting project exploring the assembly, stability and function of microbial decomposer communities.
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EMBL-EBI Training @training.ebi.embl.org · 03/02/2026
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... 🧬🖥️📊🌱
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.
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John Lees @johnlees.bacpop.org · 30/01/2026
We are hiring for group leaders again — EBI is a great place to start your research group! embl.wd103.myworkdayjobs.com/EMBL/job/Hin...
embl.wd103.myworkdayjobs.com
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...
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Ryan Wick @rrwick.bsky.social · 21/01/2026
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
P2 Solo announcement and the trade-offs of a more stable ONT
a blog for miscellaneous bioinformatics stuff
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Rebecca A. Gladstone @becctococcus.bsky.social · 20/01/2026
"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
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Alexandra Weisberg @weisbergaj.bsky.social · 14/01/2026
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!
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James McInerney @jomcinerney.bsky.social · 14/01/2026
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
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
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Pathogen Dynamics Unit @pducambridge.bsky.social · 15/01/2026
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...
cam.ac.uk
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George Bouras @gbouras13.bsky.social · 14/01/2026
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/...
academic.oup.com
Protein structure-informed bacteriophage genome annotation with Phold
Abstract. Bacteriophage (phage) genome annotation is essential for understanding their functional potential and suitability for use as therapeutic agents.
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Olaya Rendueles @olayarendueles.bsky.social · 15/01/2026
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
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Fabrizio Musacchio @fabmusacchio.bsky.social · 15/01/2026
I didn't even realize how long I had been waiting for a tool like this!
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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026
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
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Mark A. Hanson @hansonmark.bsky.social · 13/01/2026
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
direct.mit.edu
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; ...
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Kate Baker @ksbakes.bsky.social · 12/01/2026
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
shigella2026.conferences-pasteur.org
Home - EMBO Workshop Shigella: from biology to prevention
EMBO Workshop Shigella: from biology to prevention
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Nature @nature.com · 12/01/2026
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
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.
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Olivier Borkowski @oborkowski.bsky.social · 08/01/2026
Creating bacterial genomic diversity through large-scale reconfigurations reveals phenotype robustness to organizational genome change doi.org/10.64898/202...
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Hall Lab @halllab.bsky.social · 07/01/2026
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...
edzz.fa.em3.oraclecloud.com
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...
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Langridge Lab @langridgelab.bsky.social · 06/01/2026
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
tinyurl.com
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
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Rachel M. Wheatley @rachelmwheatley.bsky.social · 05/01/2026
🔊 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...
hrwebapp.qub.ac.uk
Job profile
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