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).

• Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients.

  PMID 34421903 · PMC8375662 · Frontiers in immunology · 2021 · 8 claims · 8 setups

  Has reproduction · 71

  TB patients show substantial individual variability in the intensity of hallmark IFN responses, as well as in complement system, metabolic, and other pathway responses.

  blood cynomolgus external gene differential principal

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Comparative analysis of molecular signatures reveals a hybrid approach in breast cancer: Combining the Nottingham Prognostic Index with gene expressions into a hybrid signature.

  PMID 35143511 · PMC8830616 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 48

  A hybrid signature combining the Nottingham Prognostic Index with SIS-selected gene expressions can be built in a data-driven fashion (NPI treated as a gene expression during feature selection).

  metabric scan-b gene rna-seq feature

• Integrative analysis of transcriptomic data reveals a predictive gene signature for chemoradiotherapy response in rectal cancer.

  PMID 41550766 · PMC12803930 · iScience · 2026 · 8 claims · 5 setups

  Has reproduction · 50

  A 186-gene signature derived from six GEO transcriptomic datasets predicts nCRT response in LARC with AUC 0.80 in cross-validation

  pre-treatment domingo geo bulk bulk external spatial

• Gene-expression patterns in peripheral blood classify familial breast cancer susceptibility.

  PMID 26538066 · PMC4634735 · BMC medical genomics · 2015 · 8 claims · 5 setups

  Has reproduction · 83

  A multigene peripheral-blood gene-expression biomarker accurately classifies which women from high-risk families develop familial breast cancer.

  peripheral pbmcs blood normal gene-expression lymphocyte gene

• Integrating alternative splicing detection into gene prediction.

  PMID 15705189 · PMC550657 · BMC bioinformatics · 2005 · 8 claims · 4 setups

  Full-text index only

  An integrative intrinsic/extrinsic method was implemented in the gene finder EuGÈNE (as EuGÈNE-M) to detect AS evidence from aligned transcripts and generate alternative optimal gene predictions consistent with each detected AS event.

  arabidopsis araset thaliana transcript-to-genome initio comparative

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

  Full-text index only

  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• Reconstruction of pathways associated with amino acid metabolism in human mitochondria.

  PMID 18267298 · PMC5054205 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 5 setups

  Full-text index only

  Out of 20 amino acids, the metabolic pathways of 17 utilize mitochondrial enzymes, and dysfunction of these enzymes causes over 40 known human mitochondrial diseases/disorders

  mitoproteome orthologous liver mitochondrial sequence-based computational literature

• 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

• BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

  PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

  Full-text index only

  BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

  biogps diverse tissues specified web reference exon

• VectorBase: a home for invertebrate vectors of human pathogens.

  PMID 17145709 · PMC1751530 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens

  anopheles aedes translated automated first-pass