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).

• Inverse symmetry in complete genomes and whole-genome inverse duplication.

  PMID 19898631 · PMC2771390 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Reverse and complement symmetries are essentially absent in genomic sequences at all scales.

  complete coli individual coding k-mer comparison segmental

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

  Full-text index only

  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization

• Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes.

  PMID 18989394 · PMC2566816 · PLoS computational biology · 2008 · 7 claims · 4 setups

  Full-text index only

  A novel Bayesian method, RASER, can detect site-specific evolutionary rate shifts and the lineages in which they occurred without pre-specifying candidate lineages.

  hiv-1 simulated bayesian simulation structural

• Survey of transcripts in the adult Drosophila brain.

  PMID 11276425 · PMC30707 · Genome biology · 2001 · 8 claims · 4 setups

  Full-text index only

  The adult Drosophila brain cDNA library contains approximately 6.75 million independent clones

  drosophila randomly brain cdna reverse sequence

• Adaptation to different human populations by HIV-1 revealed by codon-based analyses.

  PMID 16789820 · PMC1480537 · PLoS computational biology · 2006 · 8 claims · 8 setups

  Full-text index only

  Developed two fixed effects maximum likelihood methods: one to detect selection that persists in a population (internal vs. terminal branches) and one to detect differential selection on codons between two populations.

  hiv-1 four simulated population-based maximum bayesian

• Comparative genomics reveals functional transcriptional control sequences in the Prop1 gene.

  PMID 17557180 · PMC1998882 · Mammalian genome : official journal of the International Mammalian Genome Society · 2007 · 7 claims · 7 setups

  Full-text index only

  A BAC transgene containing Prop1 completely rescues the Prop1 mutant (dwarf) phenotype, showing all necessary regulatory elements lie within the BAC

  pig lemur cv-1 b-prop1 bac comparative transient

• Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

  PMID 18450818 · PMC2425492 · Nucleic acids research · 2008 · 8 claims · 5 setups

  Full-text index only

  Pyknons (recurrent, genome-specific, ≥16nt motifs with ≥30 intact intergenic/intronic copies and ≥1 exonic copy) span a substantial fraction of previously uncharacterized intronic space (7.4% human, 4.4% mouse)

  pyknon computational comparative term

• Genomic view of the evolution of the complement system.

  PMID 16896831 · PMC2480602 · Immunogenetics · 2006 · 8 claims · 6 setups

  Full-text index only

  Bony fish and higher vertebrates share practically the same set of complement genes, indicating most complement gene duplications occurred by the teleost/mammalian divergence (~500 MYA)

  chicken complement sponge shark comparative phylogenetic reverse

• RNAseq analysis of the parasitic nematode Strongyloides stercoralis reveals divergent regulation of canonical dauer pathways.

  PMID 23145190 · PMC3493385 · PLoS neglected tropical diseases · 2012 · 8 claims · 8 setups

  Has reproduction · 66

  S. stercoralis possesses homologs of nearly all C. elegans dauer genes, but with significant differences in protein structure, developmental regulation, and gene family expansion.

  strongyloides stercoralis mongolian adapter-ligated polyadenylated novo comparative

• Fabry disease: identification of 50 novel alpha-galactosidase A mutations causing the classic phenotype and three-dimensional structural analysis of 29 missense mutations.

  PMID 16595074 · PMC3500179 · Human genomics · 2006 · 8 claims · 7 setups

  Full-text index only

  50 novel α-Gal A mutations were identified in 49 of 66 unrelated families with classic Fabry disease.

  genomic α-gal cos-7 transcripts pcr southern microsatellite

• Metagenomic analysis of human diarrhea: viral detection and discovery.

  PMID 18398449 · PMC2290972 · PLoS pathogens · 2008 · 8 claims · 7 setups

  Full-text index only

  Micro-mass sequencing (minimal stool input, minimal purification, ~384 reads/sample) can detect known enteric viruses in diarrhea specimens

  stool divergent extract preparations sequence-independent maximum enzyme