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).

• Building disease-specific drug-protein connectivity maps from molecular interaction networks and PubMed abstracts.

  PMID 19649302 · PMC2709445 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  A computational framework can build disease-specific drug-protein connectivity maps by integrating protein interaction networks and PubMed literature mining, without gene expression profiles from drug perturbation experiments

  seed ad-related retrieved combined protein-protein network-based pubmed

• Single-cell analysis reveals multi-faceted features of B cell development, together with age-associated B cell subpopulations.

  PMID 41520091 · PMC12905261 · Communications biology · 2026 · 8 claims · 8 setups

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  18 B cell subpopulations were identified spanning the full developmental continuum from early progenitors to plasma cells, including 4 previously unappreciated minor subpopulations (FTLhi, S100A8hi immature; FOShi, HSPA1Ahi naïve).

  in-house enriched tonsil peripheral scrna-seq scvdj-seq velocity

• Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues.

  PMID 34056582 · PMC8155268 · Frontiers in artificial intelligence · 2021 · 8 claims · 6 setups

  Has reproduction · 92

  MCF-7 cell lines and human breast cancer tissues show only minimal similarity in biological processes, though some fundamental functions like cell cycle are conserved.

  mcf-7 breast wgcna-derived top bulk microarray rsem-normalized

• 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

• 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

• GREIN: An Interactive Web Platform for Re-analyzing GEO RNA-seq Data.

  PMID 31110304 · PMC6527554 · Scientific reports · 2019 · 8 claims · 7 setups

  Has reproduction · 73

  GREIN is a web application providing user-friendly interfaces to manipulate, visualize, and analyze GEO RNA-seq data.

  mcf10a nde&dt hypoxia bulk correlation pca

• Colorectal Cancer Prediction Based on Weighted Gene Co-Expression Network Analysis and Variational Auto-Encoder.

  PMID 32825264 · PMC7563725 · Biomolecules · 2020 · 6 claims · 7 setups

  Has reproduction · 80

  Combining WGCNA hub genes and VAE 10-dimensional representation as features for an SVM classifier achieves high accuracy in predicting CRC

  colorectal same combined meturquoise microarray differential batch

• A comparative gene co-expression analysis using self-organizing maps on two congener filmy ferns identifies specific desiccation tolerance mechanisms associated to their microhabitat preference.

  PMID 32019526 · PMC7001327 · BMC plant biology · 2020 · 8 claims · 6 setups

  Has reproduction · 62

  Inter-specific differences in vertical distribution/microhabitat preference are associated with distinct dynamics of gene expression during dehydration and rehydration phases

  hymenophyllum caudiculatum annotated rna-seq chlorophyll relative

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  AE networks trained on the 266 shared DEGs reveal a comorbidity (positive correlation) relationship between Alzheimer's disease and lung cancer, rather than the inverse relationship suggested by prior epidemiological studies.

  integrated expression overlapped moderated autoencoder pathway

• Identification of Key Genes in Atherosclerosis by Combined DNA Methylation and miRNA Expression Analyses.

  PMID 35949126 · PMC9682560 · Anatolian journal of cardiology · 2022 · 7 claims · 7 setups

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  10 key genes (TCF7L2, CACNA1C, NRP1, GABBR2, FANCC, DCK, CCDC88C, TCF12, ABLIM1, PBX1) are regulated by both aberrant DNA methylation and miRNA activity in atherosclerosis

  aorta cardiovascular peripheral blood methylation mirna expression

• Integrating co-expression network analysis and machine learning to reveal the regulatory landscape of GPD genes in Chlamydomonas reinhardtii under salinity stress.

  PMID 42004709 · PMC13089224 · PeerJ · 2026 · 8 claims · 8 setups

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  GPD2 and GPD3 cluster into distinct WGCNA co-expression modules (magenta and black, respectively) with contrasting temporal expression profiles

  chlamydomonas genes normalized gpd bulk weighted gene

• pmid-42103992

  PMID 42103992 · PMC13234024 · 8 claims · 7 setups

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  EU07 exposure compromises fungal cellular integrity, causing severe hyphal distortion

  graminearum five apolipophorin dual rna-seq gene

• 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

• Metabolite-Centric Reporter Pathway and Tripartite Network Analysis of Arabidopsis Under Cold Stress.

  PMID 30258841 · PMC6143811 · Frontiers in bioengineering and biotechnology · 2018 · 8 claims · 8 setups

  Has reproduction · 83

  Metabolite-centric reporter pathway analysis (RPAm) computes reporter metabolites and reporter pathways from transcriptome P-values by aggregating Z-scores of neighboring genes in a genome-scale metabolic network

  arabidopsis gene-metabolite-pathway tripartite microarray metabolite-centric reporter

• Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

  PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

  Has reproduction · 71

  AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

  aml hovon cancer tcga bulk consensus machine

• Weighted gene co-expression network analysis reveals that CXCL10, IRF7, MX1, RSAD2, and STAT1 are related to the chronic stage of spinal cord injury.

  PMID 34532385 · PMC8421925 · Annals of translational medicine · 2021 · 8 claims · 7 setups

  Has reproduction · 44

  The brown co-expression module (775 genes) is the module most significantly associated with the chronic stage of SCI

  spinal brown sci microarray functional protein-protein

• Heterogeneity and Differentiation Trajectories of Infiltrating CD8+ T Cells in Lung Adenocarcinoma.

  PMID 36358600 · PMC9658355 · Cancers · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  Infiltrating CD8+ T cells in LUAD can be divided into ten transcriptionally distinct subsets: eight cytotoxic (CTL) subsets, one naive-like (NTL) subset, and one exhausted (ETL) subset.

  luad tcga cd8+ degs single-cell cibersort survival

• Identification of Four Potential Biomarkers Associated With Coronary Artery Disease in Non-diabetic Patients by Gene Co-expression Network Analysis.

  PMID 32714363 · PMC7344232 · Frontiers in genetics · 2020 · 6 claims · 6 setups

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  The midnight blue module and the yellow module play vital roles in the pathogenesis of CAD in non-diabetic patients

  pbmcs blood apoe genes microarray rt-qpcr elisa

• Glioblastoma invasion into different organoid hosts reveals cell-intrinsic and proliferative migratory programs.

  PMID 41959666 · PMC13059114 · iScience · 2026 · 8 claims · 8 setups

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  GB cells invade both neural and endodermal organoid hosts (lineage-independent), whereas non-malignant neural progenitor cells show markedly reduced infiltration

  gbm1 gfp-gbm1 facs-sorted post-invasion image-based immunofluorescence single-cell

• ProtoCloud: A prototypical self-explaining model for single-cell analysis.

  PMID 41997134 · PMC13261663 · Cell genomics · 2026 · 8 claims · 8 setups

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  ProtoCloud matches or outperforms existing annotation methods across 11 large-scale datasets, particularly for rare cell types

  diverse pbmc10k pbmc30k tsca scrna-seq latent gene