Katherine Benjamin

Applied topology PhD student @OxUniMaths

[Katherine Benjamin @kfbenjamin]

1/5 Very happy to share our work on flexible, multiscale cell type assignment for subcellular spatial transcriptomics, now in @Nature

https://t.co/ycqRLMpo9R

[Valentina Giunchiglia @valegiunca]

This was a lot of work!

ProCyon is a model that integrates protein sequences, structures, and natural language to predict and generate protein phenotypes

Check the paper https://t.co/YvMuYylBX3

@ImperialMed @KingsCollegeLon @imperial_mrcdtp @KingsIoPPN @imperialcollege

[Katherine Benjamin @kfbenjamin]

@iolo_jones @Nature thanks so much!!

[Katherine Benjamin @kfbenjamin]

1/5 Very happy to share our work on flexible, multiscale cell type assignment for subcellular spatial transcriptomics, now in @Nature

https://t.co/ycqRLMpo9R

[Oxford Mathematics @OxUniMaths]

When a team at @NDMOxford wanted to know more about cells they were studying as part of research in to kidney disease, they found perfect partners in @OxUniMaths & @mpicbg.

Read about @BetterKidneys @haharrington @kfbenjamin & colleagues' collaboration:

https://t.co/IXy4QFTK3y

[Katherine Benjamin @kfbenjamin]

5/5 We're super excited about TopACT's ability to leverage the unparalleled resolution of next-generation spatial omics platforms.

Check out the article for more, including additional experiments on synthetic benchmark data and the mouse brain.

@OxUniMaths

[Katherine Benjamin @kfbenjamin]

2/5 This is joint work with the amazing Aneesha Bhandari, @haharrington, @BetterKidneys and many more.

We introduce TopACT, a method for automatic cell type annotation in next-generation spatial transcriptomics data which sidesteps the need for predefined cell boundaries.

[Katherine Benjamin @kfbenjamin]

4/5 In #StereoSeq data, TopACT precisely pinpoints rare immune cells in space.

We then use multiparameter persistent homology, a newly emerging method in topological data analysis, to generate and validate a hypothesis on immune cell organisation in lupus.

[Thomas Chaplin @tomrchaplin]

Arguably one of the least utilised but most powerful features of persistent homology (PH) is functoriality. Large swathes of data come pre-divided into distinguished, disjoint subsets (a priori/via clustering). A functorial PH pipeline lets us analyse how these subsets interact!

[Heather Harrington @haharrington]

Wonderful week of rainbows, maths and manuscripts! Chromatic work by Abhinav Natarajan @tomrchaplin @majirouses @adambrownphd Toric fibre products and MLE by Niharika Paul @JaneIvyCoons @tudresden_de @OxUniMaths https://t.co/VZ26pFTC1j
https://t.co/o5FglIakOA

[agnese barbensi @AgneseBarbensi]

So excited to see this 59 authors collaboration finally out! Kudos to @LucaTubiana for leading and coordinating this years long project @CostEutopia

[Katherine Benjamin @kfbenjamin]

@iolo_jones congrats iolo!! amazing work, can’t wait to read

[Iolo Jones @iolo_jones]

Really pleased to finally share my preprint: Diffusion Geometry

(1/4) Diffusion geometry defines Riemannian geometry for data and probability spaces!
https://t.co/hwldYZZCdF

[Prof. Christina Pagel - @chrischirp.bsky.social @chrischirp]

This is going to be super interesting!
Hear about how mathematical topology can shed light on actual mecahnisms going on in our immune cells!
Sign up for this free online webinar as part of our @uclchimera programme .
Fri 26 April, 10-11am

[Katherine Benjamin @kfbenjamin]

@AgneseBarbensi @StolzBernadette thanks agnese, i owe you for introducing me to TDA :)

[Katherine Benjamin @kfbenjamin]

I had a great time presenting our research on spatial transcriptomics and topological data analysis today! Incredibly honoured to have been chosen as a medallist #STEM4Brit

[STEM for Britain @STEM4Brit]

Today the first sets of winners for the STEM for Britain 4th March 2024, @Mathematics, Gold/First Place, Daniel Gardham -University of Surrey, Silver/Second Place, Katherine Benjamin -University of Oxford, Bronze/Third Place, Francisco De Melo Virssimo – London School of Economic

[Katherine Benjamin @kfbenjamin]

@StolzBernadette thank you bernadette!!

[Valentina Giunchiglia @valegiunca]

Amazing to see this paper finally published!

@ProfHampshire @imperial_mrcdtp

[Katherine Benjamin @kfbenjamin]

Thanks @osumray for a very entertaining talk on quiver laplacians and applications 🎶

[LOGML Summer School @LogmlSchool]

🌟Applications open - LOGML 2024🌟

👥 Mentor-led projects, expert talks, tutorials, socials, and a networking night
📝 Application form: https://t.co/iB0VitdZO5
📅 Apply by 26 Jan 2024 📝
📩 Questions? [email protected]

#LOGML #Geometry #MachineLearning #SummerSchool