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).

• Localized-statistical quantification of human serum proteome associated with type 2 diabetes.

  PMID 18795103 · PMC2529402 · PloS one · 2008 · 8 claims · 5 setups

  Full-text index only

  Developed LSPAD (localized statistics of protein abundance distribution) to calculate statistical significance of protein-abundance bias between two serum cohorts using a local Fisher's exact test window

  pooled computational identified additional label-free lspad pathway-associated

• Exploring Gene Expression Patterns in Alzheimer's Disease Using a Human Microarray Data Meta-Analysis.

  PMID 41744654 · PMC12938635 · Biology · 2026 · 7 claims · 7 setups

  Has reproduction · 100

  A meta-analysis of eight microarray studies (10 sub-studies) produced a combined list of 4218 statistically significant DEGs between AD and healthy brain at an adjP cut-off of 0.001

  post-mortem combined sub-studies down-regulated microarray differential statistical

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.

  PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups

  Has reproduction · 44

  DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection

  nasopharyngeal same dygaf-ranked bulk differential random

• A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

  PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

  Has reproduction · 78

  METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

  microbiome pooled hmp metarep genome assembly-based enzymatic

• 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

• Telomere-to-telomere reference genome for Panax ginseng highlights the evolution of saponin biosynthesis.

  PMID 38883331 · PMC11179851 · Horticulture research · 2024 · 8 claims · 8 setups

  Has reproduction · 92

  A telomere-to-telomere reference genome of P. ginseng was assembled (3.45 Gb, 24 chromosomes, 77266 protein-coding genes)

  panax ginseng whole-genome genome rna-seq