@astephen
Microbiologist at Queen Mary University of London. I work on anaerobes, biofilms, host-microbial models, bacterial volatile metabolites and oral microbiota-systemic axis. Passionate about guitars, motorsport and cricket. #bikerlife Views my own.
Excited to share this preprint that describes my latest work on using GPUs to accelerate processing of RNA-seq data.
The title says it all: "RNA-seq analysis in seconds using GPUs" now on biorxiv www.biorxiv.org/content/10.6... and github github.com/pachterlab/k...
Figure 1 shows they key result
I think it was a mistake to put right-wing hot-take podcasters in charge of the FDA, NIH, CDC, and CMS—the so-called “MAGA podcaster to policy pipeline”
Immune cells from the gut drive development of Parkinson’s disease in the brain www.nature.com/articles/d41...
📣 New paper alert! This is a story of molecular tricks that let spirochetes (spiral-shaped bacteria) drill through tissue. www.biorxiv.org/content/10.6...
Structural basis for curvature generation and functional specialization in spirochete flagella
#MicroSky
More #PhDOpportunities! This time, developing physiologically relevant models to study dental #erosion. The project combines fluid flow simulation, surface metrology and imaging to understand how #enamel responds to dynamic acid and mechanical challenges. 🦷🌊🧪 Based at @unisouthampton.bsky.social!
Delighted to collaborate on this exciting #PhDOpportunity exploring links between the oral #microbiome and #brain health. This project will investigate how periodontal microbial metabolites influence the #bloodbrainbarrier and neurovascular biology. @drsimonmcarthur.bsky.social
🧠🧪
Excited to advertise a new #PhDOpportunity in my lab at @qmul.bsky.social exploring how oral microbial communities regulate dietary #nitrate metabolism and shape #nitricoxide biology. We’ll combine stable #isotope tracing and #metaomics to nitrate flux in oral #biofilms.🧪 Get in touch if interested!
🦠🧪 #PhDOpportunity
Can we weaken dental plaque without killing beneficial microbes?
This PhD explores non-biocidal strategies to disrupt oral #biofilm structure, investigating how targeted interventions can destabilise plaque while preserving #microbiome balance.
📍 @glasgowcaledonian.bsky.social
🔬 Using laboratory and saliva-derived #biofilm models, this project examines how biofilm disruption affects community organisation, stability, and regrowth dynamics compared with conventional #antimicrobials.
🔗 Apply via ATOHR
Project led by Dr. Will Johnston
🔬 Using ex vivo biofilm models and multi-omics, this project investigates how repeated low-level challenges influence microbial structure, stress tolerance, and cross-kingdom dynamics in the oral ecosystem.
🔗 Apply via #ATOHR [2/2]
🧪 #PhDOpportunity
How do microbial communities adapt to everyday challenges?
This PhD explores bacterial–fungal interactions in oral biofilms and how environmental stress shapes microbial community behaviour and resilience.
📍 @glasgowcaledonian.bsky.social
At Prof. Gordon Ramage's group [1/2]
AI has huge promise for genomics -- but it has consistently failed at microbiome-based prediction.
My new post on why simple models keep winning, where deep learning actually earns its place, and where the field is headed
blekhman.substack.com/p/ai-keeps-f...
That's amazing Catherine! I was wondering how Wales had become the 'country north of England'! Scotland is wonderful and glad to hear that it is treating you well!
Nice to see you! Hope you are well.
this is what they said it would be like under socialism
@qmul.bsky.social @bartscharity.bsky.social Doctoral Training Programme - five fully funded 4 year PhD Studentships in Biomedical Research. Closing date for applications: Monday March 16th 2026 Please share - more info here: www.findaphd.com/phds/program...
Motion to stop referring to it as Next Generation Sequencing. That's like saying The Matrix is a recent movie
I mean, what are you supposed to do with people like this? It’s like saying that you wish your kids could get in some good old-fashioned car crashes without all those seatbelts and air bags.
Figure from this publication: Human foreskin-based cultivation system supports the growth of various T. pallidum strains (n=8), from the Nichols-like as well as the SS14-like cluster. Note that human foreskin fibroblast cells were prepared as an equal mixture of three tested cell lines. Each T. pallidum strain was cultivated in a single in vitro well, representing a sole experimental replicate used for data acquisition.
Major advance in T. pallidum reserach:
"First human cell-based cultivation system for the syphilis spirochete Treponema pallidum"
link.springer.com/article/10.1...
#MicroSky
Fully Funded PhD Studentship Opportunity (4 years) at Queen Mary, University of London
Why is gum disease a risk factor for dementia? Come and help us find out!
🗓 Application deadline: 15th May 2026
Apply here: tinyurl.com/4xvdzpjs
Please share! #Microbiome #Dementia #neuroskyence 🧪
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Come work with Ben Berks FRS in Oxford
2 x PDRA posts: Molecular Analysis of Bacterial Outer Membrane Protein Biogenesis
2 complementary projects investigating bacterial outer membrane protein biogenesis. Building on our recent work (Nature (2015) 647: 479-487)
my.corehr.com/pls/uoxrecru...
Ethics.
Interesting how this scandal involves for real some false claims made about Covid origin:
- doing abroad with US funds research not allowed in the US
- skipping the evaluation process and having approval straight at the director office
As if false accusations were indeed admissions of intent
"AGI is just around the corner, which will revolutionize everything. We just need to scale".
There you go - that's a $1 trillion plan, $1 billion being peanuts 😉.
I’m genuinely, unironically impressed at the idea of having a $1b plan to do… anything. A $1m plan is trivial. A $30m plan takes real work. But a priced-out plan with reasonable timelines and expenses that comes to the order of a billion? That’s not easy
Culturing microbiome therapeutics with big data
Emerging datasets from large human cohorts are dissecting the underlying mechanisms of microbiome–host interactions and accelerating progress in targeted microbiome therapeutics go.nature.com/4akDuef
Outstanding thread
Enjoy reading our "behind the paper" story: www.nature.com/articles/d41...
It's funny, my PhD advisor Dr. Goodrich-Blair would also tell stories about those exact lectures. Must have made an incredible impression! I'll do some reading and find out if anything looks like what we see in our episymbionts. I do think we're just about ready to dive into CPR regulation pathways.
