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).

• Transcriptomic profiling of skeletal muscle adaptations to exercise and inactivity.

  PMID 31980607 · PMC6981202 · Nature communications · 2020 · 8 claims · 8 setups

  Has reproduction · 52

  MetaMEx integrates transcriptomic data from 66 published human skeletal muscle studies (>1100 individuals) into an online meta-analysis resource (www.metamex.eu)

  skeletal pooled transcriptomic principal qpcr

• Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

  PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 20

  AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

  ipf common key rats microarray network protein-protein

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal

• TransOrGAN: An Artificial Intelligence Mapping of Rat Transcriptomic Profiles between Organs, Ages, and Sexes.

  PMID 37200521 · PMC10433534 · Chemical research in toxicology · 2023 · 8 claims · 5 setups

  Has reproduction · 84

  TransOrGAN can infer transcriptomic profiles between any 2 of 9 rat organs with an average cosine similarity of 0.984 versus real profiles

  fischer computational transcriptomic same bulk gan-based autoencoder

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 50

  A 186-gene signature predictive of nCRT response was derived from integrating six GEO transcriptomic datasets using machine learning.

  pre-treatment combined larc 186-gene differential machine molecular

• A systems-level analysis of the mutually antagonistic roles of RKIP and BACH1 in dynamics of cancer cell plasticity.

  PMID 37963558 · PMC10645512 · Journal of the Royal Society, Interface · 2023 · 8 claims · 7 setups

  Has reproduction · 95

  RKIP and BACH1 are negatively correlated with each other across most cancer types in TCGA

  tcga er+ ccle computational spearman correlation gene

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Pharmacogenomic screening identifies and repurposes leucovorin and dyclonine as pro-oligodendrogenic compounds in brain repair.

  PMID 39537633 · PMC11561360 · Nature communications · 2024 · 8 claims · 8 setups

  Full-text index only

  A pharmacogenomic scoring strategy (OligoScore) combining transcriptomic signatures and curated oligodendrogenesis gene sets identifies compounds with pro-oligodendrogenic transcriptional activity

  brain neonatal gene cerebellar bulk transcriptomic pharmacogenomic

• Spatially resolved integrative analysis of transcriptomic and metabolomic changes in tissue injury studies.

  PMID 41501078 · PMC12780049 · Nature communications · 2026 · 8 claims · 7 setups

  Full-text index only

  MAGPIE is a computational framework (Snakemake workflow) that co-registers Visium spatial transcriptomics with MSI metabolomics and tissue morphology images from same or consecutive sections

  lung brain publicly rodent spatial desi h&e

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Pan-cancer evaluation of regulated cell death to predict overall survival and immune checkpoint inhibitor response.

  PMID 38538696 · PMC10973470 · NPJ precision oncology · 2024 · 8 claims · 8 setups

  Full-text index only

  RCD score, defined as the sum of ssGSEA scores of 18 RCD signatures, quantifies overall RCD signaling in a sample

  tcga gtex scrna-seq cancer bulk scrna-seq transcriptomic

• mitoXplorer, a visual data mining platform to systematically analyze and visualize mitochondrial expression dynamics and mutations.

  PMID 31799603 · PMC6954439 · Nucleic acids research · 2020 · 5 claims · 5 setups

  Has reproduction · 89

  mitoXplorer integrates transcriptome, proteome, and mutation data with a manually curated mitochondrial interactome of ~1200 genes grouped into 38 mitochondrial processes across four model species.

  rpe-1 trisomic rpe yeast bulk proteomics mitotracker

• Developing a thyroid cancer differentiation state classification system using deep residual networks and metabolic signature profiling.

  PMID 40993300 · PMC12460824 · NPJ digital medicine · 2025 · 8 claims · 8 setups

  Has reproduction

  Metabolic status is closely tied to tumor differentiation state, with distinct metabolic reprogramming occurring during thyroid cancer dedifferentiation

  thyroid fuscc gse193581 aggregated untargeted whole-exome transcriptomics

• Identification of Molecular Subtypes of Clear-Cell Renal Cell Carcinoma in Patient-Derived Xenografts Using Multi-Omics.

  PMID 40282537 · PMC12026142 · Cancers · 2025 · 8 claims · 7 setups

  Full-text index only

  Each ccRCC PDX resembles one of the human molecular subtypes closely at both the transcript and protein levels.

  ccrcc differentially bulk lc-ms targeted

• Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

  PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

  Has reproduction · 64

  Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

  colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry

• Integration of multi-omics and machine learning strategies identifies immune related candidate biomarkers in inflammation-associated hypertrophic cardiomyopathy.

  PMID 41080564 · PMC12510942 · Frontiers in immunology · 2025 · 8 claims · 8 setups

  Has reproduction · 85

  Seven key immune-related genes (RNF165, SNCA, SRGN, MARCO, STEAP4, SIGLEC9, TKT) are associated with HCM by intersecting DEGs with MR-identified eQTLs

  left eqtl degs merged bulk two-sample functional

• Systems spatiotemporal dynamics of traumatic brain injury at single-cell resolution reveals humanin as a therapeutic target.

  PMID 35951114 · PMC9372016 · Cellular and molecular life sciences : CMLS · 2022 · 8 claims · 8 setups

  Has reproduction · 98

  Coordinated gene expression patterns across cell types are disrupted and re-organized by mTBI with distinct regional, cellular, and temporal (24-h vs 7-day) specificity.

  hippocampus frontal peripheral cell-type single-cell svm-based ligand-receptor

• Lipopolysaccharide distinctively alters human microglia transcriptomes to resemble microglia from Alzheimer's disease mouse models.

  PMID 36254682 · PMC9612871 · Disease models & mechanisms · 2022 · 8 claims · 8 setups

  Has reproduction · 100

  iPSC-microglia show a shared core transcriptional response to ATPγS and to LPS+IFN-γ, suggesting a convergent mechanism of action

  ipsc-derived products microglia post-mortem single-cell ca2+ protein-protein