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 49

System / cell line: sites ✕ Assay: phylogenetic ✕ Clear

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

PMID 15774015 · PMC1084245 · BMC genomics · 2005 · 6 claims · 4 setups

Full-text index only

Integrated phylogenetic foot printing and transcription factor binding site (TFBS) prediction identified a consensus putative STK11/LKB1 promoter region between nucleotides -1090 and -1472

genomic phylogenetic direct high
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
Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

PMID 19682372 · PMC2735741 · BMC evolutionary biology · 2009 · 7 claims · 7 setups

Full-text index only

Major NLRP genes duplicated before the divergence of mammals, with lineage-specific duplications in primates (NLRP7, NLRP11) and rodents (Nlrp1, Nlrp4, Nlrp9)

mammalian cattle oocyte-expressed genome phylogenetic syntenic functional
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
SARS-CoV genome polymorphism: a bioinformatics study.

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

Full-text index only

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
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

Full-text index only

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

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

Full-text index only

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
Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

PMID 15984912 · PMC1166350 · PLoS biology · 2005 · 8 claims · 6 setups

Full-text index only

Most mtDNA lineages in Taiwanese aboriginal populations are distinct from those in China and the Taiwan Han population, consistent with descent from the island's initial late Pleistocene settlers

indigenous b4a-lineage southeast populations mtdna complete rflp
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

Full-text index only

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
Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

PMID 18811940 · PMC2564943 · BMC evolutionary biology · 2008 · 8 claims · 8 setups

Full-text index only

Teleosts, unlike tetrapods, possess two closely linked paralogous AQP1 genes, aqp1a and aqp1b (formerly AQP1o), arising from a teleost-specific duplication of an ancestral AQP1 gene

aqp1-like pufferfish tissues xenopus phylogenetic genomic rt-pcr
Integrative functional genomics.

PMID 15239826 · PMC463286 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

Ultra-conserved noncoding elements exist across human, mouse and rat genomes at very high sequence identity, often far from genes

yeast tissue-cultured mammalian genomic comparative targeted chip-chip
The EH1 motif in metazoan transcription factors.

PMID 16309560 · PMC1310626 · BMC genomics · 2005 · 8 claims · 5 setups

Full-text index only

There is a statistically significant association between EH1hox motif HMM score and transcription factor function across human, Drosophila and C. elegans proteomes.

homeobox-containing forkhead-containing complete combined meme hmm logistic
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

PMID 18451061 · PMC2885628 · Microbiology (Reading, England) · 2008 · 8 claims · 6 setups

Full-text index only

N. lactamica por is less diverse than meningococcal porB2 and porB3

lactamica unique pcr distance-based population
Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

PMID 15380029 · PMC521075 · BMC genomics · 2004 · 8 claims · 6 setups

Full-text index only

Cell-cycle related CDKs (orthologs of CDK1-6) are present in all sampled eukaryotic organisms, including the most ancestral protists.

animals cdk encephalitozoon pfmrk comparative bayesian distance
Heterogeneous genomic molecular clocks in primates.

PMID 17029560 · PMC1592237 · PLoS genetics · 2006 · 7 claims · 7 setups

Full-text index only

Non-CpG site substitutions show clear generation-time dependency, consistent with a replication-error origin

baboon chimpanzee same human-chimpanzee relative phylogenetic four-species
Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

PMID 17962310 · PMC2238824 · Nucleic acids research · 2008 · 8 claims · 5 setups

Full-text index only

The Human PAML Browser is a web-accessible database of codeml-based positive selection test results for 13,721 human genes with orthologs in UCSC multispecies alignments.

same genes orangutan codeml gene sequence
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
A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.

PMID 18925953 · PMC2580767 · BMC genetics · 2008 · 8 claims · 6 setups

Full-text index only

A 460–465 bp insertion is present in intron 4 of the Amel-Y locus in most Cetartiodactyla lineages (cetaceans and ruminants) but absent in pig

cetacea amel-y amel-x cetartiodactyla pcr sanger molecular

Experiments

Sequence changes in predicted promoter elements of STK11/LKB1 are unlikely to contribute to Peutz-Jeghers syndrome.

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

Evolution and functional divergence of NLRP genes in mammalian reproductive systems.

Global genetic diversity of human metapneumovirus fusion gene.

SARS-CoV genome polymorphism: a bioinformatics study.

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

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

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

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

Traces of archaic mitochondrial lineages persist in Austronesian-speaking Formosan populations.

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

Structural and functional divergence of two fish aquaporin-1 water channels following teleost-specific gene duplication.

Integrative functional genomics.

The EH1 motif in metazoan transcription factors.

Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

Comparative genomics of cyclin-dependent kinases suggest co-evolution of the RNAP II C-terminal domain and CTD-directed CDKs.

Heterogeneous genomic molecular clocks in primates.

Human PAML browser: a database of positive selection on human genes using phylogenetic methods.

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

A highly polymorphic insertion in the Y-chromosome amelogenin gene can be used for evolutionary biology, population genetics and sexing in Cetacea and Artiodactyla.