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 1.8k

Assay: sequence ✕ Clear

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

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50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

genomic α-gal cos-7 transcripts pcr southern microsatellite
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
Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

PMID 16519801 · PMC1421398 · BMC biotechnology · 2006 · 8 claims · 8 setups

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The Creator Splice system (5' intron splicing) significantly increases protein expression levels compared to the standard Creator system

hek293t mammalian coli vector immunoblot fluorescence bacterial
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
Identifying repeat domains in large genomes.

PMID 16507140 · PMC1431705 · Genome biology · 2006 · 7 claims · 5 setups

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A repeat domain graph, built using a modified A-Bruijn graph framework, decomposes a repeat library into shared repeat domains and reveals the mosaic structure of repeat families.

repbase elegans concatenated repeat comparative dot
The fragile breakage versus random breakage models of chromosome evolution.

PMID 16501665 · PMC1378107 · PLoS computational biology · 2006 · 8 claims · 6 setups

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Sankoff and Trinh's synteny block identification algorithm (ST-Synteny) is flawed, producing erroneous block identifications even in small toy examples.

small synthetic synteny random whole-genome
Novel dengue virus type 1 from travelers to Yap State, Micronesia.

PMID 16494770 · PMC3373118 · Emerging infectious diseases · 2006 · 8 claims · 5 setups

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DENV-1 responsible for the 2004 Yap State dengue outbreak was isolated from serum of 4 Japanese travelers returning from Yap

mosquito viral denv-1 full-length virus complete sequence
Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

PMID 16469101 · PMC1457002 · BMC evolutionary biology · 2006 · 7 claims · 5 setups

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The NANOG gene and all pseudogenes except NANOGP8 occupy orthologous chromosomal positions in the chimpanzee genome, indicating they originated before the human-chimpanzee divergence.

chimpanzee megablast pcr flanking-sequence
Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

PMID 16412238 · PMC1368963 · BMC medical genetics · 2006 · 8 claims · 6 setups

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A novel PPARG nonsense mutation, Y355X, was identified in a mother and daughter with FPLD3-consistent phenotypes and was absent from unaffected relatives and 260 healthy controls

subjects nih3t3 subject healthy sequencing luciferase western
MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

PMID 16381984 · PMC1347458 · Nucleic acids research · 2006 · 8 claims · 5 setups

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MPromDb is a novel database integrating experimentally supported gene promoters, TSS annotation, cis-regulatory elements, CpG islands, and ChIP-chip data with an integrated visualization interface.

chip-chip sequence genbank
MitoP2: the mitochondrial proteome database--now including mouse data.

PMID 16381964 · PMC1347489 · Nucleic acids research · 2006 · 8 claims · 8 setups

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MitoP2 is a database integrating manually annotated mitochondrial reference proteins, functions, and disease associations for yeast, human, and mouse, with cross-species orthologue mapping

saccharomyces yeast heart liver genome-wide single transcriptome
LMPD: LIPID MAPS proteome database.

PMID 16381922 · PMC1347484 · Nucleic acids research · 2006 · 8 claims · 5 setups

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LMPD is an object-relational database of lipid-associated protein sequences and annotations, publicly available from the LIPID MAPS Consortium website.

uniprot kegg in-house oracle9i kegg database enzyme
miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

PMID 16381831 · PMC1347497 · Nucleic acids research · 2006 · 6 claims · 6 setups

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miRNAMap integrates known miRNA genes from miRBase, literature-curated validated targets, and computationally predicted miRNA genes and targets for human, mouse, rat and dog.

conserved putative mirna-target normal comparative machine mirna
ARED 3.0: the large and diverse AU-rich transcriptome.

PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

records est est-derived combined computational est sequence
Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

PMID 16319823 · PMC1477589 · European journal of human genetics : EJHG · 2006 · 7 claims · 8 setups

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ALX4 and MSX2 mutations contribute approximately equally to PFM/CB and cause skull defects that are usually clinically indistinguishable

pfm selected point-mutation-negative family dhplc bidirectional multiplex
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

PMID 18096039 · PMC2246271 · Genome biology · 2007 · 8 claims · 5 setups

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CONTRAST predicts exact coding region structures for 65% more human genes than the previous state-of-the-art de novo predictor (N-SCAN)

genome sequence drosophila novo gene coding
Long-term survival and transmission of INI1-mutation via nonpenetrant males in a family with rhabdoid tumour predisposition syndrome.

PMID 18087273 · PMC2361463 · British journal of cancer · 2008 · 8 claims · 5 setups

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The malignant brain tumours in patients III-1, III-3, and III-4, originally classified as anaplastic ependymomas, are in fact atypical teratoid/rhabdoid tumours (AT/RT)

constitutional formalin-fixed tumour blood sanger denaturing immunohistochemistry
Comparative genomics search for losses of long-established genes on the human lineage.

PMID 18085818 · PMC2134963 · PLoS computational biology · 2007 · 8 claims · 6 setups

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A novel comparative genomics method (TransMap-based syntenic mapping of gene structures between human, mouse, and dog) can detect losses of well-established single-copy genes without relying on sequence homology to a parental gene, distinguishing them from typical duplication- or retrotransposition-derived pseudogenes.

dog genome chimp gorilla comparative overlap visual
Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

cloned clinical hominis pcr culture sanger

Experiments

Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

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

Modification of the Creator recombination system for proteomics applications--improved expression by addition of splice sites.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

Identifying repeat domains in large genomes.

The fragile breakage versus random breakage models of chromosome evolution.

Novel dengue virus type 1 from travelers to Yap State, Micronesia.

Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.

Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

MPromDb: an integrated resource for annotation and visualization of mammalian gene promoters and ChIP-chip experimental data.

MitoP2: the mitochondrial proteome database--now including mouse data.

LMPD: LIPID MAPS proteome database.

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

ARED 3.0: the large and diverse AU-rich transcriptome.

Enlarged parietal foramina caused by mutations in the homeobox genes ALX4 and MSX2: from genotype to phenotype.

Personalized genomic medicine with a patchwork, partially owned genome.

CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction.

Long-term survival and transmission of INI1-mutation via nonpenetrant males in a family with rhabdoid tumour predisposition syndrome.

Comparative genomics search for losses of long-established genes on the human lineage.

Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.