Tim Downing
@downingtim@genomic.social - also downingtim.bsky.social - Head of #Genomics at The #PirbrightInstitute (UK). He/him. All posts (etc) are in a personal capacity. I log in regularly, nearly every month. #Andacyclist #genomics #virus #pathogen #evolution
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- now out in Genomics, Proteomics & Bioinformatics academic.oup.com/gpb/advance-... doi: doi.org/10.1093/gpbj... #pangenome #virus #evolution #mutation
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- Reposted by Tim DowningInterested in virome sequencing on @nanoporetech.com instruments? Check out our latest paper where we publish Twist-ONT, a modified protocol for the Twist Comprehensive Viral Research Panel (by @twistbioscience.com) so that it can be used with ONT. www.sciencedirect.com/science/arti... 🧵1/7 🧪
- Reposted by Tim DowningReally excited our paper about how H5N1 rapidly adapted to cattle (and how these adaptations also increased its ability to infect cells from the human respiratory tract) is now published! www.nature.com/articles/s41...
- Vaccination first...
- A study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...
- Reposted by Tim DowningA study on 1.7 million people in Hong Kong shows superior hybrid immunity to Covid in people who got vaccinated before infection vs. people who got infected first. "Our findings are a direct rebuttal to arguments for natural immunity," the authors write. doi.org/10.1016/j.va...
- Reposted by Tim DowningI launched version 3.0 of my browser extension "Lazy Scholar", a free in-browser research assistant. It opens automatically when you load an academic article. See: lazyscholar.org/2026/01/10/l...
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- Reposted by Tim DowningGoogle's praise of Athropic's Claude. Jaana Dogan, a Principal Engineer at Google, describing how Claude Code generated in one hour what took her Google team a year to build for distributed agent orchestrators
- Reposted by Tim DowningIf you have been following the African swine fever "mystery" in Catalonia, you would have noticed that this had the early hallmarks of a "lab leak" from a nearby facility. Turns out it wasn't, however. h/t @acritschristoph.bsky.social @flodebarre.bsky.social www.infobae.com/espana/2025/...
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- Reposted by Tim DowningThe registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31 probgen2026.github.io
- Reposted by Tim DowningWhile stories of singular DNA changes that drove evolution of human brain/behaviour remain seductive, advances across multiple fields of biology cast doubt on such simplistic narratives of our origins. A new paper from my lab shows how biobanks may speak to this fundamental question.🧪 Explainer🧵👇1/n
- Apply: Wessex One Heath (WOH) #PhD programme at Pirbright & Sussex See our project: Deciphering mutational pressures in bacterial & viral pathogens using mutational signatures Deadline: 23rd Jan See: www.surrey.ac.uk/wessex-one-h... Apply: shorturl.at/tX5Nx #virus #evolution #genomics #bacteria
- Apply for our Wessex One Heath (WOH) #PhD programme at Pirbright & collaborators See our project: Exploring the poxvirus evolutionary landscape using AI and pangenomics Deadline: 23rd Jan Details: www.surrey.ac.uk/wessex-one-h... Apply here: shorturl.at/tX5Nx #mpox #virus #evolution #genomics
- Reposted by Tim Downingabsolutely losing it at my 14yo's biology homework
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[Not loaded yet] - Reposted by Tim DowningOur January issue is live! A Focus issue on viral pathogen evolution and global health. The issue explores viral emergence, adaptation, spread, and strategies for surveillance and preparedness to detect and control evolving viral threats. Read more: www.nature.com/collections/...
- Reposted by Tim DowningThe 2026 Guarda Summer Course in Evolutionary Biology is now accepting applications. Amazing place, amazing course, amazing opportunity for early grad students. tb.ethz.ch/education/gu...
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- Reposted by Tim DowningDetails for people who like phylogenetics: virological.org/t/inter-clad...
- Reposted by Tim Downing1. In Hamburg there is a "fully autonomous train" that for some reason has a human operator to press the ON switch first thing in the morning and the OFF switch at the end of the night. In a recent talk about AI in science, I asked the audience to consider whether they want to be like that operator.
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- Reposted by Tim DowningThe connections between sugar and alcohol in the liver:
- Reposted by Tim DowningGreat culture can save lives. Literally. Amazing letter in today’s @thetimes.com about Tom Stoppard
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- Reposted by Tim DowningIf you run across a gen A.I. slop 🤖💩 diagram in an academic journal, I’d love to know about it! Please fill out this form: docs.google.com/forms/d/e/1F... Slop in journals is illuminating about journals’ quality control. And journals would like you to forget their mistakes. #AcademicChatter
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- Our work on mapping read libraries to viral #pangenome variation graphs (PVGs) to reduce reference bias Using lumpy skin disease virus #lsdv (dsDNA #virus) as an example "Using pangenome variation graphs to improve mutation detection in a large DNA virus" www.biorxiv.org/content/10.1... [1/7]
- Reposted by Tim DowningI taught (and co-taught) a course on human population genetics from 2000-2024. Having retired, I'm now making all the course materials public: github.com/alanrogers/p... #popgen #evbio
- Reposted by Tim DowningHow does fever work? Our new Science paper shows how elevated body temperature can protect against severe influenza and that avian-origin viruses escape this defence. This is likely one reason why bird flus and some pandemic influenzas can be so severe.🧵 www.science.org/doi/10.1126/...
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- Reposted by Tim Downing“AI workers said they distrust the models they work on because of a consistent emphasis on rapid turnaround time at the expense of quality.”
- Reposted by Tim DowningPublished today in @nature.com, @adititm.bsky.social & researchers from the @brianhie.bsky.social lab report that the large-scale genomic model, Evo, is capable of using surrounding genomic context to produce novel, functional genes, enabling an an emergent approach they've termed 'semantic design'.
- Reposted by Tim DowningScientific breakthroughs are rarely unique; someone else would’ve made them soon enough. But when prominent scientists cause harm, that harm isn’t inevitable; the world might simply have been better had the harm not been inflicted. liorpachter.wordpress.com/2018/05/18/j...
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- Reposted by Tim DowningNew paper with @statsepi.bsky.social and @deevybee.bsky.social in which we show there's really no evidence for a link between the gut microbiome and autism www.cell.com/neuron/fullt...
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- Reposted by Tim DowningLondon interdisciplinary #PhD position now open with myself, @sergemostowylab.bsky.social, & @gmknght.bsky.social on #phage -bacteria-host immune dynamics for WHO priority bacterial pathogens #Klebsiella, #Shigella, and #Staph. Combines cellular microbiology, genomics, & mathematical modelling.
- Reposted by Tim DowningThe link between the gut #microbiome and autism is not backed by science, researchers say. Read the full opinion piece in @cp-neuron.bsky.social: spkl.io/63322AbxpA @wiringthebrain.bsky.social, @statsepi.bsky.social, & @deevybee.bsky.social
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- Reposted by Tim DowningOn Oct 1, 2025, GISAID informed us that they had ended updates to the flat file of SARS-CoV-2 genomic sequences and associated metadata that we had used to update Nextstrain analyses since Feb 2020. GISAID's stated rationale was that their "resources are limited". 1/5
- Reposted by Tim DowningFunders must recognise that great discoveries often come from studies that seeks to advance knowledge for its own sake go.nature.com/3X5lbUg
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- Reposted by Tim DowningI still contend that >90% of the benefit of writing a review isn't the audience. It's for the author going through the literature, finding gaps in knowledge, learning how experiments are done, etc. It really isn't about writing a review. It's about doing the review yourself. AI can't do that for you
- Reposted by Tim DowningNew blogpost on my concerns about Wellcome LEAP new $50m program on autism/microbiome links. deevybee.blogspot.com/2025/10/a-le... #autism #microbiome #biomarkers #diagnostic
- Reposted by Tim DowningMyself and Alastair Wilson wrote an updated version of our 2016 primer to quantitative genetics in the wild: www.sciencedirect.com/science/arti.... Happy to share a copy if interested. It is also on research gate
