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 569

System / cell line: frequency ✕ Clear

Systems biology approaches for the study of multiple sclerosis.

PMID 18505469 · PMC3865652 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

Full-text index only

The MHC locus on chromosome 6p21 is the strongest genetic region linked to MS susceptibility.

patients lesion osteopontin monocyte-depleted genetic large-scale gene
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

Full-text index only

HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

ffpe single high direct hrm
Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

PMID 18433509 · PMC2386495 · BMC medicine · 2008 · 8 claims · 8 setups

Full-text index only

A combination of mutation-screening techniques (PTT, SSCP/HD, D-HPLC, sequencing, MLPA, mosaicism analysis, expression analysis) achieved a 100% mutation detection frequency in classical FAP

peripheral genomic cdna truncation sscp d-hplc
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

Full-text index only

Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

Full-text index only

Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct
Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

PMID 18302774 · PMC2266716 · BMC medical genetics · 2008 · 8 claims · 4 setups

Full-text index only

The SNF2L gene spans 77 kb and is encoded by 25 exons that undergo alternative splicing to generate multiple distinct transcripts.

lines genomic 293hek rt-pcr genomic indirect
Sequence context affects the rate of short insertions and deletions in flies and primates.

PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

Full-text index only

The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

chimpanzee simulans chimp primate comparative direct nucleotide
Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

PMID 18276640 · PMC2346606 · Nucleic acids research · 2008 · 8 claims · 5 setups

Full-text index only

Illumina HumanHap300 arrays are substantially more efficient than Affymetrix Genechip HindIII arrays for DNA-pooling based GWAS

pools same publicly simulated pooling individual simulation
Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

PMID 18270580 · PMC2217631 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

Pairs of unlinked SNPs showing excess genetic differentiation (LD in mouse RILs, Fst in human populations) beyond what simulations/coalescent models predict by chance represent candidate functionally interacting (epistatic) gene pairs.

bxd simulated subset populations genome-wide simulation genotype-phenotype
Mutations in mRNA export mediator GLE1 result in a fetal motoneuron disease.

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

Full-text index only

Mutations in GLE1, an mRNA export mediator, cause LCCS1

lccs1 laahd finnish healthy genomic microsatellite carrier
Associations between polycyclic aromatic hydrocarbon-related exposures and p53 mutations in breast tumors.

PMID 20064791 · PMC2854728 · Environmental health perspectives · 2010 · 8 claims · 5 setups

Full-text index only

PAH-related exposures are associated with breast cancer differently according to tumor p53 mutation status, type, effect, and number

archived breast peripheral study surveyor immunohistochemistry competitive
Fusion of short telomeres in human cells is characterized by extensive deletion and microhomology, and can result in complex rearrangements.

PMID 20026586 · PMC2847243 · Nucleic acids research · 2010 · 8 claims · 5 setups

Full-text index only

Telomere fusion in human cells is characterized by extensive sub-telomeric deletion of at least one telomere, extending up to 5.6-6.1 kb

hek293 mrc5 pcr single single-molecule southern direct
Mutation analysis of the AATF gene in breast cancer families.

PMID 20025740 · PMC2806411 · BMC cancer · 2009 · 6 claims · 6 setups

Full-text index only

No AATF sequence alteration identified was predicted to be pathogenic or showed significant association with breast cancer risk

genomic showing aatf case conformation direct pathogenicity
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

Full-text index only

SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission
SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

PMID 20008100 · PMC2836562 · Nucleic acids research · 2010 · 8 claims · 6 setups

Full-text index only

SeqBuster is a versatile web-based and stand-alone bioinformatic toolkit for processing and analyzing large-scale small RNA deep sequencing datasets.

embryonic hesc small sequence adapter
Mutation analysis of the MSMB gene in familial prostate cancer.

PMID 19997100 · PMC2816656 · British journal of cancer · 2010 · 8 claims · 5 setups

Full-text index only

No deleterious mutations were found in the MSMB coding region in 192 familial prostate cancer cases

germline blood 161-nt genotype sanger taqman transcription
PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

PMID 19969003 · PMC2822003 · Journal of molecular biology · 2010 · 7 claims · 7 setups

Full-text index only

PCP-consensus sequences of E protein show insertions/deletions that distinguish tick-borne, mosquito-borne, no-known-vector (NKV), and yellow fever virus (YFV) Flaviviruses

natural aligned ns3 denv sequence pcp-consensus physicochemical
BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

PMID 19919682 · PMC3091323 · Genome biology · 2009 · 8 claims · 4 setups

Full-text index only

BioGPS aggregates distributed, third-party gene annotation resources into a single customizable portal for human, mouse, and rat genes.

biogps diverse tissues specified web reference exon
Association of the MAPT locus with Parkinson's disease.

PMID 19912324 · PMC3906622 · European journal of neurology · 2010 · 7 claims · 5 setups

Full-text index only

H1/H2-tagging SNPs rs1052553 (MAPT) and rs62063857 (Saitohin/STH) are significantly associated with increased risk of PD

patients caucasian snp haplotype linkage
Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

Full-text index only

IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

population blood genomic hapmap snp survival allele

Experiments

Systems biology approaches for the study of multiple sclerosis.

High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

Clinical characterization and the mutation spectrum in Swedish adenomatous polyposis families.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

Characterization of novel isoforms and evaluation of SNF2L/SMARCA1 as a candidate gene for X-linked mental retardation in 12 families linked to Xq25-26.

Sequence context affects the rate of short insertions and deletions in flies and primates.

Highly cost-efficient genome-wide association studies using DNA pools and dense SNP arrays.

Genome-wide prediction of functional gene-gene interactions inferred from patterns of genetic differentiation in mice and men.

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

Associations between polycyclic aromatic hydrocarbon-related exposures and p53 mutations in breast tumors.

Fusion of short telomeres in human cells is characterized by extensive deletion and microhomology, and can result in complex rearrangements.

Mutation analysis of the AATF gene in breast cancer families.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

SeqBuster, a bioinformatic tool for the processing and analysis of small RNAs datasets, reveals ubiquitous miRNA modifications in human embryonic cells.

Mutation analysis of the MSMB gene in familial prostate cancer.

PCP consensus sequences of flaviviruses: correlating variance with vector competence and disease phenotype.

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources.

Association of the MAPT locus with Parkinson's disease.

Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.