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).

• 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

• On the association between chromosomal rearrangements and genic evolution in humans and chimpanzees.

  PMID 17971225 · PMC2246304 · Genome biology · 2007 · 8 claims · 4 setups

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  Genes located in rearranged chromosomes show lower non-coding (KI), synonymous (KS), and non-synonymous (KA) divergence than genes in colinear chromosomes.

  human-chimpanzee orthologous genome-wide pairwise lineage-specific permutation

• 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

• 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

• The gentle art of gene arrangement: the meaning of gene clusters.

  PMID 11897017 · PMC139018 · Genome biology · 2002 · 8 claims · 7 setups

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  Gene order in eukaryotic genomes is likely optimized by natural selection rather than arising purely by chance reshuffling.

  populations mhc interphase cartilaginous sequence codon comparative

• 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

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  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

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

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

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  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

• Sequence variants in the autophagy gene IRGM and multiple other replicating loci contribute to Crohn's disease susceptibility.

  PMID 17554261 · PMC2628541 · Nature genetics · 2007 · 8 claims · 8 setups

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  IRGM SNPs (rs13361189, rs4958847) show strong replicated association with Crohn disease; IRGM induces autophagy and control of intracellular bacteria

  wtccc replication population cases genome-wide taqman snp

• Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

  PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

  longitudinal backbone env intra-patient relaxed-clock correlation site-to-site

• Distinctive pattern of sequence polymorphism in the NS3 protein of hepatitis C virus type 1b reflects conflicting evolutionary pressures.

  PMID 18632963 · PMC2577380 · The Journal of general virology · 2008 · 7 claims · 6 setups

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  NS3 shows less evidence of purifying selection acting on its CTL epitopes than the other 9 HCV proteins, while outside the CTL epitopes NS3 is more conserved than the other proteins.

  complete hcv-1b sequence nonsynonymous comparative neighbor-joining maximum

• 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

• SARS-CoV genome polymorphism: a bioinformatics study.

  PMID 16144519 · PMC5172477 · Genomics, proteomics & bioinformatics · 2005 · 8 claims · 6 setups

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  SARS-CoV isolates can be classified into groups/subgroups based on the number and distribution of SNVs and INDELs relative to a 'profile' sequence, and this classification aligns with phylogenetic tree relationships and epidemiological spread.

  sars-cov annotated spike whole-genome positional codon

• Molecular evolution and multilocus sequence typing of 145 strains of SARS-CoV.

  PMID 16112670 · PMC7118731 · FEBS letters · 2005 · 8 claims · 7 setups

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  145 SARS-CoV genomes can be divided into three groups: animal-origin viruses, first-epidemic clinical viruses, and GD03T0013

  complete mutation sars-cov spike sequence phylogenetic selection

• Mutations in PIK3CA are infrequent in neuroblastoma.

  PMID 16822308 · PMC1533846 · BMC cancer · 2006 · 8 claims · 6 setups

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  PIK3CA activating mutations are infrequent in human neuroblastoma (2.9%, 2/69 tumors)

  neuroblastoma neuroblastoma-derived patients th-mycn targeted sanger rt-pcr

• Differences in the evolutionary history of disease genes affected by dominant or recessive mutations.

  PMID 16817963 · PMC1534034 · BMC genomics · 2006 · 8 claims · 8 setups

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  Dominant disease genes are more conserved at the protein level (mouse orthologues) than recessive disease genes.

  disease human-chimpanzee human-mouse-dog elegans sequence paralogue coding

• Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history.

  PMID 16440057 · PMC1331980 · PLoS genetics · 2006 · 7 claims · 6 setups

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  Complete 4.25-Mb sequence of the QBL haplotype was determined by BAC shotgun sequencing and compared with PGF (reference) and COX haplotypes

  qbl pgf classical ceph bac comparative gene

• Reverse polarization in amino acid and nucleotide substitution patterns between human-mouse orthologs of two compositional extrema.

  PMID 17895298 · PMC2533592 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2007 · 8 claims · 7 setups

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  Nucleotide and amino acid substitution trends between human-mouse orthologs are highly asymmetric and polarized in opposite directions for high-GC versus low-GC gene groups.

  human-mouse high aarm orthologous content pairwise

• Characterisation of the genetic diversity of Brucella by multilocus sequencing.

  PMID 17448232 · PMC1877810 · BMC microbiology · 2007 · 8 claims · 5 setups

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  Brucella isolates show low overall genetic diversity (1.5%) across nine sequenced loci, confirming the genus is genetically conserved.

  brucella sequenced concatenated allelic multilocus ratio neighbour-joining

• 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

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  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

• 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