New preprint from us! 🦠 Clinical metagenomics is great for sequencing pathogens directly from patient samples but for some protocols sensitivity for RNA viruses lags behind bacteria & fungi. We have shown why, and how to fix it. www.medrxiv.org/content/10.6...

Library preparation strategy critically impacts RNA virus sensitivity in clinical metagenomics

Clinical metagenomics uses sequencing for culture-independent identification of pathogens directly from clinical specimens. While a number of protocols claim to be pathogen agnostic, sensitivity for R...

medrxiv.org

We are recruiting! Join Dr Josh Quick @scalene.bsky.social as a Postdoctoral Fellow in Metagenomics edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

Research Fellow (Postdoctoral) - School of Biosciences - 107071 - Grade 7

This post-doctoral position will contribute to both complementary programmes, developing ‘broadband’ metagenomic sequencing capabilities for rapid detection and characterisation of emerging and unknow...

edzz.fa.em3.oraclecloud.com

New preprint from our Gates-funded Modjadji initiative showing that whole-genome surveillance of measles virus from wastewater greatly expands our ability for monitoring and control. Here, with our colleagues in South Africa - U.S., unfortunately, likely up next. www.medrxiv.org/content/10.6...

Integrating measles wastewater and clinical whole-genome sequencing enables high-resolution tracking of virus evolution and transmission

Measles outbreaks have surged globally in recent years, but current surveillance systems have limited capacity to monitor measles virus (MeV) transmission and evolution at population scale. Although M...

medrxiv.org

Love microbes & omics? 🦠🧬 We’re hiring a Postdoc in Public Health Genomics at @unibirmingham.bsky.social Work on cutting-edge research with wonderful people! @wvschaik.bsky.social @halllab.bsky.social @pathogenomenick.bsky.social @scalene.bsky.social @alanmcn1.bsky.social 📅 Closes 4th Feb

Research Fellow - Department of Microbes, Infection and Microbiomes - 105518 - Grade 7

The post holder will work within the newly established NIHR Health Protection Unit for Public Health Genomics, a partnership between the University of Birmingham and the UK Health Security Agency. You...

edzz.fa.em3.oraclecloud.com

Around 10% of your Nanopore reads (SQK-RBK114) are incorrectly trimmed. Here is why, and how our new tool Barbell solves it: www.biorxiv.org/content/10.1... Want to get started? github.com/rickbeeloo/b...

Interested in respiratory metagenomics? We assembled nearly all of the virus genomes in a respiratory verification panel manufactured by ZeptoMetrix. Blog: artic.network/2025-07-26_p... Assemblies: github.com/bede/zmrp @scalene.bsky.social @pathogenomenick.bsky.social @articnetwork.bsky.social

We’re continuing to expand the number of pathogens we support for Freyja (github.com/andersen-lab...), and developing corresponding low-cost and highly sensitive amplicon sequencing schemes as our Modjadji initiative (including @scalene.bsky.social ‬ and @chris.primalscheme.com

Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!

Anna (Ganna) Kovalenko@annakovalenko.bsky.social · last yr.

🚨 Tularemia mystery solved in stranded belugas in Alaska! thanks to smart-9N metagenomics & nanopore sequencing 🔬🐋 #wildhealth #onehealth Well done @bortz-virology.bsky.social and Team!! wwwnc.cdc.gov/eid/article/...

Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol.

Anna (Ganna) Kovalenko@annakovalenko.bsky.social · last yr.

the link to the preprint 🔗 www.biorxiv.org/content/10.1...

Ever had to pause genomic surveillance due to enzyme shortages?🫣 Happy to share our new preprint with the solution inside 🦹‍♀️💪 biorxiv.org/content/10.110… @scalene.bsky.social @chris.primalscheme.com @pathogenomenick.bsky.social @articnetwork.bsky.social @nanoporetech.com

And don't forget to watch the accompanying video of @scalene.bsky.social broodily walking the canals of Birmingham describing how sequencing can be useful in outbreaks: www.youtube.com/watch?embeds...

Changing how the world tracks emerging viruses | University of Birmingham

YouTube video by University of Birmingham

youtube.com

Job opportunity working with myself and @pmoyniha.bsky.social on an exciting Gates funded project developing TB lysis enzymes for rapid diagnostics. edzz.fa.em3.oraclecloud.com/hcmUI/Candid...

President Zelenskyy has been one of the greatest leaders of our time, guiding Ukraine through the darkest period of its recent history, rising up to Russia’s unwarranted aggression, being an inspiration to the Ukrainian people and ensuring that Ukraine’s voice is heard on the world stage.

Once again I am leaving the Munich Security Conference in a low mood. Amongst all the noise, the US signalled their plans for Europe, so things are becoming clearer. But things are clearly not good. This is what we now know, and what we have to do about it:🧵1/17

Working a treat here to, threw in some melt in nut inserts etc 😊

Oh and Josh, I just wanted to let you know that I refer to your excellent 'lab-in-a-suitcase' work as a primary example of situations where the DIYNAFLUOR may find utility. It typically shows up in the first 1 or 2 slides of any presentation I make. 😅

Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social

Genotype D1.1 of H5N1 confirmed in Nevada cattle, which is the one circulating in birds and not B3.13, causing the wider cattle epizootic in the U.S. In other words, this is a second observed jump from birds into cows. Keep rolling the dice, shall we? www.feedstuffs.com/agribusiness...

New HPAI genotype found in Nevada dairy cows

APHIS confirms first detection of D1.1 genotype in dairy cattle through NMTS testing.

feedstuffs.com

The @universityofleeds.bsky.social is the first Russell Group Uni to quit X! 🎉 🎉 Read more👇 tinyurl.com/2h3tyjfx @lsjleeds.bsky.social #Yorkshire #Leeds #Academia #AcademicSky #HigherEd #LawSky

Leeds becomes first Russell Group university to quit X - Research Professional News

Leeds says Elon Musk’s social media site “no longer aligns with our university values”

tinyurl.com

The world’s richest man is promoting the far right in Europe. Don’t buy a Tesla . Location: Tesla Gigafactory, Berlin www.youtube.com/watch?v=NjWl...

Heil Tesla

YouTube video by Led By Donkeys

youtube.com

President Trump will learn pretty soon that Putin cannot be convinced with money, at least not any more. He is the richest person in Russia already, though he will never say no to more billions, but that wasn't the point of him starting the full scale war in Ukraine. (Thread)

Really glad this is out there; a lot has happened in the 7 years since the original paper including: -67,000 schemes designed by the community -18M genome sequences using PrimalScheme

Chris Kent@chris.primalscheme.com · 2y ago

Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme! Preprint: www.biorxiv.org/content/10.1...

Fancy some light Christmas reading? I’m happy to share our new preprint, covering the impact and cutting edge improvements to PrimalScheme! Preprint: www.biorxiv.org/content/10.1...

PrimalScheme: open-source community resources for low-cost viral genome sequencing

Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, COVID-19 and Mpox and has seen widespread adoption due to its lo...

biorxiv.org

primalscheme3 is now live at primalscheme.com! Key features - Handle up to 20% target diversity - Create panels for multiple targets - Improved multiplexing, allowing 10x more primer per reaction Preprint to follow

Today Pathoplexus announces the inclusion of a new viral pathogen: mpox (previously known as monkeypox). Within the context of the current mpox outbreaks and ongoing health concerns, Pathoplexus aims to support sequence sharing to improve both understanding and response. 1/7

Thank you for doing this it's going to be incredibly useful!

Will Anderson@willaanderson.bsky.social · 2y ago

Hey #HiSciSky 👋. I'm a post-doc researcher with a background in scientific device dev. I have just released an open-source STEM-Education project for a $40, 3D-printed, DNA fluorometer with ng/uL levels of sensitivity. Follow for updates! GitHub Repo: github.com/traulab/DIYN... #DIYNAFLUOR #STEM

Disease prevalence in US states before & after vaccine introduction Graphic from Edward Tufte More graphics.wsj.com/infectious-d... 🧪

For a few years I've been thinking about calling somatic mutations without matched normals using long read haplotypes. I've posted a preprint with my experiments to explore when this works (and when it doesn't) and developing a prototype mutation caller ("smrest"): www.biorxiv.org/content/10.1...

Job alert 🚨 Research fellow in wastewater surveillance at the University of Birmingham working with myself and @pathogenomenick jobs.ac.uk/job/DFY639/r... Please encourage any recent PhD graduates to apply!