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).

• 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

• Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

  PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

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  Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

  genome h-invdb gene sets genome transcript-to-genome coding

• Ancient adaptive evolution of the primate antiviral DNA-editing enzyme APOBEC3G.

  PMID 15269786 · PMC479043 · PLoS biology · 2004 · 7 claims · 6 setups

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  APOBEC3G has been under strong, recurrent positive selection throughout primate evolution (~33 million years)

  apobec3g pairwise human-chimpanzee apobec1 pcr phylogenetic sliding

• 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

• 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

• Heterogeneous genomic molecular clocks in primates.

  PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

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  Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

  baboon chimpanzee same human-chimpanzee relative phylogenetic four-species

• Evolutionary toggling of the MAPT 17q21.31 inversion region.

  PMID 19165922 · PMC2684794 · Nature genetics · 2008 · 8 claims · 6 setups

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  The H2 (inverted) orientation is the most likely ancestral great ape/human configuration at 17q21.31

  chimpanzee lymphoblastoid donor whole-genome reciprocal bac

• Evolutionary analysis of the highly dynamic CHEK2 duplicon in anthropoids.

  PMID 18831734 · PMC2566985 · BMC evolutionary biology · 2008 · 8 claims · 6 setups

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  CHEK2 is present as a single copy in New World monkeys, Old World monkeys, and gibbons

  metaphase chek2 blood-derived y-chromosomal comparative phylogenetic inter-species

• Phylogenomic approaches to common problems encountered in the analysis of low copy repeats: the sulfotransferase 1A gene family example.

  PMID 15752422 · PMC555591 · BMC evolutionary biology · 2005 · 8 claims · 8 setups

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  A previously unidentified fourth human SULT1A gene (SULT1A4) exists on chromosome 16 and is transcriptionally active

  genome chimpanzee sult1a3 est blast-like comparative pairwise

• DNA sequence of human chromosome 17 and analysis of rearrangement in the human lineage.

  PMID 16625196 · PMC2610434 · Nature · 2006 · 8 claims · 7 setups

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  A finished sequence of human chromosome 17 (78,839,971 bases, ~2.8% of the euchromatic genome) was generated.

  chromosome dog macaque genomic comparative segmental

• Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability.

  PMID 17214878 · PMC1779775 · BMC genomics · 2007 · 8 claims · 7 setups

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  The proportion of subjects lacking DEFA3 varies significantly by population, from 10% to 37%

  genomic hapmap 150-kb alpha-defensin pcr-rflp snp linkage

• Comparative genomic analysis of prion genes.

  PMID 17199895 · PMC1781936 · BMC genomics · 2007 · 8 claims · 8 setups

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  SPRN and PRNP homologues are present in all vertebrates, whereas PRND is restricted to tetrapods and PRNT is restricted to primates

  vertebrate multi-tissue aligned sprn comparative gene cdna

• 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