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chownbioinf.bsky.social
Research Assistant, Imperial College London 🍄 Fungal genomics and bioinformatics
12 posts 101 followers 215 following
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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

submitted 13 days ago • 1 comment

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...

submitted 14 days ago • 0 comments

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...

submitted 15 days ago • 0 comments

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

submitted 14 days ago • 0 comments

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

submitted 18 days ago • 0 comments

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!

submitted 19 days ago • 3 comments

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

submitted 19 days ago • 0 comments

#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

submitted 21 days ago • 1 comment

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...

submitted 28 days ago • 1 comment

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

submitted 35 days ago • 0 comments

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

submitted 46 days ago • 0 comments

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

submitted 46 days ago • 1 comment

Foldseek-Multimer—now published in @naturemethods.bsky.social—our fast multimer search tool, enables complex comparisons against the full PDB in seconds. It comes with BFMD, a collection of 300K+ predictions gathered from community projects. 📄 nature.com/articles/s41... 🌐 search.foldseek.com

submitted 110 days ago • 0 comments

Hyphal growth determines spatial organization and coexistence in a pathogenic polymicrobial community within alveoli-like geometries https://www.biorxiv.org/content/10.1101/2025.03.22.644766v1

submitted 65 days ago • 0 comments

transfactor: Transcription factor activity estimation via probabilistic gene expression deconvolution https://www.biorxiv.org/content/10.1101/2025.03.19.644088v1

submitted 69 days ago • 0 comments

A large European diversity panel reveals complex azole fungicide resistance gains of a major wheat pathogen https://www.biorxiv.org/content/10.1101/2025.03.19.644200v1

submitted 68 days ago • 1 comment

We did it! We caught Starship #transposons moving between #fungal species in the lab, including between species separated by ~100my. We think Starships are a mediator of HGT in fungi, akin to conjugative elements in bacteria. Check out the preprint. www.biorxiv.org/content/10.1...

submitted 81 days ago • 3 comments

Improved reconstruction of transcripts and coding sequences from RNA-seq data https://www.biorxiv.org/content/10.1101/2025.02.27.640589v1

submitted 83 days ago • 0 comments

Friends, LiftOn is now published in @genomeresearch.bsky.social! LiftOn maps genes across genomes using a protein-centric, homology-based approach with both DNA & protein alignments @stevensalzberg.bsky.social Mihaela Pertea, Jakob Heinz, Alaina Shumate, Celine Hoh, Alan Mao doi.org/10.1101/gr.2...

submitted 85 days ago • 1 comment

I am very excited that @target-amr.bsky.social and the Fungal AMR One Health network (www.fungalamr.org) are organising an online mini-symposium on Fungal AMR Genomics on 25 March 1-4 pm GMT. Please sign up here! www.targetamr.org.uk/hdrevents/jo...

submitted 85 days ago • 2 comments

Yesterday I successfully defended my thesis. Thank you to Rhys and Chris for a great viva and thank you to all of MFIG for a brilliant 4 year 😊🎉

submitted 115 days ago • 3 comments