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Benjamin Ambrose

@single-mole.bsky.social
670 followers 514 following 32 posts

Single-molecule Biophysicist at London Institute of Medical Sciences 🧬🔬✨ My research interests are all things single-molecule fluorescence and nucleic acids. Other hobbies: archery, chess, sci-fi

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Reposted by Benjamin Ambrose
Matt Henderson @matthen.com · 03/10/2026
Visualising the distribution of substrings in the genomes of different organisms. Going up to depth eight by recursively splitting into quadrants, we get these fractal-like pictures.
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Benjamin Ambrose @single-mole.bsky.social · 25/09/2026
Your kids are correct that bird is rocking a kraft single
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Reposted by Benjamin Ambrose
Anita Meier @anitafmeier.bsky.social · 03/07/2026
Our latest paper is out! 🎉 We show that the HSV-1 origin binding protein UL9 tethers dsDNA thereby forming intramolecular DNA loops and intermolecular DNA tethers. 🤝 www.nature.com/articles/s41...
nature.com
HSV-1 origin binding protein UL9 forms intermolecular DNA tethers and intramolecular DNA loops - Nature Communications
The mechanism of herpes simplex virus type 1 (HSV-1) genome replication remains not fully understood. Here, the authors find that the HSV-1 origin binding protein UL9 does not mediate DNA looping but ...
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
Lifting happens in the browser, on the users computer. I was surprised that the AI model would work so quick but it's actually pretty light on inference (only takes a couple seconds on my Mac) even though the training needed GPUs for days. But there's a lot you can make work on a GitHub io site
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
It is mostly svelte with a little python, running on a GitHub site. Having it live is amazing for iterative development because I can add a feature or patch a bug and then users can test without having to reinstall. At some point I will package into a downloadable so people can have a static version
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
The program can currently be accessed in browser at - singlemoleculegroup.github.io/kymosketch-a..., no install required. Just drag and drop your kymos in or use the demo data already there if you want to try. (6/6)
kymosketch splash screen
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
I’ve also added fluorescence intensity analysis, and FRET. I will be adding FRET correction parameters soon, for those who like their FRET efficiencies precise and accurate. (5/6)
FRET analysis
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
Once you have your tracks, you can do diffusion analysis - whole trace MSD, rolling diffusion, or DeepDiffusion - and the results of these can be viewed globally for all tracks, including off-rate analysis taken from trajectory length (4/6)
local diffusion analysisglobal diffusion analysissurvival curve
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
You can also very easily change colours in kymolab, if you want something more colourblind friendly than RGB. If displaying only one colour you can also use perceptually uniform colourmaps like Viridis (3/6)
blue/orange kymomagenta/green kymoviridis kymo
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
It’s split into two halves, kymolab and tracklab. In kymolab you load .h5 filess (from c-trap systems) or TIFF files (from anywhere). You generate sketches (candidate tracks) using a trackspotter or manual drawing, then refine them into finalised tracks by fitting. (2/6)
schematic of kymosketch features
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Benjamin Ambrose @single-mole.bsky.social · 01/07/2026
KymoSketch started out as a GUI for our kymotracker script, but after I added DeepDiffusion to it I got suggestions to add more features and it’s since become a more fleshed out analysis platform (1/6)
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Reposted by Benjamin Ambrose
Korak Ray @korakray.bsky.social · 30/06/2026
🚨 Preprint alert 🚨 Excited to share our latest bioRxiv preprint introducing DeepDiffusion, a tool for analysing facilitated 1D diffusion! 🔗 Preprint: www.biorxiv.org/content/10.6... (1/3)
biorxiv.org
DeepDiffusion: a Physics-Informed Neural Network for Heterogeneous Facilitated 1D Diffusion
Single-molecule fluorescence microscopy combined with optical tweezers has enabled the direct observation of diffusing proteins on tethered DNA. These and complementary techniques reveal facilitated o...
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Benjamin Ambrose @single-mole.bsky.social · 21/04/2026
Technically one of these is dynamic domain
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Benjamin Ambrose @single-mole.bsky.social · 24/02/2026
stapledon for example
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Benjamin Ambrose @single-mole.bsky.social · 21/02/2026
Don't forget to pour one out for "misunderestimate"
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Reposted by Benjamin Ambrose
Steve Quinn @steve-quinn-lab.bsky.social · 22/01/2026
Congrats to Jamie et al! Our latest @york.ac.uk work dissecting the structural landscape of the Rep Helicase is now out in Nucleic Acids Research! 🧬🔬 @timcraggs.bsky.social @agnesnoy.bsky.social @bpsiyork.bsky.social @dr-mahmoud.bsky.social @single-mole.bsky.social 👇 tinyurl.com/bdznxur3
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Benjamin Ambrose @single-mole.bsky.social · 03/06/2025
Life involves significantly more squiggly lines when there are more colours
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Benjamin Ambrose @single-mole.bsky.social · 02/06/2025
Life is better with more colours!
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Benjamin Ambrose @single-mole.bsky.social · 19/05/2025
🎉 Have a good one Tim!
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Benjamin Ambrose @single-mole.bsky.social · 29/04/2025
can I add a flourophore to light it up a bit
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Benjamin Ambrose @single-mole.bsky.social · 17/02/2025
stock trajectory is invariant under Lorentz transformation
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Reposted by Benjamin Ambrose
Alex Klotz @aklotz.bsky.social · 18/12/2024
A thread on optical phenomena in The Simpsons
Lenny with a pinhole projection of the sun approaching the Drinking Time line
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Benjamin Ambrose @single-mole.bsky.social · 18/12/2024
We have to keep our washing up sponges in prison under the sink or this one will steal them and hide them
criminal sponge stealing feline
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Reposted by Benjamin Ambrose
Erin E. Cutts @eecutts.bsky.social · 16/12/2024
Please share: Still plenty of time to apply for PhD projects in my lab using single-molecule methods to look at disordered regions and condensin complexes! Contact me at e.cutts@sheffield.ac.uk For details on how to apply: www.findaphd.com/phds/project...
findaphd.com
Developing Imaging Solutions to Study the Dynamics of Human Condensin I at University of Sheffield on FindAPhD.com
PhD Project - Developing Imaging Solutions to Study the Dynamics of Human Condensin I at University of Sheffield, listed on FindAPhD.com
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Benjamin Ambrose @single-mole.bsky.social · 13/12/2024
Artificial intelligence is going to revolutionise chemistry
Google AI overview result explaining that anhydrous water is water that is free of water
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Benjamin Ambrose @single-mole.bsky.social · 05/12/2024
hopefully no bananas
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Benjamin Ambrose @single-mole.bsky.social · 04/12/2024
Whenever I see people talking about how they want to see raw data I can't help but think that everyone means something different when they say raw
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Reposted by Benjamin Ambrose
Manuel Thery @manuelthery.bsky.social · 27/11/2024
Mix two motors of opposite polarity with microtubules and they will partition space ! Microtubules will get organized in polar and active barriers, sorting the two motors in separated domains, leading to the emergence of a new type of patterns. #morphogenesis doi.org/10.1073/pnas... (1/n)
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Reposted by Benjamin Ambrose
Andrew Steele @statto.bsky.social · 21/11/2024
There’s more to rainbows than the human eye can see: here’s how a rainbow extends into the infrared and ultraviolet. Photos: 1. Infrared 2. Visible (obviously) 3. Ultraviolet, and 4. A composite showing how UV is beyond the violet in a rainbow, and IR beyond the red end. 🧪 #photography
An infrared photo of a rainbow: a strange, ghostly-looking rainbow in a mostly black and white photo, with a faintly red outer edge and a cyan inner edge, and what look like a few even fainter ‘echo’ bows insideA regular visible-light pic of a rainbowAn ultraviolet picture of a rainbow: a dark, foreboding landscape with a deep purple stripe emanating from it, and a grey stripe insideA composite of the three preceding photos, showing that the infrared bow is ‘outside’ the visible light rainbow, and the ultraviolet bow ‘inside’
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Benjamin Ambrose @single-mole.bsky.social · 19/11/2024
Beeps definitely sounds better than skeeps 😁 No snow in London yet!
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Reposted by Benjamin Ambrose
DrLachie @drlachie.bsky.social · 19/11/2024
Manuscript: "Using a simple optical setup ... "
The simple optical setup (an infinite optical breadboard with hundreds of optical components placed randomly upon it)
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Benjamin Ambrose @single-mole.bsky.social · 17/11/2024
Thanks for making this Izzy!
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Benjamin Ambrose @single-mole.bsky.social · 17/11/2024
The starter packs are good but when do we get booster packs
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Benjamin Ambrose @single-mole.bsky.social · 13/11/2024
Lots of people following me this morning even though so far I have only posted a picture of my cat, so I am raising the stakes and posting TWO cats
two fuzzy creatures
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Reposted by Benjamin Ambrose
Johannes Hohlbein @hohlbeinlab.bsky.social · 13/11/2024
First attempt in a (loosely defined) Single-Molecule Biophysics starter pack. Please share and (self-) nominate. go.bsky.app/CteFZM5
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Benjamin Ambrose @single-mole.bsky.social · 13/11/2024
This may explain why I have 20 new follows this morning! Thanks Johannes!
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Benjamin Ambrose @single-mole.bsky.social · 24/10/2024
I am always maximally suspicious when I see people fit Gaussians to diffusion coefficients plotted in linear space!
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Reposted by Benjamin Ambrose
Korak Ray @korakray.bsky.social · 20/10/2023
🚨 Preprint news!! 🚨 The collaboration with @ckinzthompson on a novel definition of resolution and how it can be used to calculate the local atomic resolution and map-to-model correspondence in cryoEM structures is finally on bioRxiv!!!! www.biorxiv.org/content/10.1... 🧵(1/6)
biorxiv.org
Scale-dependent hierarchical resolution: applications to atomic resolution and model validation in c...
bioRxiv - the preprint server for biology, operated by Cold Spring Harbor Laboratory, a research and educational institution
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Benjamin Ambrose @single-mole.bsky.social · 08/09/2023
No
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Benjamin Ambrose @single-mole.bsky.social · 30/08/2023
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Benjamin Ambrose @single-mole.bsky.social · 20/08/2023
The world isn't ready for Kubrick wonka anyway
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Benjamin Ambrose @single-mole.bsky.social · 12/08/2023
If you put a ring on the floor a cat will get in it
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Benjamin Ambrose @single-mole.bsky.social · 10/08/2023
This was very useful although it occasionally finds completely the wrong person.
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