#scrnaseq — Public Fediverse posts
Live and recent posts from across the Fediverse tagged #scrnaseq, aggregated by home.social.
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Benchmarking computational decontamination of ambient RNA
https://www.biorxiv.org/content/10.64898/2026.01.13.699237v1.full
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Last talk of the #CSSingleCells23 conference:
Karin Pelka, Gladstone/UCSF
https://pelkalab.org/Spatially organized #immune hubs in #colon #cancer
#ColonCancer
#scRNAseqhttps://pubmed.ncbi.nlm.nih.gov/34450029/
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/36702949/1/2
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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)
Looks at #PancreaticCancer with spatial #proteomics
now #scRNAseqDeveloped CoGAPS matrix factorization, can identify cell state transitions
Using PhysiCell to build models
http://physicell.org/#cancer
#SingleCell
#CSSingleCells231/2
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"predicts new biology missed by today's genomics"
#spatial #transcriptomics #genomics
#scrnaseq
#CSSingleCells23works 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
https://www.biorxiv.org/content/10.1101/2022.06.24.497555v4
https://www.biorxiv.org/content/10.1101/2023.03.17.533189v2New insights into universally expressed human genes
https://www.biorxiv.org/content/10.1101/2022.12.06.519414v12/3