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

• Using random walks to identify cancer-associated modules in expression data.

  PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

  Has reproduction

  Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

  hepatocellular breast sporadic geo gene differential interaction

• Pathway-specific canalization and plasticity of gene expression during C. elegans dauer development.

  PMID 41890963 · PMC13014971 · iScience · 2026 · 8 claims · 7 setups

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  Dauers induced by different environmental (starvation, pheromone, heat) or genetic (daf-2, daf-7, ilc-17.1, cep-1 OE) stimuli are transcriptionally distinct from each other and from continuously developing WT L2/L3 and adults

  elegans bulk principal likelihood

• Revealing the critical state and identifying individualized dynamic network biomarker for type 2 diabetes through advanced analysis methods on individual basis.

  PMID 39890881 · PMC11785715 · Scientific reports · 2025 · 8 claims · 5 setups

  Has reproduction · 75

  sJSD, NIG, and TNFE methods can detect critical states/tipping points before disease deterioration using only a single sample

  simulated adipose gastrocnemius dnb numerical microarray protein-protein

• A machine learning approach uncovers principles and determinants of eukaryotic ribosome pausing.

  PMID 39423268 · PMC11488575 · Science advances · 2024 · 8 claims · 5 setups

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  An unsupervised ML pipeline using the extended isolation forest (EIF) algorithm can reliably detect ribosome pausing sites from noisy, coverage-biased RiboSeq data across expression levels

  saccharomyces simulated yeast riboseq simulated comparative

• 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

• Flux balance analysis of mycolic acid pathway: targets for anti-tubercular drugs.

  PMID 16261191 · PMC1246807 · PLoS computational biology · 2005 · 7 claims · 7 setups

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  A comprehensive stoichiometric model of the MAP was built comprising 197 metabolites, 219 reactions, and 28 proteins

  stoichiometric map tuberculosis flux systematic drug

• Adaptive learning embedding features to improve the predictive performance of SARS-CoV-2 phosphorylation sites.

  PMID 37847658 · PMC10628388 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 6 setups

  Has reproduction · 67

  PSPred-ALE outperforms state-of-the-art SARS-CoV-2 phosphorylation site predictors (e.g. DeepIPs) and handcrafted feature-based methods in benchmarking comparisons

  a549 sequence same bulk pathway gene

• 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

• A non-parametric meta-analysis approach for combining independent microarray datasets: application using two microarray datasets pertaining to chronic allograft nephropathy.

  PMID 18302764 · PMC2276496 · BMC genomics · 2008 · 8 claims · 6 setups

  Full-text index only

  A novel non-parametric meta-analysis approach for combining independent microarray datasets is presented, requiring no distributional assumptions and being logically intuitive.

  kidney same identified additional microarray significance fisher's

• OTMODE: an optimal transport theory-based framework for identifying differential features in single-cell multi-omics data.

  PMID 41335419 · PMC12766913 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 8 setups

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  OTMODE, using an unbalanced Sinkhorn algorithm and Wald test, improves differential feature identification in single-cell multi-omics data

  simulated classical degs naive simulated bulk real

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• Transcriptome and machine learning analysis of the impact of COVID-19 on mitochondria and multiorgan damage.

  PMID 38295140 · PMC10830027 · PloS one · 2024 · 6 claims · 7 setups

  Has reproduction · 71

  Potential cardiac, hepatic, and renal impairments in COVID-19 are associated with ACE2, inflammatory cytokine storms, and mitochondrial pathways.

  nasopharyngeal heart leukocytes blood bulk pathway machine

• Clustering and machine learning-based integration identify cancer associated fibroblasts genes' signature in head and neck squamous cell carcinoma.

  PMID 37065499 · PMC10098459 · Frontiers in genetics · 2023 · 8 claims · 8 setups

  Has reproduction · 63

  Clustering of 31 CAFs genes across 868 HNSCC samples identifies two distinct molecular patterns (C1, C2) with different survival outcomes

  hnscc combined gse164690 tcga-hnsc ssgsea unsupervised immune

• Mining expressed sequence tags identifies cancer markers of clinical interest.

  PMID 17078886 · PMC1635568 · BMC bioinformatics · 2006 · 8 claims · 6 setups

  Full-text index only

  An EST-mining approach (Fisher Exact Test on tumor vs. non-tumor library hit counts) identifies differentially expressed transcripts with an estimated false discovery rate below 22% when human and mouse screens are combined.

  dbest cancer gene est human-mouse leave-one-out

• Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

  PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

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  Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

  cfs most candidate second microarray snp weighted

• Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

  PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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  Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

  surgical standardized glioma gbm western principal k-means

• Identification and characterization of tryptophan metabolism-related genes in carotid artery plaques.

  PMID 41628167 · PMC12863520 · PloS one · 2026 · 8 claims · 6 setups

  Full-text index only

  446 differentially expressed genes (DEGs) were identified between carotid plaque and normal tissue, enriched in immune and tryptophan-related pathways

  carotid degs six bulk kegg logistic

• Rare variant analyses provide insights into the genetic architecture of endometriosis.

  PMID 41736152 · PMC13001359 · Human genomics · 2026 · 7 claims · 8 setups

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  Gene-based burden testing of rare LoF and deleterious missense variants identifies SOGA1 as significantly associated with endometriosis after Bonferroni correction

  unrelated finngen biobank soga1 exome gene-based protein-protein

• Trans-ethnic association study of blood pressure determinants in over 750,000 individuals.

  PMID 30578418 · PMC6365102 · Nature genetics · 2019 · 7 claims · 8 setups

  Has reproduction

  208 novel common blood pressure SNPs and 53 rare variants were discovered in GWASs of SBP, DBP and pulse pressure in up to 776,078 participants from MVP and collaborating studies.

  multi-ethnic mvp tissues kidney genome-wide exome transcriptome-wide