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).

• Machine learning developed an intratumor heterogeneity signature for predicting clinical outcome and immunotherapy benefit in bladder cancer.

  PMID 39100839 · PMC11291408 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 40

  An integrative machine learning procedure (10 methods, 101 algorithm combinations) identified an Enet (alpha=0.2)-based intratumor heterogeneity-related signature (IRS) with the highest average C-index (0.69) across TCGA and GEO cohorts

  bladder skin bulk integrative immune

• Combining evidence of preferential gene-tissue relationships from multiple sources.

  PMID 23950964 · PMC3741196 · PloS one · 2013 · 8 claims · 8 setups

  Has reproduction · 53

  A high-level integration approach combining three methods across four human microarray datasets, merged by consensus voting and a rule-based inner/total score, predicts preferentially expressed genes while reducing method- and study-specific bias.

  normal four microarray genes microarray computational bayes

• 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

• Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS).

  PMID 17601345 · PMC1929076 · BMC genomics · 2007 · 8 claims · 8 setups

  Full-text index only

  MPSS detected 10,279 UniGene clusters, representing 7,475 known genes, in human hepatocytes

  hepatocytes promoters genes hepatocyte mpss rt-pcr hierarchical

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene

• DiRE: identifying distant regulatory elements of co-expressed genes.

  PMID 18487623 · PMC2447744 · Nucleic acids research · 2008 · 8 claims · 4 setups

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  DiRE predicts distant regulatory elements by combining gene co-expression data, comparative genomics and TFBS profiles to determine TFBS-association signatures

  liver myod transgenic microarray tfbs enhancer

• A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

  PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

  Full-text index only

  A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

  maqc hepatocytes japanese illeum microarray dasl sequence

• Molecular interactions between HNF4a, FOXA2 and GABP identified at regulatory DNA elements through ChIP-sequencing.

  PMID 19822575 · PMC2794179 · Nucleic acids research · 2009 · 8 claims · 6 setups

  Full-text index only

  ChIP-seq identified 3064 GABP peaks, 7266 FOXA2 peaks and 18783 HNF4a peaks in HepG2 cells

  hepg2 liver chip-seq quantitative co-immunoprecipitation

• DNA methylation biomarkers-based pan-cancer classifier: predictive modeling for cancer classification.

  PMID 42152108 · PMC13185202 · Genome medicine · 2026 · 8 claims · 5 setups

  Full-text index only

  Relatively simple ML models (logistic regression) outperform complex algorithms such as deep neural networks for methylation-based cancer classification

  validation cns healthy genes methylation copy-number gene-set

• TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.

  PMID 40314147 · PMC12774851 · Genetics · 2026 · 8 claims · 8 setups

  Full-text index only

  TF2TG is an online resource integrating motif scan data, ChIP-seq peaks (modENCODE/modERN), Hi-C (TADs), REDfly-curated CRMs, ATAC-seq, protein-protein interaction data, and tissue-specific expression to predict TF-target gene relationships in Drosophila

  drosophila combined motif chip-seq whole-animal

• TEDD: a comprehensive database for translation efficiency dynamics.

  PMID 41217970 · PMC12807600 · Nucleic acids research · 2026 · 8 claims · 4 setups

  Full-text index only

  TEDD integrates 1518 RNA-seq, Ribo-seq, and RNC-seq samples from 143 human projects (279 datasets) spanning 24 tissues/cell types, 74 cell lines, and 52 conditions.

  tissues reference rna-seq ribo-seq rnc-seq

• scATD: a high-throughput and interpretable framework for single-cell cancer drug resistance prediction and biomarker identification.

  PMID 40501071 · PMC12159290 · Briefings in bioinformatics · 2025 · 8 claims · 6 setups

  Has reproduction · 62

  scATD enables high-throughput single-cell drug sensitivity prediction for new patients without model parameter retraining via bidirectional Bi-AdaIN style transfer

  panglaodb cancer geo gse137829 single-cell bulk

• The systematic assessment of completeness of public metadata accompanying omics studies in the Gene Expression Omnibus data repository.

  PMID 40926267 · PMC12421755 · Genome biology · 2025 · 8 claims · 3 setups

  Has reproduction · 99

  Across 253 manually curated studies (164,000+ samples), over 25% of critical metadata are omitted, with only 74.8% of relevant phenotypes available overall.

  randomly repositories geo manual automated

• Reducing language barriers, promoting information absorption, and communication using fanyi.

  PMID 39039634 · PMC11332769 · Chinese medical journal · 2024 · 7 claims · 3 setups

  Has reproduction · 67

  The fanyi R package retrieves gene information from NCBI and translates it into multiple languages using AI-driven online translation services

  pbmcs airway gene single-cell bulk functional

• Gbdmr: identifying differentially methylated CpG regions in the human genome via generalized beta regressions.

  PMID 38443825 · PMC10916021 · BMC bioinformatics · 2024 · 8 claims · 4 setups

  Has reproduction · 62

  gbdmr models DNA methylation levels of CpG sites using a generalized beta distribution instead of assuming normality as in linear-regression-based methods

  simulated birth gene simulation methylation

• Machine learning-based DNA microarray analysis for disease detection using the MICRO-AI framework.

  PMID 41925147 · PMC13051084 · Science progress · 2026 · 8 claims · 1 setups

  Has reproduction · 22

  MICRO-AI's attention-weighted feature fusion reduces dimensionality by over 99% (from ~20,000 to ~127 genes) without loss of biological significance

  breast microarray

• MirDIP 5.2: tissue context annotation and novel microRNA curation.

  PMID 36453996 · PMC9825511 · Nucleic acids research · 2023 · 7 claims · 6 setups

  Has reproduction · 89

  mirDIP 5.2 removed eight outdated resources, added miRNATIP, and ran five prediction algorithms against miRBase and mirGeneDB miRNAs to expand and improve interaction coverage

  mirnas disease novel type mirna small bulk

• Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing.

  PMID 31443728 · PMC6708158 · Genome medicine · 2019 · 6 claims · 8 setups

  Has reproduction · 68

  A near-perfect chronological age predictor can in principle be developed from DNA methylation when training sample size is sufficiently large.

  blood unrelated sgpd lbc1921 methylation reml permutation

• miEAA 2.0: integrating multi-species microRNA enrichment analysis and workflow management systems.

  PMID 32374865 · PMC7319446 · Nucleic acids research · 2020 · 8 claims · 5 setups

  Has reproduction · 61

  miEAA 2.0 extends miRNA enrichment analysis to ten species (previously only Homo sapiens), accepting both precursor and mature miRNA input.

  kidney blood model geo bulk small agilent

• Mural cell-derived chemokines provide a protective niche to safeguard vascular macrophages and limit chronic inflammation.

  PMID 37652021 · PMC10588993 · Immunity · 2023 · 7 claims · 8 setups

  Has reproduction · 83

  Vascular macrophages form a spatiotemporal niche in direct contact with mural cells across microvascular and macrovascular beds

  cx3cr1-mφ rfp-rep coronary peritoneal intravital confocal single-cell