Published in Mol Biol Evol on October 20, 2004
On the origin and functions of RNA-mediated silencing: from protists to man. Curr Genet (2006) 3.05
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic "supergroups". Proc Natl Acad Sci U S A (2009) 3.02
Comparative genomics supports a deep evolutionary origin for the large, four-module transcriptional mediator complex. Nucleic Acids Res (2008) 2.32
Phylogenomics reveals a new 'megagroup' including most photosynthetic eukaryotes. Biol Lett (2008) 2.30
Comparative genomics and evolution of the HSP90 family of genes across all kingdoms of organisms. BMC Genomics (2006) 1.91
Steroids, triterpenoids and molecular oxygen. Philos Trans R Soc Lond B Biol Sci (2006) 1.84
The origin and diversification of eukaryotes: problems with molecular phylogenetics and molecular clock estimation. Philos Trans R Soc Lond B Biol Sci (2006) 1.71
An expanded inventory of conserved meiotic genes provides evidence for sex in Trichomonas vaginalis. PLoS One (2007) 1.67
Broadly sampled multigene trees of eukaryotes. BMC Evol Biol (2008) 1.32
Comprehensive comparative analysis of kinesins in photosynthetic eukaryotes. BMC Genomics (2006) 1.21
Evolution of four gene families with patchy phylogenetic distributions: influx of genes into protist genomes. BMC Evol Biol (2006) 1.17
Multiple secondary origins of the anaerobic lifestyle in eukaryotes. Philos Trans R Soc Lond B Biol Sci (2006) 1.17
Turning the crown upside down: gene tree parsimony roots the eukaryotic tree of life. Syst Biol (2012) 1.09
Comparative genomics uncovers novel structural and functional features of the heterotrimeric GTPase signaling system. Gene (2010) 1.08
A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution. BMC Genomics (2007) 1.01
Phylogenetic and structural analysis of translationally controlled tumor proteins. J Mol Evol (2008) 0.98
Bacterial proteins pinpoint a single eukaryotic root. Proc Natl Acad Sci U S A (2015) 0.95
Evolutionary cell biology of chromosome segregation: insights from trypanosomes. Open Biol (2013) 0.95
On the age of eukaryotes: evaluating evidence from fossils and molecular clocks. Cold Spring Harb Perspect Biol (2014) 0.93
Nuclear inheritance and genetic exchange without meiosis in the binucleate parasite Giardia intestinalis. J Cell Sci (2012) 0.83
The largest subunit of RNA polymerase II from the Glaucocystophyta: functional constraint and short-branch exclusion in deep eukaryotic phylogeny. BMC Evol Biol (2005) 0.82
Evolution of a domain conserved in microtubule-associated proteins of eukaryotes. Adv Appl Bioinform Chem (2008) 0.81
Phylogenetic detection of numerous gene duplications shared by animals, fungi and plants. Genome Biol (2010) 0.81
Phylogeny of the Centrohelida inferred from SSU rRNA, tubulins, and actin genes. J Mol Evol (2005) 0.81
Detection of fused genes in eukaryotic genomes using gene deFuser: analysis of the Tetrahymena thermophila genome. BMC Bioinformatics (2011) 0.80
Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A (2002) 5.48
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34
Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions. Proc Natl Acad Sci U S A (2006) 1.95
Large-scale phylogenomic analyses reveal that two enigmatic protist lineages, telonemia and centroheliozoa, are related to photosynthetic chromalveolates. Genome Biol Evol (2009) 1.89
Establishment of a humanized model of liver using NOD/Shi-scid IL2Rgnull mice. Biochem Biophys Res Commun (2008) 1.50
Stability of mitochondrial membrane proteins in terrestrial vertebrates predicts aerobic capacity and longevity. Genome Biol Evol (2011) 1.46
Mitochondrial phylogenetics and evolution of mysticete whales. Syst Biol (2005) 1.44
Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. Genetics (2002) 1.38
Rooting the eutherian tree: the power and pitfalls of phylogenomics. Genome Biol (2007) 1.31
Relationships between BK virus lineages and human populations. Microbes Infect (2006) 1.30
Antitumor activity of the selective ALK inhibitor alectinib in models of intracranial metastases. Cancer Chemother Pharmacol (2014) 1.30
The position of gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. Mol Biol Evol (2010) 1.24
A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times. Bioinformatics (2002) 1.21
Comment on "Nuclear genomic sequences reveal that polar bears are an old and distinct bear lineage". Science (2013) 1.17
Afrotherian phylogeny as inferred from complete mitochondrial genomes. Mol Phylogenet Evol (2003) 1.16
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol (2007) 1.16
Topological incongruence between nuclear and chloroplast DNA trees suggesting hybridization in the urophyllum group of the genus Fagopyrum (Polygonaceae). Genes Genet Syst (2003) 1.14
Further refinement of the phylogeny of the Halobacteriaceae based on the full-length RNA polymerase subunit B' (rpoB') gene. Int J Syst Evol Microbiol (2009) 1.13
A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families. Bioinformatics (2002) 1.11
Phylogeny, recombination, and mechanisms of stepwise mitochondrial genome reorganization in mantellid frogs from Madagascar. Mol Biol Evol (2008) 1.11
Evolution and phylogeny of the heterogeneous cytosolic SSU rRNA genes in the genus Plasmodium. Mol Phylogenet Evol (2008) 1.10
Recent independent evolution of msp1 polymorphism in Plasmodium vivax and related simian malaria parasites. Mol Biochem Parasitol (2007) 1.10
Split introns in the genome of Giardia intestinalis are excised by spliceosome-mediated trans-splicing. Curr Biol (2011) 1.09
Ultrastructure of the dermal chromatophores in a lizard (Scincidae: Plestiodon latiscutatus) with conspicuous body and tail coloration. Zoolog Sci (2006) 1.07
The origin of dihydroorotate dehydrogenase genes of kinetoplastids, with special reference to their biological significance and adaptation to anaerobic, parasitic conditions. J Mol Evol (2005) 1.06
Molecular phylogeny and evolution of prosimians based on complete sequences of mitochondrial DNAs. Gene (2008) 1.05
Episodic evolution and adaptation of chloroplast genomes in ancestral grasses. PLoS One (2009) 1.03
Phylogeny of primary photosynthetic eukaryotes as deduced from slowly evolving nuclear genes. Mol Biol Evol (2007) 1.03
The phylogenetic position of red algae revealed by multiple nuclear genes from mitochondria-containing eukaryotes and an alternative hypothesis on the origin of plastids. J Mol Evol (2003) 1.03
Mitochondrial phylogeny of hedgehogs and monophyly of Eulipotyphla. Mol Phylogenet Evol (2003) 1.01
Evolution of BK virus based on complete genome data. J Mol Evol (2006) 1.01
Adaptive evolution of rbcL in Conocephalum (Hepaticae, bryophytes). Gene (2008) 1.00
Balaenoptera omurai is a newly discovered baleen whale that represents an ancient evolutionary lineage. Mol Phylogenet Evol (2006) 1.00
Combining multiple data sets in a likelihood analysis: which models are the best? Mol Biol Evol (2002) 1.00
Current status of clinical background of patients with atrial fibrillation in a community-based survey: the Fushimi AF Registry. J Cardiol (2013) 0.99
Extensive mitochondrial gene arrangements in coleoid Cephalopoda and their phylogenetic implications. Mol Phylogenet Evol (2006) 0.99
The monophyletic origin of sea lions and fur seals (Carnivora; Otariidae) in the Southern Hemisphere. Gene (2009) 0.99
The Plasmodium apicoplast genome: conserved structure and close relationship of P. ovale to rodent malaria parasites. Mol Biol Evol (2012) 0.99
Case of leiomyosarcoma of the renal pelvis. Int J Urol (2004) 0.97
Mitochondrial-type hsp70 genes of the amitochondriate protists, Giardia intestinalis, Entamoeba histolytica and two microsporidians. Parasitol Int (2002) 0.95
Inositol 1,4,5-trisphosphate receptor regulates replication, differentiation, infectivity and virulence of the parasitic protist Trypanosoma cruzi. Mol Microbiol (2013) 0.93
Molecular and biochemical characterization of D-phosphoglycerate dehydrogenase from Entamoeba histolytica. A unique enteric protozoan parasite that possesses both phosphorylated and nonphosphorylated serine metabolic pathways. Eur J Biochem (2004) 0.91
Evolution of human Polyomavirus JC: implications for the population history of humans. J Mol Evol (2002) 0.91
Was the universal common ancestry proved? Nature (2010) 0.90
Regeneration of small intestinal mucosa after acute ischemia-reperfusion injury. Dig Dis Sci (2002) 0.90
Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J Eukaryot Microbiol (2002) 0.90
Domestication relaxed selective constraints on the yak mitochondrial genome. Mol Biol Evol (2010) 0.89
Why does the giant panda eat bamboo? A comparative analysis of appetite-reward-related genes among mammals. PLoS One (2011) 0.89
Three binding sites for stalk protein dimers are generally present in ribosomes from archaeal organism. J Biol Chem (2007) 0.89
Problems in speciation in the genus Blastocystis. Trends Parasitol (2004) 0.88
Intra- and interfamily relationships of Vespertilionidae inferred by various molecular markers including SINE insertion data. J Mol Evol (2002) 0.88
Centrohelida is still searching for a phylogenetic home: analyses of seven Raphidiophrys contractilis genes. Gene (2007) 0.88
Gene content evolution in Discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biol Evol (2014) 0.87
Direct evidence for cyanide-insensitive quinol oxidase (alternative oxidase) in apicomplexan parasite Cryptosporidium parvum: phylogenetic and therapeutic implications. Biochem Biophys Res Commun (2004) 0.86
Origins of plastids and glyceraldehyde-3-phosphate dehydrogenase genes in the green-colored dinoflagellate Lepidodinium chlorophorum. Gene (2007) 0.86
Green-colored plastids in the dinoflagellate genus Lepidodinium are of core chlorophyte origin. Protist (2010) 0.86
Molecular phylogenetic study on the origin and evolution of Mustelidae. Gene (2007) 0.86
Cercozoa comprises both EF-1α-containing and EFL-containing members. Eur J Protistol (2010) 0.85
Detecting excess radical replacements in phylogenetic trees. Gene (2003) 0.85
Phylogenetic relationships among JC virus strains in Japanese/Koreans and Native Americans speaking Amerind or Na-Dene. J Mol Evol (2003) 0.85
Adaptive threonine increase in transmembrane regions of mitochondrial proteins in higher primates. PLoS One (2008) 0.84
High altitude adaptation of the schizothoracine fishes (Cyprinidae) revealed by the mitochondrial genome analyses. Gene (2013) 0.84
The status of the Japanese and East Asian bats of the genus Myotis (Vespertilionidae) based on mitochondrial sequences. Mol Phylogenet Evol (2003) 0.84
Metastatic colon cancer mimicking Crohn's disease. Ann Diagn Pathol (2007) 0.84
Treatment of acute inflammatory cardiomyopathy with intravenous immunoglobulin ameliorates left ventricular function associated with suppression of inflammatory cytokines and decreased oxidative stress. Int J Cardiol (2003) 0.84
New candidate species most closely related to penguins. Gene (2006) 0.83
Ultrastructural and phylogenetic studies on Blastocystis isolates from cockroaches. J Eukaryot Microbiol (2007) 0.82
Identification of a new type of Babesia species in wild rats (Bandicota indica) in Chiang Mai Province, Thailand. J Clin Microbiol (2004) 0.82
Gene sampling can bias multi-gene phylogenetic inferences: the relationship between red algae and green plants as a case study. Mol Biol Evol (2009) 0.82
A deviant genetic code in the green alga-derived plastid in the dinoflagellate Lepidodinium chlorophorum. Mol Phylogenet Evol (2011) 0.81
Compartmentalization of a glycolytic enzyme in Diplonema, a non-kinetoplastid euglenozoan. Protist (2011) 0.81
Multigene phylogenies of diverse Carpediemonas-like organisms identify the closest relatives of 'amitochondriate' diplomonads and retortamonads. Protist (2012) 0.81
Phylogeny of the Centrohelida inferred from SSU rRNA, tubulins, and actin genes. J Mol Evol (2005) 0.81
Splintrons in Giardia intestinalis: Spliceosomal introns in a split form. Commun Integr Biol (2011) 0.81
Complete nucleotide sequence of the mitochondrial genome of a Malagasy poison frog Mantella madagascariensis: evolutionary implications on mitochondrial genomes of higher anuran groups. Mol Phylogenet Evol (2006) 0.81
Rooting for the root of elongation factor-like protein phylogeny. Mol Phylogenet Evol (2010) 0.81
Survey of rodents and ticks in human babesiosis emergence area in Japan: first detection of Babesia microti-like parasites in Ixodes ovatus. J Clin Microbiol (2004) 0.81
Some problems in proving the existence of the universal common ancestor of life on Earth. ScientificWorldJournal (2012) 0.81
Separate origins of group I introns in two mitochondrial genes of the katablepharid Leucocryptos marina. PLoS One (2012) 0.80
Cyanobacterial genes transmitted to the nucleus before divergence of red algae in the Chromista. J Mol Evol (2004) 0.80
Domestication process of the goat revealed by an analysis of the nearly complete mitochondrial protein-encoding genes. PLoS One (2013) 0.80
Successful immunoglobulin treatment for fulminant myocarditis and serial analysis of serum thioredoxin: a case report. Circ J (2002) 0.80
Temperature-dependent regulation of reproduction in the diving beetle Dytiscus sharpi (Coleoptera: Dytiscidae). Zoolog Sci (2007) 0.80
JC virus strains indigenous to northeastern Siberians and Canadian Inuits are unique but evolutionally related to those distributed throughout Europe and Mediterranean areas. J Mol Evol (2002) 0.79
Evolutionary analysis of synteny and gene fusion for pyrimidine biosynthetic enzymes in Euglenozoa: an extraordinary gap between kinetoplastids and diplonemids. Protist (2008) 0.79
Occurrence of multiple, independent gene fusion events for the fifth and sixth enzymes of pyrimidine biosynthesis in different eukaryotic groups. Gene (2007) 0.79
Molecular cloning and characterization of Trypanosoma vivax alternative oxidase (AOX) gene, a target of the trypanocide ascofuranone. Parasitol Int (2004) 0.78
Upregulation of redox-regulating protein, thioredoxin, in endomyocardial biopsy samples of patients with myocarditis and cardiomyopathies. Mol Cell Biochem (2003) 0.78
Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evol Biol (2013) 0.78
The phylogenetic position of the pelobiont Mastigamoeba balamuthi based on sequences of rDNA and translation elongation factors EF-1alpha and EF-2. J Eukaryot Microbiol (2002) 0.78