GregorySchwartz

Switching to Bluesky!

[GregorySchwartz @Schwartastic]

We are proud to announce the publication of CellNEST, deep-learning detection single cell-cell or even "relay" communication on #SpatialTrascriptomics data at single-spot or #SingleCell!

Paper: https://t.co/JG7HN9uCQU

Code: https://t.co/AoUfMxQ3FY and https://t.co/cKGy1PjLa6

[UHN Research @UHN_Research]

Scientists @PMResearch_UHN led by @Schwartastic have developed CellNEST, a powerful AI tool that maps how cells talk to each other. By detecting complex signals between cells, it could lead to new ways to target tumours and stop disease progression.

🔗https://t.co/HJyAKFElxc

[Princess Margaret Cancer Centre Research @PMResearch_UHN]

Cancer Cells Relay Messages to Coordinate the Spread

CellNEST, an AI tool developed by Dr. @Schwartastic's team, found that the tumour microenvironment may relay messages in a "two-hop" fashion, fuelling the spread of #PancreaticCancer.

@naturemethods:
https://t.co/qirz2qTxMg

[Nature Methods @naturemethods]

Out today from the Schwartz lab! A new way to study cell-cell communication from spatial transcriptomics data. Cell Neural Networks on Spatial Transcriptomics (CellNEST) can detect both signals between individual cells and relay networks of communication. https://t.co/bb0fwtp5ep

[GregorySchwartz @Schwartastic]

I am switching over to Bluesky, so check for updates at https://t.co/v161wUwrIo

[GregorySchwartz @Schwartastic]

We are proud to announce the publication of CellNEST, deep-learning detection single cell-cell or even "relay" communication on #SpatialTrascriptomics data at single-spot or #SingleCell!

Paper: https://t.co/JG7HN9uCQU

Code: https://t.co/AoUfMxQ3FY and https://t.co/cKGy1PjLa6

[GregorySchwartz @Schwartastic]

CellNEST's architecture enables finding patterns of signals, potentially detecting relay networks of communication. This work was made possible by the fantastic @ftzohora @deisha_paliwal Joshua Li @VictoriaGaoVG @k3noff @LabNotta

[GregorySchwartz @Schwartastic]

This work was led by the incredible Conor Klamann and Christie Lau!

[GregorySchwartz @Schwartastic]

Our new #singlecell #datavisualization method is now in GigaScience! With our interactive tree, you can find populations large and small in #scRNAseq, #scATACseq, #spatial, and more!

Try it: https://t.co/xAVVXpyonX

Paper: https://t.co/eFIByQbywI

Code: https://t.co/UJarN1QDMr

[GregorySchwartz @Schwartastic]

As a bonus, we include a new implementation of TooManyCells in python: TooManyCells (à la Python)

Code: https://t.co/SSzAeDS48E

[UHN Research @UHN_Research]

Research from @Schwartastic @PMResearch_UHN in collaboration with @PennMedicine have created AnnoSpat, a tool that identifies and maps cell types in tissues. It excels in analyzing complex tissues, like the pancreas. Read more > https://t.co/QgjLa7Eg4f; https://t.co/EJonY75oac

[Princess Margaret Cancer Centre Research @PMResearch_UHN]

A new tool “AnnoSpat”–developed by Dr. Gregory Schwartz (@Schwartastic) and his team @UHN–can annotate cell types and quantify cell organizations, making it easier to decipher tissue images from spatial proteomic assays. 🔬

https://t.co/cbt5xjnK1C

[Bioinformatics.ca @Bioinfodotca]

There's still time to get the early bird rate for our Pathway and Network Analysis #bioinformatics workshop!
Apply by Friday, April 26 for a discount.
Registration closes June 12.

https://t.co/c246kr9Ktw

[UofT Schmidt AI in Science Postdoctoral Fellowship @UofTSchmidt_AI]

Our #SchmidtAIinSci Postdoc @ftzohora will be presenting her work "Unraveling Cancer Cell Communication Using Deep Learning Models on Spatial Transcriptomics Data".

Host: Cornell University AI for Science Institute
🗓️Friday March 15, 2:30-3:30pm EST https://t.co/FSiOaYoTBs

[Federico Gaiti @fgaiti]

Check out our latest implementation of GoT-Splice, now at @STARProtocols!

✂️🧬GoT-Splice🧬✂️ profiles genotype, gene expression, surface markers, and splicing ... all within the same #singlecell!

https://t.co/svF4KTvLWZ

@CellStemCell publication (🧵👇): https://t.co/R1l2CdUCa6

[bioRxiv Bioinfo @biorxiv_bioinfo]

NEST: Spatially-mapped cell-cell communication patterns using a deep learning-based attention mechanism https://t.co/UVnNTmzeLk #biorxiv_bioinfo

[GregorySchwartz @Schwartastic]

Thank you to everyone who made this possible and to Fatema Zohora, who spearheaded NEST! @ftzohora @k3noff @LabNotta

@UofTSchmidt_AI @OICR_news @UHN_Research

[GregorySchwartz @Schwartastic]

Introducing NEST, our deep-learning solution for detecting cell-cell communication on #SpatialTrascriptomics data at single-spot or #SingleCell precision!

Pre-print: https://t.co/ECFK3Lnr51
NEST: https://t.co/LtY0fBfHT8
NEST-Interactive: https://t.co/SWspm5uNJR

[GregorySchwartz @Schwartastic]

@mduranfrigola Yes it can! It will work on any observation feature matrix and TMCI can visualize any tree with the appropriately structured file.

[GregorySchwartz @Schwartastic]

Want to find the right resolution for #singlecell subpopulations in your #scRNAseq, #scATACseq, #scMultiome, #spatial, and other #omics data sets?

I'm excited to share our new tool TMCI for #datavisualization!

Pre-print: https://t.co/dWXbLzwE0b

Code: https://t.co/UJarN1QDMr

[bioRxiv @biorxivpreprint]

TooManyCellsInteractive: a visualization tool for dynamic exploration of single-cell data https://t.co/vzuDrMsTOn #bioRxiv

[GregorySchwartz @Schwartastic]

This work was led by an incredible developer Conor Klamann and an amazing PhD student Christie Lau!