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).

• NETISCE: a network-based tool for cell fate reprogramming.

  PMID 35725577 · PMC9209484 · NPJ systems biology and applications · 2022 · 8 claims · 4 setups

  Has reproduction · 85

  NETISCE predicts cell fate reprogramming targets in static (GRN/signaling) networks without needing full kinetic parameterization of a dynamical model.

  ascidian pluripotent drosophila signal fvs-finding sfa

• Specific signature biomarkers highlight the potential mechanisms of circulating neutrophils in aneurysmal subarachnoid hemorrhage.

  PMID 36438795 · PMC9685413 · Frontiers in pharmacology · 2022 · 8 claims · 8 setups

  Has reproduction · 80

  A neutrophil-related co-expression gene module (blue module) is significantly associated with aSAH occurrence

  peripheral genes overlapping neutrophil-related microarray weighted kegg

• Wx: a neural network-based feature selection algorithm for transcriptomic data.

  PMID 31324856 · PMC6642261 · Scientific reports · 2019 · 8 claims · 8 setups

  Has reproduction · 50

  The Wx algorithm ranks genes using a DI score reflecting each gene's classification power for distinguishing two groups.

  tcga gse72056 gse40419 gse103322 bulk single-cell rna-seq

• Software JimenaE allows efficient dynamic simulations of Boolean networks, centrality and system state analysis.

  PMID 36725967 · PMC9892028 · Scientific reports · 2023 · 8 claims · 4 setups

  Has reproduction · 74

  JimenaE performs systematic, exhaustive calculation of all network system states rather than the heuristic approach used by SQUAD.

  mesenchymal arabidopsis dendritic comparison boolean dynamical network

• TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining.

  PMID 33705981 · PMC9403021 · Genomics, proteomics & bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 79

  TSUNAMI is a freely accessible web-based tool suite that mines gene co-expression network (GCN) modules from public (GEO, TCGA) or user-uploaded numerical omics data and performs downstream gene set enrichment analysis.

  gse17537 36th first gene circos survival

• YANA - a software tool for analyzing flux modes, gene-expression and enzyme activities.

  PMID 15929789 · PMC1175843 · BMC bioinformatics · 2005 · 7 claims · 3 setups

  Full-text index only

  YANA integrates METATOOL to provide a graphical, platform-independent front-end for editing, calculating, visualizing, and comparing elementary flux modes, with SBML support.

  redox elementary flux evolutionary

• CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

  PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups

  Has reproduction · 81

  Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL

  dlbcl ici-related degs ffpe estimate consensus differential

• Predictive genomics of cardioembolic stroke.

  PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

  Full-text index only

  A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

  blood-derived gasros same custom bayesian roc

• Development and validation of a gemcitabine sensitivity-related long noncoding RNA signature for predicting the prognosis and subtypes of bladder cancer.

  PMID 41809777 · PMC12968932 · Translational andrology and urology · 2026 · 8 claims · 8 setups

  Full-text index only

  A 37-GSRlncRNA prognostic signature stratifies BLCA patients into low- and high-risk groups with significant differences in survival, pathway enrichment, immune infiltration, and mutational profiles

  tcga-blca blca paired wgcna differential machine

• Gene regulatory network determinants of rapid recall in human memory CD4(+) T cells.

  PMID 41865369 · PMC13207208 · Cell reports · 2026 · 8 claims · 6 setups

  Full-text index only

  Memory CD4+ T cells show enhanced chromatin accessibility proximal to rapid-recall genes compared to naive cells

  blood-derived computational pseudobulk cd4+ single-nuclei maxatac grn

• Deep learning linking mechanistic models to single-cell transcriptomics data reveals transcriptional bursting in response to DNA damage.

  PMID 41779826 · PMC12959883 · eLife · 2026 · 8 claims · 5 setups

  Full-text index only

  DeepTX is an interpretable, scalable deep learning inference framework that links mechanistic transcription models to scRNA-seq data to infer genome-wide transcriptional burst kinetics

  synthetic embryonic colorectal computational stochastic scrna-seq deep

• Spatiotemporal dynamics of spermatogenesis: insights from high-resolution spatial transcriptomics and pseudotime trajectories in mouse testes.

  PMID 41602862 · PMC12832764 · Frontiers in reproductive health · 2025 · 8 claims · 7 setups

  Full-text index only

  Salus-STS (1 μm resolution) combined with the Salus Cellbins Algorithm enables accurate subcellular segmentation of individual testicular cells in dense tissue

  testicular testis seminiferous top high-resolution integration pseudotime

• Identification of Cell Subpopulation-Specific Driver Genes Reveals Ideal Candidates for Renal Cell Carcinoma Immunotherapy.

  PMID 42074110 · PMC13115843 · International journal of molecular sciences · 2026 · 8 claims · 8 setups

  Full-text index only

  25 immune-related candidate driver genes were identified from tumor, myeloid, and lymphoid cell gene regulatory networks (GRNs) using SCENIC and topological Q statistics.

  kidney lymphoid rcc tcga-kirc single-cell scenic genome-wide

• An OMICs-based meta-analysis to support infection state stratification.

  PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups

  Has reproduction · 44

  Multi-class Random Forest models built from meta-analyzed blood gene expression data can predict infection state (bacterial/viral/none) with high accuracy, correctly classifying 93% of bacterial and 89% of viral samples in the best model.

  blood merged affymetrix-trained microarray random gene

• 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

• Gene Dosage Analysis on the Single-Cell Transcriptomes Linking Cotranslational Protein Targeting to Metastatic Triple-Negative Breast Cancer.

  PMID 34577617 · PMC8472593 · Pharmaceuticals (Basel, Switzerland) · 2021 · 8 claims · 7 setups

  Has reproduction · 53

  A computational framework mapping single-cell Z-score expression to matched patient-level CNV data can identify recurrent, cross-cell-type copy-number-driven expression (dosage) events.

  tnbc independent cng-up breast single-cell gene network

• An evaluation of the performance of tag SNPs derived from HapMap in a Caucasian population.

  PMID 16532062 · PMC1391920 · PLoS genetics · 2006 · 8 claims · 5 setups

  Full-text index only

  CEU HapMap-derived tSNPs capture most of the genetic variation observed in the Estonian (EGP) population sample

  individuals hapmap egp snp tag median-joining

• Mutation screening and haplotype analysis of the rhodopsin gene locus in Japanese patients with retinitis pigmentosa.

  PMID 17653048 · PMC2776539 · Molecular vision · 2007 · 8 claims · 4 setups

  Full-text index only

  No RP patient among 68 Japanese subjects carried a RHO mutation causing an amino acid substitution

  blood-derived genomic chromosomes rho whole-locus pcr haplotype

• Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

  PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

  Full-text index only

  A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

  ebv-transformed serum combined rf-filtered snp serum random

• Variations in the transcriptome of Alzheimer's disease reveal molecular networks involved in cardiovascular diseases.

  PMID 18842138 · PMC2760875 · Genome biology · 2008 · 8 claims · 6 setups

  Full-text index only

  AD-related genes (APOE, A2M, PON2, MAP4) and CVD-associated genes (COMT, CBS, WNK1) congregate in a single co-expression module, linking AD and CVD at the transcriptional level

  entorhinal subjects expression differentially microarray significance principal