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 481

System / cell line: cross ✕ Clear

F-SNP: computationally predicted functional SNPs for disease association studies.

PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

genome protein-coding genomic genome-wide non-synonymous exonic nonsense
High incidence of human bocavirus infection in children in Spain.

PMID 17904416 · PMC7108365 · Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology · 2007 · 8 claims · 6 setups

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HBoV is a significant contributor to acute lower respiratory tract infection in young children in Spain

nasopharyngeal cloned hbov-positive urine nested multiplex sanger
Population genomics of human gene expression.

PMID 17873874 · PMC2683249 · Nature genetics · 2007 · 8 claims · 8 setups

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Gene expression levels in lymphoblastoid cell lines are a heritable trait

ebv-transformed ceu lymphoblastoid unrelated genome-wide custom cis-eqtl
Transcriptome annotation using tandem SAGE tags.

PMID 17709346 · PMC2034470 · Nucleic acids research · 2007 · 8 claims · 7 setups

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A novel algorithm pairs tandem SAGE tags anchored on two different restriction sites (CATG and GATC) to define tag-delimited genomic sequences (TDGS)

monocyte-derived unigene genome macrophage sage modified virtual
Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

PMID 17659072 · PMC1950510 · Malaria journal · 2007 · 7 claims · 6 setups

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PfMAD20 is the predominant PfMSP-1 allelic type among Indian field isolates

falciparum escherichia coli-expressed recombinant pcr recombinant sds-page
Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

genomic pnmt promoter pcr population haplotype
Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

PMID 17598913 · PMC1929078 · BMC genomics · 2007 · 8 claims · 4 setups

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Standard Affymetrix expression GeneChips (MOE430, HG-U133) contain probe sets that detect natural antisense transcripts (NATs)

moe430 pooled organs probe strand-specific microarray
Completing the map of human genetic variation.

PMID 17495918 · PMC2685471 · Nature · 2007 · 8 claims · 5 setups

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A community resource initiative will sequence fosmid and BAC clone libraries from 62 HapMap individuals to systematically discover and resolve structural genetic variants at nucleotide resolution

genomic fosmid full hapmap paired targeted genotyping
Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

PMID 17442112 · PMC1863428 · BMC cancer · 2007 · 7 claims · 5 setups

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CYYR1 mRNA undergoes a 'subtle' alternative splicing event generating two isoforms (CAG- and CAG+) differing by a single alanine codon at the exon3/exon4 junction

neuroendocrine tumors normal cyyr1 rt-pcr quantitative psti
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

longitudinal backbone env intra-patient relaxed-clock correlation site-to-site
An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

private disease uniprot snps database controlled sequence
Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

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A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

consanguineous same affected family sanger multiplex microsatellite
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
Gene-environment interaction and obesity.

PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

framingham european individuals healthy genome-wide candidate gene-diet
Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

PMID 18984079 · PMC2679897 · American journal of obstetrics and gynecology · 2008 · 8 claims · 7 setups

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Women with severe preeclampsia present a unique urinary proteomic fingerprint distinguishable from controls.

urine placenta placental seldi-tof tandem spiking
An optimized procedure for the design and evaluation of Ecotilling assays.

PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

genomic gene pcr cdna ecotilling sequence sanger
Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

PMID 18842128 · PMC2572040 · Biology direct · 2008 · 8 claims · 6 setups

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The Turmoil-1 transposable element in C. elegans incorporated two unrelated protein-coding sequences into its inverted terminal repeats (ITRs)

turmoil-1 rrm elegans predicted pairwise maximum genome-wide
The role of positive selection in determining the molecular cause of species differences in disease.

PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

orthologous omim meta-database panther comparative disease protein-protein
Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.

PMID 18828897 · PMC2760871 · Genome biology · 2008 · 8 claims · 8 setups

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The overlap between phosphoproteomes of six eukaryotes (human, mouse, fly, yeast, plant, zebrafish) is significantly greater than expected by chance.

liver fruit yeast plant high-throughput comparative
Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.

PMID 18806875 · PMC2532751 · PloS one · 2008 · 8 claims · 8 setups

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PCMT overexpression protects porcine aortic endothelial cells (PAEC) from H2O2-induced apoptosis, raising the threshold H2O2 concentration required to trigger cell death.

porcine paec umbilical huvec methyltransferase sds-page fragmentation

Experiments

F-SNP: computationally predicted functional SNPs for disease association studies.

High incidence of human bocavirus infection in children in Spain.

Population genomics of human gene expression.

Transcriptome annotation using tandem SAGE tags.

Polymorphism and epitope sharing between the alleles of merozoite surface protein-1 of Plasmodium falciparum among Indian isolates.

Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

Uncovering information on expression of natural antisense transcripts in Affymetrix MOE430 datasets.

Completing the map of human genetic variation.

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors.

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

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

Gene-environment interaction and obesity.

Proteomic profiling of urine identifies specific fragments of SERPINA1 and albumin as biomarkers of preeclampsia.

An optimized procedure for the design and evaluation of Ecotilling assays.

Transduplication resulted in the incorporation of two protein-coding sequences into the turmoil-1 transposable element of C. elegans.

The role of positive selection in determining the molecular cause of species differences in disease.

Comparative phosphoproteomics reveals evolutionary and functional conservation of phosphorylation across eukaryotes.

Protein isoaspartate methyltransferase prevents apoptosis induced by oxidative stress in endothelial cells: role of Bcl-Xl deamidation and methylation.