Mat Beale

a group of goats standing in a grassy field looking at the camera Alt: a group of goats running towards the camera

I don't think that the reviewers asking me for higher animal numbers really understand how many 40 goats are. Do you know the CHAOS that comes with dealing with 40 GOATS in an experimental setting!
Mice people cannot comprehend.
3 goats alone ate a tarp, a clock, and 2 expensive accelerometers!

It's a bit last minute, but we have an RA/junior postdoc position available in my lab (closing Sunday). Please reach out if you're interested in developing and applying methods to analyse microbial genomes and metagenomes! careers.petermac.org/job/MELBOURN...

International Syphilis Symposium Webinar Series

Announcing launch of the International Syphilis Symposium Webinar Series.

The series brings together clinicians, academics, public health agencies & community organisations to highlight research & public health interventions focused on syphilis.

First meeting 26th March this year: Register below.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature Methods This Resource paper presents a global SARS-CoV-2 phylogenetic tree of 4,471,579 high-quality genomes consistently constructed by Viridian, an efficient amplicon-aware assembler.

A long time ago in a galaxy far away, there was a SARS-CoV-2 pandemic. Our paper, led by @martibartfast.bsky.social
a) correcting errors in 4.5 million genomes & their phylogeny
b) improving representation of the Global South in public data
www.nature.com/articles/s41...
(thread 1/n)

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/...

España da un paso adelante en la lucha contra las #EnfermedadesTropicalesDesatendidas con la creación de la Coalición Española de ETD.

#ISGlobal forma parte de esta iniciativa que une ciencia, sociedad civil e instituciones.

🟠 https://tinyurl.com/5v66t6yz

#WorldNTDDay

MRC instructs grant review boards to slash funding rates - Research Professional News Boards asked to recommend just three applications for funding, as BBSRC also suspends calls

MRC instructs grant review boards to slash funding rates.

Boards asked to recommend just three applications for funding, as BBSRC also suspends calls.

www.researchprofessionalnews.com/rr-news-uk-r...

The beating heart of a broken machine

📣 A peer reviewer used #AI to create a fake review with 6 self-citation prompts. But is s/he the only perpetrator in our system? In the year's first editorial, Angela Huttner explores the depths of the academic-industrial complex.

#IDSky #clinmicro #peerreview

https://ow.ly/juoW50Y05t6

I was just thinking that…

If you're interested, MGEN (senior) editor call still open 😊 we're a nice team and you'll join a not-for-profit, community-driven journal that puts great emphasis on scientific integrity! (2/2) 🧬💻 #MicroSky #IDSky #NativeInSTEM #BlackInMicro #MicrobiomeSky microbiologysociety.org/who-we-are/j...

Amber Barton on mass drug administration to eradicate yaws in Papua New Guinea - The Lancet Microbe in conversation with Phoebe Ashley-Norman of The Lancet Microbe speaks to Amber Barton about the neglected tropical disease, yaws. Efforts to eradicate yaws were first made in the 1950s through a WHO and UNICEF campaign t...

Also, author Amber Barton discusses this work with us in this linked podcast

www.buzzsprout.com/1794195/epis...

#IDSky #ClinMicro #yaws #Treponema #MDA #AMR #OpenAccess #OA

New research article

Effect of repeated mass drug administration on the transmission of #yaws: a retrospective genomic epidemiology study

www.thelancet.com/journals/lan...

#IDSky #ClinMicro #Treponema #MDA #AMR #OpenAccess #OA

@sangerinstitute.bsky.social

The image shows two box and whisker plots. The left hand plot shows the duration of peoples ulcers stratified by sub-lineage and demonstrates that one of these sub-lineages has a longer duration of ulcers than the others. The right hand plot shows the titre of treponemal antibodies stratified by sub-lineage and demonstrates that the same sub-lineage is also associated with much lower antibody titres than the others.

Out @lancetmicrobe.bsky.social & led @amberbarton.bsky.social We used WGS to look at Treponema population dynamics during community MDA for yaws tinyurl.com/bd6zu6xm

Intriguingly found sublineage associated w longer ulcer duration & lower antibody titres. Whether occurs in syphilis needs exploring

Genomics uncovers new ways to target chronic childhood disease By sequencing the bacteria that cause the neglected disease yaws, researchers have found that while mass treatment can be successful, it can cause resistant strains to develop. They suggest that publi...

Really pleased to see our work on yaws, and how mass drug administration shapes Treponema genomes, published in @lancetmicrobe.bsky.social!

sanger.ac.uk/news_item/genomics-uncovers-new-ways-to-target-chronic-childhood-disease/

www.thelancet.com/journals/lan...

Convergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysis Klebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both…

It has been a long road, but our paper on Klebsiella plasmids is finally out in Lancet Microbe. Thanks to all co authors but especially Marjorie Gibbon and Natacha Couto www.sciencedirect.com/science/arti...

Effect of repeated mass drug administration on the transmission of yaws: a retrospective genomic epidemiology study Yaws, a neglected tropical disease caused by Treponema pallidum subspecies pertenue (T p pertenue), has evaded eradication, in part due to a high prop…

Read 'The Effect of Repeated Mass Drug Administration on the Transmission of Yaws: A Genomic Epidemiology Study' from @sangerinstitute.bsky.social @lshtm.bsky.social, @fundaciolluita.bsky.social , & others in the @lancetmicrobe.bsky.social⤵️

www.sciencedirect.com/science/arti...

Genomics uncovers new ways to target chronic childhood disease By sequencing the bacteria that cause the neglected disease yaws, researchers have found that while mass treatment can be successful, it can cause resistant strains to develop. They suggest that publi...

By sequencing the bacteria responsible for yaws, a debilitating childhood disease, experts have uncovered new insights into how these bacteria re-emerge and evade treatment 🧬

Find out how these can be used to help inform public health interventions ⤵️

www.sanger.ac.uk/news_item/ge...

🎉 New year, NEW PREPRINT!

Bacteria exhibit astonishing genetic diversity, but where do new genes come from?

My best friend Arya Kaul (/labmate in the @baym lab) investigates how advantageous deletions can spawn new genes - "deletion-born fusions." 🧵:

I’ve found similar issues with Zotero’s automated download. 😔

I’ve jotted down a few general points about paper rejection, if it’s of interest to anyone

open.substack.com/pub/onisillo...

Indy does also get paid by Marcus at the museum for the artefacts he brings them though…

On the first day of Christmas (in about 2014), @duckswabber.bsky.social gave to me - a partridge in a pear tree.

Happy Christmas everyone!

A slightly late pre-xmas reminder to please apply for these funded PhD positions in parasite genomics/genetics/molecular biology that I'm involved in – the closing date was extended and is now 4th January, so still time to put together an application.

Jobs View the current job vacancies at the Microbiology Society.

📢 Senior Editor role opportunity available with the Microbiology Society for the Pathogens & Epidemiology section. This role supports journal strategy, section development & community engagement.
More info: Voluntary Opportunities: microb.io/Vacancies

How Unethical Research Seeds Medical Mistrust The absence of equipoise can turn research into harm

"Ethical standards do not become optional because the participants are African."

bktitanji.substack.com/p/how-unethi...

As my own three year stint as an Editor comes to an end I cannot recommend doing this enough

📣 UKHSA survey on gonorrhoea testing practices in England

UKHSA is inviting sexual health services & diagnostic labs to take part in a national survey on current gonorrhoea testing practices across England.

⏱️ 15 minutes
🗓️ Deadline: 14 Jan 2026
🔗 Take part here: surveys.ukhsa.gov.uk/s/sg01bo

Wellcome Genome Campus looking very seasonal tonight.

Ancient DNA insights into diverse pathogens and their hosts Nature Reviews Genetics, Published online: 03 December 2025; doi:10.1038/s41576-025-00912-4Ancient DNA techniques are being applied to study increasingly diverse pathogens of the past. The authors review the latest insights into pathogen–host coevolution, zoonotic events and the spread of pathogens, all while highlighting the importance of a One Health approach to this research.

ICYMI: New online! Ancient DNA insights into diverse pathogens and their hosts

FlightPath: Predicting Avian Influenza Evolution through AI-Powered Phylodynamics and Bird Migration Modelling at University of Reading on FindAPhD.com PhD Project - FlightPath: Predicting Avian Influenza Evolution through AI-Powered Phylodynamics and Bird Migration Modelling at University of Reading, listed on FindAPhD.com

We’re recruiting a PhD student as part of the AI-Intervene DTP to join FlightPath, an exciting project combining viral genomics, bird migration data, and AI-powered phylodynamics to forecast how avian influenza evolves and spreads.

Project Details 🦠🧬🦅🦆🌎: tinyurl.com/2v4xaxmx.