@uthsavc Which one of us is supposed to be the old hipster in the center of this picture who’s explaining everything?
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Ben Raphael
283 posts
Ben Raphael
@benjraphael
Professor of Computer Science, Princeton University
Princeton, NJ Katılım Mart 2014
160 Takip Edilen1.6K Takipçiler
GASTON algorithm is quite natural: parametrize functions h,d with neural nets and learn from data.
Fun back-story: @benjraphael and I derived most of this model at the bar near an NCI workshop 🥂😅
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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 👇
Nature Methods@naturemethods
Gene expression topography analysis by GASTON portrays domain organization and spatial gradients of gene expression and cell type composition using spatially resolved transcriptomics data. @uthsavc @benjraphael @PrincetonCS nature.com/articles/s4159…
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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!
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 👇
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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 societyforscience.org/blog/regeneron…
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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!
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Ben Raphael retweetledi
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
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@notSoJunkDNA @uthsavc @BrianJohnArnold @hrksrkr @Cong992 Wow -- what a pleasant surprise! Much better than the Disney clip that I was expecting
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@benjraphael @uthsavc @BrianJohnArnold @hrksrkr @Cong992 Congrats. And here is a small gift! Enjoy…
m.youtube.com/watch?v=buUqko…
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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/10.110…
Led by @UthsavC w/ @BrianJohnArnold @hrksrkr @Cong992 Sereno + Kohei (1/7)
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GASTON software available at github.com/raphael-group/…. Tutorials are here with more coming soon gaston.readthedocs.io/en/latest/inde… (7/7)
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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)
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Ben Raphael retweetledi
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!
RECOMB-CCB 2023@recombccb2023
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-cc…
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Belayer first appeared @Recomb2022 and in preprint form (biorxiv.org/content/10.110…). Excited to be one of several exciting papers in the “Focus on #recomb2022” special section in @CellSystemsCP 6/6
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Belayer software and tutorial available on Github: github.com/raphael-group/… 5/6
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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/1fxla8YyDfj7…
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