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

• 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

• Long-term trends in evolution of indels in protein sequences.

  PMID 17298668 · PMC1805498 · BMC evolutionary biology · 2007 · 8 claims · 5 setups

  Full-text index only

  More than one third of protein domains show a statistically significant tendency to increase or decrease in size over evolutionary distance.

  curated individual cdd linear pearson binomial

• MEROPS: the peptidase database.

  PMID 19892822 · PMC2808883 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  MEROPS is a manually curated hierarchical classification of peptidases and protein inhibitors organized into protein species, families, and clans based on sequence and structural homology.

  archaean holotype c-x-c proteins comparative domain substrate

• nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

  PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

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  nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

  curated homologous structure random structural secondary

• Target identification for repurposed drugs active against SARS-CoV-2 via high-throughput inverse docking.

  PMID 34825285 · PMC8616721 · Journal of computer-aided molecular design · 2022 · 8 claims · 6 setups

  Has reproduction · 63

  Combining Vinardo, Ledock, and Korp-PL scoring functions (via averaged Z-scores) improves correct target identification over any single scoring function.

  curated repurposed glycosylated interior inverse molecular exploratory

• Towards alignment independent quantitative assessment of homology detection.

  PMID 17205117 · PMC1762415 · PloS one · 2006 · 8 claims · 6 setups

  Full-text index only

  The Fhom Estimator uses the prevalence of a conserved protein feature (X) in two protein sets to estimate the fraction of true homologs among paired proteins, independent of alignment quality.

  curated homologene swiss-prot fruit signalp homologene-based fhom

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

• 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

• GOLD.db: genomics of lipid-associated disorders database.

  PMID 15588328 · PMC544894 · BMC genomics · 2004 · 8 claims · 4 setups

  Full-text index only

  GOLD.db integrates annotated pathways, gene/protein reference information, and curated gene expression datasets for lipid-associated disorders research

  adipocyte adipose-specific 3t3-l1 gene curated whole-body insulin

• Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

  PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  Current syndromic disease classification lacks specificity despite historically serving clinicians well

  prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene

• In silico analysis of missense substitutions using sequence-alignment based methods.

  PMID 18951440 · PMC3431198 · Human mutation · 2008 · 8 claims · 7 setups

  Full-text index only

  Carefully validated PMSA-based computational algorithms can achieve predictive values of ~75-95% for classifying missense substitutions as pathogenic or neutral.

  clinically sequence curated deep blosum62 sift align-gvgd

• A comprehensive modular map of molecular interactions in RB/E2F pathway.

  PMID 18319725 · PMC2290939 · Molecular systems biology · 2008 · 8 claims · 4 setups

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  A comprehensive, curated map of RB/E2F pathway molecular interactions was built using SBGN notation in CellDesigner and converted to BioPAX 2.0 format

  bladder computational curated literature transcriptome gene network

• Gene Expression Atlas update--a value-added database of microarray and sequencing-based functional genomics experiments.

  PMID 22064864 · PMC3245177 · Nucleic acids research · 2012 · 8 claims · 5 setups

  Has reproduction · 83

  Gene Expression Atlas is an added-value database providing curated, re-annotated and statistically analysed gene expression data across cell types, organism parts, developmental stages, disease states and other biological/experimental conditions, derived from ArrayExpress Archive and the European Nucleotide Archive.

  species microrna atlas microarray rna-seq microrna

• Computational modeling demonstrates that glioblastoma cells can survive spatial environmental challenges through exploratory adaptation.

  PMID 31836713 · PMC6911112 · Nature communications · 2019 · 8 claims · 6 setups

  Has reproduction · 100

  Stochastic exploration of the gene-regulatory network structure confers enhanced adaptive capacity, enabling GBM cells to converge to new target phenotypes in novel environments.

  gbm glioma gbm-focused glioma-related transcriptomic differential gene-regulatory

• Intratumoral heterogeneity in microsatellite instability status at single-cell resolution.

  PMID 41767255 · PMC12936829 · iScience · 2026 · 8 claims · 8 setups

  Has reproduction · 100

  MSI status can be heterogeneous at the single-cell level within a tumor, challenging its use as a binary biomarker

  cancer aggregate single-cell homogeneously single-cell msi cancer

• 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

• Sequence similarity network reveals common ancestry of multidomain proteins.

  PMID 18475320 · PMC2377100 · PLoS computational biology · 2008 · 8 claims · 6 setups

  Full-text index only

  Traditional homology definitions do not capture multidomain evolution; the authors extend the definition to include domain insertion via a common ancestral locus model.

  curated complete well-studied sequence alignment domain

• Bioinformatics Strategies to Identify Shared Molecular Biomarkers That Link Ischemic Stroke and Moyamoya Disease with Glioblastoma.

  PMID 36015199 · PMC9413912 · Pharmaceutics · 2022 · 8 claims · 8 setups

  Has reproduction · 19

  Shared differentially expressed genes link glioblastoma with ischemic stroke and with moyamoya disease, revealing molecular associations among the diseases.

  glioblastoma ischemic moyamoya shared bulk microarray gene

• Advances in genomic and pharmacokinetic profiling for clinical stratification of metastatic breast cancer.

  PMID 41369820 · PMC12799884 · Discover oncology · 2025 · 7 claims · 8 setups

  Has reproduction · 59

  Eight gene modules linked to metastasis were identified via scored network analysis and validated through pathway databases.

  metastatic tcga-brca homo gse40622 gene bulk rt-pcr