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: natural ✕ Assay: sanger ✕ Clear

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

european-american yoruban japanese case sanger snp linkage
Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

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Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

spanish rp5 population candidate direct comparative pcr
Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

PMID 19788831 · PMC2819849 · Emerging infectious diseases · 2009 · 8 claims · 5 setups

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NA gene sequences of oseltamivir-resistant viruses (ORVs) form a distinct phylogenetic cluster separate from oseltamivir-sensitive viruses (OSVs)

influenza clinical partial sanger pyrosequencing molecular
G, N, and P gene-based analysis of Chandipura viruses, India.

PMID 15705335 · PMC3294343 · Emerging infectious diseases · 2005 · 8 claims · 4 setups

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The 2003 epidemic CHPV isolates are closely related to, and not very divergent from, the 1965 isolate, indicating the outbreak was not associated with extensive mutations in the G, N, and P genes.

chpv partial rt-pcr sequence phylogenetic
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

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N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

PMID 19890401 · PMC2768328 · PloS one · 2009 · 7 claims · 7 setups

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Reverse mutations to the wild type (HIV-1C consensus) in Gag appear significantly earlier than escape mutations from the wild type during primary infection

hiv-1 same sequenced gag single-genome mhc hypermutation
Genetic variation of SARS coronavirus in Beijing Hospital.

PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

clinical extracted rna-derived cloned nested screening direct
Genomic signatures of human versus avian influenza A viruses.

PMID 17073083 · PMC3294750 · Emerging infectious diseases · 2006 · 8 claims · 6 setups

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52 validated 'species-associated' amino acid positions distinguish human from avian influenza A viruses

throat clinical 401-genome avian rt-pcr immunofluorescent sequence
The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

pbmcs clonal env deduced nested maximum-likelihood positive
From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

PMID 33960035 · PMC9292448 · Molecular ecology · 2021 · 7 claims · 6 setups

Has reproduction · 59

382 (over 383) genomic regions contain SNPs that are consistently zonated across all surveyed intertidal habitats spanning the North Atlantic.

semibalanus individual rocky barnacles pool-seq sanger temperature
Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

tlr4 mus chimpanzee baboon genomic coding sequence
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

PMID 19747392 · PMC2754481 · BMC evolutionary biology · 2009 · 8 claims · 5 setups

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The coding sequence of FGF5 is not the critical determinant of hair length differences among elephantids, including the woolly mammoth.

asian fgf5 woolly savanna pcr structural blast
Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

PMID 19716302 · PMC2748900 · Current biology : CB · 2009 · 7 claims · 4 setups

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Direct sequencing of a 13-generation pedigree yields a Y-chromosome mutation rate of 3.0 × 10^-8 mutations/nucleotide/generation

flow-sorted cell-line family lymphoblastoid y-chromosome capillary y-str
In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

strains genomic celera blast-based targeted phred
High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

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Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

genomic ecotilling non-synonymous ecotilling sanger universal-primer
Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

PMID 19750224 · PMC2735778 · PLoS pathogens · 2009 · 7 claims · 5 setups

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The IRGM −261TT genotype is negatively associated with (protective against) pulmonary TB caused by M. tuberculosis

pulmonary tuberculosis reporter genotyped case-control gene spoligotyping
Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

PMID 16280054 · PMC1410740 · Breast cancer research : BCR · 2005 · 8 claims · 7 setups

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None of the six candidate genes (CBFA2T3, TERF2, TERF2IP, FBXL8, LRRC29, FANCA) showed inactivating mutations or expression differences clearly associated with 16q LOH status

breast quantitative fragment gene-expression
Examination of FMR1 transcript and protein levels among 74 premutation carriers.

PMID 19927162 · PMC4122982 · Journal of human genetics · 2010 · 7 claims · 4 setups

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FMR1 premutation carriers (55-199 CGG repeats) show increased FMR1 transcript levels alongside decreased FMRP levels compared to normal individuals.

peripheral subset real-time western cgg
Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.

PMID 19650937 · PMC3224928 · Malaria journal · 2009 · 8 claims · 5 setups

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Sequence group 1 (mainly from uncomplicated malaria) is significantly different in distribution from sequence group 3 (mainly from severe malaria)

falciparum falciparum-infected pcr-amplified non-identical static rosette rt-pcr

Experiments

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

Genomic diversity of oseltamivir-resistant influenza virus A (H1N1), Luxembourg, 2007-08.

G, N, and P gene-based analysis of Chandipura viruses, India.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

Timing constraints of in vivo gag mutations during primary HIV-1 subtype C infection.

Genetic variation of SARS coronavirus in Beijing Hospital.

Genomic signatures of human versus avian influenza A viruses.

The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

From tides to nucleotides: Genomic signatures of adaptation to environmental heterogeneity in barnacles.

Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

Sequence polymorphisms cause many false cis eQTLs.

Genetic variation at hair length candidate genes in elephants and the extinct woolly mammoth.

Human Y chromosome base-substitution mutation rate measured by direct sequencing in a deep-rooting pedigree.

In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

Expression analysis of candidate breast tumour suppressor genes on chromosome 16q.

Examination of FMR1 transcript and protein levels among 74 premutation carriers.

Sequence variation of PfEMP1-DBLalpha in association with rosette formation in Plasmodium falciparum isolates causing severe and uncomplicated malaria.