Sign in

Josh Quick

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

UKRI Future Leaders Fellow, University of Birmingham

PostsRepliesMedia
Josh Quick @scalene.bsky.social · 22/05/2026
Great work by @dominikaanna.bsky.social @bede.im and the HPRU PHG team @imibirmingham.bsky.social @unibirmingham.bsky.social
010
Josh Quick @scalene.bsky.social · 22/05/2026
Bottom line: library prep strategy fundamentally determines RNA virus sensitivity. Several widely-used clinical metagenomics protocols tagment cDNA directly — and may be missing viruses as a result. Avoid direct tagmentation of cDNA + dual-primer PCR when RNA virus sensitivity matters.
100
Josh Quick @scalene.bsky.social · 22/05/2026
We then spiked controls into real clinical backgrounds (low/medium/high host). SISPA methods won every time. And using a modified SMART-9N protocol, we showed single-primer PCR is a critical ingredient — switch to dual-primer PCR and enrichment collapses.
100
Josh Quick @scalene.bsky.social · 22/05/2026
This model predicts any step that disrupts fragment length will destroy the enrichment. We tested it by comparing adapter introduction during cDNA synthesis vs tagmentation. The result was clear — SISPA recovered ALL 16 RNA viruses in our control panel. Tagmenting the cDNA recovered NONE.
100
Josh Quick @scalene.bsky.social · 22/05/2026
SISPA (sequence-independent single-primer amplification) has been used to enrich viral sequences since 1991 — but nobody had explained how it actually works. We propose it exploits the PS-effect: longer viral molecules amplify preferentially over shorter host cDNA fragments on the basis of size.
100
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...
11812
Reposted by Josh Quick
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...
053
Reposted by Josh Quick
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...
17531
Reposted by Josh Quick
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...
0716
Reposted by Josh Quick
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...
35231
Josh Quick @scalene.bsky.social · 18/09/2025
Excited to finally get our hands on a production Topo kit! @articnetwork.bsky.social
010
Reposted by Josh Quick
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
0114
Reposted by Josh Quick
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.
131
Josh Quick @scalene.bsky.social · 19/06/2025
Although SMART-9N was developed for RNA viruses, DNA pathogens can be detect either via transcripts or random amplification of genomic DNA. This is the basis of the viral arm of the @nanoporetech.com rapid metagenomic sequencing protocol (nanoporetech.com/document/rap...)
nanoporetech.com
Rapid metagenomic sequencing for surveillance of bacterial, fungal and viral pathogens using SQK-RPB114.24
This protocol: - is a rapid method to perform metagenomic sequencing for identification of bacterial, fungal and viral pathogens. - consists of a two-in-one method that splits sample into bacterial/f...
040
Josh Quick @scalene.bsky.social · 19/06/2025
Francisella tularensis identified using @articnetwork.bsky.social SMART-9N metagenomics and @nanoporetech.com sequencing. Amazing work!
193
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.
082
Reposted by Josh Quick
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
41610
Reposted by Josh Quick
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
0113
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...
056
Reposted by Josh Quick
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.
275112073120752
Reposted by Josh Quick
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
19159752276
Reposted by Josh Quick
John Tyson @drt1973.bsky.social · 13/02/2025
Working a treat here to, threw in some melt in nut inserts etc 😊
111
Josh Quick @scalene.bsky.social · 13/02/2025
Looking forward to that!
010
Reposted by Josh Quick
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. 😅
131
Josh Quick @scalene.bsky.social · 13/02/2025
For ONT libraries being able to measure in the range 1-100ng/ul is perfectly adequate.
110
Josh Quick @scalene.bsky.social · 13/02/2025
A colleague here and I had an idea to use a dye with a larger Stokes shift which might help with some of the scatter but I honestly don’t think it’s necessary now.
100
Josh Quick @scalene.bsky.social · 13/02/2025
I had been wanting to do this for a while. I got as far as dismantling one and measuring the spectra of the filter set.
310
Josh Quick @scalene.bsky.social · 13/02/2025
This will be huge for LIAS because the fluorometer was one of the most expensive bits. Qubit 4 currently £2800 on our procurement system!
210
Josh Quick @scalene.bsky.social · 12/02/2025
Built our first two DIYNAFLOURS and they work great! Thanks @willaanderson.bsky.social
1120
Reposted by Josh Quick
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.
421499
Reposted by Josh Quick
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”
923785
Reposted by Josh Quick
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
21565593045
Reposted by Josh Quick
(((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)
21916176
Josh Quick @scalene.bsky.social · 22/01/2025
Same here, had the flu last week.
100
Josh Quick @scalene.bsky.social · 21/01/2025
Any error message?
100
Josh Quick @scalene.bsky.social · 24/12/2024
Turns out it works for bacteria too, can’t believe we didn’t try that! bsky.app/profile/nath...
020
Josh Quick @scalene.bsky.social · 24/12/2024
Can’t wait to see what people do with it. Merry Christmas!
031
Josh Quick @scalene.bsky.social · 24/12/2024
Massive effort by @chris.primalscheme.com and @aresti.primalscheme.com check it out now at primalscheme.com
110
Josh Quick @scalene.bsky.social · 24/12/2024
The latest version will perform sequence alignment and design primers can amplify whole viral species. It can also make massive schemes with thousands of primers.
210
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
12510
Reposted by Josh Quick
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...
1157
Josh Quick @scalene.bsky.social · 20/12/2024
If you can wait a few hours we have a preprint in the BioRxiv queue!
130
Reposted by Josh Quick
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.
1177
Josh Quick @scalene.bsky.social · 10/12/2024
That’s an old advert but I’d be happy to talk to them
000
Reposted by Josh Quick
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
28238
Josh Quick @scalene.bsky.social · 09/12/2024
Thank you for doing this it's going to be incredibly useful!
194
Josh Quick @scalene.bsky.social · 22/11/2024
The legendary Woodstock cafe in Selly oak
000
Reposted by Josh Quick
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.
12938721693
Josh Quick @scalene.bsky.social · 25/05/2024
@arambaut.bsky.social @pathogenomenick.bsky.social
000