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 62

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

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

PMID 15961730 · PMC1151590 · Nucleic acids research · 2005 · 7 claims · 5 setups

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SW-ARRAY, an adaptation of the Smith-Waterman dynamic programming algorithm, provides a sensitive and robust method for identifying copy-number changes in array CGH data

chromosome 16p array probe-by-probe sw-array
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
Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

PMID 18831757 · PMC2572624 · BMC bioinformatics · 2008 · 6 claims · 4 setups

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A dye intensity bias between the two channels (X/Y, Cy5/Cy3) of the Infinium II assay remains after BeadStudio's proprietary normalization.

urothelial hapmap snp plot baf
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
Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

PMID 15860770 · PMC1087791 · Nucleic acids research · 2005 · 8 claims · 4 setups

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A Geniom One-synthesized oligonucleotide microarray can determine the methylation status of individual CpG dinucleotides in parallel, combining high throughput with single-base resolution

hct116 p16 genomic methylation-specific combined oligonucleotide
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
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
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
An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

PMID 19925645 · PMC2791104 · BMC bioinformatics · 2009 · 7 claims · 3 setups

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The loop design compares three patients pairwise across three hybridizations instead of each patient against a normal reference, using all arrays for informative test samples and avoiding ambiguity from benign CNVs in a reference sample.

genomic e.g array karyotyping fish
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
Human and mouse oligonucleotide-based array CGH.

PMID 16361265 · PMC1316119 · Nucleic acids research · 2005 · 8 claims · 8 setups

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Oligo array CGH detects single copy gains, multi-copy amplifications, and homozygous/heterozygous deletions as small as 100 kb

bt474 normal gm01750 mda-mb-468 array fish
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
Exploiting noise in array CGH data to improve detection of DNA copy number change.

PMID 17272296 · PMC1994778 · Nucleic acids research · 2007 · 7 claims · 4 setups

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When aberrations are present, noise in BAC, 19k oligo, and 385k oligo array-CGH data is highly non-Gaussian and shows long-range spatial correlations.

atm-deficient normal simulated array simulated
High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

PMID 18344524 · PMC2367728 · Nucleic acids research · 2008 · 7 claims · 8 setups

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A protocol combining PCR-based whole genome amplification with arrays of highly purified BAC clones enables detection of DNA copy number changes in single cells

single bac amplified pi-scei array quantitative dot
A genome-wide screen for copy number alterations in Aicardi syndrome.

PMID 19760649 · PMC3640635 · American journal of medical genetics. Part A · 2009 · 7 claims · 4 setups

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Aicardi syndrome is thought to result from heterozygous defects in an essential X-linked gene, or from a sex-limited autosomal gene defect, due to its occurrence almost exclusively in females and in 47,XXY males.

genomic subject array quantitative fluorescence
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
MMASS: an optimized array-based method for assessing CpG island methylation.

PMID 17041235 · PMC1635254 · Nucleic acids research · 2006 · 8 claims · 7 setups

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MMASS-v2 (optimized AciI/HinP1I/HpyCH4IV/HpaII enzyme combination with McrBC digestion) offers improved sensitivity and statistical power for microarray-based CpG island methylation detection compared to MMASS-v1, MMASS-sub and the Nouzova method

hct116 sssi-methylated hcgi12k methylation spike-in cobra
Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

PMID 16887033 · PMC1559599 · BMC medical genetics · 2006 · 6 claims · 5 setups

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A multiplexed suspension bead array (Luminex) assay was developed to genotype 8 Ashkenazi-prevalent disease alleles including GBA c.1448T>C

genomic de-identified multiplex sanger clinical
Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.

PMID 17363414 · PMC2779891 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 6 setups

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High-density oligonucleotide/SNP platforms are superior to the BAC platform for genome-wide detection of copy-number variations smaller than 1 Mb

genomic normalized simulated tiling-resolution snp oligonucleotide

Experiments

SW-ARRAY: a dynamic programming solution for the identification of copy-number changes in genomic DNA using array comparative genome hybridization data.

Comparing whole genomes using DNA microarrays.

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios.

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

Array-based analysis of genomic DNA methylation patterns of the tumour suppressor gene p16INK4A promoter in colon carcinoma cell lines.

A statistical approach for array CGH data analysis.

High resolution array-CGH analysis of single cells.

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

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

An experimental loop design for the detection of constitutional chromosomal aberrations by array CGH.

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

Human and mouse oligonucleotide-based array CGH.

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

Exploiting noise in array CGH data to improve detection of DNA copy number change.

High-resolution array comparative genomic hybridization of single micrometastatic tumor cells.

A genome-wide screen for copy number alterations in Aicardi syndrome.

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

MMASS: an optimized array-based method for assessing CpG island methylation.

Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

Genome-wide copy number profiling on high-density bacterial artificial chromosomes, single-nucleotide polymorphisms, and oligonucleotide microarrays: a platform comparison based on statistical power analysis.