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 25

System / cell line: mutation ✕ Assay: mutation-rate ✕ Clear

Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

complete mutation sars-cov spike sequence phylogenetic selection
Genomic mutation rates: what high-throughput methods can tell us.

PMID 19644920 · PMC2952423 · BioEssays : news and reviews in molecular, cellular and developmental biology · 2009 · 8 claims · 8 setups

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High-throughput DNA analyses yield genome mutation rate estimates markedly higher than those obtained with pre-genomic strategies

cerevisiae elegans melanogaster mammals fluctuation mutation indirect
Mutation patterns of mtDNA: empirical inferences for the coding region.

PMID 18518963 · PMC2438339 · BMC evolutionary biology · 2008 · 5 claims · 3 setups

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Heteroplasmy was detected in 6.5% (3/46) of Azorean families analyzed, all caused by new point mutations with no insertions/deletions.

extended-family same direct electropherogram molecular
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

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p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser
Lineage specific recombination rates and microevolution in Listeria monocytogenes.

PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Recombination is more prevalent in lineage II than in lineage I

listeria allelic unique monocytogenes multilocus sawyer's genealogical
Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

PMID 35893303 · PMC9329910 · Journal of personalized medicine · 2022 · 8 claims · 8 setups

Has reproduction · 100

KYNU expression is decreased in melanoma despite a high KYNU mutation rate in the TCGA database

tcga-skcm melanoma keratinocytes differential copy methylation
Design and analysis issues in genome-wide somatic mutation studies of cancer.

PMID 18692126 · PMC2820387 · Genomics · 2009 · 6 claims · 4 setups

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Two-stage (discovery + validation) sequencing designs efficiently allocate resources and can produce highly informative candidate driver gene lists even with relatively small sample sizes.

hypothetical panel colorectal germline simulation targeted genome-wide
Pathogenic mitochondrial DNA mutations are common in the general population.

PMID 18674747 · PMC2495064 · American journal of human genetics · 2008 · 7 claims · 6 setups

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At least 1 in 200 healthy humans harbors a pathogenic mtDNA mutation with potential to cause disease in offspring of female carriers

neonatal independent m.1555a→g-positive mutation-positive high-throughput last-cycle cloning
Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Simple models of genomic variation in human SNP density.

PMID 17553150 · PMC1919371 · BMC genomics · 2007 · 6 claims · 4 setups

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Hierarchical Poisson model B, which allows both the mutation-rate proxy (Beta-distributed Λ) and the ARG-size proxy (Gamma-distributed T) to vary, fits the observed SNP density distribution significantly better than models with only one or neither varying.

genome observed simulated genome hierarchical coalescent
Calculating expected DNA remnants from ancient founding events in human population genetics.

PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

simulated forward-based size
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
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
Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

PMID 37032329 · PMC10084625 · Microbiome · 2023 · 8 claims · 7 setups

Has reproduction · 89

MAPQ ≥30 filtering improves precision but substantially reduces recall, especially for unrepresented/divergent eukaryotic taxa

eukdetect simulated zymobiomics read holdout mutation-rate
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
Profiling human androgen receptor mutations reveals treatment effects in a mouse model of prostate cancer.

PMID 19010817 · PMC2748651 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

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Somatic AR mutations in h/mAR-TRAMP tumors are non-random and their genomic location correlates with treatment type (castration/antiandrogen vs intact).

mar-tramp testis cv-1 ar-negative immunohistochemistry serum survival
Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

PMID 19847288 · PMC2759524 · PLoS computational biology · 2009 · 8 claims · 3 setups

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Three distinct infection types (A, B, C) emerge as maxima in the pathogen fitness landscape, each with characteristic within-host dynamics, contact network structure, and transmission mode

generic simulated hiv-1 stochastic dynamic regression
A near complete genome for goat genetic and genomic research.

PMID 34507524 · PMC8434745 · Genetics, selection, evolution : GSE · 2021 · 8 claims · 8 setups

Has reproduction · 89

Saanen_v1 is a high-quality de novo goat genome assembly from a male Saanen buck, including the first goat Y chromosome scaffold.

saanen goat testicular saanen_v1 pacbio illumina hi-c
hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

PMID 17207965 · PMC4647941 · Genomics · 2007 · 8 claims · 7 setups

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hORFeome v3.1 is a resource of 12,212 cloned human ORFs representing 10,214 genes, a 51% expansion over hORFeome v1.1

mgc cloned orfs genome gateway orf blat
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

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A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

Genomic mutation rates: what high-throughput methods can tell us.

Mutation patterns of mtDNA: empirical inferences for the coding region.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

Differential Gene Expression and Methylation Analysis of Melanoma in TCGA Database to Further Study the Expression Pattern of KYNU in Melanoma.

Design and analysis issues in genome-wide somatic mutation studies of cancer.

Pathogenic mitochondrial DNA mutations are common in the general population.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Simple models of genomic variation in human SNP density.

Calculating expected DNA remnants from ancient founding events in human population genetics.

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

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

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.

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

Profiling human androgen receptor mutations reveals treatment effects in a mouse model of prostate cancer.

Antigenic diversity, transmission mechanisms, and the evolution of pathogens.

A near complete genome for goat genetic and genomic research.

hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.