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).

Publications 1.3k Datasets 392.5k Experiments 15

System / cell line: amino ✕ Assay: neighbor-joining ✕ Clear

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

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

Full-text index only

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
Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

PMID 8903171 · PMC2626880 · Emerging infectious diseases · 1995 · 7 claims · 4 setups

Full-text index only

Romanian and Brazilian HIV-1 subtype F envelope C2-V3 sequences cluster into two related but distinct phylogenetic groups.

hiv-1 same brazilian phylogenetic bootstrap pruning
Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

PMID 18687142 · PMC2546438 · Retrovirology · 2008 · 7 claims · 6 setups

Full-text index only

Integrase displays significantly less inter- and intra-subtype amino acid diversity and lower Shannon's entropy than protease or RT.

genbank hiv-1 protease integrase blastp phylogenetic amino
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

Full-text index only

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
Evolutionary sequence analysis of complete eukaryote genomes.

PMID 15762985 · PMC1274250 · BMC bioinformatics · 2005 · 8 claims · 6 setups

Full-text index only

A conservative genome-comparison method (MIA) identifies panorthologs — strict single-copy 1:1 orthologs containing only species divergences, no paralogy — to minimize errors from gene duplication in evolutionary sequence analysis.

complete panortholog concatenated individual reciprocal sequence neighbor-joining
Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

PMID 18258114 · PMC2600181 · Emerging infectious diseases · 2008 · 8 claims · 7 setups

Full-text index only

The nonstructural genes, especially NS5, are the most variable regions between highly and less neuroinvasive lineage 2 WNV strains

lineage mice patients complete phylogenetic nucleotide
Global genetic diversity of human metapneumovirus fusion gene.

PMID 15207075 · PMC3323143 · Emerging infectious diseases · 2004 · 8 claims · 6 setups

Full-text index only

Phylogenetic analysis of the HMPV F gene identifies two main groups (A and B, 93%-96% amino acid identity) further divided into four subgroups (A1, A2, B1, B2)

hmpv llc-mk2 clinical rt-pcr sequence phylogenetic
Genome-wide diversity and selective pressure in the human rhinovirus.

PMID 17477878 · PMC1892812 · Virology journal · 2007 · 7 claims · 6 setups

Full-text index only

Whole genome and subgenomic phylogenies of HRV are essentially identical at every locus, indicating consistent phylogenetic patterns across the genome.

diverse hrv fully hrva genome phylogenetic pairwise
The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

PMID 18325125 · PMC2311284 · Virology journal · 2008 · 8 claims · 6 setups

Full-text index only

H3N2 was the prevalent influenza A strain in Denmark from 1999 to 2006, except the 2000–2001 season when H1N1 dominated

danish representative h3n2 influenza phylogenetic complete haemagglutination
Large-scale trends in the evolution of gene structures within 11 animal genomes.

PMID 16518452 · PMC1386723 · PLoS computational biology · 2006 · 8 claims · 5 setups

Full-text index only

Change in intron–exon gene structure is gradual, clock-like, and largely independent of coding-sequence (protein) evolution

annotated animal unannotated comparative all-against-all neighbor-joining
Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

PMID 18304319 · PMC2268676 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

Full-text index only

Comparative synteny conservation around a horizontally transferred gene (HTgene) can distinguish single versus multiple independent HGT events even without a robust phylogenetic tree.

poxvirus core psi-blast comparative molecular
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

PMID 19851457 · PMC2760143 · PLoS pathogens · 2009 · 8 claims · 4 setups

Full-text index only

Genetically distinct RV clades of the same G/P-type (G3P[8]) can co-circulate within a single epidemic season and cause disease

g3p[8] rv-positive concatenated deduced rt-pcr pcr-elisa phylogenetic
Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

PMID 17982176 · PMC2238928 · Nucleic acids research · 2008 · 6 claims · 7 setups

Full-text index only

Evola combines genome synteny-based computational ortholog detection with manual curation of phylogenetic trees by experts to yield more reliable orthologs than automated pairwise methods

genome h-invdb gene sets genome transcript-to-genome coding
Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

PMID 18471294 · PMC2397415 · BMC genomics · 2008 · 7 claims · 7 setups

Full-text index only

The complete genome of HAdV-37 was sequenced and annotated (35,213 bp, 56.6% GC content, 35 predicted coding sequences plus 8 hypothetical ORFs)

hadv-37 predicted select genome cpg global
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

Full-text index only

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

cloned clinical hominis pcr culture sanger

Experiments

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

Epidemiologic and evolutionary relationships between Romanian and Brazilian HIV-subtype F strains.

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors.

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

Evolutionary sequence analysis of complete eukaryote genomes.

Genetic determinants of virulence in pathogenic lineage 2 West Nile virus strains.

Global genetic diversity of human metapneumovirus fusion gene.

Genome-wide diversity and selective pressure in the human rhinovirus.

The evolution of human influenza A viruses from 1999 to 2006: a complete genome study.

Large-scale trends in the evolution of gene structures within 11 animal genomes.

Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach.

Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees.

Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism.

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