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).

• Recurring genomic breaks in independent lineages support genomic fragility.

  PMID 17090315 · PMC1636669 · BMC evolutionary biology · 2006 · 6 claims · 6 setups

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  The propensity of a chromosomal region to break is significantly correlated among independent lineages, even after accounting for covariates like region length and functional class.

  hg17 genome computationally comparative marker segmental

• Fast-evolving noncoding sequences in the human genome.

  PMID 17578567 · PMC2394770 · Genome biology · 2007 · 8 claims · 6 setups

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  1,356 conserved noncoding sequences show human-specific accelerated substitution rates (ANC sequences) relative to chimpanzee

  chimpanzee genome hapmap comparative genomic segmental

• The role of positive selection in determining the molecular cause of species differences in disease.

  PMID 18837980 · PMC2576240 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  Genes predicted to be under positive selection during human evolution are implicated in diseases (epithelial cancers, schizophrenia, autoimmune diseases, Alzheimer's disease) that differ in prevalence and symptomatology between humans and other mammals

  orthologous omim meta-database panther comparative disease protein-protein

• 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

• Patrocles: a database of polymorphic miRNA-mediated gene regulation in vertebrates.

  PMID 19906729 · PMC2808989 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Patrocles is a database compiling DSPs predicted to perturb miRNA-mediated gene regulation across seven vertebrate species, covering targets, miRNA precursors and silencing machinery.

  3'-utr mirbase hapmap comparative snp mirna

• Comparative genomics comes of age.

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

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  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

• Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

  PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

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  Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

  liver chimpanzee h-invitational tar genome blastn secondary

• CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes.

  PMID 19854943 · PMC2800233 · Nucleic acids research · 2010 · 8 claims · 6 setups

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  Functional ('bona fide') CGIs show distinct average/cumulative mutual information (AMI/CMI) distributions of neighboring CpG distances compared to non-functional CGIs and random genome segments

  genome random cd4+ six average mutual chip-seq

• DNA sequence and analysis of human chromosome 9.

  PMID 15164053 · PMC2734081 · Nature · 2004 · 8 claims · 8 setups

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  The finished euchromatic sequence of chromosome 9 comprises 109,044,351 base pairs, representing >99.6% of the region.

  bac chromosome fibres chimpanzee clone-based restriction computational

• The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample.

  PMID 19800201 · PMC2783814 · Schizophrenia research · 2009 · 8 claims · 7 setups

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  Common alleles at DTNBP1 SNPs, particularly rs760761, are associated with schizophrenia in the ICCSS sample

  irish chimpanzee dtnbp1 snp haplotype case

• Ensembl 2013.

  PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

  genome species supported variants evidence-based rna-seq chip-seq

• Genome assembly comparison identifies structural variants in the human genome.

  PMID 17115057 · PMC2674632 · Nature genetics · 2006 · 7 claims · 7 setups

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  Genome assembly comparison is a robust approach for identifying all classes of genetic variation, with no lower size limit.

  genome ceph unrelated individuals whole-genome pcr quantitative