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 262

System / cell line: using ✕ Clear

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

deposit excised pooled worn sds-page in-gel lc-ms-ms
Searching for genes underlying behavior: lessons from circadian rhythms.

PMID 18988844 · PMC3744585 · Science (New York, N.Y.) · 2008 · 8 claims · 5 setups

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Forward genetic mutagenesis screens successfully identified the molecular components of the circadian clock across Drosophila, Neurospora, cyanobacteria, Arabidopsis, and mouse.

c57bl genomic automated contextual psychostimulant-induced
Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

PMID 18986552 · PMC2625353 · BMC systems biology · 2008 · 8 claims · 6 setups

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Integrated WGCNA (IWGCNA), which adds genetic marker-based causality testing to standard WGCNA, can identify a disease-related module and its causal drivers

cfs most candidate second microarray snp weighted
Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

PMID 18722006 · PMC2566540 · Cell · 2008 · 7 claims · 8 setups

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A subtiligase-based N-terminal biotinylation and enrichment method enables global identification and sequencing of protease cleavage sites in complex mixtures

jurkat computational immunoblotting structural protein-protein
Comparison of prognostic gene expression signatures for breast cancer.

PMID 18717985 · PMC2533026 · BMC genomics · 2008 · 8 claims · 5 setups

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The three prognostic signatures (70-gene, 76-gene, GGI) show similar prognostic performance for predicting DMFS despite differing gene identity and development approach

tbagd tbvdx gene clinical survival
Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups

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E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.

e2348 hep-2 blast colony transformation
What can genome-wide association studies tell us about the genetics of common disease?

PMID 18454206 · PMC2323402 · PLoS genetics · 2008 · 8 claims · 4 setups

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Apparent patterns of common, low-effect disease-associated alleles largely reflect statistical power of studies rather than the true underlying distribution of disease variants

case gwa simulated literature cochran-armitage computer
Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

PMID 18439302 · PMC2432081 · BMC genomics · 2008 · 8 claims · 7 setups

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Adjacent cassette exon pairs can be categorized by EST-derived correlation coefficient into three groups: mutually exclusive (ME, r<=-0.7), independent (IND, -0.2<=r<=0.2), and linked (LNK, r>=0.7)

human-mouse adjacent est genome splice
Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

PMID 18304320 · PMC2292740 · BMC genetics · 2008 · 8 claims · 8 setups

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NAT2 coding region sequence variation in the Mandenka and other sub-Saharan African populations is consistent with selective neutrality and constant population size.

mandenka worldwide hapmap nat2 full snp analysis
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

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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
We are the genes we've been waiting for: rational responses to the gathering storm of personal genomics.

PMID 19998110 · PMC3749831 · The American journal of bioethics : AJOB · 2009 · 8 claims · 5 setups

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Medical establishment critics dismissed PGT information in 2008 as either not worth much or dangerous

social women relatives individuals survey epidemiological genetic
Non-imprinted allele-specific DNA methylation on human autosomes.

PMID 19958531 · PMC2812945 · Genome biology · 2009 · 8 claims · 7 setups

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SNPs within CpG islands are associated with allele-specific DNA methylation differences between alleles.

leukocytes leukocyte hek293 bisulfite methylation-sensitive cdna
Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

PMID 19956714 · PMC2776354 · PloS one · 2009 · 8 claims · 5 setups

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3,019 CNVs (2,381 autosomal, 638 X chromosome) were identified across 985 Caucasian and 692 Asian individuals using the Affymetrix 500K array

same caucasian cau autosomal snp copy population
Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

PMID 19915670 · PMC2771920 · PloS one · 2009 · 8 claims · 6 setups

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Proteomic analysis of glioma samples reveals three signaling subclasses of GBM associated with predominant EGFR activation, PDGFR activation, or loss of NF1

surgical standardized glioma gbm western principal k-means
Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

PMID 19832989 · PMC2770483 · BMC microbiology · 2009 · 8 claims · 5 setups

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The relative proportion of the three Pfmsp1 block2 allelic families (K1, Mad20, RO33) in Dielmo showed no significant temporal fluctuation over a 10-year period (1990-99).

plasmodium dielmo semi-nested direct cross-sectional
Human stool contains a previously unrecognized diversity of novel astroviruses.

PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups

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Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1

stool consensus-pcr-positive negative one consensus specific sanger
A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

PMID 19751529 · PMC2755474 · Journal of biomedical science · 2009 · 8 claims · 5 setups

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Pre-S1 and pre-S2 deletion mutants of the HBV LHBS gene are highly associated with HBV-related HCC

serum plasmids coli pcr oligonucleotide chip
Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

genome gene omim known naïve linkage disease-centric
Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

PMID 19720790 · PMC2780873 · Diabetes · 2009 · 7 claims · 8 setups

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INSR is disrupted by the chromosome 19 breakpoint, causing INSR haploinsufficiency (monoallelic expression) that explains the insulin resistance/dysglycemia phenotype

metaphase genomic ebv-transformed serum fluorescence multiplex sanger
Investigating the genetic association between ERAP1 and ankylosing spondylitis.

PMID 19692350 · PMC2758148 · Human molecular genetics · 2009 · 8 claims · 8 setups

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The genetic association between ERAP1 and AS is confirmed in an independent replication cohort

patients cases genotype comparison snp meta-analysis resequencing

Experiments

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

Searching for genes underlying behavior: lessons from circadian rhythms.

Integrated weighted gene co-expression network analysis with an application to chronic fatigue syndrome.

Global sequencing of proteolytic cleavage sites in apoptosis by specific labeling of protein N termini.

Comparison of prognostic gene expression signatures for breast cancer.

Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.

What can genome-wide association studies tell us about the genetics of common disease?

Functional importance of different patterns of correlation between adjacent cassette exons in human and mouse.

Worldwide distribution of NAT2 diversity: implications for NAT2 evolutionary history.

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

We are the genes we've been waiting for: rational responses to the gathering storm of personal genomics.

Non-imprinted allele-specific DNA methylation on human autosomes.

Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations.

Glioblastoma subclasses can be defined by activity among signal transduction pathways and associated genomic alterations.

Population diversity and antibody selective pressure to Plasmodium falciparum MSP1 block2 locus in an African malaria-endemic setting.

Human stool contains a previously unrecognized diversity of novel astroviruses.

A pre-S gene chip to detect pre-S deletions in hepatitis B virus large surface antigen as a predictive marker for hepatoma risk in chronic hepatitis B virus carriers.

Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

Severe insulin resistance and intrauterine growth deficiency associated with haploinsufficiency for INSR and CHN2: new insights into synergistic pathways involved in growth and metabolism.

Investigating the genetic association between ERAP1 and ankylosing spondylitis.