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 80

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

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
Genetic analysis of MEFV gene pyrin domain in patients with Behçet's disease.

PMID 16951489 · PMC1592598 · Mediators of inflammation · 2006 · 6 claims · 2 setups

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No deletion, insertion, or point mutations were found in the pyrin domain of the MEFV gene in any of the 54 Turkish BD patients analyzed.

genomic pcr pcr direct
Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

PMID 24782521 · PMC4066758 · Nucleic acids research · 2014 · 8 claims · 5 setups

Has reproduction · 79

EDD is a new algorithm that detects broad (megabase-size) enrichment domains from ChIP-seq data of widely distributed chromatin proteins such as A- and B-type lamins.

normal dermal analysis set chip-seq chip-qpcr rna-seq
Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

PMID 18564434 · PMC2453528 · BMC genomics · 2008 · 8 claims · 6 setups

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Jmjd6 has been misleadingly annotated as a transmembrane receptor for engulfment of apoptotic cells; recent evidence contradicts this transmembrane receptor function

species genomic jmjd6 jmjc reciprocal comparative est
Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

PMID 18673550 · PMC2533329 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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The human TRIM family is split into two groups (group 1 and group 2) that differ in domain structure, genomic organization, and evolutionary properties.

redundant mammalian genomic vertebrates blast pattern-hit tblastn
Undergraduate research. Genomics Education Partnership.

PMID 18974335 · PMC2953277 · Science (New York, N.Y.) · 2008 · 6 claims · 4 setups

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A course-embedded, multi-institution undergraduate research model (the Genomics Education Partnership) can deliver authentic research experiences during the academic year rather than only in summer programs.

drosophila dot undergraduate genomic gene comparative
Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

PMID 35899250 · PMC9309459 · Evolutionary applications · 2022 · 8 claims · 7 setups

Has reproduction · 75

XP-CLR and FST scans identify genomic regions with distorted allele frequency/differentiation patterns resulting from differential selective pressures between Vietnamese rice subpopulations

vietnamese indica subpopulation whole-genome whole-genome xp-clr fst
A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

PMID 11305939 · PMC31480 · Genome biology · 2001 · 8 claims · 8 setups

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SLC4A9 is a novel human NBC-like gene on chromosome 5q31 encoding a 990-amino-acid, 12-transmembrane-domain protein with high similarity to other sodium bicarbonate cotransporters

bac kidney genomic marathon genomic cdna pcr
ECgene: genome annotation for alternative splicing.

PMID 15608289 · PMC540072 · Nucleic acids research · 2005 · 8 claims · 5 setups

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ECgene combines genome-based EST clustering with a graph-theoretic transcript assembly procedure to predict gene models including alternative splicing events.

brca2 rgs17 organs cdna genomic genome transcript
A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

PMID 19693293 · PMC2728569 · Molecular vision · 2009 · 7 claims · 5 setups

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A novel in-frame 51 bp deletion (c.526_576del51) in TACSTD2, causing loss of 17 amino acids (codons 176-192), was identified as homozygous in two affected brothers with GDLD.

genomic excised left pcr pcr-restriction histopathology
A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

PMID 19649163 · PMC2718742 · Molecular vision · 2009 · 7 claims · 7 setups

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A novel heterozygous UBIAD1 mutation, G98S, was identified in two affected members (proband and her father) of a Chinese SCCD family.

genomic cornea corneas blood direct pcr laser
Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

PMID 16022726 · PMC1187884 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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466 Tetraodon GPCRs (Tnig-GPCRs) were identified genome-wide, of which 457 had not been previously reported

tetraodon tnig-gpcr non-rhodopsin-like domain sequence transmembrane
Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

PMID 15716312 · PMC549403 · Nucleic acids research · 2005 · 8 claims · 5 setups

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About 1000 genes across four vertebrate gene sets analyzed contain at least one RETRA marker protein domain

predicted non-masked genome interpro hmm tblastn inter-species
Comparative genomic analysis of three Leishmania species that cause diverse human disease.

PMID 17572675 · PMC2592530 · Nature genetics · 2007 · 8 claims · 6 setups

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L. infantum and L. braziliensis genomes were sequenced and show marked conservation of synteny with L. major, with only ~200 genes differentially distributed among the three species

infantum major braziliensis leishmania whole-genome comparative pcr
Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

PMID 17515881 · PMC2669507 · Molecular vision · 2007 · 8 claims · 6 setups

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Five RS1 mutations (c.574C>T, c.583A>G, c.608C>T, c.617G>A, c.637C>T) were identified in exon 6 of six unrelated Indian XLRS patients

genomic pcr xlrs retinoschisin pcr-sscp direct rflp
Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

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Mutations in USH2A are responsible for most cases of USH2

genomic family probands ush2a direct restriction single
SysZNF: the C2H2 zinc finger gene database.

PMID 18974185 · PMC2686507 · Nucleic acids research · 2009 · 7 claims · 6 setups

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SysZNF is a database that systematically catalogs C2H2-ZNF genes in human and mouse with physical location, gene models, expression probes, protein domains, homologs, and literature links

user-defined hmm domain all-to-all
Mutation screening of HSF4 in 150 age-related cataract patients.

PMID 18941546 · PMC2569895 · Molecular vision · 2008 · 8 claims · 4 setups

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Five new HSF4 sequence variants (c.1020-25G>A, c.1078A>G, c.1223C>T, c.1256+25C>T, c.1286C>T) were found in age-related cataract patients but not in 220 controls.

peripheral hsf4b hsf4 genomic secondary sequence
Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

PMID 18204449 · PMC2684619 · Nature genetics · 2008 · 8 claims · 8 setups

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Mutations in GLE1, an mRNA export mediator, cause LCCS1

lccs1 laahd finnish healthy genomic microsatellite carrier
ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

genomic red computational abo sequencing blood

Experiments

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

Genetic analysis of MEFV gene pyrin domain in patients with Behçet's disease.

Enriched domain detector: a program for detection of wide genomic enrichment domains robust against local variations.

Genomic structure and expression of Jmjd6 and evolutionary analysis in the context of related JmjC domain containing proteins.

Genomic analysis of the TRIM family reveals two groups of genes with distinct evolutionary properties.

Undergraduate research. Genomics Education Partnership.

Genomic regions and candidate genes selected during the breeding of rice in Vietnam.

A novel sodium bicarbonate cotransporter-like gene in an ancient duplicated region: SLC4A9 at 5q31.

ECgene: genome annotation for alternative splicing.

A novel TACSTD2 mutation identified in two Chinese brothers with gelatinous drop-like corneal dystrophy.

A novel UBIAD1 mutation identified in a Chinese family with Schnyder crystalline corneal dystrophy.

Genome wide survey of G protein-coupled receptors in Tetraodon nigroviridis.

Protein coding potential of retroviruses and other transposable elements in vertebrate genomes.

Comparative genomic analysis of three Leishmania species that cause diverse human disease.

Genetic variations in the hotspot region of RS1 gene in Indian patients with juvenile X-linked retinoschisis.

Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

SysZNF: the C2H2 zinc finger gene database.

Mutation screening of HSF4 in 150 age-related cataract patients.

Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.