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).

• PreTSA: computationally efficient modeling of temporal and spatial gene expression patterns.

  PMID 41673899 · PMC12998178 · Genome biology · 2026 · 7 claims · 8 setups

  Full-text index only

  PreTSA dramatically reduces computational time and memory versus GAM (Monocle, TSCAN) and PseudotimeDE for identifying temporally variable genes (TVGs) while producing highly similar results

  simulated null pbmc pancreas pseudotime tvg false-positive

• Phased differentiation of γδ T and T CD8 tumor-infiltrating lymphocytes revealed by single-cell transcriptomics of human cancers.

  PMID 34721945 · PMC8555559 · Oncoimmunology · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  In tumors, TCRVγnon9 γδ T cells (the majority γδ TIL subset) are quantitatively correlated and aligned with T CD8 cells for differentiation, exhaustion, gene expression profile, and response to immune checkpoint therapy

  pbmc tumor syngeneic scrnaseq cite-seq flow

• Interpretable trajectory inference with single-cell linear adaptive negative-binomial expression (scLANE) testing.

  PMID 41533563 · PMC12802912 · Nucleic acids research · 2026 · 8 claims · 3 setups

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  scLANE models gene expression as a piecewise negative-binomial GLM using truncated power basis (hinge) functions with adaptively chosen knots, yielding directly interpretable multiplicative effect sizes for trajectory differential expression

  zebrafish simulated diverse trajectory simulation

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

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  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• A cell atlas of multiple liver organoids and the fetal liver based on scRNA-seq.

  PMID 41736863 · PMC12927097 · iScience · 2026 · 8 claims · 8 setups

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  A unified liver organoid cell atlas of 217,025 high-quality cells was constructed by integrating scRNA-seq data from 15 organoid samples across 9 studies with human fetal liver data (5-19 weeks gestation)

  liver fetal endoderm-derived mesoderm-derived scrna-seq pseudotime pearson

• Identification and Mechanisms of Osteocyte Subsets Involved in the Pathological Progression of Osteoporosis.

  PMID 41250977 · PMC12850396 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Has reproduction · 57

  Single-cell sequencing of mouse femurs identifies six distinct osteocyte subsets (C1-C6) after excluding contaminating erythroid clusters

  femoral osteocyte dmp1-cre+ bhr-ocys single-cell monocle flow

• Autophagy Activators Normalize Aberrant Tau Proteostasis and Rescue Synapses in Human Familial Alzheimer's Disease iPSC-Derived Cortical Organoids.

  PMID 41591759 · PMC13042409 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 7 setups

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  An optimized CO differentiation protocol (Protocol 2, using 50% E6/50% hESC medium with constant rocking/orbital shaking) produces reproducible, larger, lower-necrosis organoids with consistent size across genotypes

  isogenic scrna-seq fixed cos single-cell pseudotime immunofluorescence

• Distinct senotypes in p16- and p21-positive cells across human and mouse aging tissues.

  PMID 41162753 · PMC12669595 · The EMBO journal · 2025 · 7 claims · 8 setups

  Has reproduction · 50

  p16+ and p21+ senescent cells represent largely distinct, non-overlapping populations across murine and human aging tissues

  hippocampus brain skeletal bone scrna-seq cytof velocity

• CD14(lo)CD301b(+) macrophages gathering as a proangiogenic marker in adipose tissues.

  PMID 39645040 · PMC11745947 · Journal of lipid research · 2025 · 8 claims · 8 setups

  Has reproduction · 59

  Cd14−/− mice exhibit a leaner body shape and are protected from HFD-induced obesity compared to WT mice

  epididymal adipose cd14low macrophage bulk scrna-seq pseudotime

• Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

  PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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  A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

  pca malignant tcga mda single-cell infercnv pseudotime

• Single cell snapshot analyses under proper representation reveal that epithelial-mesenchymal transition couples at G1 and G2/M.

  PMID 41611829 · PMC12894973 · Communications biology · 2026 · 7 claims · 8 setups

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  TGF-β induced EMT in MCF10A cells follows two broad paths that arise from coupling between cell cycle and EMT at either the G1 or G2/M phase

  mcf10a scrna-seq vector pseudotime

• TRAP5 Inhibition Targeting Scar-Associated Macrophages Ameliorates Acute Kidney Injury to Chronic Kidney Disease Transition.

  PMID 41773735 · PMC13159109 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  A distinct scar-associated macrophage (SM) subset marked by high Acp5/TRAP5, Ctsk, Mmp9, and Spp1 emerges and predominates during the renal remodeling/CKD phase after AAI-induced AKI

  kidney ckd aai unilateral single-cell velocity pseudotime

• Single-Cell Sequencing of iPSC-Dopamine Neurons Reconstructs Disease Progression and Identifies HDAC4 as a Regulator of Parkinson Cell Phenotypes.

  PMID 30503143 · PMC6327112 · Cell stem cell · 2019 · 8 claims · 8 setups

  Has reproduction · 30

  Single-cell transcriptomic analysis of GBA-N370S iPSC-derived dopamine neurons identifies a progressive axis of gene expression variation leading to endoplasmic reticulum stress.

  facs-purified ipsc-derived core bulk single-cell facs

• Bulk and single-cell characterisation of the immune heterogeneity of atherosclerosis identifies novel targets for immunotherapy.

  PMID 36855107 · PMC9974063 · BMC biology · 2023 · 8 claims · 8 setups

  Has reproduction · 70

  Integration of scRNA-seq datasets from human atherosclerosis samples identifies 28 distinct immune cell subpopulations with heterogeneity in tissue preference, genetics, function, immune dynamics, transcriptional regulators, metabolism, and cell communication.

  immune atherosclerotic cd4+ cd8+ scrna-seq gsea pseudotime

• Single cell analysis reveals the roles and regulatory mechanisms of type-I interferons in Parkinson's disease.

  PMID 38566100 · PMC10985960 · Cell communication and signaling : CCS · 2024 · 8 claims · 8 setups

  Has reproduction · 55

  Microglia, endothelial cells, and pericytes exhibit the highest IFN-I activity among PD midbrain cell types, with microglia and endothelial cells showing significantly elevated high-IFN-I-scoring proportions in PD versus controls

  midbrain single microglia substantia single-cell scenic monocle

• Dynamics and regulation of mitotic chromatin accessibility bookmarking at single-cell resolution.

  PMID 36696508 · PMC9876548 · Science advances · 2023 · 7 claims · 8 setups

  Has reproduction · 50

  Chromatin accessibility continually decreases from mitotic entry until metaphase, then gradually increases as chromosomes segregate.

  l02 tissues hepatoma scatac-seq immunofluorescence atac-see

• Unraveling the timeline of gene expression: A pseudotemporal trajectory analysis of single-cell RNA sequencing data.

  PMID 37994351 · PMC10663991 · F1000Research · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  A comprehensive open-source R workflow combining trajectory inference (monocle3) and pseudo-bulk time course analysis (edgeR) can be applied to multi-sample scRNA-seq data of the mouse mammary gland.

  mammary aggregated single-cell quality doublet

• Deciphering the Immune Microenvironment at the Forefront of Tumor Aggressiveness by Constructing a Regulatory Network with Single-Cell and Spatial Transcriptomic Data.

  PMID 38254989 · PMC10815467 · Genes · 2024 · 7 claims · 8 setups

  Has reproduction · 85

  High expression of transcription factors FOXA1 and EZH2 in malignant cells at the invasive front plays a key role in driving tumor progression

  breast er+ epithelial malignant scrna-seq spatial copy

• The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.

  PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups

  Has reproduction · 50

  Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.

  blood merged deg microarray coconut pseudotime

• Single-Cell Transcriptomic Landscape of Right-Sided Colon Cancer Reveals Cellular and Molecular Features of Metastatic Potential.

  PMID 41898210 · PMC13024220 · Biomedicines · 2026 · 8 claims · 6 setups

  Has reproduction · 71

  RCC_LM tumors exhibit higher genomic instability (CNV score) than RCC_noM tumors

  right-sided malignant epithelial types scrna-seq copy trajectory