Ben Raphael

Professor of Computer Science, Princeton University

[Ben Raphael @benjraphael]

@uthsavc Which one of us is supposed to be the old hipster in the center of this picture who’s explaining everything?

[Ben Raphael @benjraphael]

A great thread from @uthsavc describing some of the math behind GASTON, our new method for modeling spatial variation in gene expression, now out in @naturemethods!

[Uthsav Chitra @uthsavc]

GASTON, our method to learn “topographic maps” of gene expression, is out now @naturemethods!

IMO the coolest part is a new model of *spatial gradients in sparse data*.
As is typical for bio papers, it’s buried in Methods, but see below for a quick outline on the math 👇

[Ben Raphael @benjraphael]

Congratulations to all the winners and finalists of the 2024 @Regeneron Science Talent Search! It was inspiring to meet the next generation of leaders in science and technology!

[Society for Science @Society4Science]

🏅We're excited to announce the winners of the 2024 @Regeneron Science Talent Search. Congratulations to these extraordinary young scientists! #RegeneronSTS https://t.co/2L1GCpcbbm

[Ben Raphael @benjraphael]

Thank you @rohitsingh8080 for hosting me at @DukeCellBiology! A great visit with a packed auditorium and many stimulating conversations! This photo was me being delightfully surprised that I was speaking in a lecture series next to these truly distinguished cell biologists

[Rohit Singh @rohitsingh8080]

I forgot to take a photo during his talk, so this will have to do.

@benjraphael gave a fantastic talk at @DukeCellBiology on the creative and elegant spatial transcriptomics methods from the Raphael Lab. Check out Gaston, Belayer, PASTE2 and the rest!

[Uthsav Chitra @uthsavc]

Also, a quick observation: our 1-D coordinate is a spatial *potential function* - like the height in the famous Waddington's landscape - for some tissues

Modeling spatial information -> more accurate differentiation potential vs pseudotime methods which do not use spatial info

[Ben Raphael @benjraphael]

@notSoJunkDNA @uthsavc @BrianJohnArnold @hrksrkr @Cong992 Wow -- what a pleasant surprise! Much better than the Disney clip that I was expecting

[Ben Raphael @benjraphael]

Our new method GASTON learns a “topographic map” of a tissue slice, enabling simultaneous identification of spatial domains and gene expression gradients in spatial transcriptomics https://t.co/mnZSxzUkqx

Led by @UthsavC w/ @BrianJohnArnold @hrksrkr @Cong992 Sereno + Kohei (1/7)

[Ben Raphael @benjraphael]

GASTON software available at https://t.co/ydHTNhTyan. Tutorials are here with more coming soon https://t.co/Ox6tNbIw7Q (7/7)

[Ben Raphael @benjraphael]

In the olfactory bulb, the GASTON isodepth indicates the “differentiation potential” of neurons – with isodepth gradients showing trajectories of neural maturation. Moreover, GASTON reveals the distinct layers and cell type gradients within the layers. (6/7)

[Simone Zaccaria @ZaccaSimo]

Consider this great opportunity to submit algorithmic or analysis cancer comp bio contributions to present to the phenomenal @RECOMBconf community and to be considered for PLOS CB! Deadline extended but happening soon!

[Ben Raphael @benjraphael]

Belayer first appeared @Recomb2022 and in preprint form (https://t.co/yYoQrRTHQ2). Excited to be one of several exciting papers in the “Focus on #recomb2022” special section in @CellSystemsCP 6/6

[Ben Raphael @benjraphael]

Spatial transcriptomics meets complex analysis – our new method Belayer models spatial gene expression in layered tissues, now published in @CellSystemsCP. Work led by @Cong992 and @uthsavc with Shirley Zhang. 1/6 https://t.co/OV0Fq0Hsyo

[Ben Raphael @benjraphael]

Belayer software and tutorial available on Github: https://t.co/Z5gNd4UEBA 5/6