#SingleCellTranscriptomics
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alicefrolov.bsky.social
Rewiring of intercellular ligand-receptor communication in aged tissue

I am sharing a visualization exploring how intercellular signaling architecture is remodeled with chronological age.

#CellCommunication #LigandReceptor #SingleCellTranscriptomics #SpatialTranscriptomics #Stromalniche
Rewiring of intercellular ligand-receptor communication in aged tissue I am sharing a visualization exploring how intercellular signaling architecture is remodeled with chronological age. The figure ("Log2 fold-change (old vs young) in signaling pair activity across niches; simulated data") uses a diverging lollipop layout with a dual-panel mirror, presenting ligand-side and receptor-side activity shifts in vertically aligned registers. This mirror design allows direct visual comparison of whether a given signaling pair is being driven predominantly by altered ligand availability, receptor expression, or coordinated changes in both. I want to emphasize at the outset that the underlying data are simulated. The magnitudes and directionality, however, are parameterized to reflect trends repeatedly reported in the CellChat and CellPhoneDB-based literature on aged niches, so the figure is intended as an illustrative scaffold rather than an empirical claim. Several patterns are worth highlighting for discussion. Pro-inflammatory axes such as TNF-TNFRSF1A and CCL2-CCR2 display positive log2 fold-changes, consistent with the inflammatory remodeling and myeloid recruitment characteristic of aged stromal compartments. Conversely, WNT and NOTCH ligand-receptor pairs trend negative, mirroring reported attenuation of niche-derived regenerative and self-renewal cues. TGFB1-TGFBR2 shows a positive shift concordant with fibrotic reprogramming. The mirror arrangement makes clear that certain pairs are receptor-limited in the aged condition, which has implications for how one interprets deconvolved communication probabilities. Methodologically, I would welcome perspectives on normalization strategies for cross-niche comparison, particularly how to control for compositional shifts in cell-type abundance that can confound inferred communication strength.
August 31, 2026 at 5:03 PM
novogene-europe.bsky.social
Explore how spatial and #singlecelltranscriptomics reveal tissue architecture and cellular interactions. Watch our on-demand webinar for insights into cellular complexity and gene expression. https://bit.ly/4jc0yyo

#SpatialTranscriptomics #Genomics #CellBiology #Innovation
November 13, 2025 at 8:05 AM
novogene-europe.bsky.social
Explore how spatial and single-cell transcriptomics reveal tissue architecture and cellular interactions. Watch our on-demand webinar for insights into cellular complexity and gene expression. bit.ly/4jc0yyo #SingleCellTranscriptomics #SpatialTranscriptomics #Genomics #CellBiology #Innovation
July 23, 2025 at 7:55 AM
novogene-europe.bsky.social
Explore how spatial and single-cell transcriptomics reveal tissue architecture and cellular interactions. Watch our on-demand webinar for insights into cellular complexity and gene expression.

bit.ly/4jc0yyo

#SingleCellTranscriptomics #SpatialTranscriptomics #Genomics #CellBiology #Innovation
June 10, 2025 at 7:37 AM
horticulturer.bsky.social
Garlic clove virus study reveals meristem defense & glutathione role! 🧬🛡️ #SingleCellTranscriptomics #GarlicVirusImmunity @OxfordJournals
Details: doi.org/10.1093/hr/u...
April 4, 2025 at 3:03 PM
exo-beyondthecell.bsky.social
💡 How can we better interpret the complex data generated by spatial biology technologies? Insights into STAMP data analysis provide new perspectives.
🔗 Read the Alert: eurekalert.org/news-release...
📖 Read the Article: sciexplor.com/exo/articles...
#spatialbiology #singlecelltranscriptomics
July 17, 2026 at 3:26 AM
endosocjournals.bsky.social
Generation of a prop1 knockin zebrafish enables single-cell transcriptomics of early pituitary development. Read more in #Endocrinology: https://bit.ly/4oFnGtl #EarlyPituitaryDevelopment #zebrafish #SingleCellTranscriptomics @endocrinesociety.bsky.social
July 3, 2026 at 5:05 PM
gregorylab.bskyverified.social
New collab out with Jennifer Zhang & Amy Petty of @dukemedschool.bsky.social #Dermatology Department! #scRNAseq performed by #DukeMGC

'Insights into #Keratinocyte and Immunologic Landscape in #Cutaneous #Graft-Versus-Host Disease through #SingleCellTranscriptomics' 🧬💻

doi.org/10.1016/j.xj...
Redirecting
doi.org
May 20, 2025 at 1:03 PM
alicefrolov.bsky.social
Sharing a visualization developed in the context of our ongoing work on somatic cell reprogramming trajectories.

Figure: Single-cell transcriptomic heterogeneity during OSKM reprogramming

#CellularReprogramming #iPSC #SingleCellTranscriptomics #Pluripotency #SystemsBiology
Sharing a visualization developed in the context of our ongoing work on somatic cell reprogramming trajectories. Figure: Single-cell transcriptomic heterogeneity during OSKM reprogramming Subtitle: Distribution of pluripotency score across reprogramming day in mouse embryonic fibroblasts The plot displays violin distributions of a composite pluripotency score (aggregated expression of canonical markers including Nanog, Sox2, Esrrb, Zfp42/Rex1, and Dppa3) computed at the single-cell level across discrete time points (day 0, 3, 6, 9, 12, 15) following doxycycline-induced expression of the Yamanaka cassette (Oct4, Sox2, Klf4, c-Myc) in mouse embryonic fibroblasts. Key features illustrated: 1. Day 0 MEFs display a tight, low-score distribution consistent with a stable somatic transcriptional ground state. 2. Intermediate time points (day 6–9) exhibit pronounced multimodality and increased variance, capturing the well-documented coexistence of partially reprogrammed intermediates, including cells transiting through mesenchymal-to-epithelial transition (MET) and stochastic activation phases preceding the deterministic late phase. 3. A subpopulation bifurcation emerges around day 9–12, separating cells progressing toward the pluripotent attractor from refractory or alternative-fate trajectories (e.g., trophoblast-like or stalled XEN-like states described by Polo, Hochedlinger, and colleagues). 4. By day 15, a bimodal structure persists, reflecting the characteristically low conversion efficiency of OSKM reprogramming and the stabilization of bona fide iPSCs at the upper mode. Important caveat: the data shown are simulated. The distributions were generated to recapitulate qualitative trends consistently reported in single-cell studies of OSKM reprogramming (e.g., Buganim et al. 2012, Polo et al. 2012, Schiebinger et al. 2019), and are intended as a didactic and conceptual illustration of intermediate-state heterogeneity rather than a quantitative representation.
July 2, 2026 at 5:00 PM
ysanchez.bsky.social
Interested in applying #singlecelltranscriptomics to a difficult tissue? Please check out this #new preprint from our group and led by Dorian Xenakis. Important read for experimental design and analysis!

www.biorxiv.org/content/10.1...
The challenges of single cell transcriptomics on difficult human tissue: the placenta
Demand for the application of single cell transcriptomics on difficult tissues, processed and stored in disparate conditions, has led to the development of various single cell modalities. We focus on ...
www.biorxiv.org
November 19, 2025 at 11:44 AM
arxivlens.bsky.social
Microbial profiling and single-cell transcriptomics reveal probiotic mechanisms of coral thermal resilience
C.-H., C.-Y. et al.
Paper
Details
#MicrobialProfiling #CoralResilience #SingleCellTranscriptomics
September 4, 2025 at 8:56 PM
arxivlens.bsky.social
Missing data in single-cell transcriptomes reveals transcriptional shifts
Basu, S., Chen, R. et al.
Paper
Details
#SingleCellTranscriptomics #TranscriptionalShifts #MissingDataAnalysis
August 23, 2025 at 4:01 PM
arxivlens.bsky.social
Fundamental Limitations of Foundation Models in Single-Cell Transcriptomics
Atti, S., Subramaniam, S.
Paper
Details
#FoundationModels #SingleCellTranscriptomics #LimitationsInSCt
June 29, 2025 at 9:01 AM
arxivlens.bsky.social
Decoding Cellular Stress States for Toxicology Using Single-Cell Transcriptomics
Camiolo, S., Chambers, B. A. et al.
Paper
Details
#SingleCellTranscriptomics #ToxicologyResearch #CellularStressStates
June 14, 2025 at 1:04 PM
longtrec.bsky.social
Day 4 of the #LongTREC #SummerSchool has started! This morning, @eamonmc.bsky.social and Juan Francisco Cervilla Martínez will cover Single-cell transcriptomics with #LongReads

#LongReadsTranscriptomics #SingleCellTranscriptomics
July 17, 2025 at 10:27 AM
genesndiseases.bsky.social
#SingleCellTranscriptomics of #bonemarrow in #Type2Diabetes reveals impaired #cytokinesignaling, reduced #osteoclast activity, and diminished Cd36+ precursor differentiation, driven by dysregulated AP-1 transcription factor activity.

#OpenAccess: doi.org/10.1016/j.ge...
February 18, 2026 at 6:15 PM
bio-integration.org
This study uses #SingleCellTranscriptomics to identify C0 Atcayos+ cardiomyocytes that interact with #fibroblasts via Bmp6 and Fgf1 signaling after #IschemiaReperfusion, uncovering pathways that could reduce #fibrosis and help preserve #cardiac function.

Read: bio-integration.org/single-cell-...
Single-Cell Omics Analysis Reveals Critical Cell Subtypes and their Functional Attributes in Myocardial Ischemia-Reperfusion Injury
Announcing a new article publication for BIO Integration journal. Cardiac cell death and myocardial fibrosis after ischemia-reperfusion (I/R) injury are the primary causes of impaired cardiac function...
bio-integration.org
February 11, 2026 at 9:47 AM
mol-biomed.bsky.social
#Research
T-cell immunoglobulin and mucin domain-containing protein 3–mediated immunomodulation in myeloid cells and keratinocytes in the development of severe acne doi.org/10.1186/s435...

#SevereAcne #TIM3 #SingleCellTranscriptomics #Macrophages #Keratinocytes
T-cell immunoglobulin and mucin domain-containing protein 3–mediated immunomodulation in myeloid cells and keratinocytes in the development of severe acne - Molecular Biomedicine
Acne vulgaris is a common chronic inflammatory skin disorder with significant clinical and societal impacts. Severe acne (SA), in particular, causes scarring, disfigurement, and psychosocial distress....
doi.org
December 12, 2025 at 8:45 AM