Reposted by Mat BealeNicola Low @nicolamlow.bsky.social · 17/09/2026🧪 #HIV is still a pandemic www.theguardian.com/world/2026/s...theguardian.comFiji declares national HIV emergency as Pacific nation grapples with surge in casesGovernment estimates that one in 60 adults in Fiji now living with HIV, as escalating use of methamphetamine fuels ‘epidemic’ 0137
Reposted by Mat BealeJulian Parkhill @julianparkhill.bsky.social · 16/09/2026This 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.ukProfessorship of Veterinary ScienceThe 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... 11023
Reposted by Mat BealeTanja 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, 2026ai.ethz.chFellowship ProgramsThe 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. 01210
Reposted by Mat BealeJim Shaw @jimshaw.bsky.social · 15/09/2026The 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.ioDocumentation for sylph - ultrafast, precise metagenomic profiling 26330
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 10/09/2026Still 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. 003
Reposted by Mat BealeJulian Parkhill @julianparkhill.bsky.social · 08/09/2026Chair in Bacteriology in Cambridge Department of Medicine. A great opportunity. Please circulate. www.cam.ac.uk/jobs/researc...cam.ac.ukResearch Professor in the field of BacteriologyStrengthening 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... 02459
Reposted by Mat BealeGerry Tonkin-Hill @gerrythill.bsky.social · 02/09/2026Glad 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.orgAccurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpyGenetic 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... 12112
Reposted by Mat BealebioRxiv Microbiology @biorxiv-microbiol.bsky.social · 01/09/2026Accurate detection of metagenomic strain-level associations using average nucleotide identity with StrainSpy www.biorxiv.org/content/10.64898/20… 0102
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 18/08/2026Come & 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.socialjobs.lshtm.ac.ukJob Opportunity at LSHTM: Research FellowThe 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... 0815
Reposted by Mat BealeScott Bryan @scottygb.bsky.social · 19/07/2026Wayne Rooney speaks for everyone. 613500914
Reposted by Mat BealeCosta Samaras @costasamaras.com · 19/07/2026Could Excel be conscious? We surveyed more than Jan 1 1900 people to find out. 114137722879
Reposted by Mat BealeThe Onion @theonion.com · 16/07/2026What To Know About Cyclosporiasis theonion.com/what-to-know-about-cyc… 252689536
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 15/07/2026Delighted 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.socialovid.comAugust 2026 - Volume 53 - Issue 8 : Sexually Transmitted DiseasesDiscover the August 2026 issue of Sexually Transmitted Diseases, Volume 53, featuring peer-reviewed articles, case studies, and the latest research findings. 062
Mat Beale @typemat12.bsky.social · 09/07/2026Pleased 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.comPhylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiology - Nature CommunicationsWhole 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... 1102
Reposted by Mat BealeWellcome Sanger Institute @sangerinstitute.bsky.social · 09/07/2026Read: '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.comPhylo-Plex: a phylogenetically informed, low-cost amplicon sequencing platform for deployable high-resolution genomic epidemiologyNature 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... 063
Reposted by Mat BealeWellcome Sanger Institute @sangerinstitute.bsky.social · 09/07/2026A 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 2178
Reposted by Mat BealeKate 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! 🧫🧬💊 11311
Reposted by Mat BealeUrsula 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... 142
Reposted by Mat BealeJosie Bryant @josiebryant.bsky.social · 08/07/2026Very 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 36031
Reposted by Mat BealeLucia Ruggiero @lruggiero.bsky.social · 06/07/2026STI 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.intOverviewThe 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. ... 022
Reposted by Mat BealeKevin Ushey @kevinushey.bsky.social · 28/06/2026important 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 3368
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 17/06/2026Come 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.socialjobs.lshtm.ac.ukJob Opportunity at LSHTM: Research FellowThe 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... 0814
Reposted by Mat BealeRapid 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.eduReviews 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) | 📗📗📗📗◻️ 132
Reposted by Mat BealeMichael Payne @mjohnpayne.bsky.social · 26/05/2026Finally 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.orgDAMPA - accelerated and simplified design of probe panels for targeted metagenomics using pangenome graphsTargeted 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... 0104
Reposted by Mat BealeAdam 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.comReal signals or artificial stereotypes?Adventures with a cultural Copilot 15338141
Reposted by Mat BealeTHRU ZIM @thruzim.bsky.social · 13/04/2026Applications 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.ukCREATIVE criteria of recruitment | LSHTMIntroductionThe Clinical ResEArch Training fellowship with Industry involVEment (CREATIVE fellowship) is a multi-country, collaborative international clinical research capacity strengthening scheme in 001
Reposted by Mat BealeLeonid Schneider @forbetterscience.bsky.social · 25/03/2026Oh 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. 1521790
Mat Beale @typemat12.bsky.social · 23/03/2026Pleased 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 othersmedrxiv.org 2136
Reposted by Mat BealeCharlotte Houldcroft @virologyhouldcroft.bsky.social · 18/03/2026Have 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.orgGerm factories or immune boot camps? Infection and immunity in childcare settings | Clinical Microbiology ReviewsSUMMARYChildcare 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... 32917
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 16/03/2026Apply 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.sociallshtm.ac.uk2026-27 NIHR UK Syphilis Research Scholarship | LSHTMThe 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 0711
Reposted by Mat BealeMark Peifer (He, him) @peiferlabunc.bsky.social · 11/03/2026Holy smoke. What ultimately happened??? 921277
Reposted by Mat BealeDr. Headbutt 🌈🧪 @nicoleackermans.com · 19/02/2026I 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.coma group of goats standing in a grassy field looking at the cameraAlt: a group of goats running towards the camera 914520
Reposted by Mat BealeGerry Tonkin-Hill @gerrythill.bsky.social · 20/02/2026It'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.orgResearch Assistant - Tonkin-Hill LabResearch Assistant - Tonkin-Hill Lab 067
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 10/02/2026Announcing 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.usInternational Syphilis Symposium Webinar Series 0104
Reposted by Mat BealeZamin Iqbal @zaminiqbal.bsky.social · 09/02/2026A 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.comAddressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny - Nature MethodsThis 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. 313766
Reposted by Mat BealeMartin Hunt @martibartfast.bsky.social · 02/02/2026Ziplign 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/... 1289
Reposted by Mat BealeISGlobal @isglobal.org · 30/01/2026España 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 022
Reposted by Mat BealeResearch Professional News @resprofnews.bsky.social · 30/01/2026MRC 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.comMRC instructs grant review boards to slash funding rates - Research Professional NewsBoards asked to recommend just three applications for funding, as BBSRC also suspends calls 0514
Reposted by Mat BealeCMI 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/juoW50Y05t6ow.lyThe beating heart of a broken machine 21410
Reposted by Mat BealeEva Heinz @evaheinz7.bsky.social · 09/01/2026If 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 021
Reposted by Mat BealeThe Lancet Microbe @lancetmicrobe.bsky.social · 07/01/2026Also, author Amber Barton discusses this work with us in this linked podcast www.buzzsprout.com/1794195/epis... #IDSky #ClinMicro #yaws #Treponema #MDA #AMR #OpenAccess #OAbuzzsprout.comAmber Barton on mass drug administration to eradicate yaws in Papua New Guinea - The Lancet Microbe in conversation withPhoebe 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... 035
Reposted by Mat BealeThe Lancet Microbe @lancetmicrobe.bsky.social · 07/01/2026New 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 133
Reposted by Mat BealeMichael Marks @drmichaelmarks.bsky.social · 07/01/2026Out @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 086
Reposted by Mat BealeAmber Barton @amberbarton.bsky.social · 07/01/2026Really 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.ukGenomics uncovers new ways to target chronic childhood diseaseBy 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... 054
Reposted by Mat BealeEd Feil @edfeil.bsky.social · 07/01/2026It 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.comConvergence and global molecular epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus: a population genomic analysisKlebsiella pneumoniae is an important pathogen of humans and animals. In the past five years, increasing reports of convergent strains that carry both… 33825
Reposted by Mat BealeWellcome Sanger Institute @sangerinstitute.bsky.social · 07/01/2026Read '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.comEffect of repeated mass drug administration on the transmission of yaws: a retrospective genomic epidemiology studyYaws, a neglected tropical disease caused by Treponema pallidum subspecies pertenue (T p pertenue), has evaded eradication, in part due to a high prop… 033
Reposted by Mat BealeWellcome Sanger Institute @sangerinstitute.bsky.social · 07/01/2026By 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.ukGenomics uncovers new ways to target chronic childhood diseaseBy 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... 124
Reposted by Mat BealeEveryone'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." 🧵: 14930
Reposted by Mat BealeOnisillos @onisillos.bsky.social · 03/01/2026I’ve jotted down a few general points about paper rejection, if it’s of interest to anyone open.substack.com/pub/onisillo...open.substack.comRejection doesn't mean your paper was badIt's disappointing, but try to not take it personally. 297