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).

• Assessment tool based on fatty acid metabolic signatures for predicting the prognosis and treatment response in bladder cancer.

  PMID 38076064 · PMC10703629 · Heliyon · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  Consensus clustering of prognosis-related fatty acid metabolism genes (FAMGs) identifies three molecular subtypes of BLCA (FAMC1, FAMC2, FAMC3) with distinct prognoses and tumor microenvironments

  tcga-blca famc1-3 differentially gse32894 bulk consensus gene

• NetworKIN: a resource for exploring cellular phosphorylation networks.

  PMID 17981841 · PMC2238868 · Nucleic acids research · 2008 · 8 claims · 4 setups

  Full-text index only

  NetworKIN integrates consensus substrate motifs with probabilistic network context modelling to predict cellular kinase-substrate relations.

  phosphoproteome kinome interactome 53bp1 consensus blastp probabilistic

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• A network-guided protocol to discover susceptibility genes in genome-wide association studies using stability selection.

  PMID 36609152 · PMC9850185 · STAR protocols · 2023 · 5 claims · 5 setups

  Has reproduction · 92

  The protocol identifies genes that are both statistically associated with a phenotype and functionally interconnected in a biological network

  case-control gene-gene fictional familial snp-phenotype gene-level network-guided

• Mutation analysis of the AATF gene in breast cancer families.

  PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

  Full-text index only

  No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

  genomic showing aatf case conformation direct pathogenicity

• TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates.

  PMID 17986453 · PMC2238949 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  TranspoGene catalogs TEs within protein-coding genes of seven species (human, mouse, chicken, zebrafish, fruit fly, nematode, sea squirt), classified as proximal promoter, exonized, exonic, or intronic TEs.

  chicken normal tes genes genomic exon microrna

• Metabolic reprogramming and prognostic insights in molecular landscapes driven by glycolysis in ovarian cancer.

  PMID 40707588 · PMC12290113 · Scientific reports · 2025 · 7 claims · 8 setups

  Has reproduction · 77

  457 differentially expressed GRGs were identified between OC and normal ovarian tissue, of which 30 were significantly associated with prognosis

  tcga-oc tcga-oc-gse26193 ov_gse154600 iose-80 bulk univariate copy

• Haplotype analysis of common variants in the BRCA1 gene and risk of sporadic breast cancer.

  PMID 15743496 · PMC1064127 · Breast cancer research : BCR · 2005 · 7 claims · 5 setups

  Full-text index only

  A common BRCA1 haplotype (haplotype 2, C A G G) is associated with a modest increase in sporadic breast cancer risk

  individuals nested same nurses whole-gene snp statistical

• Mutation analysis of the ATR gene in breast and ovarian cancer families.

  PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

  Full-text index only

  ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

  index atr variant mutation direct variant

• RAId_DbS: mass-spectrometry based peptide identification web server with knowledge integration.

  PMID 18954448 · PMC2605478 · BMC genomics · 2008 · 7 claims · 4 setups

  Full-text index only

  Constructed enhanced protein databases integrating annotated SAPs, PTMs, and disease associations for 17 organisms.

  consensus sap query all-against-all blast cross-database

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

  Has reproduction · 94

  ~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

  tuberosum orthologous identified de-novo genome-wide transcriptional

• Characterization of 954 bovine full-CDS cDNA sequences.

  PMID 16305752 · PMC1314900 · BMC genomics · 2005 · 7 claims · 8 setups

  Full-text index only

  954 bovine full-length insert cDNA (bFLIC) clones representing 762 distinct loci were sequenced and characterized

  bovine translated bflic sequence est primer-walking blastp

• Identification and characterization of HLA-A*0301 epitopes in HIV-1 gag proteins using a novel approach.

  PMID 19903485 · PMC2836169 · Journal of immunological methods · 2010 · 7 claims · 7 setups

  Full-text index only

  PS mutations V7I and I34L (p17) and K403R (p7) in HIV-1 gag significantly correlate with HLA-A*0301

  hiv-1-infected genomic hiv-1 hla-a*0301 statistical pcr gag

• Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

  PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

  Full-text index only

  FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

  cerevisiae elegans randomized computational randomized microarray

• Automatic discovery of cross-family sequence features associated with protein function.

  PMID 16409628 · PMC1395344 · BMC bioinformatics · 2006 · 8 claims · 6 setups

  Full-text index only

  A self-supervised data mining approach can find relationships between sequence features and functional annotations without preconceived functional categories.

  non-redundant same evolved eukaryotic self-supervised experiment self-organizing