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).

• Leveraging RNA-seq deconvolution to improve complex in vitro model characterization.

  PMID 40701251 · PMC12391696 · The Journal of biological chemistry · 2025 · 8 claims · 6 setups

  Has reproduction · 67

  RNA-seq deconvolution can predict cell type proportions from bulk RNA-seq using scRNA-seq references, offering a useful characterization tool for CIVMs where single-cell methods are impractical

  intestine rodent duodenal neonatal bulk scrna-seq marker

• Core transcriptional signatures of phase change in the migratory locust.

  PMID 31292921 · PMC6881432 · Protein & cell · 2019 · 8 claims · 7 setups

  Has reproduction · 60

  PhaseCore genes defined by AC-PCA contribution to phase differentiation predict phase status with >87.5% accuracy

  locusta integrated bulk rnai computational

• Decoding and reconstructing disease relations between dry eye and depression: a multimodal investigation comprising meta-analysis, genetic pathways and Mendelian randomization.

  PMID 38548265 · PMC11954816 · Journal of advanced research · 2025 · 7 claims · 8 setups

  Has reproduction · 79

  Meta-analysis confirms a positive bidirectional association between DED and DEP (DED patients have increased DEP prevalence and vice versa).

  studies taiwan twb ded meta-analysis genome-wide conditional

• Filling gaps in PPAR-alpha signaling through comparative nutrigenomics analysis.

  PMID 20003344 · PMC2801700 · BMC genomics · 2009 · 7 claims · 8 setups

  Full-text index only

  Meta-analysis of 16 microarray datasets across human, mouse, rat and yeast identifies 164 genes (MDEGs) consistently differentially expressed in response to high fat diet or PPAR signaling perturbation.

  liver saccharomyces mdeg independent microarray transcription chromosomal

• Macrophages on the run: Exercise balances macrophage polarization for improved health.

  PMID 39476967 · PMC11585839 · Molecular metabolism · 2024 · 8 claims · 7 setups

  Has reproduction · 81

  Immediate/acute exercise triggers an M1 (pro-inflammatory) macrophage polarization surge.

  gene affymetrix pooled muscle meta-analysis stepminer gene

• Unveiling prognostics biomarkers of tyrosine metabolism reprogramming in liver cancer by cross-platform gene expression analyses.

  PMID 32542016 · PMC7295234 · PloS one · 2020 · 6 claims · 8 setups

  Has reproduction · 51

  Five tyrosine catabolic enzymes (TAT, HPD, HGD, GSTZ1, FAH) are downregulated in HCC versus normal liver at mRNA and protein levels

  cancer tcga-lihc gse89377 hcc pan-cancer rna-seq stage-wise

• 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

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• AI-assisted discovery of an ethnicity-influenced driver of cell transformation in esophageal and gastroesophageal junction adenocarcinomas.

  PMID 36134663 · PMC9675486 · JCI insight · 2022 · 8 claims · 8 setups

  Has reproduction · 84

  An AI-guided Boolean network approach (BoNE) models transcriptomic continuum states of normal esophagus, BE, and EAC to derive classifier gene signatures

  gene keratinocyte-derived ffpe spt6-depleted boolean rna-seq immunohistochemistry

• SGCP: a spectral self-learning method for clustering genes in co-expression networks.

  PMID 38956463 · PMC11221046 · BMC bioinformatics · 2024 · 7 claims · 4 setups

  Has reproduction · 51

  SGCP, a spectral self-learning method, yields gene co-expression modules with higher GO enrichment than WGCNA, CoExpNets, and CEMiTool across 12 real gene expression datasets.

  real microarray rna-seq same gene dna-microarray rna-sequencing

• An integrated in silico-in vitro approach for identifying therapeutic targets against osteoarthritis.

  PMID 36352408 · PMC9648005 · BMC biology · 2022 · 7 claims · 5 setups

  Has reproduction · 84

  A signal transduction/gene regulatory network model of the articular chondrocyte was built combining knowledge-based curation and data-driven (machine learning) network inference

  osteoarthritic articular chondrocyte microarray computational high-throughput

• Increased prevalence of hybrid epithelial/mesenchymal state and enhanced phenotypic heterogeneity in basal breast cancer.

  PMID 38974967 · PMC11225361 · iScience · 2024 · 7 claims · 7 setups

  Has reproduction · 95

  Luminal breast cancer gene expression signature is closely/positively associated with an epithelial signature

  breast-cancer-specific tcga ccle four single-sample survival genome-wide

• Parsimonious Gene Correlation Network Analysis (PGCNA): a tool to define modular gene co-expression for refined molecular stratification in cancer.

  PMID 30993001 · PMC6459838 · NPJ systems biology and applications · 2019 · 8 claims · 7 setups

  Has reproduction · 71

  Retaining only the top ~3 most correlated edges per gene (EPG3) combined with FastUnfold clustering (termed PGCNA) produces gene co-expression modules with significantly better separation and enrichment of known biology than using all edges or other clustering methods.

  breast colorectal brca representative gene comparative multi-omic

• Independent component analysis reveals new and biologically significant structures in micro array data.

  PMID 16762055 · PMC1557674 · BMC bioinformatics · 2006 · 7 claims · 8 setups

  Full-text index only

  ICA applied to three microarray datasets reveals many biologically significant components, including low-ranking ones not obvious by rank alone

  acute serum-stimulated head aml microarray clust term

• Deconvoluting the 'omics' for organ transplantation.

  PMID 19644370 · PMC2993238 · Current opinion in organ transplantation · 2009 · 8 claims · 5 setups

  Full-text index only

  High-throughput 'omic' technologies (genomics, proteomics, metabolomics, antibiomics) can uncover novel biomarkers for acute rejection, chronic rejection, and operational tolerance without a priori pathway bias

  kidney sera peripheral microarray non-parametric antibiomics

• CLEAN: CLustering Enrichment ANalysis.

  PMID 19640299 · PMC2734555 · BMC bioinformatics · 2009 · 8 claims · 4 setups

  Full-text index only

  The gene-specific CLEAN score improves reproducibility of cluster analysis conclusions across independent datasets compared to the traditional cluster-wide score (cwCLEAN).

  four breast combined hierarchical cluster csimm-based

• SMAGEXP: a galaxy tool suite for transcriptomics data meta-analysis.

  PMID 30698691 · PMC6354025 · GigaScience · 2019 · 8 claims · 5 setups

  Has reproduction · 82

  SMAGEXP integrates the metaMA and metaRNASeq R packages into Galaxy to provide a unified tool suite for transcriptomics meta-analysis.

  oral geo lung gene affymetrix limma

• Evaluation of classification and forecasting methods on time series gene expression data.

  PMID 33156855 · PMC7647064 · PloS one · 2020 · 6 claims · 3 setups

  Has reproduction · 74

  Deep learning based methods generally outperform traditional approaches for time series gene expression classification

  five gene microarray time

• Identification and analysis of genes associated with epithelial ovarian cancer by integrated bioinformatics methods.

  PMID 34143800 · PMC8213194 · PloS one · 2021 · 7 claims · 6 setups

  Has reproduction · 75

  306 overlapping DEGs (265 up-regulated, 41 down-regulated) were identified across three independent GEO datasets in EOC vs normal ovarian tissue.

  eoc overlapping tcga microarray kegg protein-protein

• Integrated Analysis of Multiple Microarrays Based on Raw Data Identified Novel Gene Signatures in Recurrent Implantation Failure.

  PMID 35197930 · PMC8859149 · Frontiers in endocrinology · 2022 · 6 claims · 7 setups

  Has reproduction · 85

  Robust Rank Aggregation (RRA) can integrate DEG lists from multiple independent RIF microarray datasets to identify robust DEGs.

  endometrium integrated robust ppi microarray robust gene