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 663

System / cell line: test ✕ Clear

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

PMID 17565693 · PMC1920519 · BMC genomics · 2007 · 8 claims · 4 setups

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42 different CNVs were detected in 27 phenotypically normal individuals using 1 Mb resolution BAC array-CGH

genomic metaphase computational array-cgh fish real-time
The NRG1 exon 11 missense variant is not associated with autism in the Central Valley of Costa Rica.

PMID 17519028 · PMC1888683 · BMC psychiatry · 2007 · 6 claims · 4 setups

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The NRG1 exon 11 missense variant (G>T) is not associated with autism in the CVCR.

blood genomic subjects trios taqman microsatellite clinical
Reconstruction of human protein interolog network using evolutionary conserved network.

PMID 17493278 · PMC1885812 · BMC bioinformatics · 2007 · 8 claims · 7 setups

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A relative conservation score derived from maximal quasi-cliques in protein interaction networks, combined with other interaction features, can score and rank predicted human interologs for confidence.

ppi sequences interaction predicted interolog orthology quasi-clique
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

PMID 17478504 · PMC1933151 · Nucleic acids research · 2007 · 8 claims · 8 setups

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FatiGO+ is a web-based tool for functional profiling of genome-scale experiments that integrates functional annotation, regulatory motifs and interaction data

user-supplied gene predicted interactome gene kegg transcription
Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

PMID 17477860 · PMC1871603 · BMC genetics · 2007 · 7 claims · 5 setups

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DGAT2 is a plausible positional and functional candidate gene for obesity due to its localization at chr.11q13 (a linkage region) and its key role in triglyceride synthesis

extremely families genome sanger case-control family-based
Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

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graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

neuroblastoma same normal megabladder acgh bac principal
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
Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity.

PMID 17211472 · PMC2360009 · British journal of cancer · 2007 · 5 claims · 5 setups

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Inhibiting EGFR signalling with Gefitinib alters the pattern of proteins secreted by cancer cells, and these changes can serve as an indirect quantitative assay for drug action

a431 a549 excised gel maldi-tof western
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide
Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

PMID 19059999 · PMC2632922 · Nucleic acids research · 2009 · 6 claims · 8 setups

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A novel multi-step computational method (built on approximate pattern enumeration, binomial over-representation scoring with FDR correction, and k-medoids clustering) can identify over-represented motifs in a selected set of promoters relative to a background promoter set.

myeloid reference selected genome-localized microarray promoter k-medoids
Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

PMID 19034644 · PMC2728159 · Breast cancer research and treatment · 2009 · 7 claims · 5 setups

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Family history of breast cancer is not associated with all-cause mortality after breast cancer diagnosis in women without a known germline BRCA1/BRCA2 mutation.

women same breast structured cox germline
Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

PMID 19025632 · PMC2630941 · Virology journal · 2008 · 8 claims · 4 setups

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Twelve gp41 sites (outside the overlapping rev exon2 reading frame) show positive selection conserved across multiple HIV-1 M subtypes/CRFs, making them candidate targets for broadly protective vaccines.

gp41 hiv-1 recombination site-specific comparative
Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

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The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

dbsnp best-hit omicia hgmd genome-wide correlation disease
G2Cdb: the Genes to Cognition database.

PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

brain nervous genome synaptic proteomic large-scale sequence
Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

PMID 18953408 · PMC2568805 · PloS one · 2008 · 8 claims · 8 setups

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Re-sequencing and genotyping across a 28.5 kb region delineates the prostate cancer risk association within FHIT intron 5 to a 15 kb LD block in European-Americans.

european-american yoruban japanese case sanger snp linkage
The spectrum of parkinsonian manifestations associated with glucocerebrosidase mutations.

PMID 18852351 · PMC2629407 · Archives of neurology · 2008 · 8 claims · 8 setups

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GBA mutations are associated with a spectrum of parkinsonian phenotypes ranging from Parkinson disease to Lewy body dementia

patients sequencing southern targeted
Lineage specific recombination rates and microevolution in Listeria monocytogenes.

PMID 18842152 · PMC2576243 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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Recombination is more prevalent in lineage II than in lineage I

listeria allelic unique monocytogenes multilocus sawyer's genealogical
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
Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

PMID 18828907 · PMC2760872 · Genome biology · 2008 · 8 claims · 8 setups

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A combinatorial bioinformatics pipeline (evolutionary double filtering comparative genomics, GXD/ZFIN database queries, MEDLINE text mining) can rapidly and specifically identify PAX2/5/8 direct downstream targets in the otic vesicle

genome candidate gxd medline evolutionary gene expression
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine

Experiments

Large-scale copy number variants (CNVs): distribution in normal subjects and FISH/real-time qPCR analysis.

The NRG1 exon 11 missense variant is not associated with autism in the Central Valley of Costa Rica.

Reconstruction of human protein interolog network using evolutionary conserved network.

FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.

Mutation screen and association studies in the diacylglycerol O-acyltransferase homolog 2 gene (DGAT2), a positional candidate gene for early onset obesity on chromosome 11q13.

Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

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

Proteomic identification of secreted proteins as surrogate markers for signal transduction inhibitor activity.

Genomics: applications in mechanism elucidation.

Motif discovery in promoters of genes co-localized and co-expressed during myeloid cells differentiation.

Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

Conserved positive selection signals in gp41 across multiple subtypes and difference in selection signals detectable in gp41 sequences sampled during acute and chronic HIV-1 subtype C infection.

Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

G2Cdb: the Genes to Cognition database.

Strong signature of natural selection within an FHIT intron implicated in prostate cancer risk.

The spectrum of parkinsonian manifestations associated with glucocerebrosidase mutations.

Lineage specific recombination rates and microevolution in Listeria monocytogenes.

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

Rapid identification of PAX2/5/8 direct downstream targets in the otic vesicle by combinatorial use of bioinformatics tools.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.