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).

• Genome-wide analysis of human disease alleles reveals that their locations are correlated in paralogous proteins.

  PMID 18989397 · PMC2565504 · PLoS computational biology · 2008 · 7 claims · 5 setups

  Full-text index only

  The locations of sequence variants are correlated between paralogous human proteins more than expected by chance.

  dbsnp best-hit omicia hgmd genome-wide correlation disease

• The HuRef Browser: a web resource for individual human genomics.

  PMID 19036787 · PMC2686481 · Nucleic acids research · 2009 · 7 claims · 6 setups

  Full-text index only

  The HuRef Browser is a unified web application integrating assembly, annotation, and assembly-to-assembly comparison (ATAC) views for the diploid HuRef individual human genome.

  individual huref whole-genome assembly-to-assembly variant

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

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

  Full-text index only

  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

• The heterogeneous allelic repertoire of human toll-like receptor (TLR) genes.

  PMID 19924287 · PMC2773936 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  Human TLR genes are unequally polymorphic: TLR2, 4, 7, 8 and 9 are comparatively least diverse, whereas TLR1, 5, 6 and 10 show substantial allelic diversity.

  tlr10 tlr5 tlr1 tlr6 pcr-based

• Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak.

  PMID 16700631 · PMC1463904 · PLoS medicine · 2006 · 8 claims · 6 setups

  Full-text index only

  The Indian Ocean outbreak was initiated by a strain related to East African CHIKV isolates, which subsequently evolved via a traceable microevolution history

  chikv partial pseudoscutellaris mosquito nucleotide phylogenetic focus

• Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

  PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

  Full-text index only

  The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

  healthy mrp1 population novo population functional

• Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.

  PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups

  Full-text index only

  62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation

  genome insect yy1-related zinc blast sequence synonymous

• Increased constraints on MC4R during primate and human evolution.

  PMID 19011902 · PMC9947067 · Human genetics · 2009 · 6 claims · 7 setups

  Full-text index only

  There is a significant paucity of genetic diversity at MC4R in humans but not in chimpanzees.

  hgdp-ceph germans central additional dhplc direct coding

• Exonic remnants of whole-genome duplication reveal cis-regulatory function of coding exons.

  PMID 19969543 · PMC2831330 · Nucleic acids research · 2010 · 8 claims · 8 setups

  Full-text index only

  38 candidate cis-regulatory coding exons (RCEs) with predicted target genes were identified genome-wide

  hg18 zebrafish bystander human-mouse comparative synteny orthologous

• A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

  PMID 15592405 · PMC2263125 · Nature · 2004 · 8 claims · 8 setups

  Full-text index only

  A genetic variation map of 2.8 million SNPs was constructed for chicken by comparing 3 domestic breeds to Red Jungle Fowl

  domestic red same white partial comparative pcr

• Construction and analysis of tag single nucleotide polymorphism maps for six human-mouse orthologous candidate genes in type 1 diabetes.

  PMID 15720714 · PMC551616 · BMC genetics · 2005 · 7 claims · 5 setups

  Full-text index only

  None of the six candidate gene regions showed evidence of association with type 1 diabetes (all multi-locus/single-locus test P values > 0.2)

  genomic case-control nramp1 type sanger snp microsatellite

• High-throughput discovery of rare human nucleotide polymorphisms by Ecotilling.

  PMID 16893952 · PMC1540726 · Nucleic acids research · 2006 · 7 claims · 6 setups

  Full-text index only

  Ecotilling can be adapted to accurately discover and genotype human SNPs, with error rates low relative to resequencing

  genomic ecotilling non-synonymous ecotilling sanger universal-primer

• Evolutionary genomics reveals lineage-specific gene loss and rapid evolution of a sperm-specific ion channel complex: CatSpers and CatSperbeta.

  PMID 18974790 · PMC2572835 · PloS one · 2008 · 8 claims · 6 setups

  Full-text index only

  The CatSper channel complex (four CatSpers plus CatSperβ) originated as early as primitive metazoans such as the Cnidarian Nematostella vectensis

  metazoan catsper pore chicken tblastn maximum sequence

• Assessing the genomic evidence for conserved transcribed pseudogenes under selection.

  PMID 19754956 · PMC2753554 · BMC genomics · 2009 · 8 claims · 8 setups

  Full-text index only

  1750 transcribed pseudogene annotations (TPAs) were identified in the human genome, ~11.5% of all human pseudogene annotations.

  genome rhesus vega-annotated tpas transcript-to-genome same synteny

• Molecular genetics and structural genomics of the human protein kinase C gene module.

  PMID 11897026 · PMC88812 · Genome biology · 2002 · 8 claims · 4 setups

  Full-text index only

  The nine human PKC genes are dispersed throughout the genome, with five isotypes (α, β, δ, ζ, ι) previously incorrectly assigned to chromosomes in the literature.

  metaphase genome pkc genomic fluorescence bioinformatic snp

• Comparative genomics of the neglected human malaria parasite Plasmodium vivax.

  PMID 18843361 · PMC2651158 · Nature · 2008 · 8 claims · 8 setups

  Full-text index only

  P. vivax resembles other sequenced malaria parasites (P. falciparum, P. knowlesi, P. yoelii) in gene content and metabolic potential

  vivax genome comparative microsatellite