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).

• SMAC, a computational system to link literature, biomedical and expression data.

  PMID 31324861 · PMC6642118 · Scientific reports · 2019 · 7 claims · 6 setups

  Has reproduction · 50

  SMAC is a tool that extracts, prioritises, integrates and analyses biomedical literature and molecular data according to user-defined terms, linking PubMed and GEO.

  pubmed invasive geo cancer semantic computational gene

• Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.

  PMID 41282419 · PMC12636342 · Computational and structural biotechnology journal · 2025 · 6 claims · 4 setups

  Has reproduction · 83

  POE is a web platform that semantically links GEO datasets and ENA records through their associated PubMed publications for literature-informed dataset retrieval

  pubmed natural-language representative semantic comparative qualitative

• A metadata approach for clinical data management in translational genomics studies in breast cancer.

  PMID 19948017 · PMC3225860 · BMC medical genomics · 2009 · 8 claims · 5 setups

  Full-text index only

  A metadata/CDE-based approach using CancerGrid's semantic web tools enables automatic integration of heterogeneous clinical datasets without loss of original detail

  clinical breast metadata estrogen her2

• Visualizing the genome: techniques for presenting human genome data and annotations.

  PMID 12149135 · PMC119855 · BMC bioinformatics · 2002 · 8 claims · 4 setups

  Full-text index only

  Web-based client-server genome browsers (e.g., LocusLink evidence viewer, UCSC genome browser) are limited by lack of true interactivity, requiring server round-trips for navigation

  flj22324 snurf arg1 plat cdna-to-genomic multi-track frame-of-translation

• The biological function of some human transcription factor binding motifs varies with position relative to the transcription start site.

  PMID 18367472 · PMC2377430 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  1226 eight-letter DNA words show statistically significant positional preferences relative to the TSS across 7914 human promoter regions

  putative nonredundant homo genes computational pssm semantic

• Tracing truth: dynamic temporal networks for multi-modal fake news detection.

  PMID 40989433 · PMC12453775 · PeerJ. Computer science · 2025 · 8 claims · 5 setups

  Has reproduction · 33

  The proposed dynamic temporal network (DTN) model improves multi-modal fake news detection accuracy by capturing temporal dynamics of propagation nodes and dynamically fusing multi-modal information.

  news news-related users social text image social

• Cross-species comparative hippocampal transcriptomics in Alzheimer's disease.

  PMID 38292167 · PMC10824791 · iScience · 2024 · 8 claims · 7 setups

  Has reproduction · 75

  All three mouse models (hAβ-KI, 5xFAD, APP/PS1) share more differentially expressed genes, GO biological processes, and KEGG pathways with LOAD than with EOAD patients.

  haβ-ki models degs app bulk functional master