A quick tutorial blog on a method I haven't seen before to plot gene gain/loss from e.g. CAFE5 across a phylogeny - and clearly shows I always have fungi on the mind 🤓🍄 #rstats #ggplot2 rowena-h.github.io/data-visuali...

How do GWAS and rare variant burden tests rank gene signals? In new work @nature.com with @hakha.bsky.social, @jkpritch.bsky.social, and our wonderful coauthors we find that the key factors are what we call Specificity, Length, and Luck! 🧬🧪🧵 www.nature.com/articles/s41...

Exciting news! I have two positions open in my lab at the UoManchester: one PDRA and one Research Tech. Join our team to study evolutionary mycology and help us understand antifungal resistance in fungal pathogens. A fantastic opportunity to join the brilliant Manchester Fungal Infection Group!

SWBio DTP PhD (Univ Exeter): Will global warming speed up antifungal resistance? Work with Prof Gabriel Yvon-Durocher, Prof Neil Gow & team. Experimental evolution, multi-omics & modelling on medical/crop pathogens. Apply: bpb-eu-w2.wpmucdn.com/blogs.bristo... #PhD #AMR #ClimateChange #Mycology

🚨New #PhD #adverts alert🚨 I currently have two PhD studentships being advertised on environmental #AMR ⬇️ More being advertised soon 👀 @ukceh.bsky.social @ukceh-moleco.bsky.social

New research in #GENETICS suggests accessory chromosomes in #fungi #fusarium might be maintained because of Spok genes and not because of their beneficial effects on virulence. Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O

Bernabeu, @microbiobits.bsky.social and @tonigabaldon.bsky.social use simulations to test for the robustness of inferred relative timings of gene transfers in the lineage leading to the ancestor of eukaryotes 🔗 doi.org/10.1093/gbe/evaf190 #genome #evolution

Our new paper maps the tRNA modification landscape in Vibrio cholerae! 💫 We describe differences from E. coli and discuss links to decoding of stress-related codons 🦠 Huge thanks to amazing co-authors and collaborators! @plos.org #rnasky #microsky #tRNAmodifications

Government has published one of those quiet but important documents that might get overlooked as it is not 'newsy'. The headline finding is that £1 of public R&D investment generates £8 in net economic benefits for the UK over the long term www.gov.uk/government/p...

NEW EPISODE #ScienceInContext! This week @eonore.bsky.social speaks with @chownbioinf.bsky.social about fungal disease, Aspergillus fumigatus and interactions with the soil it lives in. Harry shares his passions and insights from his work - one to watch 👇 youtu.be/ariW8UKVv-M

1/6 Movi 2 is here: faster and more space-efficient for pangenome queries. Its fastest mode uses half the memory of Movi 1 while running ~30% faster. github.com/mohsenzakeri...

OK, here it is. Come work with me at the University of Liverpool making ALL THE AI models from ALL THE prokaryote pangenome data. Heck, we will make models from ALL the pangenomes, even eukaryotes!!! (link below👇) 1/4

Each year, @unibirmingham.bsky.social offers three scholarships to international students who wish to pursue a PhD in microbiology in my department, School of Biosciences. Interested? Deadline is 7th January 2026! Message any group leader in School of Biosciences to discuss your application

Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change. Ie: it's not us (Samtools team)! Be warned

Yesterday, after 11hrs cycling and 4hrs of breaks, I completed my "Tour de Fungi" — over 200km from London to Norwich — raising funds for @aspertrust.bsky.social and attending @bsmm-meeting.bsky.social. Thanks to all who’ve donated! Still time to give: justgiving.com/page/harry-chown-2

Last practice ride completed at the weekend. 162km from Carlisle to Glasgow 🎉 There's still time to donate!

www.journalofinfection.com/article/S016... 🚨🚨🍄🍄 new research from Washington University Mycoses Group (WUMG) reveals that Invasive aspergillosis & mucormycosis show broad geographic distribution across the U.S. Regions with higher incidence report lower associated mortality. @fungaldoc.bsky.social

#MetagenomicsMonday Analysis of aDNA from 1313 ancient human remains spanning 37k years revealed that the rise of infectious diseases coincided with animal domestication around 65k years ago, with disease spread intensifying during pastoralist migrations. www.nature.com/articles/s41...

6 WEEKS LEFT before we cycle from London to Norwich for the BSMM annual scientific meeting. Raising funds for The Aspergillosis Trust. Please donate (link below) or if you want to take part get in touch ☺️ www.justgiving.com/page/harry-c...

📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social rdcu.be/exBSp

At the network launch event in April, we announce a competition for ECRs to design our logo. It is with great pleasure that we can now share the finished product, based on a winning design by @chownbioinf.bsky.social !

Nice 48km cycle from Paddington to Royal Holloway for #BMS2025

Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1

New tool for pangenome analysis! CLARC refines bacterial gene clusters using functional annotation + linkage—not just sequence. New publication by @indragon.bsky.social & collaborators, advised by @mlipsitch.bsky.social & @billhanage.bsky.social. Read more at bit.ly/4ek0Y51

Only 10 days to go! We can’t wait to see everyone at our Annual Scientific Meeting #BMS2025 and hear the latest in fungal biology research. Take a look at the programme: www.britmycolsoc.org.uk/asm.html

Walked from Victoria to South Kensington for the Imperial Fungal Network and stumbled on a Pocket Forest teeming with fungi (apparently)! Fascinating info on the SUGi project & Miyawaki forests. There are more UK sites—worth a visit! www.sugiproject.com/hertiage-for...

🚴‍♂️ Sept 6th-7th, I’m riding from London to Norwich (over 200km) to attend BSMM and to support the Aspergillosis Trust! Join me for the ride by getting in touch or donate to help raise awareness + fund research into this life-impacting fungal disease. 💛 👉 www.justgiving.com/page/harry-c...

Now published! Note that since Vikram's original post (quoted here), he's made it easy to dynamically update a set of multi-MUMs (e.g. when more genomes are added to a pangenome) and to find multi-MUMs for huge collections like HPRCv2 genomebiology.biomedcentral.com/articles/10....

Join us for the next ProSE Seminar! We are excited to welcome Sophie Heiding for a talk on "Computational Insights into Protein Adaptation Across Environmental Gradients" Date: June 10 Time: 4PM CET Register here: tinyurl.com/prose-seminar2 Please share! 🧪 #MEvoSky

I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.

Our paper shows that most ectomycorrhizal fungal species (83% of OTUs) are "dark taxa": species we detect in DNA, but can't match to known species names. We map global "darkspots" - the parts of the world most in need of more research. @spun.earth @ethz.ch www.cell.com/current-biol...

Our new paper is out! We observed a loss of function in mating compatibility for HD genes for the first time in basidiomycete fungi, and new evolutionary strata in the absence of sexually antagonistic selection! @tatianagiraud.bsky.social More details here 👉 www.nature.com/articles/s41...

🚨 New preprint! We've developed a bioassay-guided genome mining approach to identify bacterial secondary metabolites that inhibit Zymoseptoria tritici — a major fungal pathogen of wheat. Available now on bioRxiv: doi.org/10.1101/2025...

New work from @kylethedavid.bsky.social and the @rokaslab.bsky.social "Convergent expansions of keystone gene families drive metabolic innovation in Saccharomycotina yeasts" @pnas.org www.pnas.org/doi/10.1073/...

Day 18 #30DayMapChallenge I 3D-printed John Snow's 1854 cholera map of Soho. It took ages.

Do you work in mycological spaces from academic to creative art? Take the @openfung.bsky.social survey docs.google.com/forms/d/e/1F...

New preprint: we sequenced one soil sample with ultra-deep hybrid metagenomics and found… → 800+ MAGs → 11,000+ BGCs → and still nowhere near saturation. Soil is wild. Preprint here: www.biorxiv.org/content/10.1... #microbiome #metagenomics #BGCs #naturalproducts #secmet

✨Bumble bee probability of occurrence responds to interactions between local and landscape land use, climatic niche properties and climate change🐝New paper out, led by @tnewbold31.bsky.social, & with @jetkerr.bsky.social & Peter Soroye (the result of some fantastic trips across the Atlantic 🇨🇦) 🌎 🧪 🌐

New paper from my lab (first author is Sonia Ghose): www.frontiersin.org/journals/mic... Skin microbiomes of frogs vary among body regions, revealing differences that reflect known patterns of chytrid infection

We dive into the dynamics of #starships 🚀 in a fungal pathogen to ask: how might these giant #transposons impact human health? We find they drive genome-wide variation, encode clinically-relevant traits and even transpose within the same strain! 🍄🧪 out today in mBio #goteam doi.org/10.1128/mbio...

New paper by Florent Delplace - Sylvain Raffaele lab, Toulouse. Cool work on network evolution underlying quantitative defence responses. It was a pleasure to host and support Florent for a few months to work on the evolutionary analyses of the paper. :) academic.oup.com/plcell/advan...

Evaluating selection at intermediate scales within genes provides robust identification of genes under positive selection in M. tuberculosis clinical isolates https://www.biorxiv.org/content/10.1101/2025.05.07.652684v1

Mutations in transcription factors that confer fluconazole resistance also confer reduced susceptibility to manogepix in Candida auris, Candida albicans, Candida parapsilosis, and Candida glabrata (Nakaseomyces glabratus) https://www.biorxiv.org/content/10.1101/2025.05.07.652603v1

I'm incredibly grateful to be receiving this award on the basis of my work on the pangenome of Aspergillus fumigatus. A huge thank you to my friends, colleagues and mentors who have supported me!

When things add up: environmental structure and microbial interactions drive antibiotic-resistance plasmid evolution https://www.biorxiv.org/content/10.1101/2025.05.07.652652v1

#PopulationGenetics of microbial #pathogens can inform decisions that impact society; @smlatorreo.bsky.social explores a @plosbiology.org study on wheat powdery mildew #fungus which uses genomic data to predict continental-scale dispersion routes 🧪 Paper: plos.io/43qfH9F Primer: plos.io/44YjHQN

Another helpful resource is the conversion key between homologous genes from Aspergillus fumigatus strain A1163 and Af293. I've frequently shared this file amongst colleagues and realised that it may be helpful to the wider community. github.com/harrychown/a...

Vizitig: context-rich exploration of sequencing datasets https://www.biorxiv.org/content/10.1101/2025.04.19.649656v1

Curious what kind of fungi live in your neighborhood? Turns out cities in Finland host more large-spored fungi & animal/lichen pathogens than natural areas. 🔗 doi.org/10.1111/1365... Research from @uniofjyvaskyla.bsky.social | Funded by the Research Council of Finland

Tired of rewriting the same "lost" scripts over and over, so I'm finally setting them free on GitHub. First up: a little tool that converts peptide IDs in FASTA files to gene IDs — perfect if you're wrangling protein-to-genome alignments with Exonerate or Miniprot