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 26

System / cell line: transformed ✕ Assay: genomic ✕ Clear

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

PMID 16934001 · PMC1550284 · PLoS genetics · 2006 · 7 claims · 6 setups

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The E320Q, Q463H, and L706S STAT1 alleles are intrinsically deleterious for both IFNG/GAF-mediated and IFNA/ISGF3-mediated immunity when tested in STAT1-deficient transfected cells

ebv-transformed sv40-transformed nuclear stat1-deficient cdna western immunofluorescence
Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage
The personal genome project.

PMID 16729065 · PMC1681452 · Molecular systems biology · 2005 · 8 claims · 1 setups

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A Personal Genome Project (PGP) should be established as the natural successor to the Human Genome Project, providing integrated genome and phenome data for genetically diverse subjects.

ebv-transformed renewable
Investigations on a clinically and functionally unusual and novel germline p53 mutation.

PMID 12085209 · PMC2746598 · British journal of cancer · 2002 · 8 claims · 7 setups

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A novel germline 7 base pair insertion in exon 5 of p53 (causing frameshift from codon 161 with a stop at codon 182) was identified in a patient with osteosarcoma at age 22 and choroid plexus papilloma at age 29.

peripheral yeast saos-2 genomic fasay apoptotic
Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

PMID 17895983 · PMC1976591 · PloS one · 2007 · 8 claims · 5 setups

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Sequencing of complete mtDNA genomes in 23 pediatric patients identified 27 significant variants (12 novel, 15 known) associated with mitochondrial encephalomyopathies.

blood-derived lymphocytes maternal wild-type complete respiratory pcr-rflp
PAX6 gene variations associated with aniridia in south India.

PMID 15086958 · PMC419353 · BMC medical genetics · 2004 · 7 claims · 5 setups

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Mutations in PAX6 cause the aniridia phenotype via haploinsufficiency (loss-of-function/null alleles)

genomic pcr aniridia sscp automated allele-specific
Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

PMID 17010193 · PMC1599749 · BMC cancer · 2006 · 8 claims · 4 setups

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No germline deleterious mutations were identified in the ATR coding region among 54 non-BRCA1/2 high-risk French Canadian breast cancer cases.

genomic ebv-transformed normal direct linkage rt-pcr
Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.

PMID 19097825 · PMC2692687 · Clinical immunology (Orlando, Fla.) · 2009 · 8 claims · 7 setups

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CORO1A deficiency, caused by a paternal 2bp frameshift mutation combined with a maternal de novo 600kb deletion at chromosome 16p11.2, is the molecular cause of this patient's T-B+NK+ SCID

ebv-transformed genomic father peripheral intracellular snp sequencing
Mutation analysis in primary immunodeficiency diseases: case studies.

PMID 19841577 · PMC2774237 · Current opinion in allergy and clinical immunology · 2009 · 8 claims · 8 setups

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Genomic DNA Sanger sequencing is the standard first-line approach for identifying PIDD-causing mutations but has limitations that can yield false-negative or false-positive results

mother parents ebv-transformed nemo genomic flow northern
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups

Has reproduction · 83

MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.

pooled hc227 contig sets shotgun novo alignment-free
Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

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The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

rumen blood beef metagenome snp longitudinal
Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups

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Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.

blood v34a cos1 cv1 small genome-wide strip
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

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Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

PMID 17997604 · PMC2065879 · PLoS pathogens · 2007 · 8 claims · 5 setups

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Two enJSRV proviruses (enJS56A1 and enJSRV-20) independently acquired a defective, transdominant Gag (R21W substitution) that blocks late replication steps of exogenous JSRV/ENTV

sheep nih3t3 domestic enjsrv bac retroviral locus-specific
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

PMID 19728872 · PMC2745377 · BMC medical genetics · 2009 · 8 claims · 7 setups

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A novel homozygous missense mutation, c.1922G>A (p.Arg641His), in MANBA was identified in a patient with severe neurological disease featuring pyramidal and cerebellar involvement, a phenotype not previously reported in β-mannosidosis.

family hek293t lymphoid pcr-amplified fluorometric site-directed western
CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

PMID 15507145 · PMC526769 · BMC medical genetics · 2004 · 8 claims · 7 setups

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PCR amplification and sequencing of CLC-2 revealed 1 SNP in the promoter, 4 SNPs in intron 1, and none in exon 20

nasal genomic ib3-1 western pcr fisher's
Cis sequence effects on gene expression.

PMID 17727713 · PMC2077339 · BMC genomics · 2007 · 6 claims · 4 setups

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Approximately one in four genes (8 of 30, 26.7%) exhibit statistically significant cis sequence effects on gene expression in this study, consistent with a literature-wide weighted average of 26.2%

lymphoblastoid genomic oligonucleotide gene candidate snp
Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups

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A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance

saccharomyces cerevisiae hek-293t yeast yeast β-galactosidase dual
Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.

PMID 20018283 · PMC2845297 · Atherosclerosis · 2010 · 8 claims · 7 setups

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The ADIPOQ locus is the only major gene locus for plasma adiponectin, reaching genome-wide significance in combined and sex-stratified analyses

population-based cohorts gwa plasma genome-wide replication candidate

Experiments

Novel STAT1 alleles in otherwise healthy patients with mycobacterial disease.

Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

The personal genome project.

Investigations on a clinically and functionally unusual and novel germline p53 mutation.

Analysis of mitochondrial DNA sequences in childhood encephalomyopathies reveals new disease-associated variants.

PAX6 gene variations associated with aniridia in south India.

Mutation analysis and characterization of ATR sequence variants in breast cancer cases from high-risk French Canadian breast/ovarian cancer families.

Severe combined immunodeficiency (SCID) and attention deficit hyperactivity disorder (ADHD) associated with a Coronin-1A mutation and a chromosome 16p11.2 deletion.

Mutation analysis in primary immunodeficiency diseases: case studies.

Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.

Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

A paradigm for virus-host coevolution: sequential counter-adaptations between endogenous and exogenous retroviruses.

Population genomics of human gene expression.

A MANBA mutation resulting in residual beta-mannosidase activity associated with severe leukoencephalopathy: a possible pseudodeficiency variant.

CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity.

Cis sequence effects on gene expression.

Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.

Clear detection of ADIPOQ locus as the major gene for plasma adiponectin: results of genome-wide association analyses including 4659 European individuals.