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).

• Methylation patterns of the nasal epigenome of hospitalized SARS-CoV-2 positive patients reveal insights into molecular mechanisms of COVID-19.

  PMID 40170038 · PMC11963311 · BMC medical genomics · 2025 · 7 claims · 7 setups

  Has reproduction

  Differential DNA methylation occurs predominantly in intergenic regions and low methylated regions (LMRs), highlighting the role of distal regulatory elements in COVID-19 severity.

  nasal aggregated genes differentially whole-genome methylation tiling

• Exploiting convergent phenotypes to derive a pan-cancer cisplatin response gene expression signature.

  PMID 37076665 · PMC10115855 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction · 50

  A convergent-phenotype-based seed gene/co-expression method can extract consensus gene expression signatures predictive of response to chemotherapeutic drugs in the GDSC database

  epithelial-based tcga gdsc muscle-invasive differential co-expression signature

• Pathway signatures derived from on-treatment tumor specimens predict response to anti-PD1 blockade in metastatic melanoma.

  PMID 34654806 · PMC8519947 · Nature communications · 2021 · 6 claims · 8 setups

  Has reproduction · 100

  A pathway-based super signature from on-treatment samples (PASS-ON) predicts anti-PD1 response with high accuracy (validation AUC 0.85-0.89, combined AUC 0.88) and outperforms existing signatures across all four datasets.

  metastatic pathway bulk gene elastic-net

• Identification of a pediatric acute hypoxemic respiratory failure signature in peripheral blood leukocytes at 24 hours post-ICU admission with machine learning.

  PMID 37009294 · PMC10063855 · Frontiers in pediatrics · 2023 · 7 claims · 5 setups

  Full-text index only

  A machine learning stability selection approach (bootstrapped logistic regression, 100 simulations) can identify genes associated with PaO2/FiO2 < 200 vs ≥200 when standard differential expression with FDR correction shows no overlap between cohorts.

  pediatric combined top-ranked whole-blood machine pathway

• A single cell characterisation of human embryogenesis identifies pluripotency transitions and putative anterior hypoblast centre.

  PMID 34140473 · PMC8211662 · Nature communications · 2021 · 8 claims · 5 setups

  Has reproduction · 90

  The human post-implantation epiblast transitions from a naïve to a primed pluripotent state, with naïve markers (KLF4, KLF17, PRDM14, etc.) downregulated and primed markers (FGF2, DNMT3B, SOX11, etc.) upregulated between pre- and post-implantation stages

  embryo embryos single-cell logistic immunofluorescence

• Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

  PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  WGCNA identified 214 key genes in the blue module most correlated with LUAD

  tcga-luad merged tedc2-associated a549 wgcna differential machine

• A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

  PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

  Full-text index only

  A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

  cases patients postmortem whole-genome cox linear

• Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

  PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 6 setups

  Has reproduction · 76

  DRW-GM evaluates gene topological importance by directed random walk on a global gene–metabolite pathway graph integrating gene expression and metabolomic profiles to infer pathway activities

  prostate matched gse8511 gene metabolomic pathway

• A urine extracellular vesicle lncRNA classifier for high-grade prostate cancer and increased risk of progression: A multi-center study.

  PMID 37852185 · PMC10591064 · Cell reports. Medicine · 2023 · 8 claims · 8 setups

  Has reproduction · 65

  A 3-lncRNA urine extracellular vesicle classifier (Clnc: AC015987.1, CTD-2589M5.4, RP11-363E6.3) detects high-grade PCa with higher accuracy than PCA3, mpMRI, PCPT-RC 2.0, and ERSPC-RC

  urinary tcga paired urine sequencing lncrna qrt-pcr

• A comprehensive framework for analysis of microRNA sequencing data in metastatic colorectal cancer.

  PMID 35047825 · PMC8759566 · NAR cancer · 2022 · 8 claims · 7 setups

  Has reproduction · 100

  Five miRNAs (Mir-210_3p, Mir-191_5p, Mir-8-P1b_3p, Mir-1307_5p, Mir-155_5p) are up-regulated at multiple metastatic CRC sites compared to primary CRC.

  pcrc same mli ngs mirna bioinformatics differential

• Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

  PMID 18614866 · PMC2654216 · AIDS (London, England) · 2008 · 8 claims · 6 setups

  Full-text index only

  An 8-marker model combining six serum markers, age, and ART experience predicts liver fibrosis stage with an AUROC of 0.904.

  pbmcs liver serum blood microarray liver serum

• Integrative transcriptomic and machine learning framework reveals candidate genes and potential mechanisms of aflatoxin B1 exposure in breast cancer.

  PMID 41688730 · PMC12982753 · Scientific reports · 2026 · 7 claims · 8 setups

  Has reproduction · 83

  170 unique human AFB1 targets were identified by merging ChEMBL, SwissTargetPrediction, and PharmMapper predictions

  afb1 breast training candidate computational bulk weighted

• Meta-analysis of COVID-19 single-cell studies confirms eight key immune responses.

  PMID 34675242 · PMC8531356 · Scientific reports · 2021 · 8 claims · 8 setups

  Has reproduction · 69

  Only 8 of 20 previously published COVID-19 scRNA-seq findings were reproducible across all relevant datasets in a standardized meta-analysis

  pbmc bronchoalveolar nasopharyngeal combined scrna-seq tcr bcr

• Exploration of the omics evidence landscape: adding qualitative labels to predicted protein-protein interactions.

  PMID 17880677 · PMC2375035 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  Combining pairs of omics evidence types into two-dimensional 'evidence landscapes' allows regions to be identified that specifically and purely predict either physical or metabolic protein interactions

  saccharomyces correlated chip-chip gene

• L-Arabinose Alters the E. coli Transcriptome to Favor Biofilm Growth and Enhances Survival During Fluoroquinolone Stress.

  PMID 40732174 · PMC12299780 · Microorganisms · 2025 · 8 claims · 6 setups

  Has reproduction · 74

  L-arabinose increases planktonic growth rate but reduces total growth of E. coli at both 28°C and 37°C

  coli growth crystal colony