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Josh Quick

@scalene.bsky.social
2.1K followers 446 following 36 posts

UKRI Future Leaders Fellow, University of Birmingham

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Josh Quick @scalene.bsky.social · 22/05/2026
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...
medrxiv.org
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...
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Institute of Microbiology and Infection @imibirmingham.bsky.social · 12/03/2026
We are recruiting! Join Dr Josh Quick @scalene.bsky.social as a Postdoctoral Fellow in Metagenomics edzz.fa.em3.oraclecloud.com/hcmUI/Candid...
edzz.fa.em3.oraclecloud.com
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...
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Kristian G. Andersen @kgandersen.bsky.social · 24/02/2026
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...
medrxiv.org
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...
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Ed Cunningham-Oakes @edcoakes.bsky.social · 16/01/2026
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
edzz.fa.em3.oraclecloud.com
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...
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Rick Beeloo @rickbitloo.bsky.social · 23/10/2025
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...
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Bede Constantinides @bede.im · 12/08/2025
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
artic.network
Genome assemblies for a respiratory metagenomics positive control | ARTIC network - pathogen genomics from sample to response
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Josh Levy @josh-levy.bsky.social · 31/07/2025
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
github.com
GitHub - andersen-lab/Freyja-barcodes
Contribute to andersen-lab/Freyja-barcodes development by creating an account on GitHub.
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Josh Quick @scalene.bsky.social · 19/06/2025
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
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Josh Quick @scalene.bsky.social · 19/06/2025
Click the link for open-source recipes for end-preparation, barcode and adapter ligation. 60% cost saving over commercial kits for the ARTIC protocol.
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Anna (Ganna) Kovalenko @annakovalenko.bsky.social · 15/06/2025
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
biorxiv.org
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Nick Loman @pathogenomenick.bsky.social · 22/05/2025
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...
youtube.com
Changing how the world tracks emerging viruses | University of Birmingham
YouTube video by University of Birmingham
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Josh Quick @scalene.bsky.social · 08/04/2025
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...
edzz.fa.em3.oraclecloud.com
Research Associate (Genomics) - School of Biosciences - 105316 - Grade 6
The successful candidate will play a crucial role in developing an innovative TB diagnostic approach, collaborating across a multidisciplinary team to advance our novel enzymatic lysis technology. Key...
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Richard Branson @richardbranson.bsky.social · 20/02/2025
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.
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Gabrielius Landsbergis @glandsbergis.bsky.social · 15/02/2025
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
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John Tyson @drt1973.bsky.social · 13/02/2025
Working a treat here to, threw in some melt in nut inserts etc 😊
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Will Anderson @willaanderson.bsky.social · 12/02/2025
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. 😅
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Josh Quick @scalene.bsky.social · 12/02/2025
Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social
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Kristian G. Andersen @kgandersen.bsky.social · 05/02/2025
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...
feedstuffs.com
New HPAI genotype found in Nevada dairy cows
APHIS confirms first detection of D1.1 genotype in dairy cattle through NMTS testing.
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University of Leeds - School of Law @lawatleeds.bsky.social · 23/01/2025
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
tinyurl.com
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”
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Led By Donkeys @ledbydonkeys.org · 23/01/2025
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...
youtube.com
Heil Tesla
YouTube video by Led By Donkeys
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(((Tendar))) @tendar.bsky.social · 22/01/2025
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)
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Josh Quick @scalene.bsky.social · 24/12/2024
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
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Chris Kent @chris.primalscheme.com · 23/12/2024
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...
biorxiv.org
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...
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Chris Kent @chris.primalscheme.com · 09/12/2024
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
primalscheme.com
PrimalScheme3: primer panels for multiplex PCR
primalscheme is a tool for designing primer panels for multiplex PCR. It uses a greedy algorithm to find primers for tiling amplicon generation for multiple reference genomes.
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Pathoplexus @pathoplexus.org · 09/12/2024
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
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Josh Quick @scalene.bsky.social · 09/12/2024
Thank you for doing this it's going to be incredibly useful!
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Conrad Hackett @conradhackett.bsky.social · 15/11/2024
Disease prevalence in US states before & after vaccine introduction Graphic from Edward Tufte More graphics.wsj.com/infectious-d... 🧪
Graphic shows dramatic reduction in polio, rubella, mumps, measles, and hepatitis A cases after the introduction of vaccines for each disease.
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Jared Simpson @jaredsimpson.bsky.social · 29/02/2024
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...
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Josh Quick @scalene.bsky.social · 20/02/2024
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!
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Rafael Behr @rafaelbehr.bsky.social · 29/11/2023
On Rwanda scheme, small boats and a prime minister who is about as badly snookered as you can get. www.theguardian.com/commentisfre...
theguardian.com
Rwanda is a proxy in the war for the Tory soul. It’s a war Rishi Sunak is losing | Rafael Behr
A brave leader would admit he is cornered and set out a new direction to his party and the public. He’s not that guy, says Guardian columnist Rafael Behr
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Ian Dunt @iandunt.bsky.social · 17/11/2023
Rwanda: Everything you need to know about what happens next iandunt.substack.com/p/rwanda-thi...
iandunt.substack.com
Rwanda: This is what happens next
Everything you need to know about the battle for the country's soul.
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Josh Quick @scalene.bsky.social · 06/11/2023
I'm happy to announce we received BMGF support to develop amplicon sequencing for wastewater surveillance! www.birmingham.ac.uk/news/2023/1-... @pathogenomenick.bsky.social @simonrharris.bsky.social
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Josh Quick @scalene.bsky.social · 25/10/2023
Really good blog post from Ryan (as always) on latest ONT accuracy rrwick.github.io/2023/10/24/o...
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