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).

• 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

  Full-text index only

  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

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

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

  Full-text index only

  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

• Gene-resolution analysis of DNA copy number variation using oligonucleotide expression microarrays.

  PMID 17470268 · PMC1868757 · BMC genomics · 2007 · 8 claims · 7 setups

  Full-text index only

  graCNV uses re-annotated Affymetrix expression microarray probe sets and the WPP algorithm to measure DNA copy number variation at a median resolution of ~17,500 bp without genomic complexity reduction.

  neuroblastoma same normal megabladder acgh bac principal

• 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

  Full-text index only

  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 aCGH and expression profiling identifies a novel genomic subtype of ER negative breast cancer.

  PMID 17925008 · PMC2246289 · Genome biology · 2007 · 7 claims · 8 setups

  Full-text index only

  A novel subtype of high-grade ER-negative breast cancer exists, characterized by a low genomic instability index (GII)

  breast computational array-cgh gene bac

• MatchMiner: a tool for batch navigation among gene and gene product identifiers.

  PMID 12702208 · PMC154578 · Genome biology · 2003 · 8 claims · 3 setups

  Full-text index only

  MatchMiner's LookUp function automates batch translation of an input list of gene identifiers into a matching list of a different identifier type.

  nci-60 fish-mapped random batch fish-mapped cross-validation

• Twin peaks: the draft human genome sequence.

  PMID 11276423 · PMC138909 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  The predicted number of human genes (~26,000-40,000) is far lower than the widely assumed ~100,000, though downstream RNA/protein complexity can still generate substantial biological complexity.

  genome genomic genes yeast whole-genome bac computational

• A golden age of brain exploration.

  PMID 15660159 · PMC544547 · PLoS biology · 2005 · 8 claims · 3 setups

  Full-text index only

  Over 99% of neuroscience literature focuses on only 1% of the ~15,000–16,000 genes expressed in the brain, leaving most brain-expressed genes uncharacterized.

  brain transgenic situ microarray bacterial

• Computational comparison of two mouse draft genomes and the human golden path.

  PMID 12537546 · PMC151282 · Genome biology · 2003 · 8 claims · 7 setups

  Full-text index only

  The Celera and public mouse genome assemblies differ in about 10% of the mouse genome, with complementary strengths (Celera higher base-pair accuracy and overall coverage; public assembly higher quality in some finished BAC regions and freely accessible)

  newly genome chromosome genomic blat blastn repeat

• Neuroscience in the era of functional genomics and systems biology.

  PMID 19829370 · PMC3645852 · Nature · 2009 · 8 claims · 7 setups

  Full-text index only

  Omics/discovery-based approaches do not eschew hypotheses but elevate hypothesis testing to high-throughput hypothesis generation and prioritization.

  developing hippocampus bac-transgenic fetal situ gene bac-transgenic

• Comparative genomics comes of age.

  PMID 12186641 · PMC139393 · Genome biology · 2002 · 8 claims · 8 setups

  Full-text index only

  Only about 50% of conserved sequence elements (exons+introns) in orthologous human-mouse genes correspond to exons, implying substantial non-exonic conservation

  orthologous chromosome chimpanzee somatic-cell comparative targeted tiled

• The jewels of our genome: the search for the genomic changes underlying the evolutionarily unique capacities of the human brain.

  PMID 16733552 · PMC1464830 · PLoS genetics · 2006 · 8 claims · 7 setups

  Full-text index only

  Human and chimp genomes differ by ~35 million single nucleotide substitutions, corresponding to ~1.06% divergence after removing polymorphic sites

  chimpanzee chimp population non-human genome snp high-density

• More biology from the sequence.

  PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.

  schizosaccharomyces chromosome genome cervical whole-genome sequence genome

• The meso-genomic era.

  PMID 11516332 · PMC139414 · Genome biology · 2001 · 8 claims · 8 setups

  Full-text index only

  Linkage disequilibrium (LD) between SNPs extends much further in Northern European populations (~120 kb) than in a Nigerian population (<10 kb), reflecting differing population histories (bottlenecks vs. constant expansion).

  genome chromosome families tomato snp haplotype genetic