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-predicted chromatin organization landscape across pediatric tumors.

  PMID 41904260 · PMC13039956 · Scientific reports · 2026 · 8 claims · 5 setups

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  SuPreMo-Akita (built on the Akita CNN) enables systematic in silico prediction of somatic SV effects on 3D genome folding across large SV cohorts where experimental testing is infeasible

  somatic per-sample tumor paired mutagenesis dimensionality h3k27ac

• Somatic mutations of KIT in familial testicular germ cell tumours.

  PMID 15150569 · PMC2410291 · British journal of cancer · 2004 · 6 claims · 3 setups

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  No germline KIT mutations were found in constitutional DNA from 240 familial TGCT pedigrees

  blood ffpe familial csge direct contingency

• Increased frequency of the k-ras G12C mutation in MYH polyposis colorectal adenomas.

  PMID 15083190 · PMC2410274 · British journal of cancer · 2004 · 8 claims · 2 setups

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  Somatic k-ras mutations occur in 9 of 54 (16.7%) MYH polyposis colorectal tumours, with frequency increasing with degree of dysplasia.

  microdissected previously pcr literature-derived

• TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

  PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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  Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

  ovarian sporadic paraffin-embedded mutation survival extraction

• Getting started in computational immunology.

  PMID 18769677 · PMC2518523 · PLoS computational biology · 2008 · 8 claims · 7 setups

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  Affinity maturation is driven by cycles of somatic hypermutation and affinity-dependent selection acting on B cell Ig receptors.

  splenic lymphocytes lymph secondary flow microdissection intravital

• Epidemiology of doublet/multiplet mutations in lung cancers: evidence that a subset arises by chronocoordinate events.

  PMID 19005564 · PMC2579325 · PloS one · 2008 · 8 claims · 7 setups

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  Doublet mutations are significantly more frequent in EGFR (6.0%) and TP53 (2.3%) in human lung cancer than spontaneous doublets in mouse lacI (0.7%), about 8-fold and 3-fold higher respectively.

  egfr tp53 laci lung literature comparative statistical

• Analysis of the TGF beta functional pathway in epithelial ovarian carcinoma.

  PMID 11531253 · PMC2364123 · British journal of cancer · 2001 · 6 claims · 6 setups

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  IGFIIR, TGFβ1 and TGFβRII are proposed to function as a unit in the TGFβ growth inhibitory pathway

  epithelial tumor genomic ovarian sscp sequencing pcr

• Genome wide identification of recessive cancer genes by combinatorial mutation analysis.

  PMID 18846217 · PMC2557123 · PloS one · 2008 · 7 claims · 4 setups

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  A combinatorial mutation analysis identified 154 candidate recessive cancer genes (pRecessiveCancer<1.5x10-7, FDR=0.39)

  refseq tp53 tumor 154-gene est paired array

• Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning.

  PMID 36611079 · PMC9825621 · NPJ precision oncology · 2023 · 8 claims · 8 setups

  Has reproduction

  Tree-based (XGBoost, LightGBM) and deep-learning (TabNet) tabular ML classifiers achieve state-of-the-art somatic vs germline classification in tumor-only WES samples, outperforming PureCN.

  tcga same metastatic tumor-only whole-exome wes copy-number

• Molecular profiling of breast cancer in native American women reveals distinct genomic and transcriptomic features.

  PMID 41844957 · PMC13144316 · NPJ precision oncology · 2026 · 8 claims · 6 setups

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  This is the first multi-omics (mutation, CNV, RNA-seq) characterization of breast tumors from Native American women, providing a resource for future studies

  breast degs targeted panel-derived whole-transcriptome

• Chromosome alterations and E-cadherin gene mutations in human lobular breast cancer.

  PMID 10584868 · PMC2374316 · British journal of cancer · 1999 · 8 claims · 5 setups

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  LOH at chromosome 16q21-q22.1 occurs in 100% of informative lobular breast tumours, the highest frequency of any region tested

  lobular pcr loh loh pcr-sscp sequencing

• Correlations of EGFR mutations and increases in EGFR and HER2 copy number to gefitinib response in a retrospective analysis of lung cancer patients.

  PMID 17626639 · PMC1952070 · BMC cancer · 2007 · 7 claims · 4 setups

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  EGFR mutations (exon 19 deletions, exon 21 L858R) did not correlate with gefitinib response in this cohort

  microdissected formalin-fixed archival clinical pcr fluorescence laser

• Characterization of retrocopies in 663 individuals with esophageal squamous cell carcinoma.

  PMID 42058905 · PMC13122676 · iScience · 2026 · 8 claims · 7 setups

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  RIST, a new pipeline combined with GRIPper, refines retrocopy insertion site breakpoints and target-site duplication (TSD) detection, improving on existing tools (GRIPper2, sideRETRO)

  paired tool escc parent whole-genome nanopore sequencing

• Human synthetic lethal inference as potential anti-cancer target gene detection.

  PMID 20015360 · PMC2804737 · BMC systems biology · 2009 · 7 claims · 8 setups

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  Targeting the synthetic lethal partner of a gene mutated in cancer selectively damages tumor cells while sparing healthy cells, offering a rationale for anti-cancer drug design

  saccharomyces sapiens ihsln genes database phylogenetic gene

• Dynamic regulation of spermatogenesis and hybrid sterility revealed by single-cell analysis in yak and cattle.

  PMID 41622528 · PMC12916010 · Molecular biology and evolution · 2026 · 7 claims · 8 setups

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  Cattle and yak testes contain seven types of spermatogonia, ten spermatocyte subtypes, and ten spermatid types with largely conserved transcriptional programs governing spermatogenic fate transitions.

  testicular spermatocytes spermatids bc1 single-cell chromosome hematoxylin

• Mapping Genetic Regulation of Transcription to Identify Functional Variants and Genes Associated with Pancreatic Cancer Risk.

  PMID 41824785 · PMC13205582 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 8 claims · 8 setups

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  A genome-wide cis-eQTL meta-analysis of 482 pancreatic tissues (177 TCGA tumor + 305 GTEx normal) identified 1,123,483 significant SNP-gene pairs, 709,720 unique eQTLs, and 13,758 eGenes (FDR<0.05)

  tcga chinese significant egenes cis-eqtl gwas variant