David Cleary
@bacterioskeptic.bsky.social
Assistant Professor in Microbial Genomics (#microbiome, #pneumococci, #haemophilus). My views not UoB. Husband, dad, music miserablist and egg chasing.
Pinned
Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham on FindAPhD.com
PhD Project - Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham, listed on FindAPhD.com
www.findaphd.com
Interested in #Streptococcus pneumoniae genomics? Come do a PhD with me, @alanmcn1.bsky.social and @meerac.bsky.social at @unibirmingham.bsky.social UK applicants only as will be working with UKHSA through HPRU. Feel free to contact me directly www.findaphd.com/phds/project... #microsky
"It's been a while since I brought you any good news on Computerphile ... and it's going to be a while yet"
Imagine if this has already happened…
(The funny thing is that all those companies out there touting their products with added AI don’t even understand this. Remember they ignored indirect prompt injection until it happened.)
youtube.com/watch?v=wL22...
(The funny thing is that all those companies out there touting their products with added AI don’t even understand this. Remember they ignored indirect prompt injection until it happened.)
youtube.com/watch?v=wL22...
Sleeper Agents in Large Language Models - Computerphile
YouTube video by Computerphile
youtube.com
December 22, 2025 at 2:03 PM
"It's been a while since I brought you any good news on Computerphile ... and it's going to be a while yet"
Reposted by David Cleary
My first corresponding author research paper is now out in Microbiology (@microbiologysociety.org) Here, we show that the role of the major efflux pump AcrAB-TolC can differ between two widely used strains of Klebsiella pneumoniae. www.microbiologyresearch.org/content/jour...
Strain-dependent contribution of the AcrAB-TolC efflux pump to Klebsiella pneumoniae physiology
Klebsiella pneumoniae is a prominent opportunistic pathogen increasingly associated with multidrug resistance and virulence. One of the main mechanisms of antimicrobial resistance in K. pneumoniae is ...
www.microbiologyresearch.org
December 19, 2025 at 1:31 PM
My first corresponding author research paper is now out in Microbiology (@microbiologysociety.org) Here, we show that the role of the major efflux pump AcrAB-TolC can differ between two widely used strains of Klebsiella pneumoniae. www.microbiologyresearch.org/content/jour...
Been a privilege to host Uzal Umar here at @unibirmingham.bsky.social with training funding from @bactivac.bsky.social Uzal heads back to Nigeria today with great ideas around pneumococcal epidemiology in specific at risk groups. Looking forward to collaborating in the future!
December 19, 2025 at 9:13 AM
Been a privilege to host Uzal Umar here at @unibirmingham.bsky.social with training funding from @bactivac.bsky.social Uzal heads back to Nigeria today with great ideas around pneumococcal epidemiology in specific at risk groups. Looking forward to collaborating in the future!
Reposted by David Cleary
A last thought before taking off into your various breaks - Microbial Genomics is looking for editors! Scientific publishing is frustrating and so much money going to commercial publishers... be part of the change by supporting society publishing 😊 great opportunity to join a lovely community.
December 18, 2025 at 7:08 PM
A last thought before taking off into your various breaks - Microbial Genomics is looking for editors! Scientific publishing is frustrating and so much money going to commercial publishers... be part of the change by supporting society publishing 😊 great opportunity to join a lovely community.
As my own three year stint as an Editor comes to an end I cannot recommend doing this enough
📢 Voluntary opportunity
Microbial Genomics is seeking Editors to support high-quality research in microbial genomics. This unpaid, public-facing role supports peer review, editorial decisions & journal strategy.
More info: Voluntary Opportunities 👉 microb.io/Vacancies
Microbial Genomics is seeking Editors to support high-quality research in microbial genomics. This unpaid, public-facing role supports peer review, editorial decisions & journal strategy.
More info: Voluntary Opportunities 👉 microb.io/Vacancies
Jobs
View the current job vacancies at the Microbiology Society.
microb.io
December 18, 2025 at 12:21 PM
As my own three year stint as an Editor comes to an end I cannot recommend doing this enough
Reposted by David Cleary
Soon be Christmas.
a cartoon dog is sitting at a table with a cup of coffee surrounded by fire .
ALT: a cartoon dog is sitting at a table with a cup of coffee surrounded by fire .
media.tenor.com
December 17, 2025 at 4:30 PM
Soon be Christmas.
Reposted by David Cleary
End of the year vibes.
December 17, 2025 at 1:06 PM
End of the year vibes.
Reposted by David Cleary
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
Genomic rearrangement of the capsule operon in a phylogenetically distinct cluster of the multi-drug resistant Escherichia coli lineage ST131 https://www.biorxiv.org/content/10.64898/2025.12.15.689991v1
December 16, 2025 at 7:52 PM
The first preprint from @izziepotterill.bsky.social PhD. A clone within ST131 clade C with a totally unique capsule region.
Reposted by David Cleary
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
December 16, 2025 at 6:50 PM
We are recruiting for a number of PhDs in the HPRU in Public Health Genomics, based at @unibirmingham.bsky.social, in collaboration with UKHSA. 🦠🧬
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Apply below to work on cutting-edge science and public health priorities! (NB deadline of 9th January / UK only due to funding restrictions)
(1/7)
Bit late to the Noah Kahan party, but this is great! Welcome change from all the Christmas music too open.spotify.com/track/4O2rRs...
Northern Attitude
open.spotify.com
December 16, 2025 at 5:36 PM
Bit late to the Noah Kahan party, but this is great! Welcome change from all the Christmas music too open.spotify.com/track/4O2rRs...
Sobering read 😬
December 15, 2025 at 8:58 PM
Sobering read 😬
I can vividly recall his lectures as an undergraduate from 1998. Did not realise at the time he was already Emeritus! @jedwards3.bsky.social
We are saddened to learn of the recent passing of Professor Maurice O. Moss. He was
a long-time member of the Microbiology Society, where he joined in 1961.
You can read his full obituary here: microb.io/3LQCyWF
a long-time member of the Microbiology Society, where he joined in 1961.
You can read his full obituary here: microb.io/3LQCyWF
December 15, 2025 at 8:49 PM
I can vividly recall his lectures as an undergraduate from 1998. Did not realise at the time he was already Emeritus! @jedwards3.bsky.social
Reposted by David Cleary
I’m not often lost for words but…
December 15, 2025 at 4:00 PM
I’m not often lost for words but…
Reposted by David Cleary
Fascinating new paper, but I am too childish to get past this acronym.
December 14, 2025 at 6:08 PM
Fascinating new paper, but I am too childish to get past this acronym.
Reposted by David Cleary
Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration!
Feb 11th-13th, registration closing soon:
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Feb 11th-13th, registration closing soon:
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
December 11, 2025 at 12:42 PM
Work on respiratory immunology or microbes? Interested in big data, omics or the latest in vitro models?... Treat your lab to a christmas present of AIR 2026 registration!
Feb 11th-13th, registration closing soon:
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Feb 11th-13th, registration closing soon:
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Interested in #Streptococcus pneumoniae genomics? Come do a PhD with me, @alanmcn1.bsky.social and @meerac.bsky.social at @unibirmingham.bsky.social UK applicants only as will be working with UKHSA through HPRU. Feel free to contact me directly www.findaphd.com/phds/project... #microsky
Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham on FindAPhD.com
PhD Project - Leveraging genomics for improved metagenomic surveillance of Streptococcus pneumoniae at University of Birmingham, listed on FindAPhD.com
www.findaphd.com
December 15, 2025 at 9:06 AM
Interested in #Streptococcus pneumoniae genomics? Come do a PhD with me, @alanmcn1.bsky.social and @meerac.bsky.social at @unibirmingham.bsky.social UK applicants only as will be working with UKHSA through HPRU. Feel free to contact me directly www.findaphd.com/phds/project... #microsky
Reposted by David Cleary
💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
Releases · tseemann/shovill
⚡♠️ Assemble bacterial isolate genomes from Illumina paired-end reads - tseemann/shovill
github.com
December 13, 2025 at 9:15 PM
💾 Shovill 1.4.1 has been released!
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
The best way to de novo assemble microbial genomes from Illumina FASTQ.
Major fixes to the SKESA module, plasmid mode for the Spades module, and more error checking.
#bioinformatiocs #genomics #microbiology
github.com/tseemann/sho...
PCV13 reduced ESBL carriage because kids visited clinics, where they might be exposed, less often. How vaccines – and yoghurt – could reduce colonisation with antibiotic-resistant bugs www.gavi.org/vaccineswork...
December 12, 2025 at 11:06 AM
PCV13 reduced ESBL carriage because kids visited clinics, where they might be exposed, less often. How vaccines – and yoghurt – could reduce colonisation with antibiotic-resistant bugs www.gavi.org/vaccineswork...
Damn optimists. Dick Van Dyke credits his longevity to his positive outlook – and research says optimists live longer theconversation.com/dick-van-dyk...
Dick Van Dyke credits his longevity to his positive outlook – and research says optimists live longer
While we can’t control everything that impacts our health, making room for a more positive outlook in life can help support both wellbeing and longevity.
theconversation.com
December 12, 2025 at 10:27 AM
Damn optimists. Dick Van Dyke credits his longevity to his positive outlook – and research says optimists live longer theconversation.com/dick-van-dyk...
I made it 30 seconds in to this absolutely shit show. Which is how long it took for Liz to tell me Sharia law was being imposed on me 🤦♂️
The Liz Truss Show review – hapless ravings from a cupboard
The Liz Truss Show review – hapless ravings from a cupboard
Britain’s briefest PM kept her fans waiting before launching her latest plea for Maga attention in the form of a ham-fisted YouTube talk show
www.theguardian.com
December 6, 2025 at 8:27 PM
I made it 30 seconds in to this absolutely shit show. Which is how long it took for Liz to tell me Sharia law was being imposed on me 🤦♂️
Reposted by David Cleary
That thing is happening again when everyone tries to do everything before Xmas. Leave it!!
December 3, 2025 at 3:56 PM
That thing is happening again when everyone tries to do everything before Xmas. Leave it!!
Reposted by David Cleary
Absolutely delighted to have been awarded a Royal Society University Research Fellowship! I will be moving to the University of Manchester @mermanchester.bsky.social to research early endosymbiont evolution
#microsky #symbiosky
#microsky #symbiosky
Meet the new cohort of exceptional researchers who have been awarded more than £83 million worth of early career fellowships by the Royal Society, working on research spanning the sciences: #RSGrants: https://bit.ly/49jMkKx
Exceptional researchers awarded early career fellowships worth more than £83 million | Royal Society
A new cohort of exceptional researchers at have been awarded funding through the Royal Society’s early career schemes, the University Research Fellowship (URF), Dorothy Hodgkin Fellowship (DHF) and Ne...
bit.ly
November 14, 2025 at 2:31 PM
Absolutely delighted to have been awarded a Royal Society University Research Fellowship! I will be moving to the University of Manchester @mermanchester.bsky.social to research early endosymbiont evolution
#microsky #symbiosky
#microsky #symbiosky
Reposted by David Cleary
Right. Hitler's DNA. Brace yourselves for a deluge of misinformation and bad science.
I'm in Australia, so do get in touch if you want some expert debunking.
I'm in Australia, so do get in touch if you want some expert debunking.
November 13, 2025 at 6:37 AM
Right. Hitler's DNA. Brace yourselves for a deluge of misinformation and bad science.
I'm in Australia, so do get in touch if you want some expert debunking.
I'm in Australia, so do get in touch if you want some expert debunking.