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).

• SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

  PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 6 claims · 5 setups

  Has reproduction · 77

  SurvConvMixer, using pathway-level gene expression images and ConvMixer, achieves strong internal validation AUC for overall survival prediction, especially on larger datasets like LUAD

  luad lusc skcm trained deep benchmark model

• Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.

  PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups

  Has reproduction · 89

  High pretreatment abundance of Lactobacillus (and Bifidobacterium) in gut microbiota correlates with absence of ACRIII in rectal cancer patients

  fecal bacterial whole-abdomen cecal metagenomic random fecal

• Exploring the prognostic and diagnostic value of lactylation-related genes in sepsis.

  PMID 39367086 · PMC11452377 · Scientific reports · 2024 · 8 claims · 7 setups

  Has reproduction · 73

  Intersecting sepsis-associated differentially expressed genes with a curated list of 332 lactylation genes yields 55 sepsis-related lactylation genes.

  peripheral overlapping geo pbmcs bulk kegg protein-protein

• Deconvolution of the hematopoietic stem cell microenvironment reveals a high degree of specialization and conservation.

  PMID 35494238 · PMC9046238 · iScience · 2022 · 7 claims · 7 setups

  Has reproduction · 60

  Integration of three scRNA-seq datasets using a custom bootstrapping-based clustering pipeline robustly identifies 14 endothelial subclusters and 11 mesenchymal (stage-specific) subclusters in mouse bone marrow.

  bone independent scrna-seq gene singler

• Comprehensive bioinformatics analysis and experimental verification identify mitochondrial gene Dgat2 as a novel therapeutic biomarker for myocardial ischemia-reperfusion.

  PMID 40510478 · PMC12159077 · Frontiers in endocrinology · 2025 · 8 claims · 8 setups

  Has reproduction · 64

  Dgat2 is a hub mitochondria-related differentially expressed gene (MitoDEG) that can serve as a novel biomarker and therapeutic target in MI/RI

  heart degs dgat2 mitodegs microarray kegg protein-protein

• pmid-40857330

  PMID 40857330 · PMC12380325 · 6 claims · 8 setups

  Full-text index only

  90 interacting genes were identified at the intersection of AAA DEGs and periodontitis WGCNA module genes

  abdominal gingival overlapping interacting microarray weighted kegg

• 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

• Enhancing chemotherapy response prediction via matched colorectal tumor-organoid gene expression analysis and network-based biomarker selection.

  PMID 39754813 · PMC11754497 · Translational oncology · 2025 · 6 claims · 8 setups

  Has reproduction · 78

  A consensus WGCNA approach combining matched tumor-organoid and independent organoid drug-response expression data identifies gene modules and hub genes predictive of 5-FU chemotherapy response

  colorectal matched combined expression microarray rna-seq consensus

• Identification of common genetic characteristics of rheumatoid arthritis and major depressive disorder by bioinformatics analysis and machine learning.

  PMID 37415981 · PMC10320004 · Frontiers in immunology · 2023 · 7 claims · 8 setups

  Has reproduction · 58

  EAF1, SDCBP and RNF19B are common genetic characteristics (hub genes) shared by RA and MDD

  pbmc intersected candidate wgcna differential kegg

• Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.

  PMID 40160891 · PMC11951896 · Bioinformatics and biology insights · 2025 · 6 claims · 5 setups

  Has reproduction · 44

  DyGAF, a dual-model attention neural network (independent Model A + dependent Model B), identifies and ranks genes by significance for COVID-19 biomarker discovery more effectively than differential expression analysis (DEA) and random forest (RF) feature selection

  nasopharyngeal same dygaf-ranked bulk differential random