Harry Chown
@chownbioinf.bsky.social
Research Associate, Imperial College London 🍄 Fungal genomics and bioinformatics
Reposted by Harry Chown
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...
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...
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
doi.org
February 9, 2026 at 8:31 PM
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...
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...
Reposted by Harry Chown
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/...
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/...
February 3, 2026 at 3:54 PM
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/...
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/...
Reposted by Harry Chown
"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. "
Ecological context structures duplication and mobilization of antibiotic and metal resistance genes in bacteria https://www.biorxiv.org/content/10.64898/2026.02.03.703612v1
February 6, 2026 at 9:48 PM
"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. "
Reposted by Harry Chown
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
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.
huggingface.co
February 5, 2026 at 1:27 PM
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
Reposted by Harry Chown
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?
February 5, 2026 at 2:37 AM
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?
Reposted by Harry Chown
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...
January 30, 2026 at 12:34 PM
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...
Reposted by Harry Chown
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...
'Research Associate in Microbiome Ecology:Manchester
We wish to appoint a PostDoctoral Research Associate to an exciting project exploring the assembly, stability and function of microbial decomposer communities.
www.jobs.manchester.ac.uk
February 2, 2026 at 4:16 PM
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...
Reposted by Harry Chown
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/...
February 2, 2026 at 8:55 AM
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/...
Reposted by Harry Chown
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...
From #AI to drug discovery, we’re working to turn science into real-world impact.
www.imperial.ac.uk/news/article...
Imperial and DNDi strengthen partnership to accelerate treatments for neglected diseases
Researchers from Imperial College London and the Drugs for Neglected Diseases initiative (DNDi) met on 19 January to strengthen a growing partnership...
www.imperial.ac.uk
January 30, 2026 at 12:16 PM
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...
From #AI to drug discovery, we’re working to turn science into real-world impact.
www.imperial.ac.uk/news/article...
Reposted by Harry Chown
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.
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.
January 30, 2026 at 12:41 PM
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.
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.
Reposted by Harry Chown
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
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
January 29, 2026 at 1:05 PM
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
📄 www.biorxiv.org/content/10.6...
📦 github.com/marbl/anianns
Reposted by Harry Chown
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)
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)
www.biorxiv.org
January 29, 2026 at 12:07 PM
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)
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🧵
January 30, 2026 at 1:39 PM
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🧵
Reposted by Harry Chown
Big congrats to Jo and all collaborators on this paper, happy to have played a role in the lab
Emerging terbinafine-resistant Trichophyton indotineae between 2018 and 2023: a multinational genomic epidemiology study www.sciencedirect.com/science/arti...
Many thanks to my colleagues for their help in getting this published. This took a mighty 16 months to get through the peer review process.
Many thanks to my colleagues for their help in getting this published. This took a mighty 16 months to get through the peer review process.
Emerging terbinafine-resistant Trichophyton indotineae between 2018 and 2023: a multinational genomic epidemiology study
Trichophyton species cause the greatest burden of dermatophytosis worldwide, with the Trichophyton mentagrophytes species complex being particularly a…
www.sciencedirect.com
January 23, 2026 at 11:53 AM
Big congrats to Jo and all collaborators on this paper, happy to have played a role in the lab
Reposted by Harry Chown
#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
January 21, 2026 at 9:48 AM
#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
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!
A network-based model of Aspergillus fumigatus elucidates regulators of development and defensive natural products of an opportunistic pathogen
Abstract. Aspergillus fumigatus is a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Unders
doi.org
January 13, 2026 at 4:49 AM
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
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
January 8, 2026 at 2:16 AM
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
Reposted by Harry Chown
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
January 6, 2026 at 9:38 AM
Now published in Nature Biotechnology:
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
go.nature.com/44P7nSm
If you missed it, the TL;DR is in my April thread below
Reposted by Harry Chown
Reposted by Harry Chown
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
December 16, 2025 at 5:00 PM
Nature Reviews Genetics Focus issue: Eco-evolutionary genomics of microorganisms www.nature.com/collections/... 🧬🖥️🧪🦠 🧵 1/
Reposted by Harry Chown
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...
In this preprint, Lucas Paoli et al, ask what shapes antiphage systems expression in native contexts.
www.biorxiv.org/content/10.6...
Environment and physiology shape antiphage system expression
Bacteria and archaea encode on average ten antiphage systems. Quorum sensing, cellular, or transcription factors can regulate specific systems (CRISPR-Cas, CBASS). Yet, a systematic assessment of anti...
www.biorxiv.org
December 15, 2025 at 9:49 PM
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...
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/
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/
December 16, 2025 at 9:04 AM
🚨 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/
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/
Reposted by Harry Chown
Vir2vec: A Genome-Wide Viral Embedding https://www.biorxiv.org/content/10.64898/2025.12.12.693901v1
December 14, 2025 at 5:46 AM
Vir2vec: A Genome-Wide Viral Embedding https://www.biorxiv.org/content/10.64898/2025.12.12.693901v1
Reposted by Harry Chown
Come to Birmingham and do a PhD with myself and @wvschaik.bsky.social!
PhD position (Birmingham, UK)
Environmental modelling of microbial dynamics in river and flood-impacted environments
with Johanna Rhodes, Willem van Schaik, Marie Chattaway, Claire Jenkins
at University of Birmingham
More details: http://iddjobs.org/jobs/2433
Environmental modelling of microbial dynamics in river and flood-impacted environments
with Johanna Rhodes, Willem van Schaik, Marie Chattaway, Claire Jenkins
at University of Birmingham
More details: http://iddjobs.org/jobs/2433
December 12, 2025 at 6:32 AM
Come to Birmingham and do a PhD with myself and @wvschaik.bsky.social!
Reposted by Harry Chown
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...
Deadline: 5th January
www.jobs.manchester.ac.uk/Job/JobDetai...
December 10, 2025 at 9:09 PM
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...
Deadline: 5th January
www.jobs.manchester.ac.uk/Job/JobDetai...