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).

• T Cells With Activated STAT4 Drive the High-Risk Rejection State to Renal Allograft Failure After Kidney Transplantation.

  PMID 35844542 · PMC9283858 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  Unsupervised UMAP/Leiden clustering of 2,611 microarray datasets reveals 6 rejection states that diverge from traditional Banff clinical classification

  kidney scrna-seq microarray meblack microarray single-cell scissor

• Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

  PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 7 claims · 8 setups

  Has reproduction · 71

  Two distinct RNA modification patterns exist among BCa samples with radically different clinical outcomes and biological characteristics.

  bca meta-geo tcga-blca tcga bulk rna-seq somatic

• BiRNA-BERT allows efficient RNA language modeling with adaptive tokenization.

  PMID 41266599 · PMC12635123 · Communications biology · 2025 · 8 claims · 8 setups

  Has reproduction · 50

  BiRNA-BERT uses adaptive dual-tokenization that dynamically selects nucleotide-level (NUC) or byte-pair encoding (BPE) tokens based on input sequence length

  rfam plant lncrna-mirna sequences unsupervised mirna-lncrna length-binned

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

  Full-text index only

  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• Systems Analysis Reveals Ageing-Related Perturbations in Retinoids and Sex Hormones in Alzheimer's and Parkinson's Diseases.

  PMID 34680427 · PMC8533098 · Biomedicines · 2021 · 8 claims · 7 setups

  Has reproduction · 75

  AD and PD patients can be stratified by transcriptomic clustering into three subclasses with distinct gene expression and metabolic profiles

  post-mortem brain zebrafish bulk single-cell unsupervised

• Hierarchical classification-based pan-cancer methylation analysis to classify primary cancer.

  PMID 38066424 · PMC10709847 · BMC bioinformatics · 2023 · 8 claims · 5 setups

  Has reproduction · 83

  CHCT, a hierarchical classification tool, splits classification of 30 cancer types into ten smaller subproblems using a two-tier architecture to classify primary cancer by methylation profile

  cancer clinical training independent methylation upgma random

• Antibiotic Drug screening and Image Characterization Toolbox (A.D.I.C.T.): a robust imaging workflow to monitor antibiotic stress response in bacterial cells in vivo.

  PMID 35707454 · PMC9178280 · F1000Research · 2021 · 8 claims · 6 setups

  Has reproduction · 88

  A.D.I.C.T. provides a robust, reproducible semi-automated imaging workflow for monitoring antibiotic stress response in bacteria in vivo

  shewanella area imagej2 brightfield live-cell shape