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 39

System / cell line: sequences ✕ Assay: linkage ✕ Clear

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

PMID 17984073 · PMC2238967 · Nucleic acids research · 2008 · 8 claims · 8 setups

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EPGD is a gene-centered, internet-accessible database integrating paralog family and paralogon information for 26 eukaryotic genomes.

sequences homologous proteins coding pairwise single sequence
Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

PMID 17877794 · PMC2238324 · BMC bioinformatics · 2007 · 7 claims · 7 setups

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lwgv provides a lightweight alternative to large genome browsers for visualizing biological annotations and dynamic analyses without requiring a database or complex software infrastructure

chromosome user-submitted hannon-elledge gene linkage rnai shrna
Arrhythmogenic right ventricular cardiomyopathy type 6 (ARVC6): support for the locus assignment, narrowing of the critical region and mutation screening of three candidate genes.

PMID 16569242 · PMC1444927 · BMC medical genetics · 2006 · 7 claims · 4 setups

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Linkage and haplotype analysis in the South African family are highly suggestive of linkage to the ARVC6 locus on chromosome 10p12-p14

south genomic family genetic direct bioinformatic
Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

PMID 9989976 · PMC2192941 · The Journal of experimental medicine · 1999 · 8 claims · 8 setups

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The Lps locus was fine-mapped to a 0.9-cM interval spanning a 1.7-Mb genomic contig on mouse chromosome 4.

c3h genomic bac multiple-tissue genetic yac direct
A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

PMID 18958306 · PMC2573734 · Molecular vision · 2008 · 8 claims · 7 setups

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The disease locus maps to chromosome 3q21-25, linked to markers D3S2322 and D3S1541

four-generation bfsp2 wild-type microsatellite direct denaturing
Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

PMID 18616530 · PMC4732719 · Clinical genetics · 2008 · 8 claims · 8 setups

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TMC1 mutations were identified in seven of the families/patients segregating hearing loss linked to DFNA36/DFNB7-11

families affected tmc1 tjp2 genetic sequencing multiplex
Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

PMID 18334953 · PMC2268897 · Molecular vision · 2008 · 8 claims · 6 setups

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A G61C (P.G61C) missense mutation in CRYGD causes autosomal dominant congenital coralliform cataracts in this family

four-generation genomic crygd wild-type genotyping direct denaturing
PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

PMID 16430766 · PMC1434729 · BMC medical genetics · 2006 · 7 claims · 8 setups

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Linkage analysis can pre-select which gene (PKD1 or PKD2) to screen for mutations in ADPKD families with sufficient samples

genomic pcr additional cat linkage direct heteroduplex
Genotypic analysis of two hypervariable human cytomegalovirus genes.

PMID 18649324 · PMC2658010 · Journal of medical virology · 2008 · 8 claims · 8 setups

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UL146 sequences from 184 samples fall into the same 14 genotypes (G1-G14) previously defined, with no new genotypes found.

hcmv clinical pcr ul146 pcr nested molecular
A novel nonsense mutation in CRYBB1 associated with autosomal dominant congenital cataract.

PMID 18432316 · PMC2324115 · Molecular vision · 2008 · 7 claims · 5 setups

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A novel heterozygous nonsense mutation (c.C737T, p.Q223X) in CRYBB1 is responsible for autosomal dominant congenital nuclear cataract in this family.

three-generation genomic crybb1 family genotyping direct restriction
AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

PMID 17135205 · PMC1781224 · Nucleic acids research · 2007 · 7 claims · 3 setups

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AnimalQTLdb houses publicly available QTL data for multiple livestock species (pig, cattle, chicken) in one comparable database.

pig cattle blast comparative database
Ensembl 2006.

PMID 16381931 · PMC1347495 · Nucleic acids research · 2006 · 8 claims · 5 setups

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Ensembl now provides annotation for 19 genomes, up from 4 the previous year, including new mammalian (Rhesus macaque, Opossum), chordate (Ciona intestinalis), and yeast genomes.

cow ensembl snps genome gene whole-genome pairwise
Atlas - a data warehouse for integrative bioinformatics.

PMID 15723693 · PMC554782 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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Atlas is a biological data warehouse that locally stores and integrates sequences, molecular interactions, homology information, functional annotations, and ontologies

in-house gene omim genome molecular gene-disease
Species-specific protein sequence and fold optimizations.

PMID 12487631 · PMC139977 · BMC bioinformatics · 2002 · 7 claims · 7 setups

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Environmental niche is a significant factor explaining variability in amino acid composition across 100 complete genomes

predicted mean over orf principal hierarchical domain-based
Molecular characterization of retinitis pigmentosa in Saudi Arabia.

PMID 19956407 · PMC2786884 · Molecular vision · 2009 · 8 claims · 7 setups

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The causative mutation was identified in 51 of 52 (94%/98%) Saudi RP patients, including seven novel mutations.

blood-derived families pcr-amplified ethnically genome-wide linkage bidirectional
SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

PMID 19793867 · PMC2808975 · Nucleic acids research · 2010 · 8 claims · 8 setups

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A new 8.5x-coverage silkworm genome assembly with N50 scaffold size of ~3.7 Mb over a 432 Mb genome represents a significant quality improvement over the prior draft.

bombyx whole-genome snp novo
The gentle art of gene arrangement: the meaning of gene clusters.

PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

populations mhc interphase cartilaginous sequence codon comparative
Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

PMID 16150157 · PMC1236922 · BMC genomics · 2005 · 8 claims · 5 setups

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HERV-W (envW) and HERV-FRD (envFRD) envelope genes, both specifically expressed in placenta, show strong sequence conservation with only two nonsynonymous SNPs identified across 91 individuals

genomic genotype 293t pcr-amplified pcr haplotype cell-cell
Characterisation of the genetic diversity of Brucella by multilocus sequencing.

PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

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Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

brucella sequenced concatenated allelic multilocus ratio neighbour-joining
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide

Experiments

EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information.

Lightweight genome viewer: portable software for browsing genomics data in its chromosomal context.

Arrhythmogenic right ventricular cardiomyopathy type 6 (ARVC6): support for the locus assignment, narrowing of the critical region and mutation screening of three candidate genes.

Endotoxin-tolerant mice have mutations in Toll-like receptor 4 (Tlr4).

A new mutation in BFSP2 (G1091A) causes autosomal dominant congenital lamellar cataracts.

Mutation analysis of TMC1 identifies four new mutations and suggests an additional deafness gene at loci DFNA36 and DFNB7/11.

Mutation G61C in the CRYGD gene causing autosomal dominant congenital coralliform cataracts.

PKD1 and PKD2 mutations in Slovenian families with autosomal dominant polycystic kidney disease.

Genotypic analysis of two hypervariable human cytomegalovirus genes.

A novel nonsense mutation in CRYBB1 associated with autosomal dominant congenital cataract.

AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond.

Ensembl 2006.

Atlas - a data warehouse for integrative bioinformatics.

Species-specific protein sequence and fold optimizations.

Molecular characterization of retinitis pigmentosa in Saudi Arabia.

SilkDB v2.0: a platform for silkworm (Bombyx mori ) genome biology.

The gentle art of gene arrangement: the meaning of gene clusters.

Comprehensive search for intra- and inter-specific sequence polymorphisms among coding envelope genes of retroviral origin found in the human genome: genes and pseudogenes.

Characterisation of the genetic diversity of Brucella by multilocus sequencing.

Genomics: applications in mechanism elucidation.