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).

• Tissue compartment analysis for biomarker discovery by gene expression profiling.

  PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

  kidney pure serial rt-pcr sage histo-morphometry

• FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

  PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 65

  FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

  simulated four rna-seq randomly simulated paired-end read-mappability

• Examination of FMR1 transcript and protein levels among 74 premutation carriers.

  PMID 19927162 · PMC4122982 · Journal of human genetics · 2010 · 7 claims · 4 setups

  Full-text index only

  FMR1 premutation carriers (55-199 CGG repeats) show increased FMR1 transcript levels alongside decreased FMRP levels compared to normal individuals.

  peripheral subset real-time western cgg

• Of mice and men: comparative proteomics of bronchoalveolar fluid.

  PMID 20032019 · PMC3049194 · The European respiratory journal · 2010 · 8 claims · 8 setups

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  Comparative shotgun proteomics of human and mouse BALF identifies conserved pathways (immunity, defence response, protease activity) alongside species-specific divergent pathways.

  pooled oxidative unpooled balf shotgun functional protein-protein

• A platelet-related signature for predicting the prognosis and immunotherapy benefit in bladder cancer based on machine learning combinations.

  PMID 39280688 · PMC11399026 · Translational andrology and urology · 2024 · 8 claims · 8 setups

  Has reproduction · 51

  An Enet (alpha=0.4) machine-learning algorithm built from 10 platelet-related genes yields the optimal platelet-related signature (PRS) for bladder cancer prognosis, with average C-index 0.73

  bladder tcga bulk univariate integrative

• Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

  PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

  Has reproduction · 84

  A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

  tcga-brca triple-negative ffpe bulk univariate kaplan-meier

• Identification of succinylation-related genes in bladder cancer: integration of single-cell and transcriptomic data.

  PMID 42220482 · PMC13218921 · Frontiers in immunology · 2026 · 8 claims · 8 setups

  Has reproduction · 78

  KCTD16, CD3D and GSDMB are succinylation-related prognostic genes in BLCA

  paired tcga-blca geo gse135337 bulk single-cell rt-qpcr

• Discovery of molecular subtypes in leiomyosarcoma through integrative molecular profiling.

  PMID 19901961 · PMC2820592 · Oncogene · 2010 · 8 claims · 6 setups

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  Unsupervised gene expression clustering identifies 3 reproducible molecular subtypes of LMS (Group I/muscle-enriched, Group II, Group III)

  lms independent soft gene array immunohistochemistry

• Protein expression patterns in primary carcinoma of the vagina.

  PMID 15199389 · PMC2409807 · British journal of cancer · 2004 · 5 claims · 4 setups

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  Cluster analysis of 2-DE proteomic data allows accurate discrimination between normal vaginal mucosa, primary vaginal carcinoma and primary cervical carcinoma

  fresh-frozen excised normal same two-dimensional matrix-assisted hierarchical

• Molecular variants of the ATM gene in Hodgkin's disease in children.

  PMID 14735203 · PMC2409549 · British journal of cancer · 2004 · 8 claims · 4 setups

  Full-text index only

  Missense variants of the ATM gene occur in childhood Hodgkin lymphoma but at low frequency (9%), and thus do not play a major role in oncogenesis of the disease

  frozen matched paired rt-pcr germ-line sscp

• Sequence variations of GRM6 in patients with high myopia.

  PMID 19862333 · PMC2765235 · Molecular vision · 2009 · 7 claims · 8 setups

  Full-text index only

  Three novel GRM6 variations with predicted functional consequences (c.67-82delCAGGCGGGCCTGGCGCinsT, c.858-5a>g, c.1537G>A) were found in high myopia patients but absent in 96 controls

  genomic pcr mglur6 grm6 pcr heteroduplex pcr-restriction

• Evaluating Distribution and Prognostic Value of New Tumor-Infiltrating Lymphocytes in HCC Based on a scRNA-Seq Study With CIBERSORTx.

  PMID 33043022 · PMC7527443 · Frontiers in medicine · 2020 · 5 claims · 6 setups

  Has reproduction · 78

  CIBERSORTx can combine scRNA-seq-derived signatures with bulk HCC transcriptomes to estimate proportions of 11 TIL subsets and infer cell-type-specific gene expression.

  hcc tcga geo single-cell bulk microarray

• SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

  PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

  Full-text index only

  SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

  single hcc2218 nsclc array gene multi-omics

• pwrEWAS: a user-friendly tool for comprehensive power estimation for epigenome wide association studies (EWAS).

  PMID 31035919 · PMC6489300 · BMC bioinformatics · 2019 · 7 claims · 8 setups

  Has reproduction · 88

  pwrEWAS is a user-friendly tool (R package and Shiny web interface) for comprehensive power estimation in two-group EWAS using Illumina HumanMethylation BeadChip technology.

  saliva blood cord-blood pbmc illumina simulation

• The process chain for peptidomic biomarker discovery.

  PMID 16410650 · PMC3850862 · Disease markers · 2006 · 8 claims · 3 setups

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  Peptidomics (comprehensive analysis of peptides and small proteins <20 kDa) fills a methodological gap left by standard proteomics, which mainly addresses proteins in the ~10-200 kDa range.

  general body patients 2d-gel peptidomics peptidomic

• 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

• Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

  PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups

  Has reproduction · 73

  In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.

  tcga-hnscc gse65858 hpv-positive tcga bulk microarray qrt-pcr

• MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease.

  PMID 19758471 · PMC2745589 · BMC bioinformatics · 2009 · 8 claims · 5 setups

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  MtSNPscore, a weighted scoring pipeline combining literature evidence, in silico predictions, and case/control frequency, can prioritize likely pathogenic mtDNA variations

  sporadic mitochondrial reported ataxia mitochondrial functional compensatory

• Method of regulatory network that can explore protein regulations for disease classification.

  PMID 19962281 · PMC7126395 · Artificial intelligence in medicine · 2010 · 6 claims · 2 setups

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  A regulatory network (RN) can be constructed as a hopfield-like network, with nodes as biomarkers and directed weighted connections as regulatory relationships, optimized by minimizing an energy function measuring input-output disagreement.

  nasopharyngeal sars seldi-tof-ms

• Serum diagnosis of diffuse large B-cell lymphomas and further identification of response to therapy using SELDI-TOF-MS and tree analysis patterning.

  PMID 18163913 · PMC2242801 · BMC cancer · 2007 · 8 claims · 8 setups

  Full-text index only

  SELDI-TOF-MS serum proteomic patterns analyzed by decision tree classification (Biomarker Pattern Software) can discriminate DLBCL patients from healthy controls with high sensitivity and specificity.

  serum seldi dlbcl pooled seldi-tof-ms proteinchip decision