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 30

System / cell line: cell-line ✕ Assay: somatic ✕ Clear

A small-cell lung cancer genome with complex signatures of tobacco exposure.

PMID 20016488 · PMC2880489 · Nature · 2010 · 8 claims · 7 setups

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22,910 somatic substitutions, including 132 in coding exons, were identified genome-wide in the NCI-H209 SCLC genome.

nci-h209 sclc lu-135 massively pcr multiplex
A comprehensive catalogue of somatic mutations from a human cancer genome.

PMID 20016485 · PMC3145108 · Nature · 2010 · 8 claims · 7 setups

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Whole-genome sequencing of COLO-829 melanoma cells and matched COLO-829BL normal cells produced the first comprehensive catalogue of somatic mutations from an individual cancer genome

colo-829 additional whole-genome conventional pcr
Genomic variability within an organism exposes its cell lineage tree.

PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

robinia arabidopsis randomly genotyping multiplex computer
Complex landscapes of somatic rearrangement in human breast cancer genomes.

PMID 20033038 · PMC3398135 · Nature · 2009 · 8 claims · 6 setups

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There are more somatic rearrangements in some breast cancers than previously appreciated by cytogenetic methods.

breast subset confirmed paired-end fish exon-exon
TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

Has reproduction · 50

TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

t-cell hcc1395 targeted whole-exome
Nimbus: a design-driven analyses suite for amplicon-based NGS data.

PMID 29538618 · PMC6084620 · Bioinformatics (Oxford, England) · 2018 · 7 claims · 5 setups

Has reproduction · 64

Nimbus tracks the source amplicon of reads throughout alignment and SNP/InDel calling

blood na15510 twin haloplex haloplex spiked-in humanexome-12
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

nsclc 293t il-3-independent mutational site-directed cytokine-independence
A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

PMID 39950044 · PMC11823652 · PeerJ · 2025 · 8 claims · 8 setups

Has reproduction · 73

COAD patients can be divided into two molecular subtypes (S1, S2) based on 21 prognostic PCD-related genes, with S1 showing worse prognosis and immunosuppressive microenvironment, S2 showing better prognosis and stronger anti-tumor immunity

coad consensus cibersort mcp-counter
Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi.

PMID 19078957 · PMC2696133 · Nature · 2009 · 8 claims · 8 setups

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GNAQ is frequently somatically mutated in blue nevi (83%) and uveal melanoma (46%)

archival nevus htert melan-a sanger pna-clamp soft
Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

PMID 17485517 · PMC2118573 · The Journal of experimental medicine · 2007 · 8 claims · 8 setups

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AID mRNA is aberrantly expressed in Ph+ ALL but largely absent in Ph- ALL

normal ph+ semiquantitative western rt-pcr
Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

PMID 19946270 · PMC4002225 · Nature genetics · 2010 · 8 claims · 8 setups

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PARK2 is a frequently and specifically targeted gene within recurrent 6q25.2-q27 copy number losses in glioblastoma and colon cancer

colon gbm cancer dbtrg array pcr colony
AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

PMID 17485433 · PMC5947781 · Bioinformatics (Oxford, England) · 2007 · 7 claims · 2 setups

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AutoCSA is an automated algorithm, extended from the CSA protocol, that detects DNA sequence variants in cancer genomes with minimal manual intervention

training kinase capillary targeted
Personalized medicine: the future is not what it used to be.

PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

sw13 h295r drosophila acc drug synthetic gene
The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

tumor ovarian kgn high sanger taqman
Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

PMID 19737971 · PMC2994259 · Molecular cancer research : MCR · 2009 · 8 claims · 8 setups

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CLSPN is a mediator protein essential for the ATR- and CHK1-dependent checkpoint response to replicative stress or single-stranded DNA

ebv-immortalized sporadic same caucasian genomic denaturing genotyping
COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

PMID 19906727 · PMC2808858 · Nucleic acids research · 2010 · 8 claims · 6 setups

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COSMIC is the largest public resource for information on somatically acquired mutations in human cancer, freely available without restriction

cancer tumour manual semi-automated candidate
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
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 were identified as prognostic succinylation-related genes in BLCA

soochow-blca tcga-blca gse13507 gse135337 bulk scrna-seq somatic
Global variation in copy number in the human genome.

PMID 17122850 · PMC2669898 · Nature · 2006 · 8 claims · 6 setups

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A first-generation CNV map of the human genome was constructed from 270 HapMap individuals across four populations, identifying 1,447 CNV regions covering ~360 Mb (12%) of the genome.

hapmap subset blood snp array karyotyping
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping

Experiments

A small-cell lung cancer genome with complex signatures of tobacco exposure.

A comprehensive catalogue of somatic mutations from a human cancer genome.

Genomic variability within an organism exposes its cell lineage tree.

Complex landscapes of somatic rearrangement in human breast cancer genomes.

TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

Nimbus: a design-driven analyses suite for amplicon-based NGS data.

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

A gene signature related to programmed cell death to predict immunotherapy response and prognosis in colon adenocarcinoma.

Frequent somatic mutations of GNAQ in uveal melanoma and blue naevi.

Activation-induced cytidine deaminase acts as a mutator in BCR-ABL1-transformed acute lymphoblastic leukemia cells.

Somatic mutations of the Parkinson's disease-associated gene PARK2 in glioblastoma and other human malignancies.

AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes.

Personalized medicine: the future is not what it used to be.

The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

Prevalence and functional analysis of sequence variants in the ATR checkpoint mediator Claspin.

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer.

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

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

Global variation in copy number in the human genome.

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.