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 95

Assay: maximum-likelihood ✕ Clear

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

PMID 19094205 · PMC2637867 · BMC evolutionary biology · 2008 · 8 claims · 4 setups

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AR was duplicated into two paralogs, AR-A and AR-B, during a teleost-specific whole genome duplication (WGD), after the split of Acipenseriformes but before the divergence of Osteoglossiformes.

fish full-length tetraodon rt-pcr database molecular
Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

PMID 18833279 · PMC3682493 · Nature · 2008 · 7 claims · 8 setups

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Recovered and characterized HIV-1 sequences (DRC60) from a 1960 Bouin's-fixed paraffin-embedded lymph node biopsy from Léopoldville, Belgian Congo

archival hiv-1-positive cdna concatenated rt-pcr quantitative pcr
The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

PMID 18778482 · PMC2563025 · Retrovirology · 2008 · 8 claims · 7 setups

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Intra-host nucleotide diversity of the HIV-2 C2V3C3 region increases over the course of chronic infection in most patients

pbmcs clonal env deduced nested maximum-likelihood positive
Genetic variation of St. Louis encephalitis virus.

PMID 18632961 · PMC2696384 · The Journal of general virology · 2008 · 8 claims · 4 setups

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Phylogenetic analysis of 106 SLEV E gene sequences confirms seven major lineages (I-VII) and refines them into 13 clades (IA, IB, IIA, IIB, IIC, IID, IIG, III, IV, VA, VB, VI, VII)

slev rt-pcr phylogenetic recombination
The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

PMID 18452600 · PMC2396169 · BMC evolutionary biology · 2008 · 8 claims · 5 setups

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169 gene products in the Ciona genome were identified as putative GPCRs

ciona sequence molecular est
Variation in the Neisseria lactamica porin, and its relationship to meningococcal PorB.

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

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

lactamica unique pcr distance-based population
A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

PMID 25202605 · PMC4103609 · Applications in plant sciences · 2014 · 8 claims · 8 setups

Has reproduction · 87

A custom sequence capture probe set (9678 baits targeting 1061 orthologous genes) was designed to enrich COS loci across the Compositae.

compositae same species helianthus targeted genome genomic
An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

PMID 18384666 · PMC2373789 · BMC genomics · 2008 · 8 claims · 7 setups

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The bovine genome contains a cluster of eight SERPINA3 genes and one pseudogene (SERPINA3P) sharing high sequence identity and identical structural organization

bovine bac roslin deduced southern bac radiation
Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

PMID 20021660 · PMC2810298 · BMC microbiology · 2009 · 8 claims · 6 setups

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A novel Multi-Locus Sequence Typing (MLST) scheme for O. anthropi was developed for the first time, based on 7 genes (3490 nucleotides) evolving mostly by neutral mutations

anthropi same candidate multi-locus pulsed-field antibiotyping
Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

PMID 19922616 · PMC2784454 · BMC biology · 2009 · 8 claims · 7 setups

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The ratio of homologous recombination to mutation in B. pseudomallei is over two times higher than in Streptococcus pneumoniae, the highest yet reported in bacteria.

isolates genome snp snps multilocus genome bayesian
Evolutionary dynamics of human rotaviruses: balancing reassortment with preferred genome constellations.

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

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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
Bayesian coestimation of phylogeny and sequence alignment.

PMID 15804354 · PMC1087833 · BMC bioinformatics · 2005 · 7 claims · 3 setups

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Alignment and phylogenetic inference are mutually dependent, and treating them as separate sequential steps (align then infer tree) is fundamentally flawed and produces biased, overconfident estimates.

globin same four-sequence bayesian mcmc comparison
High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.

PMID 18559660 · PMC2518505 · Diabetes · 2008 · 8 claims · 3 setups

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Primary linkage finding for diabetic nephropathy is on chromosome 19q

sibpairs genotype patients genome-wide statistical urinary
A common founder for the V126D CDKN2A mutation in seven North American melanoma-prone families.

PMID 11506491 · PMC2364106 · British journal of cancer · 2001 · 8 claims · 2 setups

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All seven North American melanoma-prone families carrying V126D share a haplotype consistent with a single common founder/ancestor for the mutation

melanoma-prone haplotype microsatellite maximum
PhylomeDB: a database for genome-wide collections of gene phylogenies.

PMID 17962297 · PMC2238872 · Nucleic acids research · 2008 · 7 claims · 6 setups

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PhylomeDB is a publicly accessible database storing complete, genome-wide collections of gene phylogenies (phylomes).

seed homologous trimmed homology sequence neighbor
Web-based resources for comparative genomics.

PMID 16197736 · PMC3525128 · Human genomics · 2005 · 8 claims · 8 setups

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Comparative genomics is an indispensable tool for identifying functional genome elements and exploring evolutionary genome dynamics

yeast chimpanzee mammalian protein-coding comparative genome maximum-likelihood
Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

PMID 27832824 · PMC5105290 · Genome biology · 2016 · 8 claims · 7 setups

Has reproduction · 84

The A. glabripennis genome encodes a uniquely diverse arsenal of enzymes that degrade plant cell wall polysaccharide networks (cellulose, hemicellulose, pectin) and detoxify plant allelochemicals.

single glabripennis amino whole-genome gene busco
Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

PMID 30210471 · PMC6121073 · Frontiers in microbiology · 2018 · 8 claims · 7 setups

Has reproduction · 91

SURF_5 and SURF_17 are the first full genomes of a novel bacterial lineage, 'Candidatus Abyssubacteria,' within the candidate phylum Hydrogenedentes

deep co-assembled surf_17 surf_5 whole-genome novo 16s
Structure of the intergenic spacers in chicken ribosomal DNA.

PMID 31655542 · PMC6815422 · Genetics, selection, evolution : GSE · 2019 · 8 claims · 6 setups

Has reproduction · 80

Long-read PacBio RSII sequencing of a BAC clone plus HGAP assembly can resolve the complete, highly repetitive chicken IGS structure that short-read (Illumina) sequencing previously failed to assemble.

bac pacbio gallus_gallus-5.0 assembled long-read genome blast
Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.

PMID 41957580 · PMC13173886 · BMC genomics · 2026 · 8 claims · 8 setups

Has reproduction · 82

An isolate phenotypically identified as K. oxytoca was reclassified by genome-based taxonomy (GTDB-Tk, ANI, BLAST) as Klebsiella michiganensis

michiganensis a55848 african assembled whole-genome novo genome-based

Experiments

The fate of the duplicated androgen receptor in fishes: a late neofunctionalization event?

Direct evidence of extensive diversity of HIV-1 in Kinshasa by 1960.

The role of the humoral immune response in the molecular evolution of the envelope C2, V3 and C3 regions in chronically HIV-2 infected patients.

Genetic variation of St. Louis encephalitis virus.

The repertoire of G protein-coupled receptors in the sea squirt Ciona intestinalis.

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

A target enrichment method for gathering phylogenetic information from hundreds of loci: An example from the Compositae.

An original SERPINA3 gene cluster: elucidation of genomic organization and gene expression in the Bos taurus 21q24 region.

Multilocus sequence typing supports the hypothesis that Ochrobactrum anthropi displays a human-associated subpopulation.

Phylogeographic reconstruction of a bacterial species with high levels of lateral gene transfer.

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

Bayesian coestimation of phylogeny and sequence alignment.

High-density single nucleotide polymorphism genome-wide linkage scan for susceptibility genes for diabetic nephropathy in type 1 diabetes: discordant sibpair approach.

A common founder for the V126D CDKN2A mutation in seven North American melanoma-prone families.

PhylomeDB: a database for genome-wide collections of gene phylogenies.

Web-based resources for comparative genomics.

Genome of the Asian longhorned beetle (Anoplophora glabripennis), a globally significant invasive species, reveals key functional and evolutionary innovations at the beetle-plant interface.

Genomic Description of 'Candidatus Abyssubacteria,' a Novel Subsurface Lineage Within the Candidate Phylum Hydrogenedentes.

Structure of the intergenic spacers in chicken ribosomal DNA.

Whole-genome analysis of a multidrug-resistant Klebsiella michiganensis environmental isolate from an orthopedic ward in Mwanza, Tanzania reveals IncF-family plasmid replicon signatures associated with resistance determinants.