Harry Chown

Pangenomes, really?

Most early “pangenomes” = oligogenomes (oligo, Gr., few).

More recent “pangenomes” generally = poligenomes (polis, Gr., many).

True pangenomes (pas, Gr., every/all) would be rare indeed.

🙏🏼 @zbao.bsky.social for pointing out his review.

www.nature.com/articles/s41...

Poster of the call for abstracts fir the BMS Annual Scientific Meeting, with a photo of the Royal Holloway campus building at sunset..

📣 Call for Abstracts - British Mycological Society 2026 Annual Scientific Meeting. Inviting researchers, early-career scientists, postgraduate students, & practitioners to share their latest research👉 Event webpage & abstract submission: www.britmycolsoc.org.uk/asm.html
#BMS2026

New personal view article

The role of microbial genomics in delivering the UK’s national action plan for confronting antimicrobial resistance 2024–29

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #AMR #OpenAccess #OA

Nature security assessment on global biodiversity loss, ecosystem collapse and national security This strategic assessment explores how global biodiversity loss and the collapse of critical ecosystems could affect the UK’s resilience, security and prosperity.

“Protecting & restoring ecosystems is easier, cheaper & more reliable”

The Government’s Nature Security report has been criticised, but this conclusion about the way ahead makes all the right noises

www.gov.uk/government/p...

Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture Nature Microbiology, Published online: 03 March 2026; doi:10.1038/s41564-026-02260-3Analysis of 37 genomes together with more than 140 phenotypic traits links genomic features to ecological fitness and lifestyle diversity in Trichoderma fungi.

Out Now! Phenogenomics reveals the ecology and evolution of Trichoderma fungi for sustainable agriculture #MicroSky

Epistasis and co-adaptation in bacterial genome evolution Nature Reviews Genetics - Bacterial genome evolution is shaped by epistasis, which can constrain or promote specific evolutionary paths. The authors review how integrating the effects of epistatic...

I’ve spent a lot of time over the past two years thinking about genome evolution and how recent research revealing complex gene-gene interactions has complicated traditional ‘gene-centric’ genomic approaches to evolution. So here is a review that consolidates these thoughts!

rdcu.be/e6pHY

Predicting protein-protein interactions (PPIs) at proteome scale can take months with co-folding models due to the massive all-vs-all comparisons required.

We are excited to announce FlashPPI, a contrastive learning framework that predicts proteome wide physical interfaces in minutes. 1/🧵

#GGFungi2026 Call For Projects is now open for applications getgenome.net/callforproje...

We will be holding an information session today 3rd March at 14:00 CET (08:00 Eastern US; 18:00 PKT). To sign up please complete this short form - forms.office.com/e/DssYYkkY9Z

@thaisdalsasso.bsky.social is applying new tools to address the evolution and functional diversification of secreted proteins of fungal plant pathogen. Preprint here: www.biorxiv.org/content/10.6...

Phyloseminar #147: Antoine Koehl (UC Berkeley) Deep Models of Protein EvolutionModels of protein evolution seek to quantify how proteins evolve over time while experiencing intricate constraints and adapt...

Antoine Koehl (UC Berkeley) will be speaking on "Deep Models of Protein Evolution" in 24 hours. Link: www.youtube.com/watch?v=SgZv...

Cryptococcus neoformans responds to presence of Mycobacterium by diversifying its morphologies and remodelling its capsular material Introduction . Cryptococcus neoformans and Mycobacterium tuberculosis (MTb) are opportunistic pathogens that share overlapping geographical distributions and physiological niches within the human body...

Pleased to share that our paper on Cryptococcus neoformans-Mycobacterium tuberculosis interactions has been #published! We found that C. neoformans cells exhibit increased virulence traits in the presence of tuberculosis-causing pathogens. @mrccmm.bsky.social dx.doi.org/10.1099/jmm....

Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity - Nature Communications Here, the authors present a bioinformatic pipeline to annotate lncRNA genes in Aspergillus fumigatus. The majority of these lncRNAs are only conserved at the species level, and their expression is hig...

Full paper here: doi.org/10.1038/s414...

Grateful to collaborators at Manchester Fungal Infection Group and co-authors; especially Danielle Weaver and Tandi Qi.

These findings highlight:
• The compact nature of the A. fumigatus genome
• lncRNAs enable adaptation to antifungal exposure

This reinforces the need to study the genomic "dark matter" in fungi due to their roles in the evolution of fAMR

We found:
• 1,089 novel lncRNAs
• Low-level sequence conservation between Aspergilli
• Drug-specific and shared expression patterns
• Enhanced growth under azole stress in lncRNA knockouts

We analysed transcriptomic data across a range of MIC dosages from 7 antifungals

This allowed us to construct a lncRNA annotation library (using bioinformatic and manual methods!) and measure their transcriptional response to drugs

Azole resistance in Aspergillus fumigatus is an increasing global threat and leads to high mortality due to treatment failure

However, we still lack:
• A well characterised species genome
• Understanding of novel resistance mechanisms

This study aimed to address that

Delighted to share my first (co-)first authored paper from the Manchester Fungal Infection Group.

We identified >1,000 novel lncRNA genes and investigated their role in fungal AMR.

🧵 Here’s what we found:

One hundred unanswered questions on the dispersal ecology of fungi Abstract. Fungi comprise millions of species that play numerous varied roles in Earth’s natural and managed ecosystems, engaging in a multitude of positive

New paper out today in the ISME | International Society for Microbial Ecology Journal and the first product from our ESIIL (Environmental Data Science Innovation and Impact Lab) working group on Fungal Dispersal. Check it out!

academic.oup.com/ismej/advanc...

Such a good piece today from @jburnmurdoch.ft.com which shows that the declining graduate premium is very much a UK problem rather than a general (or inevevitable) consequence of more people going to uni www.ft.com/content/649d...

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...

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...

Top: A representative modeling example from Chimpanzee CPEB3 HDV-like ribozyme (PDB ID: 7QR3), with models predicted by four better-performing methods (blue cartoons) overlaid on experimental structure (gray cartoons). Left to right: DRFold2, DeepFoldRNA, AlphaFold3, RhoFold. Bottom: Structural visualization of the example from coxsackievirus B3 cloverleaf RNA (PDBID: 8DP3), showing experimental structure (left), AlphaFold3’s best prediction from 100 models (middle), and 5th model of DRfold2 (right), respectively. Structures are rainbow-colored from 5′ (blue) to 3′ (red) end.

Accurate RNA structure prediction remains a challenge, despite recent computational advances. This study presents DRFold2, a #DeepLearning framework that significantly enhances accuracy of de novo #RNAstructure prediction by increasing contact prediction precision @plosbiology.org 🧪 plos.io/4aoOQiX

Do you work with the Aspergillus fumigatus model isolates Af293 or CEA10? If so, we want to collaborate with you! In return for your lab's participation we will sequence your strain for free and provide co-authorship on the final paper.

Learn more here: asp-fumi-seq-project-2025.vercel.app

Co-occurrence is associated with horizontal gene transfer across marine bacteria independent of phylogeny Abstract. Understanding the drivers and consequences of horizontal gene transfer (HGT) is a key goal of microbial evolution research. Although co-occurring

Now out & nicely formatted in @isme-microbes.bsky.social

A big analysis of ocean genomes & metagenomes co-led by former postdocs, now PIs, @gmdouglas.bsky.social & @cyanophage.bsky.social along with co-PIs @lbobay.bsky.social & Samuel Chaffron.

A few highlights... 🧵 (1/n)

doi.org/10.1093/isme...

Long-read sequencing can revolutionise the way we monitor #biodiversity.

A comprehensive guide for using #ONT & #PacBio for analysis of biodiversity through #eDNA, #metabarcoding, metagenomics

Just published in @methodsinecoevol.bsky.social
besjournals.onlinelibrary.wiley.com/doi/10.1111/...

"we examined..patterns of resistance gene abundance, duplication, and mobilization across clinical, agricultural, and wastewater settings... Resistance gene profiles were strongly structured by environment, with distinct duplication patterns emerging across sources. "

Hugging Face – The AI community building the future. We’re on a journey to advance and democratize artificial intelligence through open source and open science.

Super excited to announce the release of gene and intergenic region annotation from the largest bacterial genome and MAG datasets available, including AllTheBacteria, GTDB, SPIRE, HRGM, mOTUs and MGnify - dereplicated and available from HuggingFace huggingface.co/AllTheBacteria

Interesting paper www.nature.com/articles/s41... it seems to be consistent with recent spillover event(s) discovered in a dairy farm in the northern Netherlands, but would be interesting to see how many of those potentially mammal adaptive mutations in this wave of bird migration?

Now published: our work using phylodynamics from surveillance data to quantify and experimentally validate the fitness impact of antibiotic resistance determinants & how this changes with patterns of antibiotic use: www.nature.com/articles/s41...

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...

Ziplign published in JOSS. Tool to easily interactively compare two bacteria genomes. Inspired by ACT, but easier to install and use. Drag and drop files, or download using accessions. It runs blast for you. No terminal needed. github.com/martinghunt/...