Harry Chown
@chownbioinf.bsky.social
Research Associate, Imperial College London 🍄 Fungal genomics and bioinformatics
Reposted by Harry Chown
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...
#rstats #ggplot2
rowena-h.github.io/data-visuali...
Mushroom plots to visualise gain and loss on a phylogenetic tree
A tutorial on how to visualise gene gain and loss on a phylogenetic tree
rowena-h.github.io
November 7, 2025 at 3:41 PM
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...
#rstats #ggplot2
rowena-h.github.io/data-visuali...
Reposted by Harry Chown
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...
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...
Specificity, length and luck drive gene rankings in association studies - Nature
Genetic association tests prioritize candidate genes based on different criteria.
www.nature.com
November 7, 2025 at 12:05 AM
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...
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 Chown
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!
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!
November 5, 2025 at 3:35 PM
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!
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 Chown
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
November 5, 2025 at 11:40 AM
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
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
I currently have two PhD studentships being advertised on environmental #AMR ⬇️
More being advertised soon 👀
@ukceh.bsky.social @ukceh-moleco.bsky.social
October 31, 2025 at 10:45 AM
🚨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
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 Chown
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
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
November 4, 2025 at 9:02 PM
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
Learn more about this work from @fungage-lab.bsky.social and colleagues: buff.ly/R2CRa3O
Reposted by Harry Chown
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
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
Phylogeny-aware Simulations Suggest a Low Impact of Unsampled Lineages in the Inference of Gene Flow During Eukaryogenesis
Abstract. The topologies of gene trees are broadly used to infer horizontal gene transfer events and characterize the potential donor and acceptor partners
doi.org
November 3, 2025 at 4:23 PM
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
🔗 doi.org/10.1093/gbe/evaf190
#genome #evolution
Reposted by Harry Chown
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
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
The tRNA epitranscriptomic landscape and RNA modification enzymes in Vibrio cholerae
Author summary This study charts the first genome-wide map of transfer RNA (tRNA) modifications in the cholera pathogen, Vibrio cholerae, revealing how chemical marks on tRNAs shape translation and st...
journals.plos.org
November 3, 2025 at 11:58 PM
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
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 Chown
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...
www.gov.uk/government/p...
The value of public R&D
www.gov.uk
October 30, 2025 at 1:28 PM
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...
www.gov.uk/government/p...
Reposted by Harry Chown
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
youtu.be/ariW8UKVv-M
Ep 134 Science in Context Fungal disease with Dr Harry Chown
YouTube video by MRC Centre for Global Infectious Disease Analysis
youtu.be
October 24, 2025 at 3:43 PM
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
youtu.be/ariW8UKVv-M
Reposted by Harry Chown
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...
GitHub - mohsenzakeri/Movi: Fast, Cache-Efficient, and Scalable Queries on Pangenomes
Fast, Cache-Efficient, and Scalable Queries on Pangenomes - mohsenzakeri/Movi
github.com
October 21, 2025 at 8:00 PM
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...
Reposted by Harry Chown
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
September 25, 2025 at 9:49 AM
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
Reposted by Harry Chown
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
Interested?
Deadline is 7th January 2026! Message any group leader in School of Biosciences to discuss your application
September 25, 2025 at 12:07 PM
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
Interested?
Deadline is 7th January 2026! Message any group leader in School of Biosciences to discuss your application
Reposted by Harry Chown
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
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
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
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
September 7, 2025 at 12:51 PM
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!
In just a weeks time @chownbioinf.bsky.social is cycling over 200km to the @bsmm-meeting.bsky.social in Norwich, to raise money for @aspertrust.bsky.social
This is a huge feat, and for such a great cause. Please consider sponsoring Harry! www.justgiving.com/page/harry-c...
This is a huge feat, and for such a great cause. Please consider sponsoring Harry! www.justgiving.com/page/harry-c...
September 1, 2025 at 8:47 AM
Last practice ride completed at the weekend. 162km from Carlisle to Glasgow 🎉 There's still time to donate!
Reposted by Harry Chown
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
Geographic distribution and associated mortality of invasive aspergillosis and mucormycosis among Medicare enrollees in the United States (2008-2015)
Invasive aspergillosis and mucormycosis are widely distributed in the United States,
with certain regions experiencing significantly higher incidences. For invasive aspergillosis,
each increase of 5 c...
www.journalofinfection.com
August 4, 2025 at 12:32 PM
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
Reposted by Harry Chown
#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...
www.nature.com/articles/s41...
The spatiotemporal distribution of human pathogens in ancient Eurasia - Nature
Screening shotgun-sequencing data from ancient humans covering 37,000 years of Eurasian history uncovers the widespread presence of ancient bacterial, viral and parasite DNA and zoonotic pathogens…
www.nature.com
August 4, 2025 at 7:01 AM
#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...
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...
www.justgiving.com/page/harry-c...
Tour de Fungi for The Aspergillosis Trust
Help Harry Chown raise money to support Aspergillosis Trust
www.justgiving.com
July 25, 2025 at 9:19 AM
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...
www.justgiving.com/page/harry-c...
Reposted by Harry Chown
📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp
rdcu.be/exBSp
Starship giant transposons dominate plastic genomic regions in a fungal plant pathogen and drive virulence evolution
Nature Communications - Giant transposons, known as ‘Starships’, mediate horizontal gene transfer between fungal genomes. Here, Sato et al. show that Starships occupy genome regions...
rdcu.be
July 24, 2025 at 10:40 AM
📣 Happy to see the journal publication 📄 of our work on Starships 🚀 in Verticillium fungi: terrific work led by @yukiyosato.bsky.social
rdcu.be/exBSp
rdcu.be/exBSp
Reposted by Harry Chown
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 !
July 24, 2025 at 8:26 AM
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 !
Reposted by Harry Chown
Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
July 7, 2025 at 3:48 AM
Structural motif search across the protein-universe with Folddisco https://www.biorxiv.org/content/10.1101/2025.07.06.663357v1
Reposted by Harry Chown
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
Linkage-based ortholog refinement in bacterial pangenomes with CLARC
Abstract. Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying g
bit.ly
June 25, 2025 at 4:06 PM
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
Reposted by Harry Chown
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
July 4, 2025 at 10:30 AM
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