Experiments

Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).

• Benchmarking component choices for unpaired single cell RNA and epigenomic integration.

  PMID 41987329 · PMC13192178 · Genome biology · 2026 · 7 claims · 8 setups

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  Gene activity scores (GAS) show limited correlation with actual gene expression but effectively preserve cellular neighborhood structure and support clustering.

  e18 pbmc brain kidney scrna-seq share-seq gas

• An AI-Enabled Single-Cell Transcriptomic Analysis Pipeline for Gene Signature Discovery in Natural Killer Cells Linked to Remission Outcomes in Chronic Myeloid Leukemia.

  PMID 41972591 · PMC13072394 · Biology · 2026 · 8 claims · 7 setups

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  GAFA integrates latent-space representation, pseudotime trajectory modeling, GRN inference, and machine learning-based gene panel discovery into a single coherent pipeline, unlike existing workflows that treat these steps independently.

  peripheral subset immune assigned scrna-seq latent-space automated

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• Single-cell and spatial profiling highlights TB-induced myofibroblasts as drivers of lung pathology.

  PMID 41489684 · PMC12767585 · The Journal of experimental medicine · 2026 · 8 claims · 8 setups

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  MMP1+CXCL5+ fibroblasts and SPP1+ macrophages are linked to TB disease and TB lung granuloma and reveal targetable cellular cross talk underlying TB immunopathology

  lung ffpe lymph nonhuman scrna-seq spatial bulk

• Multi-modal skin atlas identifies a multicellular immune-stromal community associated with disrupted cornification and specific T cell expansion in atopic dermatitis.

  PMID 41741455 · PMC13057205 · Nature communications · 2026 · 8 claims · 8 setups

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  Generated a multi-modal single-cell atlas of 280,518 cells from 27 samples/17 adults (healthy, AD non-lesional/lesional, scleroderma), integrated with 430,186 cells from four prior studies into a 710,704-cell human skin atlas with 86 annotated granular cell subsets.

  skin healthy keratinocytes re-annotated droplet-based scrna-seq bulk

• Comparative single-cell landscape of immune cells in human livers affected HBV and non-viral cirrhosis.

  PMID 41815278 · PMC12971635 · Frontiers in medicine · 2025 · 8 claims · 7 setups

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  Macrophage-PLCG2 (anti-inflammatory) and CD8+ T-FABP5 subsets are expanded in HBV cirrhosis compared to non-viral cirrhosis

  liver myeloid scrna-seq spatial pathway

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

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  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Tree shrew immune cell atlas identifies NR1H3⁺ tissue macrophages with conserved anti-inflammatory function.

  PMID 41957356 · PMC13223331 · Nature communications · 2026 · 8 claims · 8 setups

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  A single-cell/single-nucleus RNA-seq atlas across 12 tree shrew tissues identifies 39 distinct immune and non-immune cell types, providing a reference resource for tree shrew immunology

  tree single-cell scrna-seq cross-species functional

• A multi-omic single-cell landscape of perinatal mouse skin maps lineage specification and reveals shared dynamics in human fetal skin.

  PMID 41998142 · PMC13144478 · Experimental & molecular medicine · 2026 · 7 claims · 8 setups

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  Integrated scATAC/scRNA multi-omics analysis of developing mouse skin identifies gene network axes underlying skin lineage specification

  dorsal scrna-seq skin fibroblast scatac-seq scrna-seq spatial

• Resolving sensitivity, specificity and signal contamination in Xenium spatial transcriptomics.

  PMID 42062553 · PMC13259927 · Nature methods · 2026 · 8 claims · 6 setups

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  Xenium data show strong consistency across patients and technical replicates, with little technical variation between platforms

  ffpe matched xenium xenium single-nucleus immunohistochemistry

• Single-cell atlas of the developing Down syndrome brain cortex.

  PMID 41545595 · PMC13004680 · Nature medicine · 2026 · 8 claims · 8 setups

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  RORB/FOXP1-expressing L4-like excitatory neurons are subtype-specifically and dramatically reduced in Down syndrome fetal cortex, especially at later stages (PCW16-20)

  fetal excitatory neural humanized single-nucleus immunostaining compositional

• Deep single-cell decoding of human pancreatic islets reveals T2D β-cell gene expression defects.

  PMID 41986506 · PMC13226668 · The EMBO journal · 2026 · 8 claims · 6 setups

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  Single-cell transcriptome profiling of 245,878 islet cells from 48 donors (ND/PD/T2D) identifies 14 distinct, robust islet cell types detected in every donor

  pancreatic aggregated endoc-βh3 subset droplet-based pseudobulk unsupervised