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).

• Multi-omic identification of key transcriptional regulatory programs during endurance exercise training in rats.

  PMID 41862462 · PMC13168590 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  Gene regulatory responses to endurance exercise training (EET) are predominantly tissue-specific rather than shared across tissues

  tissues same skm-gn rna-seq atac-seq rrbs

• TBP regulates transposable element expression in early mouse embryos.

  PMID 41862641 · PMC13144441 · The EMBO journal · 2026 · 8 claims · 6 setups

  Full-text index only

  The general transcription factor TBP binds and activates MaLR transposable elements in mouse embryos

  single embryos computational embryonic rna-seq atac-seq motif

• AP-1 mediates cellular adaptation and memory formation.

  PMID 41862498 · PMC13168276 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  Cancer cells form and maintain cellular memories when becoming drug resistant, exhibiting cellular learning dependent on the transcription factor AP-1

  wm989 h2b-gfp h358 rna-seq atac-seq colony

• Single-nucleus ATAC-seq analysis resolves chromatin and transcriptional features of fibrolamellar carcinoma.

  PMID 41865105 · PMC13144680 · Scientific reports · 2026 · 8 claims · 5 setups

  Full-text index only

  snATAC-seq resolves cell-type specific chromatin accessibility, microRNA activity, transcription factor networks, and super enhancer usage in FLC tumors versus non-malignant liver (NML).

  flc bulk snatac-seq snrna-seq single-nucleus bulk motif

• TOPK Suppresses the CD8(+) T Cell Antitumor Immunity via Modulation of IRF5 Expression.

  PMID 41868885 · PMC13003159 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  A TOPK+ subset of tumor-infiltrating CD8+ T cells exists in melanoma at higher frequency than in normal lymph nodes and shows suppressed cytotoxic/cytokine programs.

  tumor-infiltrating melanoma b16-f10 unspecified scrna-seq flow multiplex

• Evaluating the Utilities of Foundation Models in Single-Cell Data Analysis.

  PMID 41869863 · PMC13170260 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

  Full-text index only

  Among ten/eleven evaluated single-cell FMs, scGPT, Geneformer, and CellFM are the top models considering both performance and user accessibility

  scrna-seq unpaired single-cell scgpt batch multi-omic cell-type

• Dynamic changes of the immune microenvironment in ovarian cancer following neoadjuvant chemotherapy.

  PMID 41872134 · PMC13039919 · Cell death discovery · 2026 · 8 claims · 8 setups

  Full-text index only

  Prostaglandin-mediated immunosuppressive microenvironment formation is a critical contributor to chemotherapy resistance following cisplatin treatment

  high-grade hgsoc bone bmdms scrna-seq cell-cell tensor

• Interpretable learning of temporal cellular dynamics from single-cell data.

  PMID 41875867 · PMC13030976 · Cell reports methods · 2026 · 7 claims · 7 setups

  Full-text index only

  NeuroVelo couples a linear latent phase-space projection with a non-linear neural ODE, using RNA velocity as a physics-informed loss penalty, to jointly model cellular dynamics and enable gene-level interpretability

  gastrulation bone pancreatic cancer scrna-seq chip-seq computational

• Comparative analysis of nuclei isolation methods for brain single-nucleus RNA sequencing.

  PMID 41875869 · PMC13030979 · Cell reports methods · 2026 · 8 claims · 8 setups

  Full-text index only

  Nuclei isolation protocol is a critical experimental variable shaping snRNA-seq data quality and biological interpretation

  cortex brain cortical snrna-seq snrna-seq bright-field nuclei

• Transcription elongation can be sufficient, but is not necessary, to advance replication timing.

  PMID 41876817 · PMC13121604 · EMBO reports · 2026 · 8 claims · 5 setups

  Full-text index only

  Transcriptional elongation can causally advance RT in a rate-dependent and context-specific manner

  musculus same tre-ptn mesc repli-seq bru-seq genome-wide

• Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

  PMID 41877584 · PMC13103941 · Cancer research communications · 2026 · 8 claims · 6 setups

  Full-text index only

  Skp2 KO improves survival, drives apoptosis, and induces antitumor immunity in Rb1/Trp53-deficient murine osteosarcoma

  tumors same osteosarcoma skp2 scrna-seq mutation copy-number

• Reprogramming of stroma-derived chemokine networks drives the loss of tissue organization in nodal B cell lymphoma.

  PMID 41882179 · PMC13035477 · Nature cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  LN-resident stromal cells (FRCs, BECs, LECs) drive chemokine-based lymphocyte zonation, and disruption of this system underlies the loss of tissue organization in nodal B cell lymphoma

  rln healthy bulk fl-ln scrna-seq multiplex bulk

• NeMO Analytics: a compendium of transcriptomic data for the exploration of neocortical development.

  PMID 41882195 · PMC13061640 · Nature neuroscience · 2026 · 8 claims · 8 setups

  Full-text index only

  NeMO Analytics is a curated compendium assembling gene-level transcriptomic (and other multiomic) data from ~200 studies of neocortical development and in vitro models for interrogation by non-coding biologists

  midgestational macaque fetal radial scrna-seq bulk spatial

• GRNFormer: accurate gene regulatory network inference using graph transformer.

  PMID 41883144 · PMC13069479 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

  Full-text index only

  GRNFormer is a generalizable graph transformer framework for GRN inference from single-cell or bulk transcriptomics data across species, cell types, and platforms without cell-type annotations or prior regulatory information

  hematopoietic embryonic dendritic hepatocytes scrna-seq chip-seq string

• A unique malignant cell type per patient tumor encoded in each cancer cell transcriptome.

  PMID 41884004 · PMC13010111 · iScience · 2026 · 8 claims · 8 setups

  Full-text index only

  Malignant cells cluster predominantly by tumor of origin, while non-malignant cells from the same tumors cluster by cell type independent of patient

  malignant non-malignant ovarian normal scrna-seq alternative paired

• A Single-Cell Atlas of Pan-Cancer Liver Metastasis Reveals Dynamic Cellular Programs Driving Metastatic Progression and Immune Modulation.

  PMID 41884334 · PMC13010057 · Research (Washington, D.C.) · 2026 · 8 claims · 4 setups

  Full-text index only

  A pan-cancer single-cell transcriptomic atlas of liver metastasis was constructed from 100 scRNA-seq samples (75 individuals, 16 studies), profiling 460,337 cells into 121 distinct cellular subtypes.

  epithelial liver-related scrna-seq copy cellular

• Deconvolving cell-type-specific gene expression profiles from bulk RNA-seq samples.

  PMID 41886524 · PMC13038110 · PLoS computational biology · 2026 · 8 claims · 6 setups

  Full-text index only

  BLUE, a U-Net-based deep learning model with dual branches (U-Net for GEPs, MLP for proportions), accurately predicts cell-type proportions and cell-type-specific gene expression profiles from bulk RNA-seq.

  pbmc pancreatic aml scrna-seq-derived real scrna-seq

• CAR-M2 immunotherapy resolves renal fibrosis via revascularization and apoptosis of profibrotic Cxcr2(+) endothelial cells.

  PMID 41887221 · PMC13130657 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

  Full-text index only

  CAR-M2 macrophages (anti-FAP CAR + IL-4-secreting, 4-1BB/CD3ζ costimulatory domains) specifically target and phagocytose FAP+ fibroblasts

  kidney car-m2 macrophages uuo scrna-seq histology live-cell

• A metrological foundation for absolute transcriptomics using International System of Units-anchored calibrators.

  PMID 41888124 · PMC13022412 · Nature communications · 2026 · 8 claims · 5 setups

  Full-text index only

  TranScale is a set of 100 biomimetic RNA spike-in standards with SI-traceable certified copy-number concentrations (via isotope dilution mass spectrometry) that anchor RNA-seq measurements to an absolute scale.

  transcale biological isotope rt-dpcr bulk

• Integrating single-cell and single-nucleus datasets improves bulk RNA-seq deconvolution.

  PMID 41895263 · PMC13106970 · Cell reports methods · 2026 · 8 claims · 5 setups

  Full-text index only

  scRNA-seq references yield significantly higher Pearson correlation and lower RMSE than snRNA-seq references for deconvolution across all four tissue datasets

  adipose same fat-cell real pseudobulk single-cell synthetic