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).

• In silico discovery of gene-coding variants in murine quantitative trait loci using strain-specific genome sequence databases.

  PMID 12537567 · PMC151180 · Genome biology · 2002 · 6 claims · 4 setups

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  Strain-specific mouse genome sequence databases can be used in a high-throughput in silico pipeline to discover gene-coding variants within murine QTLs, without de novo sequencing.

  strains genomic celera blast-based targeted phred

• Positive natural selection in the evolution of human metapneumovirus attachment glycoprotein.

  PMID 17931731 · PMC7114232 · Virus research · 2008 · 7 claims · 5 setups

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  8 amino acid sites in the extracellular domain of hMPV lineage 1a show a higher rate of nonsynonymous than synonymous substitutions (posterior probability >0.95), indicating positive selection.

  unique hmpv sequence neighbor-joining codon

• MutDB: update on development of tools for the biochemical analysis of genetic variation.

  PMID 17827212 · PMC2238958 · Nucleic acids research · 2008 · 7 claims · 5 setups

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  MutDB integrates dbSNP and Swiss-Prot genetic variation data with protein structural information, functional disruption prediction scores, and clinical phenotype links (OMIM, dbGAP)

  proteins mutdb nonsynonymous genes sequence web functional

• Conflicting selection pressures target the NS3 protein in hepatitis C virus genotypes 1a and 1b.

  PMID 19896990 · PMC3529174 · Virus research · 2010 · 7 claims · 5 setups

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  Both HCV-1a and HCV-1b show abundant slightly deleterious nonsynonymous variants subject to ongoing purifying selection across the polyprotein.

  hcv-1a phylogenetic sequence nucleotide

• Genomewide pattern of synonymous nucleotide substitution in two complete genomes of Mycobacterium tuberculosis.

  PMID 12453367 · PMC2738538 · Emerging infectious diseases · 2002 · 8 claims · 6 setups

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  Genomewide comparison of two complete M. tuberculosis genomes reveals substantially more nucleotide diversity than prior studies based on few loci suggested

  tuberculosis putative orthologous genomewide blastp clustal nei-gojobori

• Natural selection of protein structural and functional properties: a single nucleotide polymorphism perspective.

  PMID 18397526 · PMC2643940 · Genome biology · 2008 · 8 claims · 8 setups

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  The SNP A/S ratio is a robust measure of selective constraint, correlating with interspecies Ka/Ks ratios and with protein sequence conservation.

  sequence genes proteins sequences snp interspecies sequence

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• Molecular correlates of host specialization in Staphylococcus aureus.

  PMID 17971880 · PMC2040198 · PloS one · 2007 · 8 claims · 6 setups

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  Genome sequencing of ET3-1 revealed genomic elements not previously identified in S. aureus, including homologs of virulence factors from other Gram-positive pathogens

  aureus sequenced et3-1 bovine whole-genome comparative substitution

• Genetic variation of SARS coronavirus in Beijing Hospital.

  PMID 15200810 · PMC3323231 · Emerging infectious diseases · 2004 · 8 claims · 4 setups

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  113 sequence variations at 9 recurrent variant sites were identified in 29 full-length S-gene sequences compared to the BJ01 reference strain

  clinical extracted rna-derived cloned nested screening direct

• 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

• Evolutionary history of the UCP gene family: gene duplication and selection.

  PMID 18980678 · PMC2584656 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

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  The UCP gene family arose through two ancestral gene duplications early in vertebrate evolution, producing the UCP1, UCP2 and UCP3 lineages.

  vertebrate ucp human-mouse ucp1 sequence phylogenetic gene

• Relationships between emm and multilocus sequence types within a global collection of Streptococcus pyogenes.

  PMID 18405369 · PMC2359762 · BMC microbiology · 2008 · 8 claims · 5 setups

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  emm type is often a poor marker for clonal genetic background across the global S. pyogenes collection

  streptococcus pyogenes emm values multilocus emm comparative

• Genomic Correlates of Virulence Attenuation in the Deadly Amphibian Chytrid Fungus, Batrachochytrium dendrobatidis.

  PMID 26333840 · PMC4632049 · G3 (Bethesda, Md.) · 2015 · 8 claims · 8 setups

  Has reproduction · 58

  Virulence attenuation in the longer-passaged Bd isolate (JEL427-P39) is associated with loss of chromosome copy number relative to the shorter-passaged, more virulent isolate (JEL427-P9)

  strain jel427-p9 genes whole-genome snp indel

• Single nucleotide polymorphisms in bone turnover-related genes in Koreans: ethnic differences in linkage disequilibrium and haplotype.

  PMID 18036257 · PMC2222243 · BMC medical genetics · 2007 · 8 claims · 5 setups

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  Resequencing 81 candidate osteoporosis genes in 24 Koreans identified 942 variants (888 SNPs, 43 indels, 11 microsatellites)

  genomic sequenced korean common sanger sequence population

• Genetic variability of the P120' surface protein gene of Mycoplasma hominis isolates recovered from Tunisian patients with uro-genital and infertility disorders.

  PMID 18053243 · PMC2225410 · BMC infectious diseases · 2007 · 7 claims · 5 setups

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  The P120' surface-exposed N-terminal region undergoes substantial genetic variability among Tunisian M. hominis clinical isolates

  cloned clinical hominis pcr culture sanger

• Evidence for positive selection in putative virulence factors within the Paracoccidioides brasiliensis species complex.

  PMID 18820744 · PMC2553485 · PLoS neglected tropical diseases · 2008 · 8 claims · 8 setups

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  Positive selection has played an important role in the molecular evolution of putative virulence factors of P. brasiliensis

  brasiliensis gp43 ratio codon-based mutational

• Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.

  PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups

  Has reproduction · 50

  330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.

  brassica r500 rapa genomic bulk reference-based snp