We are hiring a PhD candidate! Only for non-EU graduates. To work on the molecular and genomic epidemiology of Treponema pallidum, based on our recent publication (doi:10.1128/mbio.00358-26). Interested? Send your CV and an expression of interest to fernando.gonzalez@uv.es before May 20th, 2026.

🧪 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/...

Mobile integrons encode phage defense systems

Integrons are bacterial genetic elements that capture, stockpile, and modulate the expression of genes encoded in integron cassettes. Mobile integrons (MIs) are borne on plasmids, acting as a vehicle ...

science.org

(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 🧬🖥️

Genomic surveillance reveals different transmission patterns between third-generation cephalosporin and carbapenem resistance in Klebsiella pneumoniae in the Comunidad Valenciana (Spain), 2018–2020 - ...

Background The emergence and spread of third-generation cephalosporins (3GC) and carbapenem-resistant Klebsiella pneumoniae pose a global critical challenge. Understanding the transmission dynamics wi...

go.uv.es

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

Febrero de 2020: el mes en el que España convivió con el coronavirus sin saberlo

El patógeno llegó y se propagó masivamente sin ser detectado durante esos días hasta hacer inevitables los confinamientos. Miles de casos de covid fueron confundidos con otras infecciones respiratoria...

elpais.com

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 🧪🧫🦠

The need for speed: ultra-rapid high-resolution outbreak analysis in a front-line hospital microbiology laboratory

Many hospital laboratories have technical capacity to perform whole-genome sequencing but lack bioinformatic expertise to analyse sequence data. Sending isolates to reference laboratories creates dela...

doi.org

bsky.app/profile/flod...

Flo Débarre@flodebarre.eurosky.social · 2y ago

Thread of threads: A chronology of the early days of the COVID-19 pandemic (It is not exhaustive, but hopefully it is representative.) 🧵

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...

High-throughput method characterizes hundreds of previously unknown antibiotic resistance mutations - Nature Communications

Resistance mutations are challenging to characterize because their effects are highly context dependent. Here, authors present a quantitative mutant screening technique that deconstructs how factors l...

nature.com

#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

Ecological dynamics of Enterobacteriaceae in the human gut microbiome across global populations - Nature Microbiology

Assessing more than 12,000 metagenomic samples from across the world using computational approaches, the authors determined interactions between species that co-colonize or co-exclude Enterobacteriace...

nature.com

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 victor.chai@asu.edu

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

A phylogenetic approach to comparative genomics

Nature Reviews Genetics - Controlling for phylogeny is essential in comparative genomics studies, because species, genomes and genes are not independent data points within statistical tests. The...

rdcu.be

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!

Polymerase mutations underlie adaptation of H5N1 influenza virus to dairy cattle and other mammals.

In early 2024, an unprecedented outbreak of H5N1 high pathogenicity avian influenza was detected in dairy cattle in the USA. The epidemic remains uncontrolled, with spillbacks into poultry, wild birds...

biorxiv.org

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)

Home

A tool for generating consensus long-read assemblies for bacterial genomes - rrwick/Autocycler

github.com

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...

American Ingenuity Beat the Polio Outbreak

So Why Risk Letting It Return?

brandy-schillace.medium.com

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!

Nathan Grubaugh@nathangrubaugh.bsky.social · 2y ago

Sharing our work expanding SARS-CoV-2 style tiled amplicon sequencing for whole bacteria genomes directly from clinical samples, showing examples with M.tb (>4 mb) and Strep pneumo (>2 mb). Led by Chaney Kalinich, Freddy Gonzalez, & Seth Redmond www.biorxiv.org/content/10.1...