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 116

System / cell line: array ✕ Assay: comparison ✕ Clear

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

PMID 18560825 · PMC2493868 · Immunogenetics · 2008 · 8 claims · 8 setups

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Neither transcriptional profiling alone nor genetic linkage analysis alone has been an effective approach to identify genes or gene networks that specify stemness or initiate differentiation/lineage specification.

escs fibroblasts hematopoietic bxd transcriptional forced long-term
Accurate whole human genome sequencing using reversible terminator chemistry.

PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

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A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

bac flow-sorted same yoruba reversible snp targeted
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

PMID 18704501 · PMC2525844 · Human genetics · 2008 · 6 claims · 5 setups

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Next-generation (Roche/454) resequencing of 136 kb at 8q24 in 39 prostate cancer cases and 40 controls generated a comprehensive catalog of common SNPs (MAF>1%), including 442 novel SNPs

genomic commercial plco unrelated targeted long-range genotyping
Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

PMID 19906316 · PMC2784480 · BMC genomics · 2009 · 8 claims · 7 setups

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Intronic single-block ESTs with poly(A/T) tails reveal previously unidentified novel transcript variants missed by existing databases.

genome poly est cdna est blast cdna
Targeted capture and massively parallel sequencing of 12 human exomes.

PMID 19684571 · PMC2844771 · Nature · 2009 · 8 claims · 8 setups

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Targeted exome capture combined with massively parallel sequencing sensitively and specifically identifies rare and common variants across >300 Mb of coding sequence

hapmap unrelated na18507 randomly targeted array-based molecular
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

PMID 17939873 · PMC2222656 · BMC bioinformatics · 2007 · 8 claims · 4 setups

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Yu et al.'s original comparison ran RJaCGH's MCMC sampler for a severely insufficient number of iterations (50 burn-in, 500 total)

simulated same mcmc-based direct original
A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

PMID 19941644 · PMC2789744 · BMC bioinformatics · 2009 · 7 claims · 4 setups

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Feature variability strongly influences breast cancer signature composition even when array platform and patient stratification are identical.

breast preprocessed microarray two-color perturbation
Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

PMID 17124346 · PMC3862287 · Disease markers · 2006 · 8 claims · 5 setups

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SELDI-TOF MS serum profiling can discriminate MM patients with vs without skeletal (bone lesion) involvement using peak biomarkers

serum seldi seldi-tof serum univariate
Evidence for a minimal eukaryotic phosphoproteome?

PMID 17712425 · PMC1945084 · PloS one · 2007 · 8 claims · 3 setups

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Divergence in eukaryotic kinases at the primary sequence level is not reflected at the level of substrate phosphorylation.

lysates lysate pepchip peptide labelling statistical
Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

PMID 16221972 · PMC1253841 · Nucleic acids research · 2005 · 8 claims · 6 setups

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Reducing array complexity by pooling five BACs per spot (covering a chromosome arm) increases robustness to amplification-related ratio variation compared with single-BAC spotting

normal aneuploid same genomiphi-amplified array-cgh
High resolution array-CGH analysis of single cells.

PMID 17178751 · PMC1807964 · Nucleic acids research · 2007 · 7 claims · 7 setups

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Single copy number changes as small as 8.3 Mb can be detected reliably in single cells using GenomePlex WGA combined with high-resolution tiling-path array-CGH.

769p hct116 peripheral single array-cgh gel fish
SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

PMID 18840289 · PMC2571113 · BMC bioinformatics · 2008 · 8 claims · 6 setups

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SIGMA2 is a Java-based software system that integrates and visualizes genomic, epigenomic, and transcriptomic cancer data.

single hcc2218 nsclc array gene multi-omics
Comparing whole genomes using DNA microarrays.

PMID 18347592 · PMC7097741 · Nature reviews. Genetics · 2008 · 8 claims · 6 setups

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DNA microarrays offer a relatively inexpensive and efficient alternative to genome sequencing for comparing all known classes of genomic diversity between closely related genomes.

genome saccharomyces mitochondrial sars array comparative resequencing
Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

PMID 19803774 · PMC2893889 · Twin research and human genetics : the official journal of the International Society for Twin Studies · 2009 · 7 claims · 5 setups

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Postzygotic genomic alterations are not a common cause of monozygotic twin discordance for isolated cleft lip and/or palate.

peripheral array custom snp
CGHPRO -- a comprehensive data analysis tool for array CGH.

PMID 15807904 · PMC1274268 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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CGHPRO is a user-friendly, versatile, stand-alone Java tool for normalization, visualization, breakpoint detection and comparative analysis of array-CGH data

tiling artificially array
Lineage-specific gene duplication and loss in human and great ape evolution.

PMID 15252450 · PMC449870 · PLoS biology · 2004 · 8 claims · 7 setups

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Genome-wide interspecies cDNA aCGH can identify lineage-specific gene copy number changes across five hominoid species

bonobo chimpanzee gorilla orangutan cdna fluorescence literature-based
A statistical approach for array CGH data analysis.

PMID 15705208 · PMC549559 · BMC bioinformatics · 2005 · 8 claims · 4 setups

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Existing model-selection criteria (AIC, BIC, and prior ad hoc penalties) are not well adapted to estimating the number of segments in array CGH data

fibroblast simulated bt474 dissected array numerical
Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

PMID 18990248 · PMC2585104 · BMC genomics · 2008 · 8 claims · 7 setups

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The Exon Array performs comparably to 3'-targeted platforms (Illumina, U133) at the gene expression level, though interplatform correlation is slightly lower than between the two 3' platforms.

brain exon targeted principal
Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.

PMID 18776137 · PMC2584123 · Diabetes · 2008 · 6 claims · 7 setups

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Lymphocytes (but not monocytes) from type 1 diabetic patients show a distinct subset of genes with significantly increased H3K9me2 compared with healthy controls.

blood pooled gene chip-chip conventional quantitative

Experiments

Combining transcriptional profiling and genetic linkage analysis to uncover gene networks operating in hematopoietic stem cells and their progeny.

Accurate whole human genome sequencing using reversible terminator chemistry.

Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers.

Discovery of novel human transcript variants by analysis of intronic single-block EST with polyadenylation site.

Targeted capture and massively parallel sequencing of 12 human exomes.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

A response to Yu et al. "A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array", BMC Bioinformatics 2007, 8: 145.

A comprehensive sensitivity analysis of microarray breast cancer classification under feature variability.

Biomarkers that discriminate multiple myeloma patients with or without skeletal involvement detected using SELDI-TOF mass spectrometry and statistical and machine learning tools.

Evidence for a minimal eukaryotic phosphoproteome?

Rapid detection of genomic imbalances using micro-arrays consisting of pooled BACs covering all human chromosome arms.

High resolution array-CGH analysis of single cells.

SIGMA2: a system for the integrative genomic multi-dimensional analysis of cancer genomes, epigenomes, and transcriptomes.

Comparing whole genomes using DNA microarrays.

Search for genomic alterations in monozygotic twins discordant for cleft lip and/or palate.

CGHPRO -- a comprehensive data analysis tool for array CGH.

Lineage-specific gene duplication and loss in human and great ape evolution.

A statistical approach for array CGH data analysis.

Gene expression and isoform variation analysis using Affymetrix Exon Arrays.

Lymphocytes from patients with type 1 diabetes display a distinct profile of chromatin histone H3 lysine 9 dimethylation: an epigenetic study in diabetes.