Phylogeny Concept

subject area of

• 'Outlier' lipocalins more than peripheral  Academic Article
• 17th Century Variola Virus Reveals the Recent History of Smallpox  Academic Article
• Sequence Note: Molecular Epidemiological Analysis of Human Immunodeficiency Virus Type 1 in Newfoundland, Canada  Academic Article
• Torulaspora quercuum  sp. nov. andCandida pseudohumilis  sp. nov., novel yeasts from human and forest habitats  Academic Article
• d -Ala- d -Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB  Academic Article
• A Catalog of Reference Genomes from the Human Microbiome  Academic Article
• A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods  Academic Article
• A Comprehensive Expression Analysis of the Arabidopsis Proline-rich Extensin-like Receptor Kinase Gene Family using Bioinformatic and Experimental Approaches  Academic Article
• A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals  Academic Article
• A Non-Long Terminal Repeat Retrotransposon Family Is Restricted to the Germ Line Micronucleus of the Ciliated Protozoan Tetrahymena thermophila  Academic Article
• A T-to-G Transversion at Nucleotide −567 Upstream of HBG2 in a GATA-1 Binding Motif Is Associated with Elevated Hemoglobin F  Academic Article
• A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism  Academic Article
• A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads  Academic Article
• A comparative study of an innate immune response in Lamprologine cichlid fishes  Academic Article
• A comprehensive genomic history of extinct and living elephants  Academic Article
• A comprehensive study of genic variation in natural populations of Drosophila melanogaster. IV. Mitochondrial DNA variation and the role of history vs. selection in the genetic structure of geographic populations.  Academic Article
• A divergentPseudomonas aeruginosapalmitoyltransferase essential for cystic fibrosis-specific lipid A  Academic Article
• A draft genome of Yersinia pestis from victims of the Black Death  Academic Article
• A functionally divergent hydrogenosomal peptidase with protomitochondrial ancestry  Academic Article
• A maximum likelihood approach to the detection of selection from a phylogeny  Academic Article
• A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution  Academic Article
• A new fossil assemblage shows that large angiosperm trees grew in North America by the Turonian (Late Cretaceous)  Academic Article
• A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution  Academic Article
• A phylogenetic analysis based on the gene encoding phosphoglycerate kinase  Academic Article
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Academic Article
• A phylogenomic and comparative genomic framework for resolving the polyphyly of the genus Bacillus: Proposal for six new genera of Bacillus species, Peribacillus gen. nov., Cytobacillus gen. nov., Mesobacillus gen. nov., Neobacillus gen. nov., Metabacillus gen. nov. and Alkalihalobacillus gen. nov.  Academic Article
• A phylogenomic and molecular marker based proposal for the division of the genus Borrelia into two genera: the emended genus Borrelia containing only the members of the relapsing fever Borrelia, and the genus Borreliella gen. nov. containing the members of the Lyme disease Borrelia (Borrelia burgdorferi sensu lato complex)  Academic Article
• A phylogenomic and molecular marker based taxonomic framework for the order Xanthomonadales: proposal to transfer the families Algiphilaceae and Solimonadaceae to the order Nevskiales ord. nov. and to create a new family within the order Xanthomonadales, the family Rhodanobacteraceae fam. nov., containing the genus Rhodanobacter and its closest relatives  Academic Article
• A phylogenomic and molecular markers based analysis of the phylum Chlamydiae: proposal to divide the class Chlamydiia into two orders, Chlamydiales and Parachlamydiales ord. nov., and emended description of the class Chlamydiia  Academic Article
• A phylogenomic and molecular markers based taxonomic framework for members of the order Entomoplasmatales: proposal for an emended order Mycoplasmatales containing the family Spiroplasmataceae and emended family Mycoplasmataceae comprised of six genera  Academic Article
• A phylogenomic framework and timescale for comparative studies of tunicates  Academic Article
• A phylogenomic reappraisal of family-level divisions within the class Halobacteria: proposal to divide the order Halobacteriales into the families Halobacteriaceae, Haloarculaceae fam. nov., and Halococcaceae fam. nov., and the order Haloferacales into the families, Haloferacaceae and Halorubraceae fam nov.  Academic Article
• A robust phylogenetic framework for members of the order Legionellales and its main genera (Legionella, Aquicella, Coxiella and Rickettsiella) based on phylogenomic analyses and identification of molecular markers demarcating different clades  Academic Article
• A spliceosomal intron in Giardia lamblia  Academic Article
• ANATOMIC ASYMMETRY IN THE TEMPORAL LOBES: ITS DOCUMENTATION, PHYLOGENESIS, AND RELATIONSHIP TO FUNCTIONAL ASYMMETRY  Academic Article
• AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology  Academic Article
• Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set  Academic Article
• Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China  Academic Article
• Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates  Academic Article
• Adaptive Radiation and Ecological Opportunity in Sulawesi and Philippine Fanged Frog (Limnonectes) Communities  Academic Article
• Additional molecular support for the new chordate phylogeny  Academic Article
• Adenosine kinase and ribokinase – the RK family of proteins  Academic Article
• Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses  Academic Article
• Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity  Academic Article
• Alignment/Phylogeny of the Papain Superfamily of Cysteine Proteases  Academic Article
• Amplification and sequencing of DNA from a 120–135-million-year-old weevil  Academic Article
• An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies  Academic Article
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Academic Article
• An evolutionary model for the insect vitellins  Academic Article
• An unusual myosuppressin from the blood-feeding bugRhodnius prolixus  Academic Article
• An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models  Academic Article
• Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex  Academic Article
• Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes  Academic Article
• Analysis of the legume-rhizobia symbiosis in shrubs from central western Spain  Academic Article
• Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)  Academic Article
• Ancient Antibiotics, Ancient Resistance  Academic Article
• Ancient DNA  Academic Article
• Ancient DNA and the tropics: a rodent's tale  Academic Article
• Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics  Academic Article
• Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths  Academic Article
• Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array  Academic Article
• Ancyromonadida: A New Phylogenetic Lineage Among the Protozoa Closely Related to the Common Ancestor of Metazoans, Fungi, and Choanoflagellates (Opisthokonta)  Academic Article
• Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia  Academic Article
• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life  Academic Article
• Antibiotic resistance is ancient  Academic Article
• Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions  Academic Article
• Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?  Academic Article
• Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra)  Academic Article
• Army Ants Trapped by Their Evolutionary History  Academic Article
• Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections  Academic Article
• Asymmetrical Evolution of Cytochrome bd Subunits  Academic Article
• Autoecological Approaches to Resolve Subjective Taxonomic Divisions within Arcellacea  Academic Article
• Bacillus DNA in fossil bees: an ancient symbiosis?  Academic Article
• Bacterial biogeography of the human digestive tract  Academic Article
• Bats and Coronaviruses  Academic Article
• Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution  Academic Article
• Beltrania sinensis sp. nov., an endophytic fungus from China and a key to species of the genus  Academic Article
• Broad and Differential Animal Angiotensin-Converting Enzyme 2 Receptor Usage by SARS-CoV-2  Academic Article
• Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites  Academic Article
• CLONING AND CHARACTERIZATION OF AN mRNA ENCODING AN INSULIN RECEPTOR FROM THE HORNED SCARAB BEETLEOnthophagus nigriventris(COLEOPTERA: SCARABAEIDAE)  Academic Article
• Candida auris on Apples: Diversity and Clinical Significance  Academic Article
• Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling  Academic Article
• Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co-occur on Java Island, Indonesia  Academic Article
• Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker  Academic Article
• Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil  Academic Article
• Characterization of Class I– and Class II–Like Major Histocompatibility Complex Loci in Pedigrees of North Atlantic Right Whales  Academic Article
• Characterization of a Rifampin-Inactivating Glycosyltransferase from a Screen of Environmental Actinomycetes  Academic Article
• Characterization of a cetacean aromatase (CYP19) and the phylogeny and functional conservation of vertebrate aromatase  Academic Article
• Characterization of yeast homoserine dehydrogenase, an antifungal target: the invariant histidine 309 is important for enzyme integrity  Academic Article
• Chimeric Structure of the NAD(P)+- and NADP+-dependent Malic Enzymes ofRhizobium (Sinorhizobium) meliloti  Academic Article
• Chitinase genes ( CHIA s) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals  Academic Article
• Chlamydiae-specific proteins and indels: novel tools for studies  Academic Article
• Clades of huge phages from across Earth’s ecosystems  Academic Article
• Clinical and tree hollow populations of human pathogenic yeast in Hamilton, Ontario, Canada are different  Academic Article
• Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA  Academic Article
• Clonal and Spontaneous Origins of Fluconazole Resistance in Candida albicans  Academic Article
• Cloning and Some Novel Characteristics of Mitochondrial Hsp70 from Chinese Hamster Cells  Academic Article
• Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum.  Academic Article
• Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence  Academic Article
• Codon Bias and Base Composition Are Poor Indicators of Horizontally Transferred Genes  Academic Article
• Cold-Active Winter Rye Glucanases with Ice-Binding Capacity  Academic Article
• Comment on "Hexapod Origins: Monophyletic or Paraphyletic?"  Academic Article
• Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum  Academic Article
• Comparative Gene Genealogies Indicate that Two Clonal Lineages of Cryptococcus gattii in British Columbia ResembleStrains from Other Geographical Areas  Academic Article
• Comparative Genome Analysis Provides Insights into the Evolution and Adaptation of Pseudomonas syringae pv. aesculi on Aesculus hippocastanum  Academic Article
• Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution  Academic Article
• Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness  Academic Article
• Comparative chromosome painting of pronghorn (Antilocapra americana) and saola (Pseudoryx nghetinhensis) karyotypes with human and dromedary camel probes  Academic Article
• Comparative gene genealogical analyses of strains of serotype AD identify recombination in populations of serotypes A and D in the human pathogenic yeast Cryptococcus neoformans  Academic Article
• Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis , in the south‐western Cape Province, South Africa  Academic Article
• Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria  Academic Article
• Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability  Academic Article
• Comparison of fecal biota from specific pathogen free and feral mice  Academic Article
• Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris  Academic Article
• Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths  Academic Article
• Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation  Academic Article
• Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools  Academic Article
• Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the Genus Betacoronavirus and Its Different Subgenera  Academic Article
• Conserved Signatures in Protein Sequences Reliably Demarcate Different Clades of Rodents/Glires Species and Consolidate Their Evolutionary Relationships  Academic Article
• Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria  Academic Article
• Constraining the Time Interval for the Origin of Life on Earth  Academic Article
• Control of breathing and adaptation to high altitude in the bar-headed goose  Academic Article
• Convergence of gut microbiomes in myrmecophagous mammals  Academic Article
• Corticosteroid receptor gene expression is related to sex and social behaviour in a social fish  Academic Article
• Critical Issues in Bacterial Phylogeny  Academic Article
• Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age  Academic Article
• DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms  Academic Article
• DNA methylation predicts age and provides insight into exceptional longevity of bats  Academic Article
• Dating the Ngandong Humans  Academic Article
• Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes  Academic Article
• Demographic expansion and genetic load of the halophyte model plantEutrema salsugineum  Academic Article
• Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena)  Academic Article
• Development and Evaluation of a Molecular Hepatitis A Virus Assay for Serum and Stool Specimens  Academic Article
• Development of Real-Time PCR Assays for Detection of the Streptococcus milleri Group from Cystic Fibrosis Clinical Specimens by Targeting the cpn60 and 16S rRNA Genes  Academic Article
• Differential Y‐chromosome Anatolian Influences on the Greek and Cretan Neolithic  Academic Article
• Directionality in the evolution of influenza A haemagglutinin  Academic Article
• Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella  Academic Article
• Dispersers shape fruit diversity in Ficus (Moraceae)  Academic Article
• Distinction between Borrelia and Borreliella is more robustly supported by molecular and phenotypic characteristics than all other neighbouring prokaryotic genera: Response to Margos' et al. "The genus Borrelia reloaded" (PLoS ONE 13(12): e0208432)  Academic Article
• Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum  Academic Article
• Diurnal Floc Generation from Neuston Biofilms in Two Contrasting Freshwater Lakes  Academic Article
• Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeastCryptococcus gattii  Academic Article
• Divergent respiratory and cardiovascular responses to hypoxia in bar-headed geese and Andean birds  Academic Article
• Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)  Academic Article
• Diversification of Wolbachia Endosymbiont in the Culex pipiens Mosquito  Academic Article
• Diversity Considerations in HIV-1 Vaccine Selection  Academic Article
• Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries)  Academic Article
• Diversity and relationships among strains of culturable yeasts in agricultural soils in Cameroon  Academic Article
• Diversity of Rotavirus Strains Circulating in Botswana before and after introduction of the Monovalent Rotavirus Vaccine  Academic Article
• Diversity of commensal yeasts within and among healthy hosts  Academic Article
• Diversity, Dispersal and Mode of Reproduction of Amanita exitialis in Southern China  Academic Article
• Division of the genus Borrelia into two genera (corresponding to Lyme disease and relapsing fever groups) reflects their genetic and phenotypic distinctiveness and will lead to a better understanding of these two groups of microbes (Margos et al. (2016) There is inadequate evidence to support the division of the genus Borrelia. Int. J. Syst. Evol. Microbiol. doi: 10.1099/ijsem.0.001717)  Academic Article
• Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region  Academic Article
• Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake  Academic Article
• EVOLUTION OF THE CLOSELY RELATED, SEX-RELATED GENES DM-W AND DMRT1 IN AFRICAN CLAWED FROGS (XENOPUS)  Academic Article
• Ecological Genomics of Marine Roseobacters  Academic Article
• Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps)  Academic Article
• Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks  Academic Article
• Environmental and nutritional regulation of expression and function of two peptide transporter (PepT1) isoforms in a euryhaline teleost  Academic Article
• Enzyme Evolution Explained (Sort Of)  Academic Article
• Estimating Maximum Likelihood Phylogenies with PhyML  Academic Article
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Academic Article
• Evidence for Inbreeding and Genetic Differentiation among Geographic Populations of the Saprophytic Mushroom Trogia venenata from Southwestern China  Academic Article
• Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to Giardia lamblia and Entamoeba histolytica  Academic Article
• Evidence for local DNA influences on patterns of substitutions in the human α-interferon gene family  Academic Article
• Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms  Academic Article
• Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms.  Academic Article
• Evidence for the presence of key chlorophyll-biosynthesis-related proteins in the genus Rubrobacter (Phylum Actinobacteria) and its implications for the evolution and origin of photosynthesis  Academic Article
• Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants  Academic Article
• Evidence of unique genetic diversity inAspergillus fumigatusisolates from Cameroon  Academic Article
• Evidence that Human Chlamydia pneumoniae Was Zoonotically Acquired  Academic Article
• Evolution in the Fast Lane: Rapidly Evolving Sex-Related Genes in Drosophila  Academic Article
• Evolution of Drosophila sex comb length illustrates the inextricable interplay between selection and variation  Academic Article
• Evolution of Allosteric Control in Glycogen Phosphorylase  Academic Article
• Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia  Academic Article
• Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes  Academic Article
• Evolution of Proteasome Regulators in Eukaryotes  Academic Article
• Evolution of RAG-1 in Polyploid Clawed Frogs  Academic Article
• Evolution of genes and genomes on the Drosophila phylogeny  Academic Article
• Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models  Academic Article
• Evolution of the Largest Mammalian Genome  Academic Article
• Evolution of the RpoS Regulon: Origin of RpoS and the Conservation of RpoS-Dependent Regulation in Bacteria  Academic Article
• Evolution of the chaperonin families (HSP60, HSP 10 and TCP-1) of proteins and the origin of eukaryotic cells  Academic Article
• Evolution of the nuclear-encoded cytochrome oxidase subunits in vertebrates  Academic Article
• Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling  Academic Article
• Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes  Academic Article
• Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta  Academic Article
• Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein  Academic Article
• Evolutionary and functional diversity of thePseudomonastype IVa pilin island  Academic Article
• Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales  Academic Article
• Evolutionary rate variation withinMus APRT  Academic Article
• Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis  Academic Article
• Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle  Academic Article
• Expanding the soil antibiotic resistome: exploring environmental diversity  Academic Article
• Exploratory analysis of multiple sequence alignments using phylogenies  Academic Article
• Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap  Academic Article
• Extensive Genetic Diversity and Widespread Azole Resistance in Greenhouse Populations of Aspergillus fumigatus in Yunnan, China  Academic Article
• Extracting Haplotypes from Diploid Organisms  Academic Article
• Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences  Academic Article
• Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error  Academic Article
• Fate of Cd during Microbial Fe(III) Mineral Reduction by a Novel and Cd-TolerantGeobacterSpecies  Academic Article
• First Evidence for the Presence of Iron Oxidizing Zetaproteobacteria at the Levantine Continental Margins  Academic Article
• Fish gill morphology: inside out  Academic Article
• Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality  Academic Article
• Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun  Academic Article
• Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization  Academic Article
• Functional Divergence in the Arabidopsis  -1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States  Academic Article
• Functional Diversity of Haloacid Dehalogenase Superfamily Phosphatases from Saccharomyces cerevisiae  Academic Article
• Functional analysis of CfSnf1 in the development and pathogenicity of anthracnose fungus Colletotrichum fructicola on tea-oil tree  Academic Article
• Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences  Academic Article
• Fungal mitochondrial genomes and genetic polymorphisms  Academic Article
• Fungal species concepts in the genomics era  Academic Article
• Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism  Academic Article
• Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?  Academic Article
• Gene duplication and divergence produce divergent MHC genotypes without disassortative mating  Academic Article
• Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing  Academic Article
• Genetic Analyses from Ancient DNA  Academic Article
• Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens  Academic Article
• Genetic Diversity of Dahongjun, the Commercially Important “Big Red Mushroom” from Southern China  Academic Article
• Genetic Structure of Herpetofauna on Halmahera Island, Indonesia: Implications for Aketajawe-Lolobata National Park  Academic Article
• Genetic Tracking of the Raccoon Variant of Rabies Virus in Eastern North America  Academic Article
• Genetic and biochemical properties of an alkaline phosphatase PhoX family protein found in many bacteria  Academic Article
• Genetic and epidemiological analysis of norovirus from children with gastroenteritis in Botswana, 2013–2015  Academic Article
• Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India  Academic Article
• Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China  Academic Article
• Genetic risk for dengue hemorrhagic fever and dengue fever in multiple ancestries  Academic Article
• Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from West and Central Africa  Academic Article
• Genome comparisons reveal a dominant mechanism of chromosome number reduction in grasses and accelerated genome evolution in Triticeae  Academic Article
• Genome duplication events have led to a diversification in the CPT I gene family in fish  Academic Article
• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  Academic Article
• Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family  Academic Article
• Genome structure and gene content in protist mitochondrial DNAs  Academic Article
• Genome-Scale Phylogeny and the Detection of Systematic Biases  Academic Article
• Genome-Wide Identification and Expression Analysis of Udp-Glucuronosyltransferases in the Whitefly Bemisia Tabaci (Gennadius) (HemipterA: Aleyrodidae)  Academic Article
• Genome-based phylogeny and taxonomy of the ‘Enterobacteriales’: proposal for Enterobacterales ord. nov. divided into the families Enterobacteriaceae, Erwiniaceae fam. nov., Pectobacteriaceae fam. nov., Yersiniaceae fam. nov., Hafniaceae fam. nov., Morganellaceae fam. nov., and Budviciaceae fam. nov.  Academic Article
• Genome-based taxonomic framework for the class Negativicutes: division of the class Negativicutes into the orders Selenomonadales emend., Acidaminococcales ord. nov. and Veillonellales ord. nov.  Academic Article
• Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies  Academic Article
• Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia  Academic Article
• Genomic analyses reveal low mitochondrial and high nuclear diversity in the cyclosporin-producing fungus Tolypocladium inflatum  Academic Article
• Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress  Academic Article
• Genomic insights into the evolution and ecology of botulinum neurotoxins  Academic Article
• Genomic organization and linkage via a bidirectional promoter of the AP-3 (adaptor protein-3) mu3A and AK (adenosine kinase) genes: deletion mutants of AK in Chinese hamster cells extend into the AP-3 mu3A gene  Academic Article
• Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria  Academic Article
• Genomics of Loa loa, a Wolbachia-free filarial parasite of humans  Academic Article
• Genotypic diversity and antifungal susceptibility of environmental isolates of Cryptococcus neoformans from the Yangtze River Delta region of East China  Academic Article
• HSP70 phylogeny and the relationship between archaebacteria, eubacteria, and eukaryotes  Academic Article
• HYBRIDIZATION AND POPULATION GENETICS OF TWO MACAQUE SPECIES IN SULAWESI, INDONESIA  Academic Article
• Have wing morphology or flight kinematics evolved for extreme high altitude migration in the bar-headed goose?  Academic Article
• Helicokinin alters ion transport in the secondary cell-containing region of the Malpighian tubule of the larval cabbage looper Trichoplusia ni  Academic Article
• Heterologous Complementation Reveals a Specialized Activity for BacA in the Medicago–Sinorhizobium meliloti Symbiosis  Academic Article
• Heterotachy and long-branch attraction in phylogenetics  Academic Article
• High inbreeding, limited recombination and divergent evolutionary patterns between two sympatric morel species in China  Academic Article
• Human symbionts inject and neutralize antibacterial toxins to persist in the gut  Academic Article
• Hydrocarbon-related microbial processes in the deep sediments of the Eastern Mediterranean Levantine Basin  Academic Article
• Identification and characterization of RED120: A conserved PWI domain protein with links to splicing and 3′-end formation  Academic Article
• Identification and characterization of the proteolytic flagellin from the common freshwater bacterium Hylemonella gracilis  Academic Article
• Identification and developmental expression of the full complement of Cytochrome P450 genes in Zebrafish  Academic Article
• Identification of a Hydroxyproline Transport System in the Legume Endosymbiont Sinorhizobium meliloti  Academic Article
• Identification of a Novel Group of Bacteria in Sludge from a Deteriorated Biological Phosphorus Removal Reactor  Academic Article
• Identification of a Novel Hepatitis C Virus Genotype From Punjab, India: Expanding Classification of Hepatitis C Virus Into 8 Genotypes  Academic Article
• Identification of a conserved 8 aa insert in the PIP5K protein in theSaccharomycetaceaefamily of fungi and the molecular dynamics simulations and structural analysis to investigate its potential functional role  Academic Article
• Identification of a diphtheria toxin‐like gene family beyond theCorynebacteriumgenus  Academic Article
• Identification of distinctive molecular traits that are characteristic of the phylum “Deinococcus-Thermus” and distinguish its main constituent groups  Academic Article
• Identification of numerous hepatitis C virus genotypes in Montreal, Canada  Academic Article
• Identification of the putative goldfish (Carassius auratus) magnesium transporter SLC41a1 and functional regulation in the gill, kidney, and intestine in response to dietary and environmental manipulations  Academic Article
• Identification, spatial expression analysis and functional characterization of a pyrokinin-1 receptor in the Chagas’ disease vector, Rhodnius prolixus  Academic Article
• Identifying producers of antibacterial compounds by screening for antibiotic resistance  Academic Article
• Impact of genomics on the understanding of microbial evolution and classification: the importance of Darwin's views on classification  Academic Article
• Incidence of elephant endotheliotropic herpesvirus in Asian elephants in India  Academic Article
• Increase in Carbohydrate Utilization in High-Altitude Andean Mice  Academic Article
• Indole-3-Acetic Acid Production by Endophytic Streptomyces sp. En-1 Isolated from Medicinal Plants  Academic Article
• Infants’ First Solid Foods: Impact on Gut Microbiota Development in Two Intercontinental Cohorts  Academic Article
• Inferring Bacterial Genome Flux While Considering Truncated Genes  Academic Article
• Inferring sequence regions under functional divergence in duplicate genes  Academic Article
• Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.  Academic Article
• Insulin signaling and limb-patterning: candidate pathways for the origin and evolutionary diversification of beetle ‘horns’  Academic Article
• Integrated gene and species phylogenies from unaligned whole genome protein sequences  Academic Article
• Intergenic Sequence Comparison of Escherichia coli Isolates Reveals Lifestyle Adaptations but Not Host Specificity  Academic Article
• Interspecies Recombination Contributes Minimally to Fluoroquinolone Resistance in Streptococcus pneumoniae  Academic Article
• Interspecific variation in hypoxia tolerance and hypoxia acclimation responses in killifish from the family Fundulidae  Academic Article
• Investigation of a severe SARS-CoV-2 outbreak in a long-term care home early in the pandemic  Academic Article
• Iron-Dependent Hydrogenases ofEntamoeba histolyticaandGiardia lamblia:Activity of the Recombinant Entamoebic Enzyme and Evidence for Lateral Gene Transfer  Academic Article
• Is Antigenic Sin Always “Original?” Re-examining the Evidence Regarding Circulation of a Human H1 Influenza Virus Immediately Prior to the 1918 Spanish Flu  Academic Article
• Is there convergence in the molecular pathways underlying the repeated evolution of sociality in African cichlids?  Academic Article
• Isolation and Characterization of Novel Marine-Derived Actinomycete Taxa Rich in Bioactive Metabolites  Academic Article
• Isolation and characterization of Burkholderia cenocepacia CR318, a phosphate solubilizing bacterium promoting corn growth  Academic Article
• Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production  Academic Article
• It’s Not Easy Being Blue: Are There Olfactory and Visual Trade-Offs in Plant Signalling?  Academic Article
• JOINT RECONSTRUCTION OF DIVERGENCE TIMES AND LIFE-HISTORY EVOLUTION IN PLACENTAL MAMMALS USING A PHYLOGENETIC COVARIANCE MODEL  Academic Article
• Laboratory Characterization of Methicillin‐ResistantStaphylococcus aureusin Canadian Hospitals: Results of 5 Years of National Surveillance, 1995–1999  Academic Article
• Large freshwater phages with the potential to augment aerobic methane oxidation  Academic Article
• Large-scale genome sequencing of mycorrhizal fungi provides insights into the early evolution of symbiotic traits  Academic Article
• Latent homologues for the neural crest as an evolutionary novelty  Academic Article
• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Academic Article
• Lateral gene transfer in Mycobacterium avium subspecies paratuberculosis  Academic Article
• Les datations moléculaires à l’heure de la génomique  Academic Article
• Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals  Academic Article
• Life history evolution in cichlids 1: revisiting the evolution of life histories in relation to parental care  Academic Article
• Life history evolution in cichlids 2: directional evolution of the trade-off between egg number and egg size  Academic Article
• Lineage-specific mutational clustering in protein structures predicts evolutionary shifts in function  Academic Article
• Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations  Conference Paper
• Metabolomic-guided discovery of cyclic nonribosomal peptides from Xylaria ellisii sp. nov., a leaf and stem endophyte of Vaccinium angustifolium  Academic Article
• Microbial Diversity and Host-Specific Sequences of Canada Goose Feces  Academic Article
• Microbial Geoengineers  Academic Article
• Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances  Academic Article
• Microbial systematics in the post-genomics era  Academic Article
• Microbiota at Multiple Body Sites during Pregnancy in a Rural Tanzanian Population and Effects of Moringa-Supplemented Probiotic Yogurt  Academic Article
• Middle East Respiratory Syndrome Coronavirus Infection in Dromedary Camels in Saudi Arabia  Academic Article
• Minimal ProtoHox cluster inferred from bilaterian and cnidarian Hox complements  Academic Article
• Mitochondrial DNA analysis of sympatric morphotypes of bottlenose dolphins (genus: Tursiops) in Chinese waters  Academic Article
• Mitochondrial DNA variation and genetic structure in populations of Drosophila melanogaster.  Academic Article
• Molecular Cloning and Characterization of Tetrahydroprotoberberine cis-N-Methyltransferase, an Enzyme Involved in Alkaloid Biosynthesis in Opium Poppy  Academic Article
• Molecular Evolution of Cytochrome c Oxidase Underlies High-Altitude Adaptation in the Bar-Headed Goose  Academic Article
• Molecular Markers Reveal Epidemiological Patterns and Evolutionary Histories of the Human Pathogenic Cryptococcus  Academic Article
• Molecular Phylogeny of Living Xenarthrans and the Impact of Character and Taxon Sampling on the Placental Tree Rooting  Academic Article
• Molecular Polymorphism and Divergence of Duplicated Genes in Tetraploid African Clawed Frogs <b><i>(Xenopus)</i></b>  Academic Article
• Molecular Traits of Long Non-protein Coding RNAs from Diverse Plant Species Show Little Evidence of Phylogenetic Relationships  Academic Article
• Molecular analysis of a 11 700-year-old rodent midden from the Atacama Desert, Chile  Academic Article
• Molecular and phylogenetic approaches for assessing sources of Cryptosporidium contamination in water  Academic Article
• Molecular biology and modeling analysis reveal functional roles of propionate to acetate ratios on microbial syntrophy and competition in electro-assisted anaerobic digestion  Academic Article
• Molecular caving  Academic Article
• Molecular cloning and characterization of norcoclaurine synthase, an enzyme catalyzing the first committed step in benzylisoquinoline alkaloid biosynthesis  Academic Article
• Molecular epidemiology of HIV-1 subtype A in former Soviet Union countries  Academic Article
• Molecular evidence for increased regulatory conservation during metamorphosis, and against deleterious cascading effects of hybrid breakdown in Drosophila  Academic Article
• Molecular evolution of the vesicle coat component βCOP in Toxoplasma gondii  Academic Article
• Molecular phylogenetics unveils the ancient evolutionary origins of the enigmatic fairy armadillos  Academic Article
• Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades  Academic Article
• Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus  Academic Article
• Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia  Academic Article
• Molecular signatures for the class Coriobacteriia and its different clades; proposal for division of the class Coriobacteriia into the emended order Coriobacteriales , containing the emended family Coriobacteriaceae and Atopobiaceae fam. nov., and Eggerthellales ord. nov., containing the family Eggerthellaceae fam. nov.  Academic Article
• Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations  Academic Article
• Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae  Academic Article
• Molecular signatures for the phylum Synergistetes and some of its subclades  Academic Article
• Molecular signatures in protein sequences that are characteristic of cyanobacteria and plastid homologues  Academic Article
• Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates  Academic Article
• Molecular systematics of armadillos (Xenarthra, Dasypodidae): contribution of maximum likelihood and Bayesian analyses of mitochondrial and nuclear genes  Conference Paper
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• Multicopy gene family evolution on primate Y chromosomes  Academic Article
• Multilocus Sequence Typing Reveals both Shared and Unique Genotypes of Cryptococcus neoformans in Jiangxi Province, China  Academic Article
• Multilocus sequence analyses reveal extensive diversity and multiple origins of fluconazole resistance in Candida tropicalis from tropical China  Academic Article
• Multilocus sequence typing ofCandida africanafrom patients with vulvovaginal candidiasis in New Delhi, India  Academic Article
• Multiple gene genealogical analyses reveal both common and distinct population genetic patterns among replicons in the nitrogen-fixing bacterium Sinorhizobium meliloti  Academic Article
• Multiple gene genealogical analyses suggest divergence and recent clonal dispersal in the opportunistic human pathogen Candida guilliermondii  Academic Article
• Multiple gene genealogies reveal recent dispersion and hybridization in the human pathogenic fungusCryptococcus neoformans  Academic Article
• Multiple gene genealogy reveals high genetic diversity and evidence for multiple origins of Chinese Plasmopara viticola population  Academic Article
• Multiple origins of hybrid strains of Cryptococcus neoformans with serotype AD  Academic Article
• Mycobacterial adenosine kinase is not a typical adenosine kinase  Academic Article
• Mylodon darwinii DNA sequences from ancient fecal hair shafts  Academic Article
• Naked but Not Hairless: The Pitfalls of Analyses of Molecular Adaptation Based on Few Genome Sequence Comparisons  Academic Article
• Natural Selection for Nucleotide Usage at Synonymous and Nonsynonymous Sites in Influenza A Virus Genes  Academic Article
• Necessity and rationale for the proposed name changes in the classification of Mollicutes species. Reply to: ‘Recommended rejection of the names Malacoplasma gen. nov., Mesomycoplasma gen. nov., Metamycoplasma gen. nov., Metamycoplasmataceae fam. nov., Mycoplasmoidaceae fam. nov., Mycoplasmoidales ord. nov., Mycoplasmoides gen. nov., Mycoplasmopsis gen. nov. [Gupta, Sawnani, Adeolu, Alnajar and Oren 2018] and all proposed species comb. nov. placed therein’, by M. Balish et al. (Int J Syst Evol Microbiol, 2019;69:3650–3653)  Academic Article
• New Insights into 1-Aminocyclopropane-1-Carboxylate (ACC) Deaminase Phylogeny, Evolution and Ecological Significance  Academic Article
• Newly designed primer pair revealed dominant and diverse comammox amoA gene in full-scale wastewater treatment plants  Academic Article
• Next-generation sequencing and phylogenetic signal of complete mitochondrial genomes for resolving the evolutionary history of leaf-nosed bats (Phyllostomidae)  Academic Article
• Non-neutral evolution and reciprocal monophyly of two expressed Mhc class II B genes in Leach’s storm-petrel  Academic Article
• North American matsutake: names clarified and a new species described  Academic Article
• Novel DNA Sequences from Natural Strains of the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti  Academic Article
• Novel Molecular Signatures in the PIP4K/PIP5K Family of Proteins Specific for Different Isozymes and Subfamilies Provide Important Insights into the Evolutionary Divergence of this Protein Family  Academic Article
• Novel Molecular Synapomorphies Demarcate Different Main Groups/Subgroups of Plasmodium and Piroplasmida Species Clarifying Their Evolutionary Relationships  Academic Article
• Novel insights into the origin and diversification of photosynthesis based on analyses of conserved indels in the core reaction center proteins  Academic Article
• Novel molecular, structural and evolutionary characteristics of the phosphoketolases from bifidobacteria and Coriobacteriales  Academic Article
• Nuclear Gene Sequences from a Late Pleistocene Sloth Coprolite  Academic Article
• Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi  Academic Article
• Nucleotide sequence heterogeneity of alpha satellite repetitive DNA: a survey of alphoid sequences from different human chromosomes  Academic Article
• OGRe: a relational database for comparative analysis of mitochondrial genomes  Academic Article
• Occurrence of Virulence and Antimicrobial Resistance Genes in Escherichia coli Isolates from Different Aquatic Ecosystems within the St. Clair River and Detroit River Areas  Academic Article
• Ontogeny and phylogeny: molecular signatures of selection, constraint, and temporal pleiotropy in the development of Drosophila  Academic Article
• Optimization of culturing conditions for toxicity testing with the algaOophilasp. (Chlorophyceae), an amphibian endosymbiont  Academic Article
• Oral yeast flora and its ITS sequence diversity among a large cohort of medical students in Hainan, China  Academic Article
• Origin and Spread of Photosynthesis Based upon Conserved Sequence Features in Key Bacteriochlorophyll Biosynthesis Proteins  Academic Article
• Origine des vertébrés : la tunique fait-elle le moine ?  Academic Article
• OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals  Academic Article
• OrthoMaM: A database of orthologous genomic markers for placental mammal phylogenetics  Academic Article
• Osteocalcin protein sequences of Neanderthals and modern primates  Academic Article
• Out of America: Ancient DNA Evidence for a New World Origin of Late Quaternary Woolly Mammoths  Academic Article
• PCR–restriction fragment length polymorphism (RFLP) analyses reveal both extensive clonality and local genetic differences inCandidaalbicans  Academic Article
• Pan-African phylogeography of a model organism, the African clawed frog ‘Xenopus laevis’  Academic Article
• Partial 28S rDNA Sequences and the Antiquity of Hydrothermal Vent Endemic Gastropods  Academic Article
• Partial characterization of the genome of nine animal caliciviruses  Academic Article
• Pattern and timing of diversification of Cetartiodactyla (Mammalia, Laurasiatheria), as revealed by a comprehensive analysis of mitochondrial genomes  Academic Article
• Patterns of Bacterial Gene Movement  Academic Article
• Peripheral Chemoreceptors in Air- Versus Water- Breathers  Chapter
• Pervasive Cryptic Epistasis in Molecular Evolution  Academic Article
• Phenotypic Divergence along Geographic Gradients Reveals Potential for Rapid Adaptation of the White-Nose Syndrome Pathogen, Pseudogymnoascus destructans, in North America  Academic Article
• PhyloExplorer: a web server to validate, explore and query phylogenetic trees  Academic Article
• Phylogenetic Analysis of Mycoplasmas Based on Hsp70 Sequences: Cloning of the dnaK (hsp70) Gene Region of Mycoplasma capricolum  Academic Article
• Phylogenetic Analysis of the Cytochrome P450 3 (CYP3) Gene Family  Academic Article
• Phylogenetic Diversity and Molecular Detection of Bacteria in Gull Feces  Academic Article
• Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria  Academic Article
• Phylogenetic Gaussian Process Model for the Inference of Functionally Important Regions in Protein Tertiary Structures  Academic Article
• Phylogenetic analyses and antimicrobial resistance profiles of Campylobacter spp. from diarrhoeal patients and chickens in Botswana  Academic Article
• Phylogenetic analyses of mitochondrial and nuclear data in haematophagous flies support the paraphyly of the genus Stomoxys (Diptera: Muscidae)  Academic Article
• Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives  Academic Article
• Phylogenetic analysis of 70 kD heat shock protein sequences suggests a chimeric origin for the eukaryotic cell nucleus  Academic Article
• Phylogenetic analysis of emergent Streptococcus pneumoniae serotype 22F causing invasive pneumococcal disease using whole genome sequencing  Academic Article
• Phylogenetic analysis of the 90 kD heat shock family of protein sequences and an examination of the relationship among animals, plants, and fungi species.  Academic Article
• Phylogenetic analysis of the caliciviruses  Academic Article
• Phylogenetic analysis of the diacylglycerol kinase family of proteins and identification of multiple highly-specific conserved inserts and deletions within the catalytic domain that are distinctive characteristics of different classes of DGK homologs  Academic Article
• Phylogenetic and Functional Analysis of the Vertebrate Cytochrome P450 2 Family  Academic Article
• Phylogenetic and environmental components of inter-specific variability in the antioxidant defense system in freshwater anomurans Aegla (Crustacea, Decapoda)  Academic Article
• Phylogenetic and functional analyses of the cytochrome P450 family 4  Academic Article
• Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexi class. nov. into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov.  Academic Article
• Phylogenetic framework for the phylum Tenericutes based on genome sequence data: proposal for the creation of a new order Mycoplasmoidales ord. nov., containing two new families Mycoplasmoidaceae fam. nov. and Metamycoplasmataceae fam. nov. harbouring Eperythrozoon, Ureaplasma and five novel genera  Academic Article
• Phylogenetic reconciliation reveals the natural history of glycopeptide antibiotic biosynthesis and resistance  Academic Article
• Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation  Academic Article
• Phylogenetics of Fanged Frogs: Testing Biogeographical Hypotheses at the Interface of the Asian and Australian Faunal Zones  Academic Article
• Phylogenomic analyses and molecular signatures for the class Halobacteria and its two major clades: a proposal for division of the class Halobacteria into an emended order Halobacteriales and two new orders, Haloferacales ord. nov. and Natrialbales ord. nov., containing the novel families Haloferacaceae fam. nov. and Natrialbaceae fam. nov.  Academic Article
• Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)  Academic Article
• Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)  Academic Article
• Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis  Academic Article
• Phylogenomic and comparative genomic analyses of Leuconostocaceae species: identification of molecular signatures specific for the genera Leuconostoc, Fructobacillus and Oenococcus and proposal for a novel genus Periweissella gen. nov.  Academic Article
• Phylogenomic and comparative genomic analyses of species of the family Pseudomonadaceae: Proposals for the genera Halopseudomonas gen. nov. and Atopomonas gen. nov., merger of the genus Oblitimonas with the genus Thiopseudomonas, and transfer of some misclassified species of the genus Pseudomonas into other genera  Academic Article
• Phylogenomic and comparative genomic studies robustly demarcate two distinct clades of Pseudomonas aeruginosa strains: proposal to transfer the strains from an outlier clade to a novel species Pseudomonas paraeruginosa sp. nov.  Academic Article
• Phylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family  Academic Article
• Phylogenomics and molecular signatures for the order Neisseriales: proposal for division of the order Neisseriales into the emended family Neisseriaceae and Chromobacteriaceae fam. nov.  Academic Article
• Phylogenomics and molecular signatures support division of the order Neisseriales into emended families Neisseriaceae and Chromobacteriaceae and three new families Aquaspirillaceae fam. nov., Chitinibacteraceae fam. nov., and Leeiaceae fam. nov.  Academic Article
• Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria  Academic Article
• Phylogenomics and signature proteins for the alpha Proteobacteria and its main groups  Academic Article
• Phylogenomics and the reconstruction of the tree of life  Academic Article
• Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B  Academic Article
• Phylogenomics: the beginning of incongruence?  Academic Article
• Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species  Academic Article
• Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades  Academic Article
• Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups  Academic Article
• Phylogeny and shared conserved inserts in proteins provide evidence that Verrucomicrobia are the closest known free-living relatives of chlamydiae  Academic Article
• Phylogeny of Helicobacter Isolates from Bird and Swine Feces and Description of Helicobacter pametensis sp. nov.  Academic Article
• Phylogeography and evolution of a fungal-insect association on the Tibetan Plateau  Academic Article
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• Plasmodium possesses dynein light chain classes that are unique and conserved across species  Academic Article
• Pleistocene mitogenomes reconstructed from the environmental DNA of permafrost sediments  Academic Article
• Polymorphism of human papillomavirus type 31 isolates infecting the genital tract of HIV-seropositive and HIV-seronegative women at risk for HIV infection  Academic Article
• Population Genetic Analyses of the Fungal Pathogen Colletotrichum fructicola on Tea-Oil Trees in China  Academic Article
• Population Genetics Without Intraspecific Data  Academic Article
• Population-specific incidence of testicular ovarian follicles in Xenopus laevis from South Africa: A potential issue in endocrine testing  Academic Article
• Predicting West Nile virus transmission in North American bird communities using phylogenetic mixed effects models and eBird citizen science data  Academic Article
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• Predicting the recombination potential of severe acute respiratory syndrome coronavirus 2 and Middle East respiratory syndrome coronavirus  Academic Article
• Prevalence of Epistasis in the Evolution of Influenza A Surface Proteins  Academic Article
• Prevalence of specific and phylogenetically closely related genotypes in the population of Candida albicans associated with genital candidiasis in China  Academic Article
• Prokaryote populations of extant microbialites along a depth gradient in Pavilion Lake, British Columbia, Canada  Academic Article
• Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes  Academic Article
• Protein Signatures Distinctive of Alpha Proteobacteria and Its Subgroups and a Model for α –Proteobacterial Evolution  Academic Article
• Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution  Academic Article
• Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase  Academic Article
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• Protein signatures (molecular synapomorphies) that are distinctive characteristics of the major cyanobacterial clades  Academic Article
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• Protein-based phylogenies support a chimeric origin for the eukaryotic genome.  Academic Article
• Proteins of the Glycine Decarboxylase Complex in the Hydrogenosome of Trichomonas vaginalis  Academic Article
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• RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences  Academic Article
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• Rapidly Evolving Genes of Drosophila: Differing Levels of Selective Pressure in Testis, Ovary, and Head Tissues Between Sibling Species  Academic Article
• Reconstructing the Prior Probabilities of Allelic Phylogenies  Academic Article
• Regulatory Evolution of a Duplicated Heterodimer Across Species and Tissues of Allopolyploid Clawed Frogs (Xenopus)  Academic Article
• Resolving the root of the avian mitogenomic tree by breaking up long branches  Academic Article
• Retroposed Elements and Their Flanking Regions Resolve the Evolutionary History of Xenarthran Mammals (Armadillos, Anteaters, and Sloths)  Academic Article
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• Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species  Academic Article
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• Signature proteins for the major clades of Cyanobacteria  Academic Article
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• Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome  Academic Article
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• The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes  Academic Article
• The Evolutionary Origins of Eukaryotic Protein Disulfide Isomerase Domains: New Evidence from the Amitochondriate Protist Giardia lamblia  Academic Article
• The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance  Academic Article
• The Genetic Secrets Some Fossils Hold  Academic Article
• The Location of Substitutions and Bacterial Genome Arrangements  Academic Article
• The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes  Academic Article
• The Natural Evolutionary Relationships among Prokaryotes  Academic Article
• The Pattern of Amino Acid Replacements in α/β-Barrels  Academic Article
• The Phylogeny and Signature Sequences Characteristics ofFibrobacteres,Chlorobi, andBacteroidetes  Academic Article
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• The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes  Academic Article
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• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Academic Article
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• The mosaic nature of the eukaryotic nucleus  Academic Article
• The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis  Academic Article
• The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances  Academic Article
• The origin of the eukaryotic cell  Academic Article
• The paradox of HBV evolution as revealed from a 16th century mummy  Academic Article
• The phylogenetic affinities of the extinct glyptodonts  Academic Article
• The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes  Academic Article
• The role of laterally transferred genes in adaptive evolution  Academic Article
• The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria  Academic Article
• The structural basis of molecular adaptation  Academic Article
• The use of signature sequences in different proteins to determine the relative branching order of bacterial divisions: evidence that Fibrobacter diverged at a similar time to Chlamydia and the Cytophaga–Flavobacterium–Bacteroides division The GenBank accession numbers for the sequences reported in this paper are AY017380, AY017381, AY017382 and AY017383.  Academic Article
• Thrice better than once: quality control guidelines to validate new mitogenomes  Academic Article
• Timings of major glaciations, inherent selection schemes and the origins of cold hardy animal phyla.  Academic Article
• Tracking Host Sources of Cryptosporidium spp. in Raw Water for Improved Health Risk Assessment  Academic Article
• Transmission of HIV and HCV within Former Soviet Union Countries  Academic Article
• Trends in DNA barcoding and metabarcoding  Academic Article
• Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny  Academic Article
• Tunicates and not cephalochordates are the closest living relatives of vertebrates  Academic Article
• Two new unusualLeucoagaricusspecies (Agaricaceae) from tropical China with blue-green staining reactions  Academic Article
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Academic Article
• Unmelanized Plumage Patterns in Old World Leaf Warblers Do Not Correspond to Sequence Variation at the Melanocortin-1 Receptor Locus (MC1R)  Academic Article
• Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes  Academic Article
• Upregulating Nrf2-dependent antioxidant defenses in Pacific oysters Crassostrea gigas: Investigating the Nrf2/Keap1 pathway in bivalves  Academic Article
• Using a Nonrecursive Formula to Determine Cladogram Probabilities  Academic Article
• Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods  Academic Article
• World-wide genetic differentiation ofEubalaena: questioning the number of right whale species  Academic Article
• Xenopus fraseri: Mr. Fraser, where did your frog come from?  Academic Article
• Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis  Academic Article
• Yersinia pestis and the three plague pandemics–Authors' reply  Academic Article
• Yersinia pestis: New Evidence for an Old Infection  Academic Article
• [Soil microbial diversity of artificial peashrub plantation on North Loess Plateau of China].  Academic Article
• markophylo: Markov chain analysis on phylogenetic trees  Academic Article