Reposted by Benjamin AmbroseMatt Henderson @matthen.com · 03/10/2026Visualising 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. 816634
Benjamin Ambrose @single-mole.bsky.social · 25/09/2026Your kids are correct that bird is rocking a kraft single 010
Reposted by Benjamin AmbroseAnita Meier @anitafmeier.bsky.social · 03/07/2026Our 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.comHSV-1 origin binding protein UL9 forms intermolecular DNA tethers and intramolecular DNA loops - Nature CommunicationsThe 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 ... 4126
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026Lifting 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 120
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026It 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 120
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026The 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) 140
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026I’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) 130
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026Once 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) 110
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026You 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) 110
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026It’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) 110
Benjamin Ambrose @single-mole.bsky.social · 01/07/2026KymoSketch 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) 1112
Reposted by Benjamin AmbroseKorak 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.orgDeepDiffusion: a Physics-Informed Neural Network for Heterogeneous Facilitated 1D DiffusionSingle-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... 2154
Benjamin Ambrose @single-mole.bsky.social · 21/02/2026Don't forget to pour one out for "misunderestimate" 020
Reposted by Benjamin AmbroseSteve Quinn @steve-quinn-lab.bsky.social · 22/01/2026Congrats 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 01910
Benjamin Ambrose @single-mole.bsky.social · 03/06/2025Life involves significantly more squiggly lines when there are more colours 010
Benjamin Ambrose @single-mole.bsky.social · 29/04/2025can I add a flourophore to light it up a bit 140
Benjamin Ambrose @single-mole.bsky.social · 17/02/2025stock trajectory is invariant under Lorentz transformation 020
Reposted by Benjamin AmbroseAlex Klotz @aklotz.bsky.social · 18/12/2024A thread on optical phenomena in The Simpsons 5345
Benjamin Ambrose @single-mole.bsky.social · 18/12/2024We have to keep our washing up sponges in prison under the sink or this one will steal them and hide them 1192
Reposted by Benjamin AmbroseErin E. Cutts @eecutts.bsky.social · 16/12/2024Please 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.comDeveloping Imaging Solutions to Study the Dynamics of Human Condensin I at University of Sheffield on FindAPhD.comPhD Project - Developing Imaging Solutions to Study the Dynamics of Human Condensin I at University of Sheffield, listed on FindAPhD.com 11314
Benjamin Ambrose @single-mole.bsky.social · 13/12/2024Artificial intelligence is going to revolutionise chemistry 030
Benjamin Ambrose @single-mole.bsky.social · 04/12/2024Whenever 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 050
Reposted by Benjamin AmbroseManuel Thery @manuelthery.bsky.social · 27/11/2024Mix 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) 8365102
Reposted by Benjamin AmbroseAndrew Steele @statto.bsky.social · 21/11/2024There’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 722011652
Benjamin Ambrose @single-mole.bsky.social · 19/11/2024Beeps definitely sounds better than skeeps 😁 No snow in London yet! 010
Reposted by Benjamin AmbroseDrLachie @drlachie.bsky.social · 19/11/2024Manuscript: "Using a simple optical setup ... " 6468
Benjamin Ambrose @single-mole.bsky.social · 17/11/2024The starter packs are good but when do we get booster packs 060
Benjamin Ambrose @single-mole.bsky.social · 13/11/2024Lots 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 2251
Reposted by Benjamin AmbroseJohannes Hohlbein @hohlbeinlab.bsky.social · 13/11/2024First attempt in a (loosely defined) Single-Molecule Biophysics starter pack. Please share and (self-) nominate. go.bsky.app/CteFZM5 6510760
Benjamin Ambrose @single-mole.bsky.social · 13/11/2024This may explain why I have 20 new follows this morning! Thanks Johannes! 000
Benjamin Ambrose @single-mole.bsky.social · 24/10/2024I am always maximally suspicious when I see people fit Gaussians to diffusion coefficients plotted in linear space! 110
Reposted by Benjamin AmbroseKorak 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.orgScale-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 1102
Benjamin Ambrose @single-mole.bsky.social · 20/08/2023The world isn't ready for Kubrick wonka anyway 110
Benjamin Ambrose @single-mole.bsky.social · 12/08/2023If you put a ring on the floor a cat will get in it 010
Benjamin Ambrose @single-mole.bsky.social · 10/08/2023This was very useful although it occasionally finds completely the wrong person. 040