@AaronNewmanLab

Computational biology, cancer genomics, & stem cell bioinformatics lab @Stanford @czbiohub

 Stanford, CA
anlab.stanford.edu
Joined October 2021
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1/ Thrilled to share our new paper, out today in @Nature: "Non-invasive profiling of the tumour microenvironment with spatial ecotypes". Paper (open access): nature.com/articles/s41586-0…

Non-invasive profiling of the tumour microenvironment with spatial ecotypes

Nature - Multimodal machine learning reveals that tumour microenvironments can be decomposed into spatially organized multicellular ecosystems, termed spatial ecotypes, that can be accessed...

nature.com
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An honor to discuss our recent @Nature paper with @EricTopol on his Ground Truths podcast! See his fantastic thread below and a link to our conversation here: erictopol.substack.com/p/a-b…
Eric Topol
@EricTopolJul 5
For treatment and outcomes for cancer, the tumor microenvironment (TME) is pivotal, but we've never had a non-invasive way to assess it. Until now, a blood test breakthrough! (<-a term I use sparingly) Pictured below, schematically, the TME surrounds the cancer cells and consists of immune cells, blood vessel (endothelial) cells, fibroblasts and matrix
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15/ We are grateful to our funding sources including @theNCI, @TheVFoundation, @CancerRF, @MelanomaReAlli, and @Ludwig_Cancer. We deeply thank the patients and their families whose generous contribution of samples made this research possible.
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16/ GitHub: github.com/digitalcytometry/… Web interface: spatialecotyper.stanford.edu

GitHub - digitalcytometry/spatialecotyper: Deciphering spatial ecotypes from spatial, single-cell,...

Deciphering spatial ecotypes from spatial, single-cell, and bulk transcriptomic data - digitalcytometry/spatialecotyper

github.com
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Thanks @IamLinghua !!
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SCI @AaronNewmanLab & others unveil CytoTRACE 2, a deep learning tool that predicts absolute cell developmental potential from #SingleCell RNA-seq data, outperforming prior methods and refining maps of cell fate and potency across tissues. brnw.ch/21wX6j4 @kang_minji_
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Aaron Newman Lab retweeted
Nature Methods@naturemethods29 Oct 2025
CytoTRACE 2: an interpretable deep-learning method that uses scRNA-seq data to predict absolute developmental potential across datasets. nature.com/articles/s41592-0…

Improved reconstruction of single-cell developmental potential with CytoTRACE 2

Nature Methods - CytoTRACE 2 is an interpretable deep learning framework that leverages single-cell RNA sequencing data to predict absolute developmental potential across datasets.

nature.com
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