Professor of Computer Science, Princeton University
Princeton, NJ
Joined March 2014
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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!
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 👇
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!
🏅We're excited to announce the winners of the 2024 @Regeneron Science Talent Search. Congratulations to these extraordinary young scientists! #RegeneronSTS societyforscience.org/blog/r…
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
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!
Ben Raphael retweeted
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
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 biorxiv.org/content/10.1101/…
Led by @UthsavC w/ @BrianJohnArnold @hrksrkr @Cong992 Sereno + Kohei (1/7)
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)
GASTON software available at github.com/raphael-group/GAS…. Tutorials are here with more coming soon gaston.readthedocs.io/en/lat… (7/7)
Ben Raphael retweeted
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!
We have extended the RECOMB-CBB deadline for papers submission to February 7, 2023 23:59, AoE.
Send your #Cancer #Computational #Biology papers to #RECOMB_CCB at @RECOMBconf. This year's edition in Istanbul follows the previous amazing @2022Ccb ! #rt
sites.google.com/view/recomb…
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 authors.elsevier.com/a/1fxla…
Belayer software and tutorial available on Github: github.com/raphael-group/bel… 5/6
Belayer first appeared @Recomb2022 and in preprint form (biorxiv.org/content/10.1101/…). Excited to be one of several exciting papers in the “Focus on #recomb2022” special section in @CellSystemsCP 6/6
Ben Raphael retweeted
Five computer science graduate students have been named 2023 @SiebelScholars. The award recognizes academic achievement and leadership.
Congratulations! 🎉
bit.ly/3xGJyeU
ALT Siebel Scholars Class of 2023 photos in a grid
Ben Raphael retweeted
Princeton Bioengineering is hiring! (please ReTweet!). The search is open rank, but we're particularly interested in talented postdocs on the faculty job market. Applications due Nov15. Come join our vibrant and growing Bioengineering community! puwebp.princeton.edu/AcadHir…
