2009
Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies
Otto W, Stadler PF, López-Giraldéz F, Townsend JP, Lynch VJ, Wagner GP. Measuring Transcription Factor–Binding Site Turnover: A Maximum Likelihood Approach Using Phylogenies. Genome Biology And Evolution 2009, 1: 85-98. PMID: 20333180, PMCID: PMC2817405, DOI: 10.1093/gbe/evp010.Peer-Reviewed Original ResearchTranscription factor-binding sitesCis-regulatory elementsHOXA clusterSelective pressureGene expression evolutionMethionine biosynthesis pathwayLow sequence similarityFactor-binding sitesClade-specific differencesTurnover rateExpression evolutionSpecies treeBiosynthesis pathwayRelated speciesSequence similaritySite turnoverDifferent organismsSequence evolutionTranscription factorsDifferent cladesFungal dataProgesterone response elementMaximum likelihood modelVertebratesTurnover
2000
Hox cluster genomics in the horn shark, Heterodontus francisci
Kim C, Amemiya C, Bailey W, Kawasaki K, Mezey J, Miller W, Minoshima S, Shimizu N, Wagner G, Ruddle F. Hox cluster genomics in the horn shark, Heterodontus francisci. Proceedings Of The National Academy Of Sciences Of The United States Of America 2000, 97: 1655-1660. PMID: 10677514, PMCID: PMC26491, DOI: 10.1073/pnas.030539697.Peer-Reviewed Original ResearchConceptsHox gene clustersHox clustersHOXA clusterGene clusterHeterodontus francisciVertebrate body planHorn sharkGene-coding sequencesDivergence timesEvolutionary historyBody planHoxD clusterEvolutionary significanceSequence motifsVertebrate phylogenyDevelopmental processesGenetic entitiesStructural similarityControl motifsSharksCluster organizationMotifPhylogenyGenomicsNoncoding