@RonZeira

Research scientist

 Israel
Joined March 2021
  • Tweets12
  • Following52
  • Followers41
Happy to share that our paper on inferring spatially resolved expression from H&E images is published in #PLOSCompBio I want to thank @leon_anavy , Zohar Yakhini, Ehud Rivlin and Daniel Freedman for their guidance and support driving this project doi.org/10.1371/journal.pcbi…

HIPI: Spatially resolved multiplexed protein expression inferred from H&E WSIs

Author summary We present HIPI (H&E Image Interpretation and Protein Expression Inference) for predicting cell marker expression from tumor H&E images. We process paired H&E and CyCIF images taken...

journals.plos.org
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Ben Raphael is next, PASTE2: Partial Alignment of Multi-slice Spatially Resolved transcriptomics data. #RECOMB2023
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Our work on "Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data" was accepted to #RECOMB2023. @benjraphael #XinhaoLiu PASTE2 uses a novel partial optimal transport formulation for 3D reconstruction of partially overlapping ST slices biorxiv.org/content/10.1101/…

PASTE2: Partial Alignment of Multi-slice Spatially Resolved Transcriptomics Data

Spatially resolved transcriptomics (SRT) technologies measure mRNA expression at thousands of locations in a tissue slice. However, nearly all SRT technologies measure expression in two dimensional...

biorxiv.org
RECOMB Conference Series@RECOMBconf10 Jan 2023
15 more papers are accepted to #RECOMB2023 after a round of revisions. The list is now updated: recomb2023.bilkent.edu.tr/pr…
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Many tools can only analyze spatial gene expression in 2D, so researchers from @Princeton developed #PASTE, a tool that integrates spatial transcriptomic data from multiple slices to generate a 3D view of gene expression biotechniques.com/molecular-… @benjraphael @RonZeira 🖥️(4/8)
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Now published in revised form in @naturemethods after a constructive review process. rdcu.be/cNFXO
Ben Raphael@benjraphael17 Mar 2021
Our new method PASTE aligns and integrates spatial transcriptomics data from multiple tissue sections. Great work by @RonZeira and @mrland99 1/4 biorxiv.org/content/10.1101/…

Alignment and Integration of Spatial Transcriptomics Data

Spatial transcriptomics ( ST ) is a new technology that measures mRNA expression across thousands of spots on a tissue slice, while preserving information about the spatial location of spots. ST is...

biorxiv.org
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A beautiful summary of our method PASTE by @MollySharlach @mrland99 @polishstudent17 @benjraphael engineering.princeton.edu/ne…

Princeton Engineering - New method melds data to make a 3-D map of cells’ activities

Princeton engineers are using a cell's surroundings to help biologists make more sense of gene expression information. Their new system could open the door to identifying rare cell types and choosing...

engineering.princeton.edu
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And read the accompanying News & Views here: nature.com/articles/s41592-0…
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Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices. @RonZeira @benjraphael nature.com/articles/s41592-0…
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Check out our presentation on “Alignment and Integration of Spatial Transcriptomics Data” tomorrow at #RECOMB2021
recomb2021@recomb2128 Aug 2021
#RECOMB2021 begins tomorrow at 10 am US ET with a fantastic program (recomb2021.org/program). The first day of the conference will feature welcome remarks from the organizing committee, two distinguished keynote talks, and four sessions.
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How close is a copy number profile to a whole genome duplication event? Check out our #WABI2021 paper on “Genome Halving and Aliquoting Under the Copy Number Distance” with Geoffrey Mon and @benjraphael drops.dagstuhl.de/opus/vollt…
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Preprint of our method PASTE for alignment and integration of spatial transcriptomics data.
Ben Raphael@benjraphael17 Mar 2021
Our new method PASTE aligns and integrates spatial transcriptomics data from multiple tissue sections. Great work by @RonZeira and @mrland99 1/4 biorxiv.org/content/10.1101/…

Alignment and Integration of Spatial Transcriptomics Data

Spatial transcriptomics ( ST ) is a new technology that measures mRNA expression across thousands of spots on a tissue slice, while preserving information about the spatial location of spots. ST is...

biorxiv.org
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