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).

• GoMiner: a resource for biological interpretation of genomic and proteomic data.

  PMID 12702209 · PMC154579 · Genome biology · 2003 · 8 claims · 4 setups

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  GoMiner organizes 'interesting' gene lists (e.g., differentially expressed genes) into the Gene Ontology hierarchy for biological interpretation, displaying results as both a tree and a directed acyclic graph (DAG).

  du145 gene gominer cdna flow category

• A taxonomy of epithelial human cancer and their metastases.

  PMID 20017941 · PMC2806369 · BMC medical genomics · 2009 · 8 claims · 6 setups

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  Unsupervised hierarchical clustering of 1566 primary epithelial tumors yields large tissue-enriched clusters (breast, colon/GI, lung, ovary, kidney) plus smaller prostate, thyroid-kidney, and mixed clusters

  epithelial tumor metastatic breast microarray gene fisher

• Topologically inferring pathway activity toward precise cancer classification via integrating genomic and metabolomic data: prostate cancer as a case.

  PMID 26286638 · PMC4541321 · Scientific reports · 2015 · 6 claims · 4 setups

  Has reproduction · 76

  DRW-GM integrates gene expression and metabolomic profiles via directed random walk on a global gene–metabolite pathway graph to weight genes by topological importance and infer reproducible pathway activities

  prostate global gene metabolomic computational

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

  Has reproduction · 80

  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Identification of gene interactions associated with disease from gene expression data using synergy networks.

  PMID 18234101 · PMC2258206 · BMC systems biology · 2008 · 8 claims · 4 setups

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  Synergy of a gene pair with respect to disease, defined as I(G1,G2;C) - [I(G1;C)+I(G2;C)], identifies gene pairs that interact cooperatively with respect to a phenotype rather than independently.

  prostate simulated microarray simulated permutation

• PCR-free method detects high frequency of genomic instability in prostate cancer.

  PMID 19797393 · PMC2794161 · Nucleic acids research · 2009 · 7 claims · 6 setups

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  A novel PCR-free random cloning/sequencing method can detect genomic variants that PCR-based approaches miss in heterogeneous tumor genomes.

  blood normal prostate matched pcr-free degenerate-pcr blastn

• Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

  PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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  Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

  european-american yoruban japanese case sanger snp linkage

• PALB2 variants in hereditary and unselected Finnish prostate cancer cases.

  PMID 20003494 · PMC2806404 · Journal of negative results in biomedicine · 2009 · 8 claims · 6 setups

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  None of the detected PALB2 variants, including 1592delT, show significant association with PRCA at the population level in Finland

  blood finnish combined formalin-fixed direct additional statistical

• Rare germline mutations in the BRCA2 gene are associated with early-onset prostate cancer.

  PMID 17700570 · PMC2360390 · British journal of cancer · 2007 · 8 claims · 3 setups

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  Germline protein-truncating BRCA2 mutations confer an elevated relative risk (~7.8-fold) of early-onset prostate cancer in Caucasian men

  peripheral population-based same germline epidemiological genotype-phenotype

• Mutation analysis of the MSMB gene in familial prostate cancer.

  PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

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  No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

  germline blood 161-nt genotype sanger taqman transcription

• Positive selection for the male functionality of a co-retroposed gene in the hominoids.

  PMID 19832993 · PMC2773790 · BMC evolutionary biology · 2009 · 8 claims · 8 setups

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  PIPSL is an extraordinary co-retroposed protein-coding gene that may participate in male-specific functions of humans and close relatives

  african chimpanzee orangutan reconstructed population hka comparative

• Correcting scale distortion in RNA sequencing data.

  PMID 39875825 · PMC11776150 · BMC bioinformatics · 2025 · 8 claims · 8 setups

  Has reproduction · 76

  Local averaging reveals expression-level-dependent biases that differ from sample to sample across all RNA-seq datasets studied, and are not corrected by conventional normalization (TPM/FPKM)

  tcga su2c gse47774 gtex bulk computational d'agostino

• Identification of genes associated with multiple cancers via integrative analysis.

  PMID 19919702 · PMC2785840 · BMC genomics · 2009 · 8 claims · 8 setups

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  Mc.TGD (Multi-cancer Threshold Gradient Descent) is the first regularized approach to conduct two-dimensional selection of genes with joint effects on cancer development across multiple cancers.

  breast kidney liver lung gene wilcoxon

• CanCellCap: robust cancer cell capture across tissue types on single-cell RNA-seq data by multi-domain learning.

  PMID 40739511 · PMC12312500 · BMC biology · 2025 · 8 claims · 8 setups

  Has reproduction · 42

  CanCellCap, a multi-domain learning framework integrating domain adversarial learning and Mixture of Experts, identifies cancer cells across all tissues, cancers, and sequencing platforms by extracting tissue-common and tissue-specific gene expression patterns.

  testing datasets tisch2 prostate scrna-seq simulated spatial