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 35

System / cell line: whole-genome ✕ Assay: mutation ✕ Clear

Characterizing natural variation using next-generation sequencing technologies.

PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups

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Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.

pichia individuals saccharomyces individual whole-genome partial comparative
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
Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

PMID 15361934 · PMC515368 · PLoS biology · 2004 · 7 claims · 8 setups

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The HIF-1/VHL-1/EGL-9 hydroxylase pathway is tightly conserved in C. elegans

elegans whole-genome rnase pharmacological
The field of tissue injury in the lung and airway.

PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

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Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific
TAC3 and TACR3 mutations in familial hypogonadotropic hypogonadism reveal a key role for Neurokinin B in the central control of reproduction.

PMID 19079066 · PMC4312696 · Nature genetics · 2009 · 8 claims · 5 setups

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Homozygous loss-of-function mutations in TAC3 or TACR3 cause congenital hypogonadotropic hypogonadism in four consanguineous families

consanguineous genomic hek293a hek293 genome sanger calcium
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
A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

PMID 25392735 · PMC4228822 · GigaScience · 2014 · 8 claims · 8 setups

Has reproduction · 61

T. melanosporum shows a high rate of cytosine methylation (>44%) that selectively targets transposable elements rather than genes, with a strong preference for CpG sites.

tuber ectomycorrhizal melanosporum rna-seq whole-genome sequencing guided
Evolution of genomic sequence inhomogeneity at mid-range scales.

PMID 19891785 · PMC2779198 · BMC genomics · 2009 · 7 claims · 3 setups

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MRI regions have comparable levels of de novo mutations to control genomic sequences with average base composition.

chimpanzee population genome whole-genome snp indel
Candida albicans genome sequence: a platform for genomics in the absence of genetics.

PMID 15239821 · PMC463275 · Genome biology · 2004 · 8 claims · 5 setups

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Publication of the complete diploid C. albicans genome sequence will accelerate research into the pathogenesis of Candida infections

candida sc5314 whole-genome fingerprinting multi-locus
Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

PMID 24221193 · PMC3912411 · Genome research · 2014 · 8 claims · 8 setups

Has reproduction · 30

Treatment-naïve epithelial ovarian cancers show extensive intra-tumor heterogeneity of genomic rearrangements, with the most substantial differences occurring between omentum/peritoneum metastases and ovarian tumor sites.

tumor each rna-seq whole-genome targeted pcr-based
Genome-wide diversity and selective pressure in the human rhinovirus.

PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

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Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

diverse hrv fully hrva genome phylogenetic pairwise
Biodefense versus bioterrorism.

PMID 18771576 · PMC2575524 · Genome biology · 2008 · 5 claims · 4 setups

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Whole-genome sequencing and comparative genomics of the attack strain were used to trace the anthrax letters to a specific laboratory flask

bacillus ancestral cultures anthrax whole-genome comparative colony
Widespread ultraconservation divergence in primates.

PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

hg18 genome genes computed comparative snp gene
Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

PMID 19706363 · PMC3525194 · Human genomics · 2009 · 8 claims · 6 setups

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A novel HPV type (HPV-85) was identified and phylogenetically characterized, showing closest relatedness to HPV-70/39/18/45/59 within the A7 genital HPV group

novel hpv gene h5n1 whole-genome intrinsic statistical
The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

PMID 11178241 · PMC138858 · Genome biology · 2000 · 8 claims · 4 setups

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The V. cholerae O1 (El Tor) genome consists of two chromosomes with asymmetrically distributed gene functions

vibrio whole-genome microarray expression
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups

Has reproduction · 93

Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.

melanogaster dgrp complete wolbachia-infected whole-genome diagnostic coverage-based
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

PMID 37160956 · PMC10169776 · Scientific reports · 2023 · 7 claims · 8 setups

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Spontaneous ΦD5-resistant D. solani mutants DsR34 and DsR207 show significantly reduced virulence and colonization ability in planta compared to wild-type

potato solani planta maceration genome
A critical reassessment of the role of mitochondria in tumorigenesis.

PMID 16187796 · PMC1240051 · PLoS medicine · 2005 · 8 claims · 8 setups

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A significant number of published medical mtDNA cancer studies are based on obviously flawed sequencing results.

hepatocellular papillary prostate tissues mtdna mutational
Human genome research in China.

PMID 15168679 · PMC7079922 · Journal of molecular medicine (Berlin, Germany) · 2004 · 8 claims · 8 setups

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China completed its assigned 1% share of the international Human Genome Project sequencing effort and contributed ~10% of the HapMap effort

genome chinese high-risk nb4 large-scale mutation positional

Experiments

Characterizing natural variation using next-generation sequencing technologies.

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

Genetic analysis of pathways regulated by the von Hippel-Lindau tumor suppressor in Caenorhabditis elegans.

The field of tissue injury in the lung and airway.

TAC3 and TACR3 mutations in familial hypogonadotropic hypogonadism reveal a key role for Neurokinin B in the central control of reproduction.

Recurring mutations found by sequencing an acute myeloid leukemia genome.

A comprehensive resource of genomic, epigenomic and transcriptomic sequencing data for the black truffle Tuber melanosporum.

Evolution of genomic sequence inhomogeneity at mid-range scales.

Candida albicans genome sequence: a platform for genomics in the absence of genetics.

Genomic and transcriptomic plasticity in treatment-naive ovarian cancer.

Genome-wide diversity and selective pressure in the human rhinovirus.

Biodefense versus bioterrorism.

Widespread ultraconservation divergence in primates.

Human genomic diversity, viral genomics and proteomics, as exemplified by human papillomaviruses and H5N1 influenza viruses.

The complete genome sequence of Vibrio cholerae: a tale of two chromosomes and of two lifestyles.

Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.

Massively parallel pyrosequencing in HIV research.

Spontaneous mutations in hlyD and tuf genes result in resistance of Dickeya solani IPO 2222 to phage ϕD5 but cause decreased bacterial fitness and virulence in planta.

A critical reassessment of the role of mitochondria in tumorigenesis.

Human genome research in China.