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).

• Capturing genomic signatures of DNA sequence variation using a standard anonymous microarray platform.

  PMID 17000641 · PMC1636412 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  An anonymous SHyP oligonucleotide microarray can capture genomic signatures of DNA sequence variation from any organism, including a previously unsequenced species

  genomic gonystylus subset restriction-digested custom self-self blast

• CGH-Profiler: data mining based on genomic aberration profiles.

  PMID 16042799 · PMC1183191 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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  CGH-Profiler circumvents ISCN nomenclature by importing CGH data from different vendor systems and converting it into a table format suitable for statistical analysis.

  tumour cgh metaphase comparative metaphase

• More breast cancer genes?

  PMID 11305950 · PMC138680 · Breast cancer research : BCR · 2001 · 8 claims · 7 setups

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  A new high-risk breast cancer gene termed BRCAX may exist on chromosome 13q, identified via CGH and linkage analysis in Nordic families

  tumours five independent ataxia-telangiectasia comparative haplotype linkage

• 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

• Comparative genomic analysis of Campylobacter jejuni associated with Guillain-Barré and Miller Fisher syndromes: neuropathogenic and enteritis-associated isolates can share high levels of genomic similarity.

  PMID 17919333 · PMC2174954 · BMC genomics · 2007 · 8 claims · 4 setups

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  GBS/MFS strains are genomically heterogeneous, falling into about six major lineages rather than a single clonal group

  jejuni subset matched comparative fisher's hierarchical

• Challenges and standards in integrating surveys of structural variation.

  PMID 17597783 · PMC2698291 · Nature genetics · 2007 · 7 claims · 5 setups

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  There is no standard approach to collecting, assessing the quality of, or describing structural variants, risking the entire genome eventually being labeled 'structurally variant' based on uncurated nondisease-sample data.

  genomic hapmap reference independent comparative snp fosmid

• 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

• High-throughput molecular analysis in lung cancer: insights into biology and potential clinical applications.

  PMID 19648524 · PMC4648268 · The European respiratory journal · 2009 · 8 claims · 8 setups

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  High-throughput -omics technologies have revolutionised understanding of lung cancer biology and hold promise for personalised management of lung cancer

  tumour serum nsclc comparative snp methylation

• Colorectal cancer genomics: evidence for multiple genotypes which influence survival.

  PMID 11720434 · PMC2363933 · British journal of cancer · 2001 · 6 claims · 3 setups

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  Genetic grade (total number of CGH-detected gains+losses) varies greatly among Dukes' C CRC tumours and shows a multimodal (non-normal) distribution

  dukes colorectal comparative kaplan-meier

• 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

• Re-evaluating early breast neoplasia.

  PMID 18279539 · PMC2374963 · Breast cancer research : BCR · 2008 · 8 claims · 7 setups

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  The classic single linear model of breast cancer progression requires revision based on high-throughput molecular genetic and gene expression data.

  dcis breast patient-matched premalignant comparative combined cdna

• Recurrent DNA copy number changes in 1q, 4q, 6q, 9p, 13q, 14q and 22q detected by comparative genomic hybridization in malignant mesothelioma.

  PMID 9052404 · PMC2063309 · British journal of cancer · 1997 · 7 claims · 2 setups

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  This is the first genome-wide screening for DNA sequence gains and losses using CGH in malignant pleural mesothelioma tumours.

  pleural cgh comparative statistical

• From microarrays to genome duplications.

  PMID 12914655 · PMC193639 · Genome biology · 2003 · 8 claims · 8 setups

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  Gene3D shows that most genes across sequenced genomes can be assigned to known structural domain families, many of which are shared across kingdoms of life

  tumor cancer plated saccharomyces comparative nonsense-mediated cell-based

• 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

• 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

• Copy number variations are a rare cause of non-CMT1A Charcot-Marie-Tooth disease.

  PMID 19949810 · PMC2865568 · Journal of neurology · 2010 · 7 claims · 4 setups

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  CNVs are a rare cause of non-CMT1A Charcot-Marie-Tooth disease

  unrelated genomic mtmr2 array quantitative sanger

• Paired-end mapping reveals extensive structural variation in the human genome.

  PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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  Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

  genomic na15510 stretched reference paired-end pcr array

• High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians.

  PMID 19900272 · PMC3091319 · Genome biology · 2009 · 7 claims · 4 setups

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  Custom whole-genome scan arrays (~200 bp resolution) discover CNV regions not previously reported in the literature

  yoruba selected subset whole-genome targeted pcr

• 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

• BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).

  PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups

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  oaCGH, not BAC CGH arrays, is the platform that will prevail in the future

  genomic lung genetics bt474 array exon