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 37

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

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

PMID 18281252 · PMC2443276 · Carcinogenesis · 2008 · 7 claims · 4 setups

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Cigarette smoking is associated with a higher frequency of somatic mtDNA mutations in buccal cells

buccal subject ttge real-time pcr-based
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
Prostate cancer genomics: towards a new understanding.

PMID 19104501 · PMC2721916 · Nature reviews. Genetics · 2009 · 8 claims · 8 setups

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Multiple GWAS have identified over a dozen replicated germline SNPs each associated with a modest increase in prostate cancer risk

germline families african-american combined genome-wide linkage admixture
Alcohol consumption and breast tumor mitochondrial DNA mutations.

PMID 19847642 · PMC4403627 · Breast cancer research and treatment · 2010 · 8 claims · 6 setups

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Somatic mtDNA mutations are a frequent occurrence in breast tumors

breast paraffin-embedded blood study ttge sequencing immunohistochemistry
Complex genetic diseases: controversy over the Croesus code.

PMID 11532206 · PMC138948 · Genome biology · 2001 · 8 claims · 3 setups

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The common disease/common variant hypothesis is predicted by population genetic theory (founder population dynamics, mutation-drift-selection balance) and supported by empirical examples such as APOE*E4.

chromosome northern disease large-scale genome-wide database
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
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
Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

PMID 35028613 · PMC8714941 · Cell reports. Medicine · 2021 · 8 claims · 8 setups

Has reproduction · 75

Stage-stratified molecular subclassification (analyzing Ta and T1 separately) is more biologically and clinically informative than subtypes derived from all NMIBC combined, especially for T1 tumors.

stage combined patients copy genome-wide targeted
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
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
DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

PMID 18987736 · PMC2603574 · Nature · 2008 · 8 claims · 8 setups

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Whole genome sequencing can identify unbiased, novel somatic mutations in a cytogenetically normal AML genome that would not have been found by candidate-gene resequencing.

aml tumor novo additional genome snp comparative
B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

PMID 9236193 · PMC2198998 · The Journal of experimental medicine · 1997 · 6 claims · 3 setups

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EBV-transformed B cells from NER-defective patients (XP-B, XP-D, XP-V, CS-A) show a high frequency of point mutations in Ig heavy and light chain V regions but not in C regions

ebv-transformed cloned rt-pcr southern sequence
Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

PMID 15867095 · PMC2213188 · The Journal of experimental medicine · 2005 · 7 claims · 6 setups

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IgVH genes have evolved precise placement of coding-strand Cs so that AID-induced C-to-T mutations are predominantly silent, especially in the CDRs.

igvh germline non-igv immunogenetics flow cdna bioinformatic
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
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups

Has reproduction · 89

TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency

melanogaster simulated long-read whole-genome genome
Recurring mutations found by sequencing an acute myeloid leukemia genome.

PMID 19657110 · PMC3201812 · The New England journal of medicine · 2009 · 8 claims · 8 setups

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Deep paired tumor/normal whole-genome sequencing of a cytogenetically normal AML-M1 genome identified 12 somatic coding (tier 1) mutations and 52 somatic tier 2 (conserved/regulatory) mutations.

aml-m1 tumor bone additional whole-genome snp gene-expression
Recurrent KRAS codon 146 mutations in human colorectal cancer.

PMID 16969076 · PMC2714972 · Cancer biology & therapy · 2006 · 8 claims · 8 setups

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KRAS A146 missense mutations are a recurrent, previously unrecognized class of somatic mutation in colorectal cancer

colorectal sporadic familial cancer pcr direct chi-squared
Development of a fluorescent multiplex assay for detection of MSI-High tumors.

PMID 15528789 · PMC3839403 · Disease markers · 2004 · 8 claims · 7 setups

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Mononucleotide markers are the most sensitive and specific microsatellite marker type for detecting MSI-H tumors with MMR defects

colorectal blood healthy non-msi-h microsatellite fluorescent immunohistochemistry
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
ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.

PMID 18416817 · PMC2377272 · BMC cancer · 2008 · 8 claims · 7 setups

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Five genes (NQO1, ATBF1, DBNDD1, HSBP1, CGI-38) at 16q show significantly lower mRNA expression in breast tumors with LOH at 16q compared to tumors without LOH

ductal same sporadic paired cdna quantitative genotyping

Experiments

Associations between cigarette smoking and mitochondrial DNA abnormalities in buccal cells.

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

Prostate cancer genomics: towards a new understanding.

Alcohol consumption and breast tumor mitochondrial DNA mutations.

Complex genetic diseases: controversy over the Croesus code.

Getting started in computational immunology.

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

Stage-stratified molecular profiling of non-muscle-invasive bladder cancer enhances biological, clinical, and therapeutic insight.

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

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

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome.

B lymphocytes of xeroderma pigmentosum or Cockayne syndrome patients with inherited defects in nucleotide excision repair are fully capable of somatic hypermutation of immunoglobulin genes.

Intricate targeting of immunoglobulin somatic hypermutation maximizes the efficiency of affinity maturation.

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

TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

Recurrent KRAS codon 146 mutations in human colorectal cancer.

Development of a fluorescent multiplex assay for detection of MSI-High tumors.

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.

ATBF1 and NQO1 as candidate targets for allelic loss at chromosome arm 16q in breast cancer: absence of somatic ATBF1 mutations and no role for the C609T NQO1 polymorphism.