I've used it to re analyse my neutrophil single cell proteomics data. The representation was excellent and made much biological sense. Mature neutrophils sit close together. Immature branch off. NETing populations are far off. Its great ill keep using Bonsai! Great tool!

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Hey, I heard about Bonsai, but now I heard there is another method called MILK that also visualizes scRNA-seq on trees. And it is much faster! Should I just use that then? A tree is a tree, right? TLDR: No. #methodsmatter Not even close. On realistic synthetic data MILK performs worse than UMAP.

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Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22

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It's been on BioRxiv since May 2025. And it's not that it went unnoticed in the community. www.biorxiv.org/content/10.1...

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How does it compare to Bonsai? www.nature.com/articles/s41...

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