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).

• 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-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

• 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

• SIGMA: a system for integrative genomic microarray analysis of cancer genomes.

  PMID 17192189 · PMC1764892 · BMC genomics · 2006 · 7 claims · 6 setups

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  SIGMA is a user-friendly, web-based Java application for visualization and integrative analysis of array CGH data across multiple platforms.

  cancer lung breast array medip segmentation

• Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution.

  PMID 18410676 · PMC2375447 · BMC genomics · 2008 · 8 claims · 7 setups

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  Chicken and turkey genomes differ by only two inter-chromosomal rearrangements (GGA2 orthologous to MGA3+6; GGA4 orthologous to MGA4+9), both involving centromeres.

  chicken turkey broiler chromosome single fish

• Free energy of DNA duplex formation on short oligonucleotide microarrays.

  PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

  mapping50k_xba240 dgcr hg-u133a pdnn free correlation

• 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

• Large-scale molecular analysis of a 34 Mb interval on chromosome 6q: major refinement of the RP25 interval.

  PMID 18510646 · PMC2689154 · Annals of human genetics · 2008 · 7 claims · 5 setups

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  Direct sequencing of 43 candidate genes in 7 Spanish arRP families identified 244 sequence variants (76 novel), none pathogenic, excluding these genes as disease-causing.

  spanish rp5 population candidate direct comparative pcr

• 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