David Cleary

David Cleary

@bacterioskeptic.bsky.social

Scientist (pathogen genomics). Husband, dad, music miserablist and egg chasing.

376 followers354 following159 posts

David Cleary reposted

Joe Hanly
@hanliconius.bsky.social

I've complained on here a few times about synteny plots that are harder to read than they need to be. I decided it was time to actaully do something about it: introducing SynTangle, a tool for untangling whole-genome synteny plots github.com/Hanliconius/... 1/

github.comGitHub - Hanliconius/SynTangle: On synteny plots, intrinsic tangledness is real, layout tangledness is noise. This tool is for removing layout tangledness.On synteny plots, intrinsic tangledness is real, layout tangledness is noise. This tool is for removing layout tangledness. - Hanliconius/SynTangle
Joe Hanly@hanliconius.bsky.social

I hate to do this with real data, but this is a persistent data vis issue in chromosome synteny riparian plots that we Need to get better at. Left, a synteny plot published today. Right, a rearranged version with exactly the same gross arrangement but with reordered chromosomes:

David Cleary reposted

God
@thegodshow.com

Elon cut off Starlink to Ukraine because they blew up his Russian bots and so now his posts don’t get enough likes? Do I have that right?

David Cleary reposted

Strep GBI, 1-2 April 2027 in Durham
@strepgbi.bsky.social

Save the date and spread the word! The 2nd Streptococcus Great Britain & Ireland meeting in Durham on April 1st/2nd 2027 will bring together ECRs and experts to highlight cutting-edge research on streptococcal biology.

David Cleary reposted

Ian Dunt
@iandunt.bsky.social

Sorry but the colander thing is such a piece of shit. Fine, it's not safe to stare right at the sun. But let's not pretend I'm going to have a great time watching a tiny shadow on a piece of paper through a fucking kitchen utensil.

David Cleary
@bacterioskeptic.bsky.social

This is fucking insane … but wholly predictable

The Associated Press@apnews.com

BREAKING: President Trump to sign an executive order calling for spacing out childhood shots, among other changes to vaccine recommendations.

bit.lyTrump to sign executive order calling for spacing out childhood shotsPresident Donald Trump will sign an executive order calling for spacing out childhood vaccines into separate medical visits and splitting the combined measles, mumps and rubella vaccine into three different shots.
David Cleary
@bacterioskeptic.bsky.social

‘Historically accurate’

The Guardian@theguardian.com

Elon Musk says Grok Imagine will make ‘historically accurate’ AI adaptation of Homer’s Odyssey

theguardian.comElon Musk says Grok Imagine will make ‘historically accurate’ AI adaptation of Homer’s OdysseyThe billionaire says the AI-generated film will stay true to Homer’s original, after repeatedly criticising Christopher Nolan’s blockbuster over its casting choices Elon Musk has said his AI platform Grok Imagine will make a “historically accurate” adaptation of Homer’s Odyssey, after the success of Christopher Nolan’s blockbusting treatment which the SpaceX founder has regularly criticised over its casting. In a post on X, Musk said: “Before this year ends, Grok Imagine will make a full-length movie of The Odyssey that is historically accurate and true to the art of Homer.” Musk also linked to a post containing a three-minute clip of footage that the user said had been generated from Grok Imagine, showing a scene between Odysseus and the nymph Calypso. Continue reading...

David Cleary reposted

Dr Claire Smith
@drclairesmith.bsky.social

Delighted to share our new paper, out now in @natureportfolio.nature.com where we show that neutrophil myeloperoxidase (MPO) tracks RSV severity in infants, and can be used as a functional readout of therapeutic efficacy in the lab. 📄 Read it (open access) 👉 rdcu.be/ftx53

rdcu.beNeutrophil myeloperoxidase as a functional biomarker for RSV severity: implications for in vitro therapeutic screeningNature Communications - Preclinical human models are needed to investigate mechanisms and evaluate therapies for severe respiratory syncytial virus (RSV) infection in children. The authors here...

David Cleary reposted

Chris Newfield
@cnewf.bsky.social

the FT has two pieces on the slow-motion collapse of UK higher ed. 4/5ths of unis are doing voluntary layoffs; 38% are doing compulsory. Meanwhile Britain and its flatlined productivity growth sleepwalks through its unprecedented loss of advanced capabilities www.ft.com/content/8097...

David Cleary
@bacterioskeptic.bsky.social

A little write up of Uzal's (Lecturer and Research Associate at University of Jos Plateau State in Nigeria) @bactivac.bsky.social supported visit to learn pneumococcal genomics with me and biofilms with @allan-lab.bsky.social www.birmingham.ac.uk/news/2026/sp...

birmingham.ac.ukSpotlight on BactiVac Network training opportunities - University of BirminghamUzal shares his story of resilience, which features a successful training opportunity in the UK, awarded and funded by the BactiVac Network.

David Cleary reposted

Respiratory Microbiomes
@resp-micro.bsky.social

Question: anyone struggle with Streptococcus pneumoniae growth in plasticware? Eliminated almost every other variable and it's lovely in glass but terrible in polystyrene plates. Anyone observed, got a mechanism or a fix? Driving us potty!

David Cleary reposted

James O’Brien
@mrjamesob.bsky.social

However you dice it, it’s been a great night for Thai-based cryptocurrency billionaires & Vladimir Putin - who, incredibly, is currently getting more good news from the UK than Ukraine.

David Cleary
@bacterioskeptic.bsky.social

Saw a review of this and looks great. It’s on my list!

Willem van Schaik@wvschaik.bsky.social

Sounds like a great read for the Summer holidays, especially for the microbiologist in your life The Black Death by Thomas Asbridge — portrait of a medieval killer share.google/vGVs0044vRqI...

share.googleThe Black Death by Thomas Asbridge — portrait of a medieval killerA gripping and authoritative global history of the plague that killed more than 100mn people in the 14th century
David Cleary
@bacterioskeptic.bsky.social

Immunogenicity and safety of co-administration of adjuvanted respiratory syncytial virus prefusion F protein vaccine with 20-valent pneumococcal conjugate vaccine in adults aged ≥60 years: a randomized, non-inferiority trial academic.oup.com/cid/article/...

academic.oup.comImmunogenicity and safety of co-administration of adjuvanted respiratory syncytial virus prefusion F protein vaccine with 20-valent pneumococcal conjugate vaccine in adults aged ≥60 years: a randomize...AbstractBackground. Respiratory syncytial virus (RSV) illness and pneumococcal disease present high disease burden and health risks to older adults. Vaccin

David Cleary reposted

A. Murat Eren (Meren)
@merenbey.bsky.social

How every layer of science's "self-correcting machinery" failed when Iva Veseli and I simply wanted to reproduce the findings of a high-profile study on gut microbiome and autism: merenlab.org/2026/04/15/u...

merenlab.orgUnfalsifiable by Design: A Year of Trying and Failing to Reproduce a Human Microbiome and Autism StudyThe myth of open data, reproducibility, responsibility, and accountability in science, and your role in it
David Cleary
@bacterioskeptic.bsky.social

#pneumococci continue to be the leading cause of LRI deaths globally: Global burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023 - The Lancet Infectious Diseases www.thelancet.com/journals/lan...

thelancet.comGlobal burden of lower respiratory infections and aetiologies, 1990–2023: a systematic analysis for the Global Burden of Disease Study 2023This comprehensive analysis underscores both the gains achieved through vaccination and the challenges that remain in controlling the LRI burden globally. Furthermore, it demonstrates persistent dispa...

David Cleary reposted

Raymond Kiu
@raymondkiu.bsky.social

Here I would like to introduce a genome downloading tool: GenomeFetch 👇🧬 This is a Linux tool written in pure Shell/Bash for downloading bacterial genomes (genome assemblies) from RefSeq or GenBank 🧫

github.comGitHub - raymondkiu/GenomeFetch: GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank.GenomeFetch: a fast, user-friendly bacterial genome assembly retrieval tool for RefSeq and GenBank. - raymondkiu/GenomeFetch

David Cleary reposted

Mehrzad Mohsseni Pour
@drmehrzadmp.bsky.social

I had the opportunity to present my research at #AIR2026 (Wellcome Genome Campus), focusing on how lactate shapes host-microbe interactions in the lung It was a great experience to share this work, receive valuable feedback, and engage with researchers across microbiology and immunology. #microbiome