Harry Chown
Research Associate, Imperial College London 🍄 Fungal genomics and bioinformatics
- Reposted by Harry Chown[Not loaded yet]
- Reposted by Harry ChownSuper 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
- Reposted by Harry ChownInteresting 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?
- Interessante reconstructie van de tijdlijn van de diagnostische tests van katten, koeien en mensen op vogelgriep H5N1 op het Friese melkveebedrijf, en de informatieverstrekking daarover door de overheid, gezien door de bril van dierenarts ‘hogvet51’ uit de V.S. hogvet51.substack.com/p/h5n1-in-ca...
- Reposted by Harry ChownNow 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...
- New preprint! How much does antibiotic use shape bacterial lineage dynamics, and how does that relate to the fitness costs/benefits of resistance determinants? All sorts of fun findings and a method that we hope will be broadly useful. See @dhelekal.bsky.social's thread and the preprint!
- Reposted by Harry ChownWe'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...
- Reposted by Harry ChownZiplign 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/...
- Just published in JOSS: 'Ziplign: a simple-to-use interactive tool to compare bacterial genomes' doi.org/10.21105/joss.09004
- Reposted by Harry ChownOn #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...
- Reposted by Harry ChownThis 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.
- Determining presence-absence variation (PAV) across reference genomes is a major goal of pangenome analysis. It turns out that A LOT of gene PAV is due to methodological artifacts. We explore the causes of this in soybean and cotton datasets in our recent preprint: www.biorxiv.org/content/10.1...
- Reposted by Harry ChownNew 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
- Reposted by Harry ChownCalling 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🧵
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- Reposted by Harry Chown[Not loaded yet]
- Reposted by Harry Chown
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! - Reposted by Harry Chown[Not loaded yet]
- Reposted by Harry ChownNow published in Nature Biotechnology: go.nature.com/44P7nSm If you missed it, the TL;DR is in my April thread below
- I am very happy (and anxious) to share with you our most recent work in which we evaluated four of the most popular long-read assemblers, www.biorxiv.org/content/10.1... and tell you just a little bit about it in the following 🧵
- Reposted by Harry Chown
- Reposted by Harry ChownNature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
- Reposted by Harry ChownBacterial 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...
- Reposted by Harry Chown🚨 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/
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- Reposted by Harry ChownCome to Birmingham and do a PhD with myself and @wvschaik.bsky.social!
- Reposted by Harry ChownWe 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...
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- Reposted by Harry ChownNow officially published in Current Biology 🥳🥳 @mfseidl.bsky.social @binfutrecht.bsky.social www.cell.com/current-biol...
- Reposted by Harry ChownMetaPointFinder: 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/...
- Reposted by Harry ChownAnyone 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!
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- Reposted by Harry ChownA recent shift in centromere size and DNA content in Podospora pseudocomata co-occurs with the loss of a fungal genome defense system biorxiv.org/content/10.64898/20…
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- Reposted by Harry ChownWe 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
- Reposted by Harry ChownOur paper on Zymoseptoria tritici 3D genome organization is officially out! @iglavincheska.bsky.social link.springer.com/article/10.1...
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- Reposted by Harry ChownAI 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...
- Reposted by Harry ChownPhD 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
- Reposted by Harry ChownExciting 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.
- Reposted by Harry ChownFungal 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...
- Reposted by Harry ChownWe'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/...
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- Reposted by Harry Chown“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
- Reposted by Harry ChownA 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....
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- Reposted by Harry ChownA 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...
- Reposted by Harry ChownHow 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...
- Reposted by Harry ChownExciting 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!
- Reposted by Harry ChownSWBio 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
- Reposted by Harry Chown🚨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
- Reposted by Harry ChownNew 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
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- Reposted by Harry ChownOur 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
- Reposted by Harry ChownGovernment 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...
