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 852

Assay: relative ✕ Clear

Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

PMID 18701470 · PMC2562548 · Cancer research · 2008 · 7 claims · 4 setups

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Carriers of common ATM variants (>=1% frequency) have a statistically significant reduction in risk of contralateral breast cancer (CBC)

peripheral wecare atm mutation case-control variant
A general definition and nomenclature for alternative splicing events.

PMID 18688268 · PMC2467475 · PLoS computational biology · 2008 · 6 claims · 4 setups

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Existing AS nomenclatures (Malko et al.'s 5-letter strings, Nagasaki et al.'s bit matrices, and the ASD/ATD/AEdb system) are redundant, ambiguous, or incapable of representing complex or large splicing variations.

refseq reference metazoan example computational comparative
Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

PMID 18684996 · PMC2532738 · Nucleic acids research · 2008 · 8 claims · 7 setups

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SISSRs identifies binding sites from ChIP-Seq short reads with much higher resolution than the standard region-clustering approach

cd4+ jurkat hela computational chip-seq novo motif
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups

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PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers

breast hormone early-stage mass sanger reverse-phase
Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

PMID 18655731 · PMC2515324 · BMC genomics · 2008 · 7 claims · 6 setups

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A collection of 132,577 ESTs from four Actinidia species was generated and clustered into 41,858 non-redundant clusters (18,070 TCs and 23,788 singletons)

cdna full-length tentative non-redundant est codon snp
Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

PMID 18654633 · PMC2464715 · PLoS genetics · 2008 · 8 claims · 5 setups

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A Bayesian-inspired penalised maximum likelihood stochastic search method can simultaneously analyse all SNPs (up to 500K) from a GWA study in a few hours on a desktop workstation

fregene-simulated 80k-snp 480k 192k simulated null whole-genome
A network model for the correlation between epistasis and genomic complexity.

PMID 18648534 · PMC2481279 · PloS one · 2008 · 8 claims · 5 setups

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In small networks with multifunctional nodes, lack of redundancy, and absence of alternative pathways, epistasis is antagonistic on average.

two-pathway network
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

PMID 18613715 · PMC2601597 · Journal of proteome research · 2008 · 8 claims · 5 setups

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A NCI source coupled via an added octopole and the c-trap to a QLT-orbitrap enables fast, efficient ETD reagent anion injection (4-8 ms)

saccharomyces histone glioblastoma fluoranthene lc-ms etd anion
Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

PMID 18590534 · PMC2481270 · BMC genomics · 2008 · 8 claims · 6 setups

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B. pertussis strains carrying the ptxP3 allele gradually replaced ptxP1 strains and became predominant from 1998, coinciding with the Dutch pertussis resurgence

dutch additional pertussis ptxp3 multi-locus multiple-locus microarray-based
Calibrating the performance of SNP arrays for whole-genome association studies.

PMID 18584036 · PMC2432039 · PLoS genetics · 2008 · 8 claims · 7 setups

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Previous SNP array genetic coverage estimates are inflated due to SNP overfitting and sample overfitting, since they were evaluated on the same HapMap SNPs/individuals used to design the arrays.

american liver simulated hapmap snp gene simulation-based
Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

PMID 18588709 · PMC2464599 · BMC genetics · 2008 · 8 claims · 7 setups

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Porcine PNAS-4 encodes a 194-amino-acid protein that localizes to the Golgi complex

chinese tissues skeletal pk15 full-length real-time gfp
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion
A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

PMID 18518950 · PMC2464610 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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A new method for building reference gene-expression profiles and scoring/testing connections improves on the original Connectivity Map by enabling statistical significance testing of connections.

lines random gene-expression connectivity
Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

PMID 18500686 · PMC2516917 · The Prostate · 2008 · 8 claims · 5 setups

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Identified 32 genes (38 cDNAs) with an expression pattern of highest levels in seminal vesicle, lower in normal prostate, and lowest in prostate cancer

normal prostate microarray cdna cross-tissue gene
Inferring human colonization history using a copying model.

PMID 18497854 · PMC2367454 · PLoS genetics · 2008 · 8 claims · 6 setups

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A copying-model approach using SNP haplotype sharing can infer both the order of population founding and the donor populations contributing ancestry to each new population.

simulated populations coalescent snp ascertainment
Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

PMID 18490959 · PMC2386506 · Molecular vision · 2008 · 7 claims · 6 setups

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A novel affinity-enrichment strategy using UV cross-linked protease inhibitor peptides on Protein A/G columns improves capture of the TM protease proteome compared to SDS-PAGE fractionation alone

cytosolic affinity-eluted porcine affinity-enriched affinity western sds-page
Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

PMID 18492229 · PMC2408590 · BMC microbiology · 2008 · 8 claims · 6 setups

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The mcrA gene serves as a useful biomarker for methanogen detection in the human gut

faecal mcra pure pcr rflp 16s
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race

Experiments

Variants in the ATM gene associated with a reduced risk of contralateral breast cancer.

A general definition and nomenclature for alternative splicing events.

Genome-wide identification of in vivo protein-DNA binding sites from ChIP-Seq data.

An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening.

Simultaneous analysis of all SNPs in genome-wide and re-sequencing association studies.

A network model for the correlation between epistasis and genomic complexity.

Massively parallel pyrosequencing in HIV research.

A proteomics grade electron transfer dissociation-enabled hybrid linear ion trap-orbitrap mass spectrometer.

Comparative genomic profiling of Dutch clinical Bordetella pertussis isolates using DNA microarrays: identification of genes absent from epidemic strains.

Calibrating the performance of SNP arrays for whole-genome association studies.

Characterization, expression profiles, intracellular distribution and association analysis of porcine PNAS-4 gene with production traits.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

A simple and robust method for connecting small-molecule drugs using gene-expression signatures.

Identification of candidate prostate cancer genes through comparative expression-profiling of seminal vesicle.

Inferring human colonization history using a copying model.

Technical Brief: a novel strategy for enrichment of trabecular meshwork protease proteome.

Human methanogen diversity and incidence in healthy and diseased colonic groups using mcrA gene analysis.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.