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).

• Widespread ultraconservation divergence in primates.

  PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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  The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

  hg18 genome genes computed comparative snp gene

• Chimp genome: branching out.

  PMID 16136102 · PMC7420934 · Nature · 2005 · 8 claims · 8 setups

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  The Chimpanzee Sequencing and Analysis Consortium published the initial draft chimpanzee genome sequence and compared it to the human genome.

  chimpanzee primate rhesus fossil whole-genome phylogenetic genome

• 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

• Sequence context affects the rate of short insertions and deletions in flies and primates.

  PMID 18291026 · PMC2374710 · Genome biology · 2008 · 8 claims · 6 setups

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  The rate of insertion or deletion of specific lengths can vary by more than 100-fold depending on the surrounding sequence context

  chimpanzee simulans chimp primate comparative direct nucleotide

• Ensembl 2009.

  PMID 19033362 · PMC2686571 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  Ensembl provides comprehensive, consistently annotated genome information for chordate genomes with automatically generated genesets and comparative genomics data

  horse mammalian chromosome ensembl post-gene-build genome gerp

• Genome-wide analysis of the human Alu Yb-lineage.

  PMID 15588477 · PMC3525081 · Human genomics · 2004 · 8 claims · 6 setups

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  1,733 Alu Yb-lineage elements are present on human autosomal chromosomes

  genome genomic non-human yb7 computational pcr-based pcr

• 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

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  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

• Endonuclease-independent insertion provides an alternative pathway for L1 retrotransposition in the human genome.

  PMID 17517773 · PMC1920257 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  An endonuclease-independent pathway (NCLI) for L1 insertion has been active in recent human genome evolution

  genome chimpanzee genomic pcr computational triple pcr

• 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

• Getting positive about selection.

  PMID 12914654 · PMC193638 · Genome biology · 2003 · 8 claims · 4 setups

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  Purifying selection is the predominant form of molecular evolution, preserving fitness by eliminating deleterious mutations, while positive selection is rare but critical for adaptation.

  genome chimpanzee human-chimpanzee humans whole-genome ratio maximum-likelihood

• Analysis of the human Alu Ye lineage.

  PMID 15725352 · PMC554112 · BMC evolutionary biology · 2005 · 8 claims · 6 setups

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  Two new Alu subfamilies, Ye4 and Ye6, were discovered, complementing the previously described Ye5 subfamily.

  draft genomic non-human geographically blast sequence pcr

• Identification, characterization and comparative genomics of chimpanzee endogenous retroviruses.

  PMID 16805923 · PMC1779541 · Genome biology · 2006 · 8 claims · 6 setups

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  The chimpanzee genome contains at least 42 separate families of endogenous retroviruses, 9 newly identified

  chimpanzee domains genomic hg16 genome-wide sequence ltr-ltr

• TB database: an integrated platform for tuberculosis research.

  PMID 18835847 · PMC2686437 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  TBDB is an integrated database providing access to TB genomic data and resources relevant to discovery/development of TB drugs, vaccines and biomarkers.

  tuberculosis streptomyces tb-infected whole-genome sequence trna

• Genome-wide survey for biologically functional pseudogenes.

  PMID 16680195 · PMC1456316 · PLoS computational biology · 2006 · 8 claims · 6 setups

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  A subset of ancient, cross-species-conserved pseudogenes (30 of 1,453 candidate quartets) show evidence consistent with retained biological function

  human-mouse chimpanzee cross-species maximum-likelihood synteny

• Network of Cancer Genes: a web resource to analyze duplicability, orthology and network properties of cancer genes.

  PMID 19906700 · PMC2808873 · Nucleic acids research · 2010 · 7 claims · 4 setups

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  NCG is a web database integrating duplicability, orthology, evolutionary appearance, and network topology data for 736 human cancer genes

  cancer proteome pten genome orthology protein-protein

• Kangaroo--a pattern-matching program for biological sequences.

  PMID 12150718 · PMC119856 · BMC bioinformatics · 2002 · 7 claims · 2 setups

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  Kangaroo is a web-based regular expression pattern-matching program that searches DNA, protein, or coding-region sequences across ten organisms with no restriction on query length or complexity.

  coding regular-expression mutation

• The UCSC Genome Browser Database: update 2009.

  PMID 18996895 · PMC2686463 · Nucleic acids research · 2009 · 8 claims · 6 setups

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  The UCSC Genome Browser Database (GBD) is a publicly available, integrated collection of genome assembly sequences and annotations across many organisms, including extensive comparative-genomic resources.

  chimp vertebrate mrnas genome genome-wide multiz blat

• In silico and in vitro comparative analysis to select, validate and test SNPs for human identification.

  PMID 18076761 · PMC2222643 · BMC genomics · 2007 · 8 claims · 7 setups

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  A panel of 24 SNPs was selected and validated for human identification using 1,040 unrelated samples from three populations (Italian, Benin Gulf, Mongolian)

  genomic genome pan blood snp sequence cross-species

• Accelerated evolution of the ASPM gene controlling brain size begins prior to human brain expansion.

  PMID 15045028 · PMC374243 · PLoS biology · 2004 · 8 claims · 6 setups

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  The ASPM gene shows accelerated (positively selected) evolution in the African hominoid clade, and this acceleration precedes hominid brain expansion by several million years.

  chimpanzee retrofitted primate aspm tar restriction genomic

• Analysis of the prostate cancer cell line LNCaP transcriptome using a sequencing-by-synthesis approach.

  PMID 17010196 · PMC1592491 · BMC genomics · 2006 · 8 claims · 7 setups

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  High-throughput 454 sequencing-by-synthesis of LNCaP cDNA can profile transcript abundance across the transcriptome

  lncap lncap-derived r1881-treated massively blast blat