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).

• Genomics--from Neanderthals to high-throughput sequencing.

  PMID 16934106 · PMC1779599 · Genome biology · 2006 · 8 claims · 8 setups

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  Next-generation sequencing platforms (GS20/454 and Solexa) can deliver the throughput and cost reductions needed for population-scale and medical resequencing.

  bacterial ion-channel drosophila arrays next-generation pooled multiplex

• Epigenetics and phenotypic variation in mammals.

  PMID 16688527 · PMC3906716 · Mammalian genome : official journal of the International Mammalian Genome Society · 2006 · 8 claims · 8 setups

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  Epigenetic modifications are mitotically heritable, but the fidelity of meiotic/transgenerational inheritance in mammals is poorly understood and evidence in mammals is scanty.

  mammalian mhc chromosomes embryonic methylation high-throughput chip

• Paircomp, FamilyRelationsII and Cartwheel: tools for interspecific sequence comparison.

  PMID 15790396 · PMC1087472 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Paircomp, FamilyRelationsII, and Cartwheel together form an integrated system for comparing, viewing, and managing analyses of BAC-sized (~100 kb) genomic sequence pairs.

  otx sea elegans endo16 windowed reporter comparative

• Interaction of vitamin D receptor with HLA DRB1 0301 in type 1 diabetes patients from North India.

  PMID 19956544 · PMC2780726 · PloS one · 2009 · 8 claims · 6 setups

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  Interaction between VDR and HLA alleles is mediated by a VDRE present in the promoter region of HLA-DRB1*0301, which may be detrimental in the absence of 1,25-(OH)2D3 in early childhood.

  blood genotype hla-drb1*0301 drb1*0301-carrying pcr-rflp pcr haplotype

• Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).

  PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups

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  The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species

  tlr4 mus chimpanzee baboon genomic coding sequence

• Molecular phylogeny of the antiangiogenic and neurotrophic serpin, pigment epithelium derived factor in vertebrates.

  PMID 17020603 · PMC1609119 · BMC genomics · 2006 · 8 claims · 8 setups

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  A single PEDF gene is present in all examined vertebrate species but is absent from invertebrates (D. melanogaster, C. elegans, C. intestinalis)

  vertebrate cdna pedf complete genomic rt-pcr phylogenetic

• Personalized genomic medicine with a patchwork, partially owned genome.

  PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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  Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

  phenotypically single genome chimpanzee molecular diploid encode

• F-SNP: computationally predicted functional SNPs for disease association studies.

  PMID 17986460 · PMC2238878 · Nucleic acids research · 2008 · 6 claims · 8 setups

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  F-SNP is a database integrating functional effect predictions for SNPs from 16 bioinformatics tools/databases across four categories: splicing, transcription, translation, and post-translation

  genome protein-coding genomic genome-wide non-synonymous exonic nonsense

• Resequencing PNMT in European hypertensive and normotensive individuals: no common susceptibilily variants for hypertension and purifying selection on intron 1.

  PMID 17645789 · PMC1947951 · BMC medical genetics · 2007 · 7 claims · 7 setups

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  Resequencing of PNMT found no common susceptibility variants that distinguish hypertensive from normotensive individuals

  genomic pnmt promoter pcr population haplotype

• Comparative genomics.

  PMID 14624258 · PMC261895 · PLoS biology · 2003 · 8 claims · 7 setups

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  Conserved DNA between species tends to encode shared functional features, while divergent DNA underlies species differences

  caenorhabditis yeast mammalian vertebrate whole-genome comparative interspecies-similarity-informed

• Genomic rearrangements by LINE-1 insertion-mediated deletion in the human and chimpanzee lineages.

  PMID 16034026 · PMC1179734 · Nucleic acids research · 2005 · 8 claims · 6 setups

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  L1 insertions are directly responsible for genomic deletions (L1IMDs) confirmed in both human and chimpanzee genomes

  hg16 genomic individuals element computational pcr pcr-based

• A genome-wide screen for noncoding elements important in primate evolution.

  PMID 18215302 · PMC2242780 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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  A new likelihood ratio test (LRT) method, using nearby ancestral repeats to control for local mutation rate, can identify noncoding elements with lineage-specific accelerated substitution rates.

  phastcons global genome accelerated comparative targeted fisher's

• Identification of transcription start sites and preferential expression of select CB2 transcripts in mouse and human B lymphocytes.

  PMID 19757078 · PMC2843092 · Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2009 · 7 claims · 8 setups

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  Human B cells express one CB2 transcript while mouse B cells express three CB2 transcripts

  splenocytes pbmc-derived splenic genbank race pcr quantitative

• Of rats and men.

  PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups

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  The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)

  rattus cftr fugu transgenic whole-genome comparative genome