Tim Downing

Accurate plasmid reconstruction from metagenomics data using assembly–alignment graphs and contrastive learning www.nature.com/articles/s41... 🧬💻🧪 github.com/RasmussenLab...

now out in Genomics, Proteomics & Bioinformatics

academic.oup.com/gpb/advance-...

doi: doi.org/10.1093/gpbj...

#pangenome #virus #evolution #mutation

Race is not a biological category: challenging this misconception will help tackle racism in healthcare Healthcare professionals must reject flawed racial generalisations, writes Jasmeen Kanwal Institutional racism in healthcare has received increased coverage in recent years, including in The BMJ ’s ...

Excellent piece about why race is not a biological category and how medical education needs to respond. www.bmj.com/content/392/...

Twist-ONT: Combining nanopore sequencing with the twist comprehensive viral research panel The Twist Comprehensive Viral Research Panel (Twist CVRP) is a probe-based hybridization capture enrichment method for whole-genome sequencing, design…

Interested 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...
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Really 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...

I 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...

Holiday Inn turned away homeless men despite rooms being paid for Charity worker describes incident at Manchester hotel as disgusting and ‘complete discrimination on appearance’ Two homeless men were turned away from a Holiday Inn in sub-zero temperatures despite their booking already being paid for, a charity has said. The hotel in Manchester city centre refused to accommodate the men and staff members apparently told them: “I know that you’re from the street and the hotel doesn’t allow it.” Continue reading...

Holiday Inn turned away homeless men despite rooms being paid for

Viral tweet (3.1M views) from Jaana Dogan, a Princiapl Engineer at Google, describing how Claude Code generated in one hour what took her Google team a year to build for distributed agent orchestrators

Google'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

La Generalitat descarta que el origen del brote de peste porcina africana en Cataluña comenzara en un laboratorio de Barcelona “La secuenciación genética nos dice que no coinciden las muestras de jabalí con las del IRTA-CResa”, ha declarado el conseller de Agricultura, Òscar Ordeig

If 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/...

Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa In November 2024, a highly divergent BA.3-related SARS-CoV-2 lineage, designated BA.3.2, was detected in South Africa, marking the first appearance of a BA.3-derived lineage in over two years. Phyloge...

SARS-CoV-2 continue to surprise us with evolutionary jumps. In this pre-print, we describe the Identification and genomic characterisation of BA.3.2: a highly divergent BA.3-related SARS-CoV-2 lineage from southern Africa. A thread 🧵 www.medrxiv.org/content/10.6...

Sisyphus pushing a rock up a hill. Sisyphus is labelled "Me trying to work", and the rock is labelled "Microsoft Authenticator popups". God I hate microsoft authenticator.

The registration deadline is fast approaching for probgen 2026! Abstracts due by January 15, registration by January 31

probgen2026.github.io

Evaluating the effects of archaic protein-altering variants in living human adults Promise and pitfalls of using large biobanks to study impacts of archaic protein-coding variants in living humans.

While 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 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

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

screenshot of a homework worksheet that includes the sentence: "Methyl groups, a type of chemical group, are present in the environment and may enter cells and attach to the DNA as a person ages, as shown in the diagram below"

absolutely losing it at my 14yo's biology homework

Fond of this one...

“We conclude that apparent effects of growth mindset interventions on academic achievement are likely attributable to inadequate study design, reporting flaws, and bias.”
statmodeling.stat.columbia.edu/2025/12/11/w...

Viral pathogen evolution and global health Viral pathogen evolution and global health

Our 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/...

Summer school:<br> Evolutionary Biology in Guarda Information about the annual summer school Evolutionary Biology in Guarda

The 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...

Mandatory specific impact test - Statutory Equalities Duties Complete Statutory Equalities Duties The Home Office assess that there may be some indirect impacts as a result of the changes including raising the skills threshold and salary requirements. These are more likely to affect younger people who are likely to be earlier in their career and therefore less likely to have reached the higher salary of more experienced colleagues. It may also affect those where there is still evidence of lower pay including women and those with disabilities. However, the Home Office consider that these changes are justified for legitimate policy aims of lowering net migration and reducing reliance on overseas workers. In relation to social care, the Home Office assess that there may be some indirect impact of closing the route on those from countries which make up the majority of care workers including Nigeria, Zimbabwe, Ghana, India and Pakistan. This may indirectly affect characteristics including ethnicity, religion, race. The department also know that the sector is more commonly occupied by women so likely to have a greater impact on women than men from those countries. The Home Office also recognise that this may have an impact on user of care services who are likely to be older people and those with disabilities. The Home Office believes that despite these points the changes are justified for a number of policy reasons including reducing net migration and ending reliance on overseas recruitment.

There are some spectacularly misguided "assumptions" in the Home Office's impact assessment on its changes to immigration rules. More than that though, it confirms not only will these changes cost the country billions, they are also discriminatory. 1/
assets.publishing.service.gov.uk/media/6937e6...

Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Inter-Clade Recombinant Mpox Virus Detected in England in a Traveller Recently Returned from Asia Authors: Steven T. Pullan1, Isobel Everall1, Rebecca Doherty1, Lucy Crossman1, Emma Wise1, Hassan Ha...

Details for people who like phylogenetics: virological.org/t/inter-clad...

YouTube video by euronews All aboard except the driver? A fully autonomous train takes to the tracks in Germany

1. 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.

I think you just discovered a meme

Alcohol And Fructose, Tangled (and Untangled?)

The connections between sugar and alcohol in the liver:

Great culture can save lives. Literally.

Amazing letter in today’s @thetimes.com about Tom Stoppard