Arjan Boltjes

... specific functional expression programs correlated with fluctuations in various #Tcell subsets, which may be associated with #AML progression and relapse. Furthermore, our analysis of cellular communication networks led to the identification of #VISTA, #CD244, and #TIM3 as potential #immunotherapeutic targets in pediatric AML."

https://pubmed.ncbi.nlm.nih.gov/38844062/

Nice work by Yuan et al., using #scRNAseq and #scTCRseq. No huge discoveries, but of interest nonetheless.

#science #cancer #immunology

Single-cell transcriptomic analysis of the immune microenvironment in pediatric acute leukemia - PubMed

Relapse and treatment resistance pose significant challenges in the management of pediatric B cell acute lymphoblastic leukemia (B-ALL) and acute myeloid leukemia (AML). The efficacy of immunotherapy in leukemia remains limited due to factors such as the immunosuppressive tumor microenvironment (TME …

PubMed
Jun 20, 2024 at 7:35amWeb
Show threadArjan BoltjesJun 20, 2024

Of specific interest for #pediatric #cancer researchers might be the n=4 pediatric healthy control samples included, of which the #scRNAseq according to the statement in the paper is available.

#OpenData

Show threadArjan BoltjesJun 20, 2024

While going over the methods, I noticed they used #NMF where #PCA is mostly used. And while refreshing ;) my knowledge of the differences between the two, I stumbled upon a simple question/answer on #CrossValidated: https://stats.stackexchange.com/questions/502072/what-is-the-main-difference-between-pca-and-nmf-and-why-to-choose-one-rather-tha

This links to a book from #TrevorHastie, offered for free on his website: https://hastie.su.domains/publications.html

Another reason to finally have a look at "An Introduction to #Statistical Learning with Applications in R (second edition)" by James, Witten, et al.

#rstats

What is The Main Difference between PCA and NMF and why to choose one rather than the other?

I have to develop some analyses to study cancer data. I want to use NMF and PCA. Basically these tools choose the best factorization rank and the number of components that is meaningful to your ana...

Cross Validated