🧪 Finally out after peer review, our work showing that "Mobile #Integrons carry Phage Defense Systems" is now published in Science 🎉 Short 🧵 www.science.org/doi/10.1126/...

(1/2) 🌍 Don't miss this groundbreaking study by Guo et al., 2025 and the 10,000 Plant Genomes Project. Profiling over one million nuclei across 20 tissues, the authors have further unraveled the genome of one of the most well studied plant genera: Arabidopsis. #plantgenomics #agriculture

New vacancy in my team! PhD student position on microbial genome evolution, focusing on the evolutionary principles underlying bacterial genome architecture. Please repost and share with talented MSc students in #evobio, bioinformatics or related :) www.uu.nl/en/organisat... #MEvoSky #MicroSky

Good papers, like good wine, need maturing. I'm proud and thrilled to share our work on genomic epidemiology of K.pneumoniae in Valencia and differential transmission patterns of resistances, part of Neris Garcia's PhD thesis and the NLSAR consortium. go.uv.es/td8iL4c #publichealth #EpiSky 🧬🖥️

Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo #publichealth #publichealthsky elpais.com/sociedad/202...

The PopGen Vienna Seminar series schedule is ready for the next term (Mar-Jun). It's jam-packed with fantastic speakers in #evolution, #genetics, #genomics, #popgen, and more! Details and streaming link signup can be found on our website www.popgen-vienna.at/news/seminars/

📌The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory |@medrxivpreprint See how hospital labs can analyse outbreaks fast - no on-site #Bioinformatics needed, cutting delays doi.org/10.1101/2025... 🖥️🧬💻 #AcademicSky #MicroSky 🧪🧫🦠

CompBio method developers: software that only runs on your computer and is not available via a repository like CRAN, PyPI, Bioconductor, is not a proper research output — just like a set of scribbled notes on your desktop is not the same as a preprint or a paper. Finish the job.

Very excited that my 1st first-author paper has just been published!! We present a novel mutant screening technique that can rapidly identify 100s of antibiotic resistance mutations, while evaluating how likely they are in different genetic backgrounds. www.nature.com/articles/s41...

#IDSky #MedSky required reading: Multidrug-resistant Gram-negative bacterial infections Nenad Macesic, Anne-Catrin Uhlemann, Anton Peleg Review in @thelancet.bsky.social doi.org/10.1016/S014...

Five years ago (Sunday 12 Jan 2020), five sequences of the new coronavirus were officially shared via GISAID, on a dedicated page revealed by a link on the GISAID homepage. ▫️1/ (🖼️: virological.org/t/novel-2019... by @arambaut.bsky.social)

H5 bird flu was found in wastewater in Los Angeles, San Francisco, Palo Alto, Paso Robles, Redwood City, Sacramento, San Jose, Santa Rosa, Sunnyvale and Turlock, according to WastewaterSCAN.

Five years ago (Saturday 11 Jan 2020), first public announcement and availability of a sequence of the new coronavirus. It was posted by @eddieholmes.bsky.social at 01:05 UTC on Virological, and announced on Twitter at 01:08 UTC. ▫️1/ web.archive.org/web/20200118... archive.is/z880d

Delighted to share the first peer-reviewed paper from our team @camvetschool.bsky.social where we investigate the ecological dynamics of Enterobacteriaceae in the human gut #microbiome: www.nature.com/articles/s41... @naturemicrobiol.bsky.social

Suppose a new flu pandemic were to emerge. How quickly could we get going with key epidemiological analysis and modelling? To find out, I went back through the dozens of reports I was involved in for SPI-M for COVID and estimated where we currently stand: epiverse-trace.github.io/posts/covid-...

🔥 Webinar Series Launch! 🔥 ‘#Genomics and Beyond: A Holistic Approach to Tackling #AMR in East Africa’ 🌍 Don't miss Prof. Matthew Holden #StAndMedicine sharing his expertise. Register Now www.targetamr.org.uk/hdrevents/ja...

🥁 Announcing the Public Domain Image Archive! 🥁 We are v excited to share our new sister-project, the Public Domain Image Archive (PDIA), a curated collection of 10k+ out-of-copyright historical images, all free to explore and reuse: pdimagearchive.org @pdimagearchive

*** Notification: New class in Evolutionary Cell Biology open to the public during Spring 2025 semester The class is taught by Dr. Michael Lynch every Tuesday and Thursday, 9:00-10:15 am (MST), starting on 16 January 2025 Join the class on asu.zoom.us/j/86824596554 Details [email protected]

Our review is out in Nature Reviews Genetics! rdcu.be/d5AY2 We show how phylogeny-based methods can resolve the problem of non-independence in genomic datasets. These methods must be considered an essential part of the comparative genomics toolkit. @lauriebelch.bsky.social @stuwest.bsky.social

Very excited to share our recent publication with Verena Schuenemann and other excellent collaborators, including my former student Marta Pla-Diaz. We have improved the analysis of Treponema pallidum genomes with a Multiple_Reference_Based mapping. Useful for many other bacteria Enjoy rdcu.be/d5GGx

Really proud to share our preprint describing early adaptation of H5N1 to US dairy cattle, and showing how these mutations enhance the ability of the virus to infect other mammals, such as pigs and humans. With @influenzal.bsky.social @vidhid.bsky.social @drclairesmith.bsky.social and many more!

New year, new assemblies! I'm excited to announce Autocycler, my new tool for consensus assembly of long-read bacterial genomes! It's the successor to Trycycler, designed to be faster and less reliant on user intervention. Check it out: github.com/rrwick/Autoc... (1/5)

History doesn’t lie. Polio—and other disease epidemics—killed, paralyzed, ravaged lives. It’s still here, waiting. 🧪♿️🗃️ #vaccines #polio brandy-schillace.medium.com/american-ing...

Incredibly excited to share that our manuscript was just published in @nature.com ! What a way to start the new year! 🎉 https://buff.ly/4gyYCzx We present phylowave, a framework that enables to learn the fitness dynamics of pathogens from phylogenies. 🧵 A thread... 1/n #IDSky #IDModelling

⚠️ BREAKING: H5N1 bird flu virus levels in San Francisco wastewater surged to a record high of 228.8, according to WastewaterSCAN. This wastewater treatment plant handles 80% of the city's wastewater.

🎁 Early Xmas present from your friends at the MRC-University of Glasgow Centre for Virus Research @cvrinfo.bsky.social We're thrilled to unwrap Viro3D - a comprehensive database of virus protein structures: >85,000 predicted structures from 4,400 human & animal viruses! 🦠 viro3d.cvr.gla.ac.uk

1/ Highly pathogenic avian influenza (HPAI) in Great Britain & Europe - DEFRA outbreak assessment for 18 Dec 2024. #IDsky 🧪 🗓️ Report period: 06 Nov – 18 Dec 2024 🔗 to report: assets.publishing.service.gov.uk/media/6765a0...

This is super interesting, have never seen tiled amplicons for bacteria. I can see why it works with (non recombining, v few mobile elements) Mtb, seems like it would be v hard to design primer schemes for other things. V keen to see the pneumococcus results . Will read!

Bioart, courtesy of the NIH. All images are in the public domain and available for download as high-quality SVGs. bioart.niaid.nih.gov

Today, the Ministry of Health of #Rwanda has declared the end of the #Marburg virus disease outbreak, following a 42 day case-free countdown. As of 19 December 2024, 66 cases were confirmed, including 15 deaths (CFR 23%) and 51 recovered cases. More here: www.who.int/emergencies/...

Ngl, I think this will be one of the more meaningful tools I've ever engineered. Orthogroups inferred using HMMs have greater precision and recall compared to traditional sequence search approaches bsky.app/profile/jlst...

For months now, the CDC has described H5N1 as “mild” compared to prior H5N1 viruses. I disagree—the virus alone doesn’t determine pathogenicity. I hypothesize that the 2 most critical determinants of H5N1 severity are the host (it’s always the host 🥰) & the route of infection.

Really glad I could contribute to this work exploring biofilm formation, mucoidy and tip adhesin diversity in #klebsiella. For those in #KLEBS2024, I provided a sneak peak of the potential relation between K3 serotype & HMV This is also my first publication since I joined @cbitoulouse.bsky.social !

A widely quoted COVID theory was that once individuals with lots of contacts become immume, outbreaks will end with relatively small % infected. But when we looked at real-life networks, we found popularity isn't stable enough to predict 'superspreaders': royalsocietypublishing.org/doi/10.1098/...

We identified protein domains in LUCA (Last Universal Common Ancestor). Their distinctive amino acid usage reveals the order amino acids were added to the genetic code, based mostly on size. Older proteins hint at earlier alternative codes. 1/15 @seekingluca.bsky.social www.pnas.org/doi/10.1073/...

New paper with @snaildit.bsky.social❗ You can use paralogs to reduce long-branch attraction! This will be especially helpful when there are no extant taxa that can be sampled to break up these branches. www.biorxiv.org/content/10.1...

Gene flow between Homo sapiens and Neanderthals started ~50,000 years ago and lasted around 6000 years (~100 generations) 🧪🧬🖥️ #AnthroSky #EvoSky #PaleoSky www.science.org/doi/10.1126/...

Pathogenomics group leader Mireia Coscolla had a talk at FiSABIO about their M. #tuberculosis research 🔬🦠🧫🖥🧬

Grateful for @who.int updates on the undiagnosed illness in #DRC. - 10/12 samples (+) for #malaria. - Could be solely malaria or a mix with another disease. - Important to remember malnutrition may increase severity and risk of complications. - Critical to monitor developments closely.

And if you want to read more about this new research program in English, here you have an article in #PRBBellipse :) 👍 #genomics #evolution ellipse.prbb.org/harnessing-e...

"Given the clinical presentation and symptoms reported, and a number of associated deaths, acute pneumonia, influenza, COVID-19, measles and malaria are being considered as potential causal factors with malnutrition as a contributing factor." Update on outbreak unfolding in DRC" #IDSky #MedSky

Question of how is #H5N1 spreading in North America given in theory its been isolated to poultry/cattle herds that are quarantined. One metric to look at is a weighted diffusion coefficient (WDC). Using this, avian influenzas rank in the upper-echelon of dispersal potential: 🧪🛟 #EpiSky #IDSky 1/🧵

1/ Influenza wastewater activity levels are currently low across the US, aside from conspicuous areas in CA where #H5N1 is spreading in dairy cows. A deeper dive into the Wastewater Scan data paints a very concerning picture and should add to our sense of urgency.

Dudar de la #evolución a día de hoy no tiene ningún sentido: desde el registro fósil a la embriología, un sinfín de evidencias confirman que Darwin tenía razón.

Do mutations that drive evolution improve many traits or few? Does this change over the course of evolution? Excited to share our work in PLOS Biology exploring these questions in the first 2 adaptive steps w/ Yuping Li, @gsherloc.bsky.social, @petrovadmitri.bsky.social 🧵 doi.org/10.1371/jour...

The process of producing flu vaccines with eggs: I didn't realise that 1 egg supplies only around 1 dose.