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Mat Beale

@typemat12.bsky.social
620 followers 546 following 127 posts

Microbial (meta)genomics researcher @sangerinstitute interested in genomic epidemiology and evolutionary dynamics of STIs/NTDs/AMR in complex samples. Views my own. www.sanger.ac.uk/person/beale-mathew

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Reposted by Mat Beale
Nicola Low @nicolamlow.bsky.social · 17/09/2026
🧪 #HIV is still a pandemic www.theguardian.com/world/2026/s...
theguardian.com
Fiji declares national HIV emergency as Pacific nation grapples with surge in cases
Government estimates that one in 60 adults in Fiji now living with HIV, as escalating use of methamphetamine fuels ‘epidemic’
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Julian Parkhill @julianparkhill.bsky.social · 16/09/2026
This will be an amazing opportunity for the right person. The Department of Veterinary Medicine in Cambridge is recruiting for an established chair who will also be our Head of Department. Your research can be in any area of veterinary science. Please circulate. www.cam.ac.uk/jobs/profess...
cam.ac.uk
Professorship of Veterinary Science
The Board of Electors to the Professorship of Veterinary Science invite applications for this Professorship from persons whose work is connected with veterinary science (ideally in research aligned wi...
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Tanja Stadler @tanjastadler.bsky.social · 15/09/2026
🚀 Interested in joining our Computational Evolution group at ETH Zürich in Basel @bsse.ethz.ch as a Postdoc? We will be hosting ETH AI Center's Postdoc Fellows on AI x evolution, AI x single cell biology as well as AI x public health. Apply now 👉 ai.ethz.ch/apply Deadline: Oct 27, 2026
ai.ethz.ch
Fellowship Programs
The application portal for the ETH AI Center Fellowship Programs is now closed. The deadline for submitting reference letters is 23:59 CET on November 14, 2025.
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Jim Shaw @jimshaw.bsky.social · 15/09/2026
The sylph metagenome profiler is v1.0.0! sylph-docs.github.io A new DB format + approach --> huge performance gains: GTDB-R232 (200k species) now takes < 5 GB of RAM and ~30s (2GB fq.gz). Huge thanks to @benjwoodcroft.bsky.social and his ongoing performance efforts (github.com/wwood/weebill)
sylph-docs.github.io
Documentation for sylph - ultrafast, precise metagenomic profiling
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Michael Marks @drmichaelmarks.bsky.social · 10/09/2026
Still 1 week to apply. Looking for a great mathematical modeller to come and do a post-doc @lshtm.bsky.social focused on STI modelling in the UK.
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Julian Parkhill @julianparkhill.bsky.social · 08/09/2026
Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate. www.cam.ac.uk/jobs/researc...
cam.ac.uk
Research Professor in the field of Bacteriology
Strengthening Cambridge's leadership in bacteriology research Bacterial infection and antimicrobial resistance remain among the most pressing global health challenges of our time. At Cambridge, the De...
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Gerry Tonkin-Hill @gerrythill.bsky.social · 02/09/2026
Glad to share StrainSpy, a new method developed by Sudaraka and co which identifies strain-level associations in metagenomics using ANI estimates from tools like Sylph. www.biorxiv.org/content/10.6...
biorxiv.org
Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy
Genetic variation among microbial strains of the same species can profoundly influence their phenotypes, ecological functions, and impacts on human health. Traditionally, the relative abundance of a s...
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 01/09/2026
Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy www.biorxiv.org/content/10.64898/20…
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Michael Marks @drmichaelmarks.bsky.social · 18/08/2026
Come & join our group. Modelling post @lshtm.bsky.social working on STI transmission & new interventions in the UK. Working closely with @ukhsa.bsky.social Applications close 17th September. @adamjkucharski.bsky.social @rozeggo.bsky.social @bquilty.bsky.social @grahammedley.bsky.social
jobs.lshtm.ac.uk
Job Opportunity at LSHTM: Research Fellow
The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...
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Scott Bryan @scottygb.bsky.social · 19/07/2026
Wayne Rooney speaks for everyone.
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Costa Samaras @costasamaras.com · 19/07/2026
Could Excel be conscious? We surveyed more than Jan 1 1900 people to find out.
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The Onion @theonion.com · 16/07/2026
What To Know About Cyclosporiasis theonion.com/what-to-know-about-cyc…
Q: How many cases have been recorded?

A: Oh, the CDC doesn’t do that anymore.
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Michael Marks @drmichaelmarks.bsky.social · 15/07/2026
Delighted to see our special issue of Sexually Transmitted Diseases featuring a large number of outputs arising from the 2025 Shanghai International Syphilis Symposium & related work. Lots of great work & insights on the recent scientific progress. @typemat12.bsky.social @thelovetankcic.bsky.social
ovid.com
August 2026 - Volume 53 - Issue 8 : Sexually Transmitted Diseases
Discover the August 2026 issue of Sexually Transmitted Diseases, Volume 53, featuring peer-reviewed articles, case studies, and the latest research findings.
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Mat Beale @typemat12.bsky.social · 09/07/2026
Pleased to share our paper on low cost amplicon methods, part of a collaboration between the Sanger Institute and researchers at BRTI in Zimbabwe and NICD in South Africa www.nature.com/articles/s41...
nature.com
Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology - Nature Communications
Whole genome sequencing of pathogens is costly to implement, and partial sequencing sacrifices information. Here, the authors present Phylo-Plex, a method for identifying information-rich genomic regi...
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Wellcome Sanger Institute @sangerinstitute.bsky.social · 09/07/2026
Read: 'Phylo-Plex: A phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology' in @natcomms.nature.com here 👇 www.nature.com/articles/s41467-026-…
nature.com
Phylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology
Nature Communications - Whole genome sequencing of pathogens is costly to implement, and partial sequencing sacrifices information. Here, the authors present Phylo-Plex, a method for identifying...
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Wellcome Sanger Institute @sangerinstitute.bsky.social · 09/07/2026
A faster, lower-cost way to track microbes. 🦠 Researchers have developed a new platform that sequences DNA of bacteria and other harmful microbes more efficiently, making it easier to monitor outbreaks in resource-limited settings. Read more here 👇 bit.ly/4phwvdu
A person in gloves uses a pipette to transfer liquid into a 96-well plate at a laboratory bench with test tubes and lab equipment.
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Kate Baker @ksbakes.bsky.social · 09/07/2026
👀👇 New work on sexually transmitting Shigella (press-friendly: bit.ly/4bBarEL) From continued collaboration with @clairejenkins2.bsky.social @ukhsa.bsky.social, @pducambridge.bsky.social co-lead @hsalje.bsky.social, a talented student Julia Marshall www.linkedin.com/in/julia--ma..., and others! 🧫🧬💊
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Ursula Hofer @hoferu.bsky.social · 09/07/2026
~1/3 of Shigella cases are in MSM and rising, resistance increasingly becoming a problem. Emerging STI, in my opinion...
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Josie Bryant @josiebryant.bsky.social · 08/07/2026
Very proud of this preprint out of my lab, our first (of hopefully many) host-microbe spatial transcriptomics paper. www.biorxiv.org/content/10.6... Amazing insights into P. aeruginosa biology and chronic airway disease @cysticfibrosis.org.uk @sangerinstitute.bsky.social @asthmaandlung.org.uk
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Lucia Ruggiero @lruggiero.bsky.social · 06/07/2026
STI Prevalence Atlas A global resource that brings together prevalence data on sexually transmitted infections (STIs) in low- and middle-income countries (LMICs) data.who.int/dashboards/s...
data.who.int
Overview
The Atlas is a first of its kind global resource that brings together prevalence data on sexually transmitted infections (STIs) in low- and middle-income countries (LMICs) collected in 2010 or later. ...
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Kevin Ushey @kevinushey.bsky.social · 28/06/2026
important knowledge for anyone who doesn't want the big AI button in rstudio: right click, wave bye. also discoverable in the "Assistant" preferences pane. #rstats
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Michael Marks @drmichaelmarks.bsky.social · 17/06/2026
Come work @lshtm.bsky.social modelling STIs in UK & evaluation of new interventions. 3yr research fellow modelling post - feel free to get in touch to discuss. Current closing date 30th June @rozeggo.bsky.social @adamjkucharski.bsky.social @grahammedley.bsky.social @drlouisedyson.bsky.social
jobs.lshtm.ac.uk
Job Opportunity at LSHTM: Research Fellow
The London School of Hygiene & Tropical Medicine (LSHTM) is one of the world’s leading public health universities. Our mission is to improve health and health equity in the UK and worldwide; working i...
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Reposted by Mat Beale
Rapid Reviews\Infectious Diseases Journal @rapidreviews-id.bsky.social · 11/06/2026
‼️🚨Read reviews on a preprint analyzing more than 300 African Treponema pallidum genomes revealing unexpectedly high local diversity and distinct transmission patterns. rrid.mitpress.mit.edu/pub/mosfrcfr...
rrid.mitpress.mit.edu
Reviews of: "High Diversity amongst African Treponema pallidum Genomes Provides a Window into Global Transmission Dynamics of Syphilis: A Genomic Epidemiology Study"
Reviewers: F Gonzalez-Candelas (University of Valencia) | 📗📗📗📗◻️ • T Mortimer (University of Georgia) | 📘📘📘📘📘 • A Pillay (Centers for Disease Control and Prevention) | 📗📗📗📗◻️
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Michael Payne @mjohnpayne.bsky.social · 26/05/2026
Finally a preprint for our tool DAMPA (Australiana included) that generates efficient probe panels for targeted metagenomics from pangenome graphs. Presented at ABPHM and ABACBS last year. www.medrxiv.org/content/10.6...
medrxiv.org
DAMPA - accelerated and simplified design of probe panels for targeted metagenomics using pangenome graphs
Targeted metagenomics, where samples are enriched for multiple organisms of interest using oligonucleotide probes, is a highly efficient sequencing methodology that is becoming standard practice for g...
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Adam Kucharski @adamjkucharski.bsky.social · 06/05/2026
"Based on the dataset you shared, US and UK responses differ mainly in tone, intensity, and wording style, even though they express similar emotional states" New post on what happened when I got Copilot to do some data analysis: kucharski.substack.com/p/real-signa...
kucharski.substack.com
Real signals or artificial stereotypes?
Adventures with a cultural Copilot
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THRU ZIM @thruzim.bsky.social · 13/04/2026
Applications are OPEN for the 𝗖𝗥𝗘𝗔𝗧𝗜𝗩𝗘 𝗙𝗲𝗹𝗹𝗼𝘄𝘀𝗵𝗶𝗽! A unique opportunity to build clinical research capacity in sub-Saharan Africa through: • Academic training (MSc via LSHTM) • Hands-on research experience • Industry exposure 🗓 Deadline: 29 May 2026 🔗 www.lshtm.ac.uk/study/fees-a...
lshtm.ac.uk
CREATIVE criteria of recruitment | LSHTM
IntroductionThe Clinical ResEArch Training fellowship with Industry involVEment (CREATIVE fellowship) is a multi-country, collaborative international clinical research capacity strengthening scheme in
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Leonid Schneider @forbetterscience.bsky.social · 25/03/2026
Oh nothing, just a peer reviewed paper my colleagues found... doi.org/10.1016/j.ma... "1 mL of the mass killing of an ethnic group was opposed to 20 mL of the skin sample and unprotected to light for 7 min." Even AI knows what's wrong here, but @elsevierconnect.bsky.social doesn't.
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Mat Beale @typemat12.bsky.social · 23/03/2026
Pleased to share our new preprint on genomic epi of #treponema www.medrxiv.org/content/10.6... focusing on genomic diversity and transmission of #syphilis in Africa with @drmichaelmarks.bsky.social @sangerinstitute.bsky.social @thruzim.bsky.social and many others
medrxiv.org
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Charlotte Houldcroft @virologyhouldcroft.bsky.social · 18/03/2026
Have you ever wondered why children starting nursery/daycare pick up so many germs? I certainly did, and with a crack team of parent-scientists/clinicians, we set out to answer that question. Is childcare a germ factory or an immune bootcamp? journals.asm.org/doi/10.1128/...
journals.asm.org
Germ factories or immune boot camps? Infection and immunity in childcare settings | Clinical Microbiology Reviews
SUMMARYChildcare outside the home is a common experience for many children in high-income countries. It is associated with an increase in the incidence of infectious diseases—not just for the child bu...
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Michael Marks @drmichaelmarks.bsky.social · 16/03/2026
Apply by 11th May to do a PhD @lshtm.bsky.social Work with epidemiologists, social scientists & modellers to understand quality of life measures in Syphilis and develop evidence on cost-effectiveness of interventions & public health strategies. @thelovetankcic.bsky.social @joetucker.bsky.social
lshtm.ac.uk
2026-27 NIHR UK Syphilis Research Scholarship | LSHTM
The London School of Hygiene and Tropical Medicine (LSHTM) is pleased to invite applications for a 3-year full-time PhD studentship, starting in September 2026.The award will cover a tax-free stipend
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Mark Peifer (He, him) @peiferlabunc.bsky.social · 11/03/2026
Holy smoke. What ultimately happened???
Image from their link showing evidence of fabricated references
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Dr. Headbutt 🌈🧪 @nicoleackermans.com · 19/02/2026
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!
media.tenor.com
a group of goats standing in a grassy field looking at the camera
Alt: a group of goats running towards the camera
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Gerry Tonkin-Hill @gerrythill.bsky.social · 20/02/2026
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...
careers.petermac.org
Research Assistant - Tonkin-Hill Lab
Research Assistant - Tonkin-Hill Lab
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Michael Marks @drmichaelmarks.bsky.social · 10/02/2026
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.
events.zoom.us
International Syphilis Symposium Webinar Series
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Zamin Iqbal @zaminiqbal.bsky.social · 09/02/2026
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)
nature.com
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.
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Martin Hunt @martibartfast.bsky.social · 02/02/2026
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/...
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ISGlobal @isglobal.org · 30/01/2026
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. 🟠 tinyurl.com/5v66t6yz #WorldNTDDay
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Research Professional News @resprofnews.bsky.social · 30/01/2026
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...
researchprofessionalnews.com
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
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CMI Communications @cmicomms.bsky.social · 20/01/2026
📣 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 ow.ly/juoW50Y05t6
ow.ly
The beating heart of a broken machine
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Eva Heinz @evaheinz7.bsky.social · 09/01/2026
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...
microbiologysociety.org
<i>Microbial Genomics</i> Senior Editor and Editors: call for expressions of interest
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The Lancet Microbe @lancetmicrobe.bsky.social · 07/01/2026
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
buzzsprout.com
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...
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The Lancet Microbe @lancetmicrobe.bsky.social · 07/01/2026
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
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Michael Marks @drmichaelmarks.bsky.social · 07/01/2026
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
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.
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Amber Barton @amberbarton.bsky.social · 07/01/2026
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...
sanger.ac.uk
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...
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Ed Feil @edfeil.bsky.social · 07/01/2026
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...
sciencedirect.com
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…
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Wellcome Sanger Institute @sangerinstitute.bsky.social · 07/01/2026
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...
sciencedirect.com
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…
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Wellcome Sanger Institute @sangerinstitute.bsky.social · 07/01/2026
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...
sanger.ac.uk
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...
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Everyone's least favorite lab mate @kepatitis-c.bsky.social · 06/01/2026
🎉 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." 🧵:
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Onisillos @onisillos.bsky.social · 03/01/2026
I’ve jotted down a few general points about paper rejection, if it’s of interest to anyone open.substack.com/pub/onisillo...
open.substack.com
Rejection doesn't mean your paper was bad
It's disappointing, but try to not take it personally.
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