Benjamin Ambrose

Benjamin Ambrose

@single-mole.bsky.social

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

671 followers516 following32 posts

Benjamin Ambrose reposted

Matt Henderson
@matthen.com

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.

Benjamin Ambrose reposted

Anita Meier
@anitafmeier.bsky.social

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.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 ...
Benjamin Ambrose
@single-mole.bsky.social

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)

Korak Ray@korakray.bsky.social

🚨 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...
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Benjamin Ambrose
@single-mole.bsky.social

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)

Korak Ray@korakray.bsky.social

🚨 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...
View full thread
Benjamin Ambrose
@single-mole.bsky.social

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)

Benjamin Ambrose
@single-mole.bsky.social

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)

Benjamin Ambrose
@single-mole.bsky.social

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)

Korak Ray@korakray.bsky.social

🚨 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...
Benjamin Ambrose
@single-mole.bsky.social

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)

Benjamin Ambrose reposted

Korak Ray
@korakray.bsky.social

🚨 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...

Benjamin Ambrose reposted

Erin E. Cutts
@eecutts.bsky.social

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.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

Benjamin Ambrose reposted

Manuel Thery
@manuelthery.bsky.social

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)

Benjamin Ambrose reposted

Andrew Steele
@statto.bsky.social

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

Benjamin Ambrose reposted

Korak Ray
@korakray.bsky.social

🚨 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
Benjamin Ambrose
@single-mole.bsky.social

This was very useful although it occasionally finds completely the wrong person.

Anne Carpenter@drannecarpenter.bsky.social

Hey all you SciTwitter arrivals! You can quickly find many of your old follows using: skeet.labnotes.org And be sure to edit your X/Twitter bio to add your bluesky profile - some tools use this to find you! (like https://bsky.app/profile/drannecarpenter.bsky.social)

skeet.labnotes.orgSkeet @ labnotes.orgFind your Twitter/Mastodon follows on BlueSky

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