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).

• Ex Vivo Immuno-Oncology Platform Reveals Spatial T-cell Infiltration Patterns Linked to ATR Inhibition Responses in High-Grade Serous Ovarian Cancer.

  PMID 41563843 · PMC7618831 · Cancer immunology research · 2026 · 8 claims · 8 setups

  Full-text index only

  iPDCs cultured on human omentum gel (OmGel) recapitulate tumor genomic and histologic characteristics while retaining intratumoral immune cells

  formalin-fixed blood dissociated ipdcs histopathology whole-exome flow

• Small molecule inhibition rescues the skeletal dysplasia phenotype of Trpv4 mutant mice.

  PMID 41574606 · PMC12892883 · JCI insight · 2026 · 8 claims · 8 setups

  Full-text index only

  Chondrocyte-specific (Col2a1-Cre-driven) expression of the p.R594H Trpv4 mutation reproduces the human TRPV4 skeletal dysplasia phenotype in mice, including short stature, long bone and craniofacial abnormalities, and vertebral defects.

  col2a1-cre proximal growth cervical radiography histology rnascope

• Babesia divergens host cell egress is mediated by essential and druggable kinases and proteases.

  PMID 41593365 · PMC12872469 · Nature microbiology · 2026 · 8 claims · 8 setups

  Full-text index only

  PKG, CDPK4, ASP2 and ASP3 mediate distinct sequential steps of B. divergens egress and/or invasion of red blood cells

  divergens flow time-lapse live

• Integrative miRNA-mRNA Network and Molecular Dynamics-Based Identification of Therapeutic Candidates for Paroxysmal Nocturnal Hemoglobinuria.

  PMID 41599741 · PMC12845513 · Pharmaceuticals (Basel, Switzerland) · 2026 · 8 claims · 8 setups

  Full-text index only

  A PIGA-knockout (PIGA-KO) THP-1 cell model was successfully established using CRISPR/Cas9 RNP technology as a PNH model

  thp-1 literature-validated pnh cxcl8 crispr rt-qpcr bulk

• Therapeutic synergies that overcome carboplatin resistance in triple-negative breast cancer.

  PMID 41630032 · PMC13037280 · Journal of experimental & clinical cancer research : CR · 2026 · 8 claims · 8 setups

  Full-text index only

  Four isogenic carboplatin-resistant (CR) PDX pairs (WHIM30, BCM-2147, BCM-3887, BCM-7482) were generated via serial in vivo carboplatin exposure to model acquired resistance in TNBC

  isogenic pdx ffpe carboplatin-resistant bulk single-cell nuclear

• ChromAcS: an automated and flexible GUI for end-to-end reproducible ATAC-seq analysis across multiple species.

  PMID 41639613 · PMC12973882 · BMC bioinformatics · 2026 · 8 claims · 8 setups

  Full-text index only

  ChromAcS is a comprehensive open-source, GUI-based ATAC-seq analysis pipeline supporting multi-species genomes with real-time progress monitoring and modular re-execution.

  pc9 paired-end sorted atac-seq quality read

• Mitochondrial DNA methylation predicts immunotherapy response and prognosis in lung adenocarcinoma: evidence from scRNA-Seq and machine learning.

  PMID 41663976 · PMC12997902 · BMC cancer · 2026 · 8 claims · 8 setups

  Full-text index only

  Differentially expressed MTDM-related genes (DEMTDMRGs) are significantly enriched in cell cycle regulation, ferroptosis, and ABC transporter pathways

  luad demtdmrgs gse131907 wgcna kegg univariate

• Genome-wide discovery and phenotyping of non-coding transcripts in A. fumigatus reveals lncRNAs with a role in antifungal drug sensitivity.

  PMID 41673015 · PMC12921299 · Nature communications · 2026 · 7 claims · 8 setups

  Full-text index only

  Genome-wide pipeline generated a manually curated database of 1089 novel lncRNAs from 2388 candidate loci in A. fumigatus

  fumigatus distinct non-fumigatus niger rna-seq comparative qrt-pcr

• Ribosomal RNA synthesis by RNA polymerase I is subject to premature termination of transcription.

  PMID 41677783 · PMC12900514 · eLife · 2026 · 8 claims · 6 setups

  Full-text index only

  SuperPol (RPA135-F301S) produces 1.5-fold more rRNA than WT Pol I in vivo

  cerevisiae pol pol crac northern

• Multi-omics analyses related to unfolded protein response in prostate cancer implicate pro-tumor role of IFRD1.

  PMID 41694360 · PMC12894258 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Full-text index only

  Luminal prostate epithelial cells, especially the LE-KLK3 subpopulation, show elevated UPR activity compared to other cell types

  pca tcga-prad external scrna-seq bulk immune

• Identification of Poor Prognosis-Associated Fibroblast Subpopulation Signature Genes Utilizing the Scissor Algorithm to Classify Colorectal Cancer Subtypes and Evaluate the Immune Landscape.

  PMID 41787974 · PMC13180509 · Gut and liver · 2026 · 8 claims · 8 setups

  Full-text index only

  Scissor+ fibroblast subpopulations significantly correlated with prognosis were identified in CRC using the Scissor algorithm integrating scRNA-seq, bulk RNA-seq, and clinical data

  tcga gse39582 gse166555 scrna-seq bulk single-cell cell-cell

• Illuminating cell states by a comprehensive and interpretable single cell foundation model.

  PMID 41839876 · PMC13139411 · Nature communications · 2026 · 6 claims · 6 setups

  Full-text index only

  CellVQ, incorporating a Single-Cell Discretization (SCD) module that converts cell embeddings into a discrete 'cell code' via a unified codebook, mitigates data heterogeneity and batch effects while improving interpretability

  pancreas sampled bulk lines scrna-seq type property

• Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity.

  PMID 41842971 · PMC13132380 · The Journal of clinical investigation · 2026 · 8 claims · 8 setups

  Full-text index only

  PRC2i/EZH2i alone or combined with AR inhibitors induce diverse cell state programs (CSPs) that increase tumor cell invasion, metastasis, and drug resistance despite only modest suppression of tumor growth.

  lncap pca pdx clinical viability tumor ic50

• Distinct origins and niches determine the cellular responsiveness of CNS macrophages after repopulation.

  PMID 41851525 · PMC13132723 · Nature immunology · 2026 · 8 claims · 8 setups

  Full-text index only

  Microglia repopulate rapidly and exclusively cell-autonomously from surviving microglia after CSF-1R inhibitor (BLZ945) depletion.

  brain cerebral cd11b+cd45int-hi leptomeninges flow confocal single-cell

• Establishment of a canine urothelial carcinoma-derived organoid biobank: A platform for comparative and translational research.

  PMID 41889014 · PMC13140855 · Clinical and translational medicine · 2026 · 8 claims · 6 setups

  Full-text index only

  Canine urothelial carcinoma closely resembles human muscle-invasive bladder cancer in histopathology, molecular features, biological behavior, metastatic patterns, therapeutic response, and clinical outcome

  canine matched paired urine immunohistochemistry bulk single-nuclei

• pmid-41907410

  PMID 41907410 · PMC13018870 · 8 claims · 8 setups

  Full-text index only

  scRNA-seq of 17 HGSOC tissue samples reveals seven major cell types and extensive intra-tumoral heterogeneity

  hgsoc epithelial tcga gse165897 single-cell copy kegg

• Toxicogenomic response of Pseudomonas aeruginosa to ortho-phenylphenol.

  PMID 18847467 · PMC2577666 · BMC genomics · 2008 · 6 claims · 2 setups

  Full-text index only

  OPP exposure upregulates transcription of ribosomal, virulence, and membrane transport protein genes after both 20 and 60 minutes of treatment.

  pseudomonas growth whole-genome

• Method of regulatory network that can explore protein regulations for disease classification.

  PMID 19962281 · PMC7126395 · Artificial intelligence in medicine · 2010 · 6 claims · 2 setups

  Full-text index only

  A regulatory network (RN) can be constructed as a hopfield-like network, with nodes as biomarkers and directed weighted connections as regulatory relationships, optimized by minimizing an energy function measuring input-output disagreement.

  nasopharyngeal sars seldi-tof-ms

• SeqExpressionAnalyser: An R Package for Automated End-to-End RNA-Seq Analysis From Reads to Differential Expression.

  PMID 41602550 · PMC12833196 · Bioinformatics and biology insights · 2026 · 8 claims · 2 setups

  Full-text index only

  SeqExpressionAnalyser is a novel R package/Shiny web application that provides the first R-based, fully integrated interface for interactive end-to-end RNA-Seq differential gene expression analysis, from FASTQ reads to results.

  escherichia mammary rna-seq

• Integromics: challenges in data integration.

  PMID 12186644 · PMC139396 · Genome biology · 2002 · 8 claims · 7 setups

  Full-text index only

  There is no simple solution to database integration in genomics/bioinformatics

  lines molecular gene monsanto high-throughput cluster-correlation microarray