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).

• SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

  PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

  Full-text index only

  SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

  msi-h aggregated genome mnr sigmoid genome-wide

• An analysis of human microRNA and disease associations.

  PMID 18923704 · PMC2559869 · PloS one · 2008 · 8 claims · 8 setups

  Full-text index only

  MicroRNAs tend to show similar dysfunctional evidence (both up- or both down-regulated) for diseases within the same disease cluster, and different dysfunctional evidence between different disease clusters.

  literature-derived diseases mirnas mirna literature bipartite mirna

• Seeded Bayesian Networks: constructing genetic networks from microarray data.

  PMID 18601736 · PMC2474592 · BMC systems biology · 2008 · 8 claims · 4 setups

  Full-text index only

  Seeding Bayesian Network analysis with prior networks derived from literature and/or PPI data improves recovery of known gene-gene interactions compared to BN analysis without a seed

  leukemia interactome pubmed-indexed computational microarray yeast literature

• What can genome-wide association studies tell us about the genetics of common disease?

  PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

  Full-text index only

  Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

  case gwa simulated literature cochran-armitage computer

• Biased exon/intron distribution of cryptic and de novo 3' splice sites.

  PMID 16141195 · PMC1197134 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  Cryptic 3'ss (from 3'YAG consensus mutations) are significantly more frequent in exons than in introns

  disease authentic hek293t nuclear literature shapiro-senapathy splicing

• A biomedically enriched collection of 7000 human ORF clones.

  PMID 18231609 · PMC2211400 · PloS one · 2008 · 8 claims · 4 setups

  Full-text index only

  Produced and made available over 7000 fully sequence-verified plasmid ORF clones representing over 3400 unique human genes, in both closed (stop codon) and fusion (no stop codon) formats.

  genes mgc plasmid literature pcr sequence

• Integrative network modeling reveals mechanisms underlying T cell exhaustion.

  PMID 32024856 · PMC7002445 · Scientific reports · 2020 · 8 claims · 6 setups

  Has reproduction · 59

  An integrative, literature-curated and data-driven gene regulatory network underlies CD8+ T cell exhaustion and accurately captures expression states in chronic infection and tumor settings.

  cd8+ tce activated manual gene principal

• A global database for modeling tumor-immune cell communication.

  PMID 37438390 · PMC10338499 · Scientific data · 2023 · 7 claims · 6 setups

  Has reproduction · 66

  TICCom integrates 739 experimentally-validated or manually-curated TIC interactions collected from more than 3,000 literatures

  pubmed scrna-seq tcga basal manual scrna-seq bulk

• A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

  PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

  Full-text index only

  mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

  nonredundant database high-throughput homology

• Systematic review of human post-mortem immunohistochemical studies and bioinformatics analyses unveil the complexity of astrocyte reaction in Alzheimer's disease.

  PMID 34297416 · PMC8766893 · Neuropathology and applied neurobiology · 2022 · 8 claims · 5 setups

  Has reproduction · 92

  Systematic review of 306 eligible articles identified 196 distinct proteins constituting the ADRA (AD reactive astrocyte) protein set

  post-mortem adra immunohistochemistry protein-protein pathway

• Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

  PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

  Full-text index only

  Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

  egfr tp53 laci lung literature comparative statistical

• Comparative Toxicogenomics Database: a knowledgebase and discovery tool for chemical-gene-disease networks.

  PMID 18782832 · PMC2686584 · Nucleic acids research · 2009 · 8 claims · 5 setups

  Full-text index only

  CTD is a manually curated knowledgebase that integrates chemical-gene interactions, chemical-disease relationships, and gene-disease relationships into a chemical-gene-disease triad

  pubmed ctd manual computational case-study

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

  Full-text index only

  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• The Universal Protein Resource (UniProt) in 2010.

  PMID 19843607 · PMC2808944 · Nucleic acids research · 2010 · 8 claims · 5 setups

  Full-text index only

  UniProt is a centralized, freely accessible, comprehensive knowledgebase of protein sequence and functional annotation maintained by the EBI, SIB and PIR consortium.

  uniprotkb oceanic proteome manual automated sequence

• GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets.

  PMID 40208796 · PMC11984350 · GigaScience · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  GeneSetCart is a web-based platform that lets users assemble, augment, combine, visualize, and analyze gene sets from multiple sources in one place

  user-assembled archs4 generif-derived aggregated gene gene-gene literature

• Analysis of nucleotide diversity of NAT2 coding region reveals homogeneity across Native American populations and high intra-population diversity.

  PMID 16847467 · PMC3099416 · The pharmacogenomics journal · 2007 · 8 claims · 6 setups

  Full-text index only

  NAT2 variants are homogeneously distributed across native populations of the American continent

  chromosomes same inferred american pcr statistical haplotype

• The Edinburgh human metabolic network reconstruction and its functional analysis.

  PMID 17882155 · PMC2013923 · Molecular systems biology · 2007 · 8 claims · 7 setups

  Full-text index only

  EHMN is a high-quality, manually curated human metabolic network combining genome-based and literature-based (EMP) reconstruction, containing nearly 3000 reactions and over 2000 metabolic genes.

  enzyme emp kegg humancyc genome literature-based comparative

• Public health genomics: translating obesity genomics research into population health benefits.

  PMID 19037221 · PMC2736102 · Obesity (Silver Spring, Md.) · 2008 · 8 claims · 6 setups

  Full-text index only

  Obesity genomics research is mostly in the discovery phase (T1); a four-phase translational framework (T1-T4) is needed to move discoveries to population health impact

  populations white mice humans genetic pharmacogenetic gene-by-environment

• Sys-BodyFluid: a systematical database for human body fluid proteome research.

  PMID 18978022 · PMC2686600 · Nucleic acids research · 2009 · 6 claims · 4 setups

  Full-text index only

  Sys-BodyFluid is a web-based database integrating proteomic data from 11 human body fluids (plasma/serum, urine, cerebrospinal fluid, saliva, bronchoalveolar lavage fluid, synovial fluid, nipple aspirate fluid, tear fluid, seminal fluid, milk, amniotic fluid), containing over 10,000 proteins

  body curated proteins literature sequence cross-body-fluid

• Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

  PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

  Full-text index only

  A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

  ebv-transformed serum combined rf-filtered snp serum random