#scrnaseq — Public Fediverse posts on home.social

Benchmarking computational decontamination of ambient RNA

#scrnaseq

Last talk of the #CSSingleCells23 conference:
Karin Pelka, Gladstone/UCSF
https://pelkalab.org/

Then: predict cellular interaction networks via correlations of gene program activities across #tumors

anti-tumor hubs in tumors, ISGs including CXCR3 ligands, differs between tumor types (MMR+ or -)

have data from clinical trial (biopsies before and after treatment)
https://pubmed.ncbi.nlm.nih.gov/36702949/

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#tumors #scrnaseq #coloncancer #cancer #colon #immune

First speaker of the session (Cell identity in situ)
is Elana Fertig
of Convergence Institute at Johns Hopkins
https://fertiglab.com/

She has background in weather prediction (!) ⛈️ which has convergence with predictive medicine (such as huge data sets)

Developed CoGAPS matrix factorization, can identify cell state transitions

Using PhysiCell to build models
http://physicell.org/

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#cssinglecells23 #singlecell #cancer #scrnaseq #proteomics #pancreaticcancer

works by unified detection of sample-specific sequence variation... sample can be different cells, sequence is raw reads

method chooses an "anchor" sequence then looks for neighboring sequence that varies. thus is independent of any reference genome

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#cssinglecells23 #scrnaseq #genomics #transcriptomics #spatial