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 381

System / cell line: acid ✕ Clear

A novel mutation in the WFS1 gene identified in a Taiwanese family with low-frequency hearing impairment.

PMID 17517145 · PMC1890544 · BMC medical genetics · 2007 · 7 claims · 6 setups

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A novel heterozygous missense mutation Y669H (2005T>C) in exon 8 of WFS1 was identified in affected family members but not in 100 controls (200 chromosomes)

family genomic 10-member wfs1 pure direct pcr-rflp
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

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MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Fucosylated glycoproteins as markers of liver disease.

PMID 19126969 · PMC3827789 · Disease markers · 2008 · 8 claims · 6 setups

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Core alpha 1,6-linked fucosylation of AFP (AFP-L3) is increased in HCC and is a more specific marker of HCC than total AFP

afp pooled larger igg lectin fucose-specific immunoblot
Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

PMID 19112531 · PMC2610290 · Molecular vision · 2008 · 8 claims · 4 setups

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A novel STRA6 missense variant (p.G217E, exon 8) and a novel STRA6 nonsense variant (p.Q592X, exon 18) were identified in one A/M subject and absent from 89 controls, implicating STRA6 in this subject's A/M phenotype.

genomic stra6 direct variant
targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

PMID 19099550 · PMC2651862 · BMC systems biology · 2008 · 8 claims · 8 setups

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A comprehensive in silico target identification pipeline (targetTB) integrating interactome, reactome, essentiality, sequence and structural analyses can identify high-confidence drug targets for Mtb

tuberculosis mtb protein-protein flux transposon
The genomic analysis of lactic acidosis and acidosis response in human cancers.

PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

mammary hmec gene breast gene real-time bayesian
Cataloging coding sequence variations in human genome databases.

PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

coding hapmap concurrent nssnps database hapmap amino
Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

PMID 18957099 · PMC2582241 · Malaria journal · 2008 · 7 claims · 8 setups

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pfhrp2 and pfhrp3 genes show markedly higher polymorphism than the P. falciparum and P. vivax aldolase and pldh genes

falciparum vivax extracted febrile pcr nested species-specific
A computational screen for type I polyketide synthases in metagenomics shotgun data.

PMID 18953415 · PMC2568958 · PloS one · 2008 · 8 claims · 6 setups

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Combining HMM domain searches with maximum-likelihood phylogenetic trees can discriminate true PKS I sequences from evolutionarily related but functionally different enzymes (e.g., FAS I) in metagenomic data.

predicted hmm-identified reference hmm hmm maximum-likelihood robinson-foulds
The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

PMID 18949050 · PMC2569417 · PloS one · 2008 · 6 claims · 5 setups

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Within individual hosts, proteasome and TAP escape mutations in HIV-1 occur frequently

hiv-1 hla-genotyped predicted bioinformatic longitudinal ancestral
Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

PMID 18948357 · PMC3044481 · Journal of medical genetics · 2009 · 8 claims · 6 setups

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TGM1 germline mutations were identified in 55% (57/104) of patients with ARCI

arci unrelated dog direct sequence blast
Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

PMID 18847511 · PMC2571112 · BMC genomics · 2008 · 8 claims · 8 setups

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[BF/S+L/Ep] butanol fraction from E. purpurea enhances maturation of human immature dendritic cells (increased CD83 expression)

immature idcs [bf phytocompounds flow mtt lal
Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

PMID 18842779 · PMC3014055 · The American journal of clinical nutrition · 2008 · 8 claims · 4 setups

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A significant gene x diet interaction exists between 5-LO promoter short alleles (3,4 repeats) and dietary AA intake in determining MI risk

costa buffy genetic real-time allele-specific
Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

PMID 18820594 · PMC2905378 · Pharmacogenetics and genomics · 2008 · 7 claims · 8 setups

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The tRNA-Thr G15927A mutation has a potential modifier role that increases penetrance and expressivity of A1555G-associated deafness.

blood genomic lymphoblastoid same pcr-rflp mitochondrial northern
The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

PMID 18718264 · PMC3835188 · The Journal of pediatrics · 2008 · 6 claims · 5 setups

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The patient carries two identical homozygous mutations (GC>AA at positions 197/198) in exon 1 of PCFT, causing a premature stop codon (C66X)

parental rfc hela blood genomic [3h]5-methyltetrahydrofolate northern
Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

PMID 18712842 · PMC2906129 · Journal of medical virology · 2008 · 8 claims · 5 setups

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Coverage of naturally occurring BKV strains varies substantially among current PCR diagnostic assays due to primer/probe mismatches

bkv virus sequence primer cross-reactivity
Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

h3n2 meme sequence entropy
Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices.

PMID 18398479 · PMC2276316 · PloS one · 2008 · 8 claims · 6 setups

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The first singular component of a PSSM acts to disfavor substitutions, penalizing potentially functionally important residues at conserved sites more severely.

representative pfam pdb right psi-blast hidden singular
Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

PMID 18304319 · PMC2268676 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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Comparative synteny conservation around a horizontally transferred gene (HTgene) can distinguish single versus multiple independent HGT events even without a robust phylogenetic tree.

poxvirus core psi-blast comparative molecular
Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.

PMID 20069058 · PMC2801467 · Journal of biomedicine & biotechnology · 2009 · 7 claims · 5 setups

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NUCKS is highly overexpressed in invasive ductal carcinoma (IDC) of the breast compared to matched normal tissue.

matched idc nucks rabbits lc-ms sds-page western

Experiments

A novel mutation in the WFS1 gene identified in a Taiwanese family with low-frequency hearing impairment.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Fucosylated glycoproteins as markers of liver disease.

Identification of STRA6 and SKI sequence variants in patients with anophthalmia/microphthalmia.

targetTB: a target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis.

The genomic analysis of lactic acidosis and acidosis response in human cancers.

Cataloging coding sequence variations in human genome databases.

Country-wide assessment of the genetic polymorphism in Plasmodium falciparum and Plasmodium vivax antigens detected with rapid diagnostic tests for malaria.

A computational screen for type I polyketide synthases in metagenomics shotgun data.

The specificity and polymorphism of the MHC class I prevents the global adaptation of HIV-1 to the monomorphic proteasome and TAP.

Novel transglutaminase-1 mutations and genotype-phenotype investigations of 104 patients with autosomal recessive congenital ichthyosis in the USA.

Genomics and proteomics of immune modulatory effects of a butanol fraction of echinacea purpurea in human dendritic cells.

Nutrigenetic association of the 5-lipoxygenase gene with myocardial infarction.

Mitochondrial tRNAThr G15927A mutation may modulate the phenotypic manifestation of ototoxic 12S rRNA A1555G mutation in four Chinese families.

The clinical course and genetic defect in the PCFT gene in a 27-year-old woman with hereditary folate malabsorption.

Biologic diversity of polyomavirus BK genomic sequences: Implications for molecular diagnostic laboratories.

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

Nature of protein family signatures: insights from singular value analysis of position-specific scoring matrices.

Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

Immunohistochemical and proteomic evaluation of nuclear ubiquitous casein and cyclin-dependent kinases substrate in invasive ductal carcinoma of the breast.