#scrnaseq — Public Fediverse posts

Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant!
Single-cell/nuclei pipeline for data derived from Oxford Nanopore and 10X Genomics
Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0

#10xgenomics #longreadsequencing #nanopore #rnaseq #rnaseq #scrnaseq #singlecell #nfcore #openscience #nextflow #bioinformatics

Join us for a 2-part workshop on Mastering Reproducible Enrichment Analysis! 📊

Presented by Anusuiya Bora and myself, with a focus on reproducibility and best practices.

📅 When: 12 and 13 May 2026
🕑 Time: 2:00 PM – 4:00 PM (AEST)
📍 Where: Online
💰 Cost: FREE for academic sector (places are limited!)

🔗Registration form link: https://lnkd.in/gQcHggGF

#Bioinformatics #RNAseq #scRNAseq #Genomics #ReproducibleResearch #OpenScience #RStats

... 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

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

Spatially organized #immune hubs in #colon #cancer
#ColonCancer
#scRNAseq

https://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

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 #scRNAseq

Developed CoGAPS matrix factorization, can identify cell state transitions

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

#cancer
#SingleCell
#CSSingleCells23

1/2

"predicts new biology missed by today's genomics"
#spatial #transcriptomics #genomics
#scrnaseq
#CSSingleCells23

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

https://www.biorxiv.org/content/10.1101/2022.06.24.497555v4
https://www.biorxiv.org/content/10.1101/2023.03.17.533189v2

New insights into universally expressed human genes
https://www.biorxiv.org/content/10.1101/2022.12.06.519414v1

2/3

" Instead, #Hepatoblastoma #tumors contain a large suppressive #myeloid compartment which poses opportunities for targeting. Specifically, therapeutic antibodies
targeting the #tumor antigen #GPC3 to induce ADCP by #macrophages, in combination with myeloid
#ImmuneCheckpointBlockade (#CD47/SIRPa, or VISTA) could be a feasible strategy to explore in future studies"

Krijgsman et al. from Vercoulen lab in the #UMCUtrecht, on #bioRXiv:
https://www.biorxiv.org/content/10.1101/2023.06.28.546852v1

#scRNAseq #spatial #CyTOF #immunology