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. "

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/...

On #WorldNTDDay, @imperialcollegeldn.bsky.social + @dndi.org strengthen their partnership to speed up new treatments for #NeglectedDiseases affecting 1 billion+ people worldwide. 🌍 From #AI to drug discovery, we’re working to turn science into real-world impact. www.imperial.ac.uk/news/article...

This article is now published! academic.oup.com/nargab/artic... We’ve added a few new analyses. First off, we show that, while gene presence absence variation (PAV) scales with evolutionary distance in both plants and animals, the base level and rate of accrual are both twice as high in plants.

New tool from @alexsweeten.bsky.social to find and classify all your satellites: "AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates" 📄 www.biorxiv.org/content/10.6... 📦 github.com/marbl/anianns

Calling all OrthoFinder users! We’ve just released GLADE, a tool to infer gene gains, losses, duplications, and ancestral genomes across a phylogeny. GLADE runs directly on OrthoFinder results. www.biorxiv.org/content/10.6... github.com/lauriebelch/... (1/10)

In response to introducing regulations as per Awaab's law, Scottish Housing Secretary Màiri McAllan says: "In Scotland, while 90% of homes are free from damp and mould, we want to make sure everyone is protected". Here is why I think this statistic is flawed 1/5🧵

Big congrats to Jo and all collaborators on this paper, happy to have played a role in the lab

#Plant pathogens secrete effectors to establish infections, but resistant crops select for resistance-breaking #pathogens. @mfseidl.bsky.social &co use #pangenome graph analyses of 19 resistance-breaking races of an #oomycete pathogen to identify several effectors @plosbiology.org 🧪 plos.io/4qA6nKC

Very happy to see this published: doi.org/10.1093/nar/...: a GRN-based approach to predict regulatory subnetworks for developmental and pathogenic processes in Aspergillus fumigatus and GRAsp: a network viz tool: grasp.wid.wisc.edu with @jeanmichelane.bsky.social and Nancy Keller labs!

A long non-coding RNA, afu-254, is required for the oxidative stress response, cell wall stress response, azole susceptibility and virulence in Aspergillus fumigatus https://www.biorxiv.org/content/10.64898/2026.01.07.698160v1

Now published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below

Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/

Bacterial genomes encode a rich repertoire of antiphage systems, but we still know surprisingly little about when these systems are actually expressed. In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts. www.biorxiv.org/content/10.6...

🚨 What if evolution is the ”law”… and networks are the machines that do the work? In this paper (just published) I try to formalize how living systems are non-equilibrium, information-processing, adaptive matter. With a great biological flavor! 🧪🌐🌍🧬🦠 👉 iopscience.iop.org/article/10.1... 🧵 1/

Vir2vec: A Genome-Wide Viral Embedding https://www.biorxiv.org/content/10.64898/2025.12.12.693901v1

Come to Birmingham and do a PhD with myself and @wvschaik.bsky.social!

We are recruiting a Research Tech! Funded by the @wellcometrust.bsky.social, join us to work on Mucorales adaption in collaboration with Becky Hall (University of Kent) Deadline: 5th January www.jobs.manchester.ac.uk/Job/JobDetai...

🎨🔬 Art meets Science! 50 Exeter College Fashion & Textiles students teamed up with MRC CMM researchers to explore fungi & create stunning designs. We enjoyed an inspiring evening of art and science, while celebrating the students achievements 👏 #STEM #ScienceArt

Now officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...

MetaPointFinder: A new approach for detecting mutation-driven antimicrobial resistance directly from metagenomic reads. Fills a major gap in current resistome profiling by capturing chromosomal AMR mutations that metagenome tools miss. github.com/aldertzomer/...

Anyone looking for roommates for #Fungal26 in Asilomar? I will participate and I am looking for someone to share a room for the week! I'm a female PhD student, looking to share a room with another female. Please DM me if you'd like to team up with me 😄 Reposts appreciated!

Our paper with the results of Citizen Science project ‘Fungal Radar’ are now out! @evelinesnelders.bsky.social @benauxier.bsky.social academic.oup.com/ismej/articl...

A recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system https://www.biorxiv.org/content/10.64898/2025.12.02.690432v1

k-mer-based GWAS reveals a candidate avirulence gene and structural variation in Puccinia triticina linked to gain of Lr20 virulence doi.org/10.1186/s128...

We are thrilled to announce the first official release (v0.1.8) of #𝗯𝗲𝗱𝗱𝗲𝗿, the successor to one of our flagship tool, #𝗯𝗲𝗱𝘁𝗼𝗼𝗹𝘀! Based on ideas we conceived of long ago (!), this was achieved thanks to the dedication of Brent Pedersen. 1/n

Our paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...

Optimized k-mer search across millions of bacterial genomes on laptops https://www.biorxiv.org/content/10.1101/2025.11.23.690050v1

AI model Helixer predicts eukaryotic genes ab initio, directly from a plain text FASTA file. No RNA-seq. No protein homology. No repeats, hints, or curated evidence. Raw genome → accurate gene models. Deep learning + HMM, published in @natmethods.nature.com www.nature.com/articles/s41...

PhD position available to study the immune response to the terbinafine resistant dermatophyte T. Indotinea. www.surrey.ac.uk/wessex-one-h... @mrccmm.bsky.social @youngecmm.bsky.social @ishamycology.bsky.social @britsocimm.bsky.social @britmycolsoc.org.uk

Exciting day at London’s Science Museum for the #InnovationforGrowth meeting where we’re showing off AirSeq technology from @earlhaminst.bsky.social and @nhm.org Meeting organised by @ukri.org to highlight the importance of research and innovation for economic growth.

Fungal friends: The University of Minnesota is hiring a tenure track medical mycologist, with emphasis on emergence of pathogens, genomics and evolution! www.nature.com/naturecareer...

We're looking for a PhD student! If you're interested in #fungal #genomics & #TEs, meiotic drive, or pathogens, please consider applying. The project is about toxin/antidote genes in the human fungal pathogen A. fumigatus. uu.varbi.com/en/what:job/...

Whilst this research is available currently as a preprint only www.researchsquare.com/article/rs-7... I would like to acknowledge all the researchers on this study who have made this possible. It's great to see the fruition of collaborative science! Thank you 🙏

“Bin Chicken” is now published in Nature Methods! It substantially improves genome recovery through rational coassembly 🧬🖥️. Applied to public 🌍 metagenomes, we recovered 24,000 novel species 🦠, including 6 new phyla. doi.org/10.1038/s415... @benjwoodcroft.bsky.social @rhysnewell.bsky.social 🧵1/6

A great genomics paper from my friend and colleague @drandiwilson.bsky.social on the expansion of heat stress related proteins in Rhizina undulata bmcgenomics.biomedcentral.com/articles/10....

🔥 At conferences, who asks the questions shapes who gets seen. Across 24 ID&CM meetings, women were 55% of delegates but asked 36% of questions. 💬 When women moderate or speak first, others follow. Let’s change the pattern bit.ly/47VL0eH 🙏 @maudsalmona.bsky.social & MicroID EmpowHERment consortium

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