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).

• Gene losses during human origins.

  PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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  A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

  pseudogene chimpanzee human-specific population comparative phylogenetic fisher's

• 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

• Retropseudogenes derived from the human Ro/SS-A autoantigen-associated hY RNAs.

  PMID 15817567 · PMC1074747 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  966 pseudogenes derived from the four human Y (hY) RNAs were characterized in the human genome

  genome chimpanzee pseudogenes genomic megablast blat sequence

• PolyA_DB 2: mRNA polyadenylation sites in vertebrate genes.

  PMID 17202160 · PMC1899096 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  PolyA_DB 2 catalogs poly(A) sites for genes in human, mouse, rat, chicken and zebrafish, identified by aligning cDNA/ESTs with genome sequences

  sequences poly cdna trace pssm-based

• New approaches to the analysis of palindromic sequences from the human genome: evolution and polymorphism of an intronic site at the NF1 locus.

  PMID 16340004 · PMC1310899 · Nucleic acids research · 2005 · 7 claims · 8 setups

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  Long pure palindromes (>~200 bp) cannot be stably cloned in E.coli due to cruciform-driven instability, and no E.coli mutant fully overcomes this cloning block.

  individuals e.coli cerevisiae yeast pcr plasmid phi-29

• 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

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• 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