Phylogeny Concept

subject area of

• 'Outlier' lipocalins more than peripheral  Journal Articles
• 17th Century Variola Virus Reveals the Recent History of Smallpox  Journal Articles
• Sequence Note: Molecular Epidemiological Analysis of Human Immunodeficiency Virus Type 1 in Newfoundland, Canada  Journal Articles
• Burkholderia from Fungus Gardens of Fungus-Growing Ants Produces Antifungals That Inhibit the Specialized Parasite Escovopsis  Journal Articles
• Helicobacter apodemussp. nov., a newHelicobacterspecies identified from the gastrointestinal tract of striped field mice in Korea  Journal Articles
• Torulaspora quercuum  sp. nov. andCandida pseudohumilis  sp. nov., novel yeasts from human and forest habitats  Journal Articles
• d -Ala- d -Ala ligases from glycopeptide antibiotic-producing organisms are highly homologous to the enterococcal vancomycin-resistance ligases VanA and VanB  Journal Articles
• A 14th century CE Brucella melitensis genome and the recent expansion of the Western Mediterranean clade  Journal Articles
• A Catalog of Reference Genomes from the Human Microbiome  Journal Articles
• A Comprehensive Analysis of Mammalian Mitochondrial Genome Base Composition and Improved Phylogenetic Methods  Journal Articles
• A Comprehensive Expression Analysis of the Arabidopsis Proline-rich Extensin-like Receptor Kinase Gene Family using Bioinformatic and Experimental Approaches  Journal Articles
• A Highly Unstable Recent Mutation in Human mtDNA  Journal Articles
• A Large and Consistent Phylogenomic Dataset Supports Sponges as the Sister Group to All Other Animals  Journal Articles
• A Machine Learning Framework Identifies Plastid-Encoded Proteins Harboring C3 and C4 Distinguishing Sequence Information  Journal Articles
• A Non-Long Terminal Repeat Retrotransposon Family Is Restricted to the Germ Line Micronucleus of the Ciliated Protozoan Tetrahymena thermophila  Journal Articles
• A T-to-G Transversion at Nucleotide −567 Upstream of HBG2 in a GATA-1 Binding Motif Is Associated with Elevated Hemoglobin F  Journal Articles
• A Type VI Secretion-Related Pathway in Bacteroidetes Mediates Interbacterial Antagonism  Journal Articles
• A coalescent framework for comparing alternative models of population structure with genetic data: evolution of Celebes toads  Journal Articles
• A comparative study of an innate immune response in Lamprologine cichlid fishes  Journal Articles
• A comprehensive genomic history of extinct and living elephants  Journal Articles
• 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.  Journal Articles
• A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis‐specific lipid A  Journal Articles
• A draft genome of Yersinia pestis from victims of the Black Death  Journal Articles
• A functionally divergent hydrogenosomal peptidase with protomitochondrial ancestry  Journal Articles
• A genomic catalog of Earth’s microbiomes  Journal Articles
• A high‐quality carabid genome assembly provides insights into beetle genome evolution and cold adaptation  Journal Articles
• A maximum likelihood approach to the detection of selection from a phylogeny  Journal Articles
• A mitochondrial DNA phylogeny of African clawed frogs: phylogeography and implications for polyploid evolution  Journal Articles
• A new fossil assemblage shows that large angiosperm trees grew in North America by the Turonian (Late Cretaceous)  Journal Articles
• A novel strain of cynomolgus macaque cytomegalovirus: implications for host-virus co-evolution  Journal Articles
• A phylogenetic analysis based on the gene encoding phosphoglycerate kinase  Journal Articles
• A phylogenetic analysis of the pSymB replicon from the Sinorhizobium meliloti genome reveals a complex evolutionary history  Journal Articles
• 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.  Journal Articles
• 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)  Journal Articles
• 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  Journal Articles
• 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  Journal Articles
• 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  Journal Articles
• A phylogenomic framework and timescale for comparative studies of tunicates  Journal Articles
• 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.  Journal Articles
• 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  Journal Articles
• A spliceosomal intron in Giardia lamblia  Journal Articles
• ANATOMIC ASYMMETRY IN THE TEMPORAL LOBES: ITS DOCUMENTATION, PHYLOGENESIS, AND RELATIONSHIP TO FUNCTIONAL ASYMMETRY*  Journal Articles
• AXIOME3: Automation, eXtension, and Integration Of Microbial Ecology  Journal Articles
• Abundance and community composition of comammox bacteria in different ecosystems by a universal primer set  Journal Articles
• Abundant sequence variation around the mitochondrial origin of replication in the human opportunistic yeast pathogen Candida albicans from a tropical island in China  Journal Articles
• Accelerated Evolutionary Rate of Housekeeping Genes in Tunicates  Journal Articles
• Adaptive Radiation and Ecological Opportunity in Sulawesi and Philippine Fanged Frog (Limnonectes) Communities  Journal Articles
• Additional molecular support for the new chordate phylogeny  Journal Articles
• Adenosine kinase and ribokinase – the RK family of proteins  Journal Articles
• Aerobic proteobacterial methylotrophs in Movile Cave: genomic and metagenomic analyses  Journal Articles
• Agricultural soil denitrifiers possess extensive nitrite reductase gene diversity  Journal Articles
• Alignment/Phylogeny of the Papain Superfamily of Cysteine Proteases  Journal Articles
• Amplification and sequencing of DNA from a 120–135-million-year-old weevil  Journal Articles
• An Assessment of Sub-Meter Scale Spatial Variability of Arcellinida (Testate Lobose Amoebae) Assemblages in a Temperate Lake: Implications for Limnological Studies  Journal Articles
• An Insect Herbivore Microbiome with High Plant Biomass-Degrading Capacity  Journal Articles
• An evaluation of logic regression-based biomarker discovery across multiple intergenic regions for predicting host specificity in Escherichia coli  Journal Articles
• An evolutionary model for the insect vitellins  Journal Articles
• An unusual myosuppressin from the blood-feeding bugRhodnius prolixus  Journal Articles
• An updated 18S rRNA phylogeny of tunicates based on mixture and secondary structure models  Journal Articles
• Analyses of the Global Multilocus Genotypes of the Human Pathogenic Yeast Cryptococcus neoformans Species Complex  Journal Articles
• Analysis of Canis mitochondrial DNA demonstrates high concordance between the control region and ATPase genes  Journal Articles
• Analysis of the legume-rhizobia symbiosis in shrubs from central western Spain  Journal Articles
• Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)  Journal Articles
• Ancient Antibiotics, Ancient Resistance  Journal Articles
• Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains  Journal Articles
• Ancient DNA  Journal Articles
• Ancient DNA and the tropics: a rodent's tale  Journal Articles
• Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics  Journal Articles
• Ancient Mitogenomes Reveal the Evolutionary History and Biogeography of Sloths  Journal Articles
• Ancient Tripartite Coevolution in the Attine Ant-Microbe Symbiosis  Journal Articles
• Ancient pathogen DNA in archaeological samples detected with a Microbial Detection Array  Journal Articles
• Ancyromonadida: A New Phylogenetic Lineage Among the Protozoa Closely Related to the Common Ancestor of Metazoans, Fungi, and Choanoflagellates (Opisthokonta)  Journal Articles
• Annexin-like alpha giardins: a new cytoskeletal gene family in Giardia lamblia  Journal Articles
• AnnoTree: visualization and exploration of a functionally annotated microbial tree of life  Journal Articles
• Antagonistic Bacterial Interactions Help Shape Host-Symbiont Dynamics within the Fungus-Growing Ant-Microbe Mutualism  Journal Articles
• Antibiotic resistance is ancient  Journal Articles
• AppIndels.com server: a web-based tool for the identification of known taxon-specific conserved signature indels in genome sequences. Validation of its usefulness by predicting the taxonomic affiliation of >700 unclassified strains of Bacillus species  Journal Articles
• Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions  Journal Articles
• Are similarity- or phylogeny-based methods more appropriate for classifying internal transcribed spacer (ITS) metagenomic amplicons?  Journal Articles
• Armadillos exhibit less genetic polymorphism in North America than in South America: nuclear and mitochondrial data confirm a founder effect in Dasypus novemcinctus (Xenarthra)  Journal Articles
• Army Ants Trapped by Their Evolutionary History  Journal Articles
• Assessment of the Microbial Constituents of the Home Environment of Individuals with Cystic Fibrosis (CF) and Their Association with Lower Airways Infections  Journal Articles
• Association between Pseudonocardia symbionts and Atta leaf-cutting ants suggested by improved isolation methods.  Journal Articles
• Asymmetrical Evolution of Cytochrome bd Subunits  Journal Articles
• Autoecological Approaches to Resolve Subjective Taxonomic Divisions within Arcellacea  Journal Articles
• Bacillus DNA in fossil bees: an ancient symbiosis?  Journal Articles
• Bacteria Contribute to Plant Secondary Compound Degradation in a Generalist Herbivore System  Journal Articles
• Bacterial biogeography of the human digestive tract  Journal Articles
• Bats and Coronaviruses  Journal Articles
• Bayesian Phylogenetics Using an RNA Substitution Model Applied to Early Mammalian Evolution  Journal Articles
• Beltrania sinensis sp. nov., an endophytic fungus from China and a key to species of the genus  Journal Articles
• Biogeography of Bacterial Communities and Specialized Metabolism in Human Aerodigestive Tract Microbiomes  Journal Articles
• Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites  Journal Articles
• CLONING AND CHARACTERIZATION OF AN mRNA ENCODING AN INSULIN RECEPTOR FROM THE HORNED SCARAB BEETLE Onthophagus nigriventris (COLEOPTERA: SCARABAEIDAE)  Journal Articles
• Candida auris on Apples: Diversity and Clinical Significance  Journal Articles
• Capturing the diversity of the human gut microbiota through culture-enriched molecular profiling  Journal Articles
• Carving out turf in a biodiversity hotspot: multiple, previously unrecognized shrew species co‐occur onJavaIsland,Indonesia  Journal Articles
• Cellulolytic Streptomyces Strains Associated with Herbivorous Insects Share a Phylogenetically Linked Capacity To Degrade Lignocellulose  Journal Articles
• Characterization and assessment of an avian repetitive DNA sequence as an icterid phylogenetic marker  Journal Articles
• Characterization and genomic analysis of a diesel-degrading bacterium, Acinetobacter calcoaceticus CA16, isolated from Canadian soil  Journal Articles
• Characterization of Class I– and Class II–Like Major Histocompatibility Complex Loci in Pedigrees of North Atlantic Right Whales  Journal Articles
• Characterization of a Rifampin-Inactivating Glycosyltransferase from a Screen of Environmental Actinomycetes  Journal Articles
• Characterization of a cetacean aromatase (CYP19) and the phylogeny and functional conservation of vertebrate aromatase  Journal Articles
• Characterization of yeast homoserine dehydrogenase, an antifungal target: the invariant histidine 309 is important for enzyme integrity  Journal Articles
• Chemical Analyses of Wasp-Associated Streptomyces Bacteria Reveal a Prolific Potential for Natural Products Discovery  Journal Articles
• Chimeric Structure of the NAD(P)+- and NADP+-dependent Malic Enzymes ofRhizobium (Sinorhizobium) meliloti  Journal Articles
• Chitinase genes ( CHIA s) provide genomic footprints of a post-Cretaceous dietary radiation in placental mammals  Journal Articles
• Chlamydiae-specific proteins and indels: novel tools for studies  Journal Articles
• Clades of huge phages from across Earth’s ecosystems  Journal Articles
• Clinical and tree hollow populations of human pathogenic yeast in Hamilton, Ontario, Canada are different  Journal Articles
• Clonal Genotype of Geomyces destructans among Bats with White Nose Syndrome, New York, USA  Journal Articles
• Clonal and Spontaneous Origins of Fluconazole Resistance in Candida albicans  Journal Articles
• Cloning and Some Novel Characteristics of Mitochondrial Hsp70 from Chinese Hamster Cells  Journal Articles
• Cloning of Giardia lamblia heat shock protein HSP70 homologs: implications regarding origin of eukaryotic cells and of endoplasmic reticulum.  Journal Articles
• Cloning of the hsp70 (dnaK) genes from Rhizobium meliloti and Pseudomonas cepacia: phylogenetic analyses of mitochondrial origin based on a highly conserved protein sequence  Journal Articles
• Codon Bias and Base Composition Are Poor Indicators of Horizontally Transferred Genes  Journal Articles
• Coevolved Crypts and Exocrine Glands Support Mutualistic Bacteria in Fungus-Growing Ants  Journal Articles
• Cold-Active Winter Rye Glucanases with Ice-Binding Capacity  Journal Articles
• Comment on "Hexapod Origins: Monophyletic or Paraphyletic?"  Journal Articles
• Comment: Characterization of Two Historic Smallpox Specimens from a Czech Museum  Journal Articles
• Common biosynthetic origins for polycyclic tetramate macrolactams from phylogenetically diverse bacteria  Journal Articles
• Comparative Gene Genealogies Indicate that Two Clonal Lineages ofCryptococcus gattiiin British Columbia ResembleStrains from Other Geographical Areas  Journal Articles
• Comparative analysis of function and interaction of transcription factors in nematodes: Extensive conservation of orthology coupled to rapid sequence evolution  Journal Articles
• 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  Journal Articles
• Comparative chromosome painting of pronghorn (Antilocapra americana) and saola (Pseudoryx nghetinhensis) karyotypes with human and dromedary camel probes  Journal Articles
• 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  Journal Articles
• Comparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants  Journal Articles
• Comparative molecular phylogeography of two Xenopus species, X. gilli and X. laevis, in the south‐western Cape Province, South Africa  Journal Articles
• Comparative proteome analysis of Acidaminococcus intestini supports a relationship between outer membrane biogenesis in Negativicutes and Proteobacteria  Journal Articles
• Comparison of 26 Sphingomonad Genomes Reveals Diverse Environmental Adaptations and Biodegradative Capabilities  Journal Articles
• Comparison of Bayesian and Maximum Likelihood Bootstrap Measures of Phylogenetic Reliability  Journal Articles
• Comparison of biochemical and genotypic speciation methods for vancomycin-resistant enterococci isolated from urban wastewater treatment plants  Journal Articles
• Comparison of fecal biota from specific pathogen free and feral mice  Journal Articles
• Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris  Journal Articles
• Complete Columbian mammoth mitogenome suggests interbreeding with woolly mammoths  Journal Articles
• Complete mitochondrial genomes of living and extinct pigeons revise the timing of the columbiform radiation  Journal Articles
• Completion of draft bacterial genomes by long-read sequencing of synthetic genomic pools  Journal Articles
• Complex host-pathogen coevolution in the Apterostigma fungus-growing ant-microbe symbiosis.  Journal Articles
• Conserved Molecular Signatures in the Spike, Nucleocapsid, and Polymerase Proteins Specific for the Genus Betacoronavirus and Its Different Subgenera  Journal Articles
• Conserved Signatures in Protein Sequences Reliably Demarcate Different Clades of Rodents/Glires Species and Consolidate Their Evolutionary Relationships  Journal Articles
• 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  Journal Articles
• Constraining the Time Interval for the Origin of Life on Earth  Journal Articles
• Control of breathing and adaptation to high altitude in the bar-headed goose  Journal Articles
• Convergence of gut microbiomes in myrmecophagous mammals  Journal Articles
• Convergent Bacterial Microbiotas in the Fungal Agricultural Systems of Insects  Journal Articles
• Convergent evolution of complex structures for ant–bacterial defensive symbiosis in fungus-farming ants  Journal Articles
• Corticosteroid receptor gene expression is related to sex and social behaviour in a social fish  Journal Articles
• Critical Issues in Bacterial Phylogeny  Journal Articles
• Culture and molecular-based profiles show shifts in bacterial communities of the upper respiratory tract that occur with age  Journal Articles
• DNA Sequence Analyses Reveal Abundant Diversity, Endemism and Evidence for Asian Origin of the Porcini Mushrooms  Journal Articles
• DNA methylation predicts age and provides insight into exceptional longevity of bats  Journal Articles
• Dating the Ngandong Humans  Journal Articles
• Deep Sequencing of Mixed Total DNA without Barcodes Allows Efficient Assembly of Highly Plastic Ascidian Mitochondrial Genomes  Journal Articles
• Demographic expansion and genetic load of the halophyte model plant Eutrema salsugineum  Journal Articles
• Detecting recent speciation events: the case of the finless porpoise (genus Neophocaena)  Journal Articles
• Development and Evaluation of a Molecular Hepatitis A Virus Assay for Serum and Stool Specimens  Journal Articles
• 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  Journal Articles
• Differential Y‐chromosome Anatolian Influences on the Greek and Cretan Neolithic  Journal Articles
• Directionality in the evolution of influenza A haemagglutinin  Journal Articles
• Discovery of a proteolytic flagellin family in diverse bacterial phyla that assembles enzymatically active flagella  Journal Articles
• Dispersers shape fruit diversity in Ficus (Moraceae)  Journal Articles
• 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)  Journal Articles
• Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum  Journal Articles
• Diurnal Floc Generation from Neuston Biofilms in Two Contrasting Freshwater Lakes  Journal Articles
• Divergence, hybridization, and recombination in the mitochondrial genome of the human pathogenic yeast Cryptococcus gattii  Journal Articles
• Divergent respiratory and cardiovascular responses to hypoxia in bar-headed geese and Andean birds  Journal Articles
• Divergent subgenome evolution after allopolyploidization in African clawed frogs (Xenopus)  Journal Articles
• Diversification of Wolbachia Endosymbiont in the Culex pipiens Mosquito  Journal Articles
• Diversity Considerations in HIV-1 Vaccine Selection  Journal Articles
• Diversity and abundance of the bacterial 16S rRNA gene sequences in forestomach of alpacas (Lama pacos) and sheep (Ovis aries)  Journal Articles
• Diversity and relationships among strains of culturable yeasts in agricultural soils in Cameroon  Journal Articles
• Diversity of Rotavirus Strains Circulating in Botswana before and after introduction of the Monovalent Rotavirus Vaccine  Journal Articles
• Diversity of commensal yeasts within and among healthy hosts  Journal Articles
• Diversity, Dispersal and Mode of Reproduction of Amanita exitialis in Southern China  Journal Articles
• 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)  Journal Articles
• Draft genome of the globally widespread and invasive Argentine ant ( Linepithema humile )  Journal Articles
• Draft genome of the red harvester ant Pogonomyrmex barbatus  Journal Articles
• Drainage isolation and climate change-driven population expansion shape the genetic structures of Tuber indicum complex in the Hengduan Mountains region  Journal Articles
• Dynamic evolution of eukaryotic mitochondrial and nuclear genomes: a case study in the gourmet pine mushroom Tricholoma matsutake  Journal Articles
• EPHEMERAL WINDOWS OF OPPORTUNITY FOR HORIZONTAL TRANSMISSION OF FUNGAL SYMBIONTS IN LEAF-CUTTING ANTS  Journal Articles
• EVOLUTION OF THE CLOSELY RELATED, SEX-RELATED GENES DM-W AND DMRT1 IN AFRICAN CLAWED FROGS (XENOPUS)  Journal Articles
• Ecological Genomics of Marine Roseobacters  Journal Articles
• Ecological and physical barriers shape genetic structure of the Alpine porcini (Boletus reticuloceps)  Journal Articles
• Emergence, continuity, and evolution of Yersinia pestis throughout medieval and early modern Denmark  Journal Articles
• Enabling genomic island prediction and comparison in multiple genomes to investigate bacterial evolution and outbreaks  Journal Articles
• Environmental and nutritional regulation of expression and function of two peptide transporter (PepT1) isoforms in a euryhaline teleost  Journal Articles
• Enzyme Evolution Explained (Sort Of)  Journal Articles
• Erratum to “Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms” [Phytochemistry 66 (2005) 1374–1393]  Journal Articles
• Estimating Maximum Likelihood Phylogenies with PhyML  Journal Articles
• Estimating the Frequency of Horizontal Gene Transfer Using Phylogenetic Models of Gene Gain and Loss  Journal Articles
• Evidence for Inbreeding and Genetic Differentiation among Geographic Populations of the Saprophytic Mushroom Trogia venenata from Southwestern China  Journal Articles
• Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to Giardia lamblia and Entamoeba histolytica  Journal Articles
• Evidence for local DNA influences on patterns of substitutions in the human α-interferon gene family  Journal Articles
• Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms  Journal Articles
• Evidence for the monophyletic evolution of benzylisoquinoline alkaloid biosynthesis in angiosperms.  Journal Articles
• 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  Journal Articles
• Evidence of Naturalized Stress-Tolerant Strains of Escherichia coli in Municipal Wastewater Treatment Plants  Journal Articles
• Evidence of unique genetic diversity in Aspergillus fumigatus isolates from Cameroon  Journal Articles
• Evolution in the Fast Lane: Rapidly Evolving Sex-Related Genes in Drosophila  Journal Articles
• Evolution of Drosophila sex comb length illustrates the inextricable interplay between selection and variation  Journal Articles
• Evolution of Allosteric Control in Glycogen Phosphorylase  Journal Articles
• Evolution of Eukaryotic Transcription: Insights From the Genome of Giardia lamblia  Journal Articles
• Evolution of HSP70 gene and its implications regarding relationships between archaebacteria, eubacteria, and eukaryotes  Journal Articles
• Evolution of High Cellulolytic Activity in Symbiotic Streptomyces through Selection of Expanded Gene Content and Coordinated Gene Expression  Journal Articles
• Evolution of Proteasome Regulators in Eukaryotes  Journal Articles
• Evolution of RAG-1 in Polyploid Clawed Frogs  Journal Articles
• Evolution of genes and genomes on the Drosophila phylogeny  Journal Articles
• Evolution of mitochondrial-encoded cytochrome oxidase subunits in endothermic fish: The importance of taxon-sampling in codon-based models  Journal Articles
• Evolution of the Largest Mammalian Genome  Journal Articles
• Evolution of the RpoS Regulon: Origin of RpoS and the Conservation of RpoS-Dependent Regulation in Bacteria  Journal Articles
• Evolution of the chaperonin families (HSP60, HSP 10 and TCP‐1) of proteins and the origin of eukaryotic cells  Journal Articles
• Evolution of the nuclear-encoded cytochrome oxidase subunits in vertebrates  Journal Articles
• Evolution-guided discovery of antibiotics that inhibit peptidoglycan remodelling  Journal Articles
• Evolutionary affinity of billfishes (Xiphiidae and Istiophoridae) and flatfishes (Plueronectiformes): Independent and trans-subordinal origins of endothermy in teleost fishes  Journal Articles
• Evolutionary analysis of selective constraints identifies ameloblastin (AMBN) as a potential candidate for amelogenesis imperfecta  Journal Articles
• Evolutionary and Functional Analyses of the Interaction between the Myeloid Restriction Factor SAMHD1 and the Lentiviral Vpx Protein  Journal Articles
• Evolutionary and functional diversity of the Pseudomonas type IVa pilin island  Journal Articles
• Evolutionary innovations through gain and loss of genes in the ectomycorrhizal Boletales  Journal Articles
• Evolutionary rate variation withinMus APRT  Journal Articles
• Evolutionary relationships among photosynthetic prokaryotes (Heliobacterium chlorum, Chloroflexus aurantiacus, cyanobacteria, Chlorobium tepidum and proteobacteria): implications regarding the origin of photosynthesis  Journal Articles
• Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus.  Journal Articles
• Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle  Journal Articles
• Expanding the soil antibiotic resistome: exploring environmental diversity  Journal Articles
• Exploratory analysis of multiple sequence alignments using phylogenies  Journal Articles
• Exploring the Potential for Actinobacteria as Defensive Symbionts in Fungus-Growing Termites  Journal Articles
• Expressed sequence tags from the Yukon ecotype of Thellungiella reveal that gene expression in response to cold, drought and salinity shows little overlap  Journal Articles
• Extensive Genetic Diversity and Widespread Azole Resistance in Greenhouse Populations of Aspergillus fumigatus in Yunnan, China  Journal Articles
• Extracting Haplotypes from Diploid Organisms  Journal Articles
• Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences  Journal Articles
• Factors That Affect Large Subunit Ribosomal DNA Amplicon Sequencing Studies of Fungal Communities: Classification Method, Primer Choice, and Error  Journal Articles
• Fate of Cd during Microbial Fe(III) Mineral Reduction by a Novel and Cd-Tolerant Geobacter Species  Journal Articles
• First Evidence for the Presence of Iron Oxidizing Zetaproteobacteria at the Levantine Continental Margins  Journal Articles
• Fish gill morphology: inside out  Journal Articles
• Fossil Rhabdoviral Sequences Integrated into Arthropod Genomes: Ontogeny, Evolution, and Potential Functionality  Journal Articles
• Frequent heteroplasmy and recombination in the mitochondrial genomes of the basidiomycete mushroom Thelephora ganbajun  Journal Articles
• Functional Biogeography of Ocean Microbes Revealed through Non-Negative Matrix Factorization  Journal Articles
• Functional Divergence in the Arabidopsis  -1,3-Glucanase Gene Family Inferred by Phylogenetic Reconstruction of Expression States  Journal Articles
• Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome  Journal Articles
• Functional analysis of CfSnf1 in the development and pathogenicity of anthracnose fungus Colletotrichum fructicola on tea-oil tree  Journal Articles
• Functional metagenomics reveals novel β-galactosidases not predictable from gene sequences  Journal Articles
• Fungal mitochondrial genomes and genetic polymorphisms  Journal Articles
• Fungal species concepts in the genomics era  Journal Articles
• Galactitol catabolism in Sinorhizobium meliloti is dependent on a chromosomally encoded sorbitol dehydrogenase and a pSymB-encoded operon necessary for tagatose catabolism  Journal Articles
• Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?  Journal Articles
• Gene duplication and divergence produce divergent MHC genotypes without disassortative mating  Journal Articles
• Generation and Analysis of a Mouse Intestinal Metatranscriptome through Illumina Based RNA-Sequencing  Journal Articles
• Genetic Analyses from Ancient DNA  Journal Articles
• Genetic Analyses of the Internal Transcribed Spacer Sequences Suggest Introgression and Duplication in the Medicinal Mushroom Agaricus subrufescens  Journal Articles
• Genetic Diversity of Dahongjun, the Commercially Important “Big Red Mushroom” from Southern China  Journal Articles
• Genetic Structure of Herpetofauna on Halmahera Island, Indonesia: Implications for Aketajawe‐Lolobata National Park  Journal Articles
• Genetic Tracking of the Raccoon Variant of Rabies Virus in Eastern North America  Journal Articles
• Genetic and biochemical properties of an alkaline phosphatase PhoX family protein found in many bacteria  Journal Articles
• Genetic differentiation, recombination and clonal expansion in environmental populations of Cryptococcus gattii in India  Journal Articles
• Genetic diversity of the endemic gourmet mushroom Thelephora ganbajun from south-western China  Journal Articles
• Genetic risk for dengue hemorrhagic fever and dengue fever in multiple ancestries  Journal Articles
• Genetics, Morphology, Advertisement Calls, and Historical Records Distinguish Six New Polyploid Species of African Clawed Frog (Xenopus, Pipidae) from West and Central Africa  Journal Articles
• Genome duplication events have led to a diversification in the CPT I gene family in fish  Journal Articles
• Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes  Journal Articles
• Genome skimming by shotgun sequencing helps resolve the phylogeny of a pantropical tree family  Journal Articles
• Genome structure and gene content in protist mitochondrial DNAs  Journal Articles
• Genome-Scale Phylogeny and the Detection of Systematic Biases  Journal Articles
• Genome-Wide Identification and Expression Analysis of Udp-Glucuronosyltransferases in the Whitefly Bemisia Tabaci (Gennadius) (HemipterA: Aleyrodidae)  Journal Articles
• 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.  Journal Articles
• 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.  Journal Articles
• Genomic Analyses Identify Novel Molecular Signatures Specific for the Caenorhabditis and other Nematode Taxa Providing Novel Means for Genetic and Biochemical Studies  Journal Articles
• Genomic Minimalism in the Early Diverging Intestinal Parasite Giardia lamblia  Journal Articles
• Genomic analyses reveal low mitochondrial and high nuclear diversity in the cyclosporin-producing fungus Tolypocladium inflatum  Journal Articles
• Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress  Journal Articles
• Genomic diversification of the specialized parasite of the fungus-growing ant symbiosis  Journal Articles
• Genomic insights into the evolution and ecology of botulinum neurotoxins  Journal Articles
• 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  Journal Articles
• Genomics as a means to understand bacterial phylogeny and ecological adaptation: the case of bifidobacteria  Journal Articles
• Genomics of Loa loa, a Wolbachia-free filarial parasite of humans  Journal Articles
• Genotypic diversity and antifungal susceptibility of environmental isolates of Cryptococcus neoformans from the Yangtze River Delta region of East China  Journal Articles
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• INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances  Journal Articles
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• Lateral Transfers of Serine Hydroxymethyltransferase (glyA) and UDP-N-Acetylglucosamine Enolpyruvyl Transferase (murA) Genes from Free-living Actinobacteria to the Parasitic Chlamydiae  Journal Articles
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• Microbial Geoengineers  Journal Articles
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• Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades  Journal Articles
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• Molecular signatures for members of the genus Dehalococcoides and the class Dehalococcoidia  Journal Articles
• 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.  Journal Articles
• 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  Journal Articles
• 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  Journal Articles
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• Sequence evolution within populations under multiple types of mutation.  Journal Articles
• Sequence signatures within the genome of SARS-CoV-2 can be used to predict host source  Journal Articles
• Sequence-directed mutagenesis: evidence from a phylogenetic history of human alpha-interferon genes.  Journal Articles
• Sequencing of heat shock protein 70 (DnaK) homologs from Deinococcus proteolyticus and Thermomicrobium roseum and their integration in a protein-based phylogeny of prokaryotes  Journal Articles
• Sex-Linked Inheritance in Macaque Monkeys: Implications for Effective Population Size and Dispersal to Sulawesi  Journal Articles
• Shotgun Mitogenomics Provides a Reference Phylogenetic Framework and Timescale for Living Xenarthrans  Journal Articles
• Signature proteins for the major clades of Cyanobacteria  Journal Articles
• Signature proteins that are distinctive characteristics of Actinobacteria and their subgroups  Journal Articles
• Signature proteins that are distinctive of alpha proteobacteria  Journal Articles
• Signature sequences in diverse proteins provide evidence for the late divergence of the Order Aquificales.  Journal Articles
• Significant differences in type IV pilin allele distribution among Pseudomonas aeruginosa isolates from cystic fibrosis (CF) versus non-CF patients  Conferences
• Single-locus species delimitation: a test of the mixed Yule–coalescent model, with an empirical application to Philippine round-leaf bats  Journal Articles
• Slr4, a newly identified S‐layer protein from marine Gammaproteobacteria, is a major biofilm matrix component  Journal Articles
• Small genome of the fungus Escovopsis weberi , a specialized disease agent of ant agriculture  Journal Articles
• Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality  Journal Articles
• Soil pH is equally important as salinity in shaping bacterial communities in saline soils under halophytic vegetation  Journal Articles
• Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation  Journal Articles
• Species and Genotypic Diversities and Similarities of Pathogenic Yeasts Colonizing Women  Journal Articles
• Specificity in the symbiotic association between fungus-growing ants and protective Pseudonocardia bacteria  Journal Articles
• Specificity of the mutualistic association between actinomycete bacteria and two sympatric species of Acromyrmex leaf‐cutting ants  Journal Articles
• Stability of Microbial Community Profiles Associated with Compacted Bentonite from the Grimsel Underground Research Laboratory  Journal Articles
• Statistical models and computational algorithms for discovering relationships in microbiome data  Journal Articles
• Statistical universals reveal the structures and functions of human music  Journal Articles
• Stem responses to damage: the evolutionary ecology of Quercus species in contrasting fire regimes  Journal Articles
• Stingless Bee Larvae Require Fungal Steroid to Pupate  Journal Articles
• Structural and Functional Plasticity of Antibiotic Resistance Nucleotidylyltransferases Revealed by Molecular Characterization of Lincosamide Nucleotidylyltransferases Lnu(A) and Lnu(D)  Journal Articles
• Structural and functional studies of an IRF-7-like gene from Atlantic salmon  Journal Articles
• Structural and phylogenetic analysis of a conserved actinobacteria-specific protein (ASP1; SCO1997) from Streptomyces coelicolor  Journal Articles
• Structural motif screening reveals a novel, conserved carbohydrate-binding surface in the pathogenesis-related protein PR-5d  Journal Articles
• Structure, Gene Flow, and Recombination among Geographic Populations of a Russula virescens Ally from Southwestern China  Journal Articles
• Substitution rate variation in closely related rodent species  Journal Articles
• Symbiont recognition of mutualistic bacteria by Acromyrmex leaf-cutting ants  Journal Articles
• Symbiotic Nitrogen Fixation in the Fungus Gardens of Leaf-Cutter Ants  Journal Articles
• Symbiotic complexity: discovery of a fifth symbiont in the attine ant–microbe symbiosis  Journal Articles
• Synchronous diversification of Sulawesi's iconic artiodactyls driven by recent geological events  Journal Articles
• Taxonomy of the order Mononegavirales: update 2016  Journal Articles
• Temporal Dynamics and Evolution of SARS-CoV-2 Demonstrate the Necessity of Ongoing Viral Genome Sequencing in Ontario, Canada  Journal Articles
• Temporal and spatial variations on accumulation of nomilin and limonin in the pummelos  Journal Articles
• Testing the Infinitely Many Genes Model for the Evolution of the Bacterial Core Genome and Pangenome  Journal Articles
• Tetrahymena glochidiophila n. sp., a new species of Tetrahymena (Ciliophora) that causes mortality to glochidia larvae of freshwater mussels (Bivalvia)  Journal Articles
• Thaxtomin A-deficient endophytic Streptomyces sp. enhances plant disease resistance to pathogenic Streptomyces scabies  Journal Articles
• The Closest BLAST Hit Is Often Not the Nearest Neighbor  Journal Articles
• The Complete Genome Sequence of Fibrobacter succinogenes S85 Reveals a Cellulolytic and Metabolic Specialist  Journal Articles
• The Conserved Tetratricopeptide Repeat-Containing C-Terminal Domain of Pseudomonas aeruginosa FimV Is Required for Its Cyclic AMP-Dependent and -Independent Functions  Journal Articles
• The Cytochrome P450 Superfamily Complement (CYPome) in the Annelid Capitella teleta  Journal Articles
• The DY genes of the cattle MHC: expression and comparative analysis of an unusual class II MHC gene pair  Journal Articles
• The Divided Bacterial Genome: Structure, Function, and Evolution  Journal Articles
• The Evolution of tRNA-Leu Genes in Animal Mitochondrial Genomes  Journal Articles
• The Evolutionary Origins of Eukaryotic Protein Disulfide Isomerase Domains: New Evidence from the Amitochondriate Protist Giardia lamblia  Journal Articles
• The Family Borreliaceae (Spirochaetales), a Diverse Group in Two Genera of Tick-Borne Spirochetes of Mammals, Birds, and Reptiles  Journal Articles
• The Genesis and Spread of Reassortment Human Influenza A/H3N2 Viruses Conferring Adamantane Resistance  Journal Articles
• The Genetic Secrets Some Fossils Hold  Journal Articles
• The Location of Substitutions and Bacterial Genome Arrangements  Journal Articles
• The Mechanisms of Codon Reassignments in Mitochondrial Genetic Codes  Journal Articles
• The Natural Evolutionary Relationships among Prokaryotes  Journal Articles
• The Pattern of Amino Acid Replacements in α/β-Barrels  Journal Articles
• The Phylogeny and Signature Sequences Characteristics ofFibrobacteres,Chlorobi, andBacteroidetes  Journal Articles
• The Pipid Root  Journal Articles
• The Population Structure of Antibiotic-Producing Bacterial Symbionts ofApterostigma dentigerumAnts: Impacts of Coevolution and Multipartite Symbiosis  Journal Articles
• The Recovery, Interpretation and Use of Ancient Pathogen Genomes  Journal Articles
• The Relationship Between the Rate of Molecular Evolution and the Rate of Genome Rearrangement in Animal Mitochondrial Genomes  Journal Articles
• The Rift Valley is a major barrier to dispersal of African clawed frogs (Xenopus) in Ethiopia  Journal Articles
• The Role of Palmitoylation for Protein Recruitment to the Inner Membrane Complex of the Malaria Parasite  Journal Articles
• The Selective Cause of an Ancient Adaptation  Journal Articles
• The Unique Lifestyle of Crohn's Disease-Associated Adherent-Invasive Escherichia coli  Journal Articles
• The advantages and disadvantages of horizontal gene transfer and the emergence of the first species  Journal Articles
• The branching order and phylogenetic placement of species from completed bacterial genomes, based on conserved indels found in various proteins  Journal Articles
• The coevolution of fungus-ant agriculture.  Journal Articles
• The cytochrome P450 (CYP) superfamily in cnidarians  Journal Articles
• The detection of deleterious selection using ancestors inferred from a phylogenetic history  Journal Articles
• The draft genome sequence of the nematode Caenorhabditis briggsae, a companion to C. elegans.  Journal Articles
• The dynamic balance of the skin microbiome across the lifespan  Journal Articles
• The effects of environmental and genetic factors on the germination of basidiospores in the Cryptococcus gattii species complex  Journal Articles
• The evolution of substrate discrimination in macrolide antibiotic resistance enzymes  Journal Articles
• The evolution of the class A scavenger receptors  Journal Articles
• The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis  Journal Articles
• The fate of laterally transferred genes: Life in the fast lane to adaptation or death  Journal Articles
• The genomic evolutionary dynamics and global circulation patterns of respiratory syncytial virus  Journal Articles
• The mosaic nature of the eukaryotic nucleus  Journal Articles
• The natural history and genetic diversity of Haemophilus influenzae infecting the airways of adults with cystic fibrosis  Journal Articles
• The newly characterized colicin Y provides evidence of positive selection in pore-former colicin diversification During the time this manuscript was being prepared for publication, our colleague James V. Neel passed away. The other authors wish to dedicate this work to his memory. The GenBank accession number for the sequence reported in this paper is AF197335.  Journal Articles
• The origin of the eukaryotic cell  Journal Articles
• The paradox of HBV evolution as revealed from a 16th century mummy  Journal Articles
• The phylogenetic affinities of the extinct glyptodonts  Journal Articles
• The phylogeny of proteobacteria: relationships to other eubacterial phyla and eukaryotes  Journal Articles
• The role of fire in terrestrial vertebrate richness patterns  Journal Articles
• The role of laterally transferred genes in adaptive evolution  Journal Articles
• The sequences of heat shock protein 40 (DnaJ) homologs provide evidence for a close evolutionary relationship between the Deinococcus- Thermus group and cyanobacteria  Journal Articles
• The structural basis of molecular adaptation  Journal Articles
• The use of E. coli phylogrouping and microbial source tracking (non-species specific, human-specific, bovine-specific bacteroidales markers) to elucidate hydro(geo)logical contamination mechanisms in southeastern Ontario, Canada.  Journal Articles
• 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.  Journal Articles
• Thousands of small, novel genes predicted in global phage genomes  Journal Articles
• Thrice better than once: quality control guidelines to validate new mitogenomes  Journal Articles
• Timings of major glaciations, inherent selection schemes and the origins of cold hardy animal phyla.  Journal Articles
• Tracking Host Sources of Cryptosporidium spp. in Raw Water for Improved Health Risk Assessment  Journal Articles
• Transmission of HIV and HCV within Former Soviet Union Countries  Journal Articles
• Trends in DNA barcoding and metabarcoding  Journal Articles
• Tunicate mitogenomics and phylogenetics: peculiarities of the Herdmania momus mitochondrial genome and support for the new chordate phylogeny  Journal Articles
• Tunicates and not cephalochordates are the closest living relatives of vertebrates  Journal Articles
• Two new unusualLeucoagaricusspecies (Agaricaceae) from tropical China with blue-green staining reactions  Journal Articles
• Ultrastructural and microbial analyses of cellulose degradation in leaf-cutter ant colonies  Journal Articles
• Uncovering rate variation of lateral gene transfer during bacterial genome evolution  Journal Articles
• Unmelanized Plumage Patterns in Old World Leaf Warblers Do Not Correspond to Sequence Variation at the Melanocortin-1 Receptor Locus (MC1R)  Journal Articles
• Unreliable mtDNA data due to nuclear insertions: a cautionary tale from analysis of humans and other great apes  Journal Articles
• Upregulating Nrf2-dependent antioxidant defenses in Pacific oysters Crassostrea gigas: Investigating the Nrf2/Keap1 pathway in bivalves  Journal Articles
• Using a Nonrecursive Formula to Determine Cladogram Probabilities  Journal Articles
• Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods  Journal Articles
• World‐wide genetic differentiation of Eubalaena: questioning the number of right whale species  Journal Articles
• Xenopus fraseri: Mr. Fraser, where did your frog come from?  Journal Articles
• Xenorhabdus bovienii Strain Diversity Impacts Coevolution and Symbiotic Maintenance with Steinernema spp. Nematode Hosts  Journal Articles
• Yersinia pestis and the Plague of Justinian 541–543 AD: a genomic analysis  Journal Articles
• Yersinia pestis and the three plague pandemics–Authors' reply  Journal Articles
• Yersinia pestis: New Evidence for an Old Infection  Journal Articles
• [Soil microbial diversity of artificial peashrub plantation on North Loess Plateau of China].  Journal Articles
• markophylo: Markov chain analysis on phylogenetic trees  Journal Articles