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).

Publications 1.3k Datasets 392.5k Experiments 153

System / cell line: somatic ✕ Clear

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
An integrated genomic analysis of human glioblastoma multiforme.

PMID 18772396 · PMC2820389 · Science (New York, N.Y.) · 2008 · 8 claims · 7 setups

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IDH1 is recurrently mutated at its active site (R132) in 12% of GBM patients, a previously unrecognized alteration in GBM.

gbm additional missense exome targeted snp
Oncogenic mutations in GNAQ occur early in uveal melanoma.

PMID 18719078 · PMC2634606 · Investigative ophthalmology & visual science · 2008 · 8 claims · 7 setups

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Activating GNAQ mutations at codon 209 occur in 33/67 (49%) of primary uveal melanomas, making it the most common known oncogenic mutation in UM

uveal peripheral normal well-characterized pcr sequencing array-based
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

PMID 18535014 · PMC2464741 · Molecular biology and evolution · 2008 · 8 claims · 7 setups

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Repair genes are numerically less common than apoptosis genes in the genomes of multicellular organisms

yeast familial human-mouse comparative gene mutation
Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

PMID 19861435 · PMC2783876 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 7 claims · 7 setups

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Comprehensive genomic analysis shows thymic carcinomas are molecularly distinct from thymomas

resected thymic previously mass dideoxynucleotide array
Divide and conquer: progress in the molecular stratification of cancer.

PMID 19718393 · PMC2730607 · Yonsei medical journal · 2009 · 8 claims · 8 setups

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Cancers exhibit significant clinical, histopathologic, and molecular heterogeneity between individual patients

breast nsclc colon early-stage immunohistochemistry gene comparative
Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

PMID 19671847 · PMC2892178 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2009 · 8 claims · 5 setups

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Genomic profiling by aCGH can distinguish clonal tumors from independent primaries with high confidence by identifying matching versus non-matching regions of allelic gain/loss.

fresh-frozen same banked resected array mutational pcr
BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

PMID 19668202 · PMC3661775 · Nature methods · 2009 · 8 claims · 8 setups

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BreakDancer (BreakDancerMax + BreakDancerMini) is a software package that predicts a wide variety of structural variants including deletions, insertions, inversions, and intra/inter-chromosomal translocations from paired-end short-insert sequencing reads.

reads yoruban cytogenetically predicted simulated paired-end whole-genome
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr
DNA demethylation is associated with malignant progression of lower-grade gliomas.

PMID 30760837 · PMC6374451 · Scientific reports · 2019 · 8 claims · 8 setups

Has reproduction

Nearly half of IDH-mutant glioblastomas that progressed from lower-grade gliomas show characteristic partial DNA demethylation in previously methylated (G-CIMP) genomic regions of their initial tumor.

gliomas neural analysis tcga methylation whole-exome sequencing
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 6 claims · 8 setups

Has reproduction · 89

STEC prevalence in surface water varies by watershed and by season in the Lower Mainland of British Columbia.

surface sediment isolate presumptive hydrophobic stx monoplex
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted
Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

PMID 41758938 · PMC12947870 · Science advances · 2026 · 8 claims · 8 setups

Has reproduction · 84

MYOD1 L122R-mutant SRMS tumors contain three coexisting, conserved cell states (progenitor, transition, differentiated) reflecting aberrant myogenic differentiation

patient-derived tumor single paired single-nucleus infercnv aracne-ap
Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

PMID 37106072 · PMC10181940 · Nature genetics · 2023 · 8 claims · 8 setups

Has reproduction · 78

CODEC concatenates both strands of an original DNA duplex into a single NGS read pair via an adapter quadruplex and strand-displacing extension, enabling single-duplex resolution

cfdna na12878 genomic sperm targeted whole-genome whole-exome
Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

PMID 11879542 · PMC128918 · Arthritis research · 2002 · 8 claims · 6 setups

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Antibody sequences that violate normal ontogenic/developmental constraints indicate a failure of B-cell regulation

peripheral diseased rheumatoid autoimmune immunoglobulin single-cell cloning
High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

PMID 11207044 · PMC2363776 · British journal of cancer · 2001 · 8 claims · 4 setups

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The SAFB locus region on chromosome 19p13.2-3 shows a very high rate of loss of heterozygosity (LOH) in primary breast cancer, indicating presence of a breast tumour-suppressor gene locus

breast microdissected loh rt-pcr pcr
Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

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PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

pancreatic same tumor pet sscp methylation-specific microsatellite
Comparative genomics comes of age.

PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

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Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

Experiments

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

An integrated genomic analysis of human glioblastoma multiforme.

Oncogenic mutations in GNAQ occur early in uveal melanoma.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

Programmed genetic instability: a tumor-permissive mechanism for maintaining the evolvability of higher species through methylation-dependent mutation of DNA repair genes in the male germ line.

Comprehensive genomic analysis reveals clinically relevant molecular distinctions between thymic carcinomas and thymomas.

Divide and conquer: progress in the molecular stratification of cancer.

Genomic and mutational profiling to assess clonal relationships between multiple non-small cell lung cancers.

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

DNA demethylation is associated with malignant progression of lower-grade gliomas.

Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

Single-cell protein activity analysis reveals aberrant myogenesis and IGF2-PI3K pathway dependencies in MYOD1-mutant rhabdomyosarcoma.

Single duplex DNA sequencing with CODEC detects mutations with high sensitivity.

Clues to the etiology of autoimmune diseases through analysis of immunoglobulin genes.

High rates of loss of heterozygosity on chromosome 19p13 in human breast cancer.

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

Comparative genomics comes of age.