XML for evolutionary biology and comparative genomics.
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XML for evolutionary biology and comparative genomics.
metasource: Fairsharing.org
version: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
phyloXML
metasource: Fairsharing.org
version: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
More detailed information about this field from each metasource.
XML for evolutionary biology and comparative genomics.
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
phyloXML
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Names
More detailed information about this field from each metasource.
XML for evolutionary biology and comparative genomics.
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
phyloXML
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
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PhyloXML is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events.
Description
More detailed information about this field from each metasource.
PhyloXML is an XML language designed to describe phylogenetic trees (or networks) and associated data. PhyloXML provides elements for commonly used features, such as taxonomic information, gene names and identifiers, branch lengths, support values, and gene duplication and speciation events.
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Webpage:
http://www.phyloxml.org/Webpage
More detailed information about this field from each metasource.
http://www.phyloxml.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
phyloXML: XML for evolutionary biology and comparative genomics
PMID: 19860910
metasource: Fairsharing.org
version: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
Publications
More detailed information about this field from each metasource.
phyloXML: XML for evolutionary biology and comparative genomics
PMID: 19860910
metasource: Fairsharing.org
version: FAIRsharing.org: phyloXML; XML for evolutionary biology and comparative genomics.; DOI: https://doi.org/10.25504/FAIRsharing.3mprr8; Last edited: May 20, 2021, 1:25 p.m.; Last accessed: Jan 03 2022 7:10 p.m.
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phyloXML: XML for evolutionary biology and comparative genomics
PubMed citations: 256.
256 articles citing: phyloXML: XML for evolutionary biology and comparative genomics
Expanding the Database of Signal-Anchor-Release Domain Endolysins Through Metagenomics. PMID:35525881
Genomic characterisation of an entomopathogenic strain of Serratia ureilytica in the critically endangered phasmid Dryococelus australis. PMID:35442959
Long-Term Cellulose Enrichment Selects for Highly Cellulolytic Consortia and Competition for Public Goods. PMID:35258341
A peptide toxin in ant venom mimics vertebrate EGF-like hormones to cause long-lasting hypersensitivity in mammals. PMID:35131940
The importance of accessory protein variants in the pathogenicity of SARS-CoV-2. PMID:35085577
Maturation trajectories and transcriptional landscape of plasmablasts and autoreactive B cells in COVID-19. PMID:34723157
Immune Response in Mice Immunized with Chimeric H1 Antigens. PMID:34696290
Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection. PMID:34682285
TYGS and LPSN: a database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. PMID:34634793
Implications derived from S-protein variants of SARS-CoV-2 from six continents. PMID:34571123
Drought and Plant Community Composition Affect the Metabolic and Genotypic Diversity of Pseudomonas Strains in Grassland Soils. PMID:34442756
Scattered migrating colony formation in the filamentous cyanobacterium, Pseudanabaena sp. NIES-4403. PMID:34399691
Tracking Fungal Growth: Establishment of Arp1 as a Marker for Polarity Establishment and Active Hyphal Growth in Filamentous Ascomycetes. PMID:34356959
Morphometric relationships and their contribution to biomass and cannabinoid yield in hybrids of hemp (Cannabis sativa). PMID:34286838
Ecophysiology of the Cosmopolitan OM252 Bacterioplankton (Gammaproteobacteria). PMID:34184914
Analysis of genomes of bacterial isolates from lameness outbreaks in broilers. PMID:34077848
Lineage-level divergence of copepod glycerol transporters and the emergence of isoform-specific trafficking regulation. PMID:34059783
Weed-infecting viruses in a tropical agroecosystem present different threats to crops and evolutionary histories. PMID:33909644
Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. PMID:33885785
SARS-CoV-2 Genome from the Khyber Pakhtunkhwa Province of Pakistan. PMID:33748571
HLA class I-associated expansion of TRBV11-2 T cells in multisystem inflammatory syndrome in children. PMID:33705359
Genomic characterization and evolution of SARS-CoV-2 of a Canadian population. PMID:33662015
Resolving cryptic species complexes in marine protists: phylogenetic haplotype networks meet global DNA metabarcoding datasets. PMID:33589768
Genetic variation among 481 diverse soybean accessions, inferred from genomic re-sequencing. PMID:33558550
Phylogenetic analyses suggest centipede venom arsenals were repeatedly stocked by horizontal gene transfer. PMID:33547293
Diel transcriptional oscillations of light-sensitive regulatory elements in open-ocean eukaryotic plankton communities. PMID:33547239
The Glyoxysomal Protease LON2 Is Involved in Fruiting-Body Development, Ascosporogenesis and Stress Resistance in Sordaria macrospora. PMID:33530609
Empirical evidence for concerted evolution in the 18S rDNA region of the planktonic diatom genus Chaetoceros. PMID:33437054
Putative Epigenetic Biomarkers of Stress in Red Blood Cells of Chickens Reared Across Different Biomes. PMID:33240310
Identification of a unique TCR repertoire, consistent with a superantigen selection process in Children with Multi-system Inflammatory Syndrome. PMID:33200133
MpeV is a lyase isomerase that ligates a doubly linked phycourobilin on the β-subunit of phycoerythrin I and II in marine Synechococcus. PMID:33154169
Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria. PMID:33042072
Autoantibodies against type I IFNs in patients with life-threatening COVID-19. PMID:32972996
Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley. PMID:32698771
Next-Generation Sequencing of T and B Cell Receptor Repertoires from COVID-19 Patients Showed Signatures Associated with Severity of Disease. PMID:32668194
Unravelling the Complex Duplication History of Deuterostome Glycerol Transporters. PMID:32664262
Habitat diversity and type govern potential nitrogen loss by denitrification in coastal sediments and differences in ecosystem-level diversities of disparate N2O reducing communities. PMID:32662514
Single-Cell Genomics of Novel Actinobacteria With the Wood-Ljungdahl Pathway Discovered in a Serpentinizing System. PMID:32655506
Synthesis of glucooligosaccharides with prebiotic potential by glucansucrase URE 13-300 acceptor reactions with maltose, raffinose and lactose. PMID:32624884
Expanding the Diversity of Bacterioplankton Isolates and Modeling Isolation Efficacy with Large-Scale Dilution-to-Extinction Cultivation. PMID:32561583
A single-cell view on alga-virus interactions reveals sequential transcriptional programs and infection states. PMID:32490206
An evolutionary path to altered cofactor specificity in a metalloenzyme. PMID:32483131
Whole-Genome Comparisons of Staphylococcus agnetis Isolates from Cattle and Chickens. PMID:32245765
Genetic Differentiation of the Two Types of Polish Cold-blooded Horses Included in the National Conservation Program. PMID:32214005
Iroki: automatic customization and visualization of phylogenetic trees. PMID:32149022
The vertebrate Aqp14 water channel is a neuropeptide-regulated polytransporter. PMID:31840107
The mycolic acid reductase Rv2509 has distinct structural motifs and is essential for growth in slow-growing mycobacteria. PMID:31785114
Efa6 protects axons and regulates their growth and branching by inhibiting microtubule polymerisation at the cortex. PMID:31718774
Identification and Characterization of New RNA Tetraloop Sequence Families. PMID:31714066
Haplotype Networking of GWAS Hits for Citrulline Variation Associated with the Domestication of Watermelon. PMID:31671884
Whole genome sequencing of a novel, dichloromethane-fermenting Peptococcaceae from an enrichment culture. PMID:31592187
Global distribution and diversity of Chaetoceros (Bacillariophyta, Mediophyceae): integration of classical and novel strategies. PMID:31489261
Cuticular hydrocarbons as potential mediators of cryptic species divergence in a mutualistic ant association. PMID:31463013
Advances in Visualization Tools for Phylogenomic and Phylodynamic Studies of Viral Diseases. PMID:31428595
Parallel Evolution of Complex Centipede Venoms Revealed by Comparative Proteotranscriptomic Analyses. PMID:31396628
JPhyloIO: a Java library for event-based reading and writing of different phylogenetic file formats through a common interface. PMID:31331268
T-BAS Version 2.1: Tree-Based Alignment Selector Toolkit for Evolutionary Placement of DNA Sequences and Viewing Alignments and Specimen Metadata on Curated and Custom Trees. PMID:31320426
Interactive web-based visualization and sharing of phylogenetic trees using phylogeny.IO. PMID:31114886
Tracing the evolution of novel features of human Toll-like receptor 4. PMID:31075178
Interactive Tree Of Life (iTOL) v4: recent updates and new developments. PMID:30931475
mtProtEvol: the resource presenting molecular evolution analysis of proteins involved in the function of Vertebrate mitochondria. PMID:30813887
Different Ways of Doing the Same: Variations in the Two Last Steps of the Purine Biosynthetic Pathway in Prokaryotes. PMID:30785193
BioJava 5: A community driven open-source bioinformatics library. PMID:30735498
An expanded molecular phylogeny of Plumbaginaceae, with emphasis on Limonium (sea lavenders): Taxonomic implications and biogeographic considerations. PMID:30619554
Classification, substrate specificity and structural features of D-2-hydroxyacid dehydrogenases: 2HADH knowledgebase. PMID:30577795
Evolution of asexual and sexual reproduction in the aspergilli. PMID:30425416
NAT/NCS2-hound: a webserver for the detection and evolutionary classification of prokaryotic and eukaryotic nucleobase-cation symporters of the NAT/NCS2 family. PMID:30418564
An RND transporter in the monoterpene metabolism of Castellaniella defragrans. PMID:30334144
High-resolution genetic linkage map of European pear (Pyrus communis) and QTL fine-mapping of vegetative budbreak time. PMID:30165824
phylotree.js - a JavaScript library for application development and interactive data visualization in phylogenetics. PMID:30045713
The Biological Object Notation (BON): a structured file format for biological data. PMID:29941895
Gene family innovation, conservation and loss on the animal stem lineage. PMID:29848444
RecPhyloXML: a format for reconciled gene trees. PMID:29762653
Molecular phylogenetic species in Alternaria pathogens infecting pistachio and wild relatives. PMID:29755919
RitR is an archetype for a novel family of redox sensors in the streptococci that has evolved from two-component response regulators and is required for pneumococcal colonization. PMID:29750817
Human local adaptation of the TRPM8 cold receptor along a latitudinal cline. PMID:29723195
IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing. PMID:29722813
Cultivation and genomics of the first freshwater SAR11 (LD12) isolate. PMID:29599519
A Novel Glaesserella sp. Isolated from Pigs with Severe Respiratory Infections Has a Mosaic Genome with Virulence Factors Putatively Acquired by Horizontal Transfer. PMID:29572210
Differences in microbial community structure and nitrogen cycling in natural and drained tropical peatland soils. PMID:29549345
Spatio-temporal dynamics of soil bacterial communities as a function of Amazon forest phenology. PMID:29531240
Occurrence, evolution, and functions of DNA phosphorothioate epigenetics in bacteria. PMID:29531068
True Lies: Using Proteomics to Assess the Accuracy of Transcriptome-Based Venomics in Centipedes Uncovers False Positives and Reveals Startling Intraspecific Variation in Scolopendra Subspinipes. PMID:29495554
Genetic Architecture of Capitate Glandular Trichome Density in Florets of Domesticated Sunflower (Helianthus annuus L.). PMID:29375602
Screening and Genomic Characterization of Filamentous Hemagglutinin-Deficient Bordetella pertussis. PMID:29358336
Structural, Biochemical, and Evolutionary Characterizations of Glyoxylate/Hydroxypyruvate Reductases Show Their Division into Two Distinct Subfamilies. PMID:29309127
CRISPR-Cas Systems in Bacteroides fragilis, an Important Pathobiont in the Human Gut Microbiome. PMID:29218031
Comprehensive Genome-Wide Classification Reveals That Many Plant-Specific Transcription Factors Evolved in Streptophyte Algae. PMID:29216360
NumtS colonization in mammalian genomes. PMID:29180746
Immune Repertoire after Immunization As Seen by Next-Generation Sequencing and Proteomics. PMID:29085363
PLAZA 4.0: an integrative resource for functional, evolutionary and comparative plant genomics. PMID:29069403
Computational Population Biology: Linking the inner and outer worlds of organisms. PMID:29051719
MAFFT online service: multiple sequence alignment, interactive sequence choice and visualization. PMID:28968734
VCFtoTree: a user-friendly tool to construct locus-specific alignments and phylogenies from thousands of anthropologically relevant genome sequences. PMID:28950836
Venomics of Remipede Crustaceans Reveals Novel Peptide Diversity and Illuminates the Venom's Biological Role. PMID:28933727
Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis. PMID:28855266
A Brief View of the Surface Membrane Proteins from Trypanosoma cruzi. PMID:28656101
Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell. PMID:28642439
Essential role for GABARAP autophagy proteins in interferon-inducible GTPase-mediated host defense. PMID:28604719
Comprehensive classification of the PIN domain-like superfamily. PMID:28575517
Spatial Structure of the Mormon Cricket Gut Microbiome and its Predicted Contribution to Nutrition and Immune Function. PMID:28553263
β-Carboxysome bioinformatics: identification and evolution of new bacterial microcompartment protein gene classes and core locus constraints. PMID:28419380
IcyTree: rapid browser-based visualization for phylogenetic trees and networks. PMID:28407035
A Critical Review on the Use of Support Values in Tree Viewers and Bioinformatics Toolkits. PMID:28369572
Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region. PMID:28333343
Adaptation to Blue Light in Marine Synechococcus Requires MpeU, an Enzyme with Similarity to Phycoerythrobilin Lyase Isomerases. PMID:28270800
Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes. PMID:28182402
A Comprehensive Analysis of RALF Proteins in Green Plants Suggests There Are Two Distinct Functional Groups. PMID:28174582
The History of Bordetella pertussis Genome Evolution Includes Structural Rearrangement. PMID:28167525
Sepsis and Hemocyte Loss in Honey Bees (Apis mellifera) Infected with Serratia marcescens Strain Sicaria. PMID:28002470
Rapid Production of Virus Protein Microarray Using Protein Microarray Fabrication through Gene Synthesis (PAGES). PMID:27965274
Risk assessment of recent Egyptian H5N1 influenza viruses. PMID:27922116
Discovery and structural characterisation of new fold type IV-transaminases exemplify the diversity of this enzyme fold. PMID:27905516
TransportDB 2.0: a database for exploring membrane transporters in sequenced genomes from all domains of life. PMID:27899676
The Evolution of Silicon Transport in Eukaryotes. PMID:27729397
B Cell Receptor Activation Predominantly Regulates AKT-mTORC1/2 Substrates Functionally Related to RNA Processing. PMID:27487157
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly. PMID:27392085
Artificial Seawater Media Facilitate Cultivating Members of the Microbial Majority from the Gulf of Mexico. PMID:27303734
Delineating ecologically significant taxonomic units from global patterns of marine picocyanobacteria. PMID:27302952
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases. PMID:27226617
Orthology Analysis and In Vivo Complementation Studies to Elucidate the Role of DIR1 during Systemic Acquired Resistance in Arabidopsis thaliana and Cucumis sativus. PMID:27200039
Visual Omics Explorer (VOE): a cross-platform portal for interactive data visualization. PMID:27153572
Efficient Coalescent Simulation and Genealogical Analysis for Large Sample Sizes. PMID:27145223
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. PMID:27095192
Evolution of Pentameric Ligand-Gated Ion Channels: Pro-Loop Receptors. PMID:26986966
ncRNA orthologies in the vertebrate lineage. PMID:26980512
Activation of Myenteric Glia during Acute Inflammation In Vitro and In Vivo. PMID:26964064
A Glycosyltransferase from Nicotiana alata Pollen Mediates Synthesis of a Linear (1,5)-α-L-Arabinan When Expressed in Arabidopsis. PMID:26850276
UET: a database of evolutionarily-predicted functional determinants of protein sequences that cluster as functional sites in protein structures. PMID:26590254
RPA homologs and ssDNA processing during meiotic recombination. PMID:26520106
Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes. PMID:26493560
Bacteriophages of wastewater foaming-associated filamentous Gordonia reduce host levels in raw activated sludge. PMID:26349678
ReproPhylo: An Environment for Reproducible Phylogenomics. PMID:26335558
Oligoribonuclease is a central feature of cyclic diguanylate signaling in Pseudomonas aeruginosa. PMID:26305928
Phylogenetic and 2D/3D Analysis of HCV 1a NS4A Gene/Protein in Pakistani Isolates. PMID:26288631
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution. PMID:26286928
Phylogenomic and functional analyses of salmon lice aquaporins uncover the molecular diversity of the superfamily in Arthropoda. PMID:26282991
Inactivation of ca10a and ca10b Genes Leads to Abnormal Embryonic Development and Alters Movement Pattern in Zebrafish. PMID:26218428
Novel molecular markers for the detection of methanogens and phylogenetic analyses of methanogenic communities. PMID:26217325
Potential regulatory phosphorylation sites in a Medicago truncatula plasma membrane proton pump implicated during early symbiotic signaling in roots. PMID:26188545
Insect glycerol transporters evolved by functional co-option and gene replacement. PMID:26183829
Compact graphical representation of phylogenetic data and metadata with GraPhlAn. PMID:26157614
The Mitochondrial Genomes of a Myxozoan Genus Kudoa Are Extremely Divergent in Metazoa. PMID:26148004
BGD: a database of bat genomes. PMID:26110276
Diversity and Evolutionary History of Iron Metabolism Genes in Diatoms. PMID:26052941
Naturally Occurring Resistance-Associated Variants of Hepatitis C Virus Protease Inhibitors in Poor Responders to Pegylated Interferon-Ribavirin. PMID:25926499
The aspartate-less receiver (ALR) domains: distribution, structure and function. PMID:25875291
Siglec receptors impact mammalian lifespan by modulating oxidative stress. PMID:25846707
MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree. PMID:25826378
Explosive tandem and segmental duplications of multigenic families in Eucalyptus grandis. PMID:25769696
Genome evolution in the primary endosymbiont of whiteflies sheds light on their divergence. PMID:25716826
CompPhy: a web-based collaborative platform for comparing phylogenies. PMID:25496383
Transcriptional and post-transcriptional regulation of the jasmonate signalling pathway in response to abiotic and harvesting stress in Hevea brasiliensis. PMID:25443311
The lineage-specific evolution of aquaporin gene clusters facilitated tetrapod terrestrial adaptation. PMID:25426855
An AGEF-1/Arf GTPase/AP-1 ensemble antagonizes LET-23 EGFR basolateral localization and signaling during C. elegans vulva induction. PMID:25329472
Aerobic methanotrophic communities at the Red Sea brine-seawater interface. PMID:25295031
Novel residues in avian influenza virus PB2 protein affect virulence in mammalian hosts. PMID:25289523
The mitochondrial genomes of the glaucophytes Gloeochaete wittrockiana and Cyanoptyche gloeocystis: multilocus phylogenetics suggests a monophyletic archaeplastida. PMID:25281844
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. PMID:25280501
Microbiology, genomics, and clinical significance of the Pseudomonas fluorescens species complex, an unappreciated colonizer of humans. PMID:25278578
The Ensembl REST API: Ensembl Data for Any Language. PMID:25236461
The Antibody Germline/Maturation Hypothesis, Elicitation of Broadly Neutralizing Antibodies Against HIV-1 and Cord Blood IgM Repertoires. PMID:25221552
Identification of diversity-generating retroelements in human microbiomes. PMID:25196521
Phylogenomic analysis of glycogen branching and debranching enzymatic duo. PMID:25148856
Phylogenetic analysis and evolutionary origins of DNA polymerase X-family members. PMID:25112931
Cloning and functional expression in E. coli of a polyphenol oxidase transcript from Coreopsis grandiflora involved in aurone formation. PMID:25109778
Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). PMID:25007843
Osiris: accessible and reproducible phylogenetic and phylogenomic analyses within the Galaxy workflow management system. PMID:24990571
Best practices for data sharing in phylogenetic research. PMID:24987572
The Supertree Toolkit 2: a new and improved software package with a Graphical User Interface for supertree construction. PMID:24891820
Ribosomal oxygenases are structurally conserved from prokaryotes to humans. PMID:24814345
Origin and evolution of the sodium -pumping NADH: ubiquinone oxidoreductase. PMID:24809444
Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase. PMID:24742328
Molecular characterization of human T-cell lymphotropic virus type 1 full and partial genomes by Illumina massively parallel sequencing technology. PMID:24686382
Exercise prevents weight gain and alters the gut microbiota in a mouse model of high fat diet-induced obesity. PMID:24670791
HIV-1 transmission patterns in antiretroviral therapy-naïve, HIV-infected North Americans based on phylogenetic analysis by population level and ultra-deep DNA sequencing. PMID:24586911
Network analysis reveals ecological links between N-fixing bacteria and wood-decaying fungi. PMID:24505405
Crystal structure of an (R)-selective ω-transaminase from Aspergillus terreus. PMID:24498081
Characterization and differential expression of CPD and 6-4 DNA photolyases in Xiphophorus species and interspecies hybrids. PMID:24496042
New insights into the phylogeny and molecular classification of nicotinamide mononucleotide deamidases. PMID:24340054
TRAPID: an efficient online tool for the functional and comparative analysis of de novo RNA-Seq transcriptomes. PMID:24330842
Exploring the uncultured microeukaryote majority in the oceans: reevaluation of ribogroups within stramenopiles. PMID:24196325
The Candida Genome Database: the new homology information page highlights protein similarity and phylogeny. PMID:24185697
Simian foamy virus infection of rhesus macaques in Bangladesh: relationship of latent proviruses and transcriptionally active viruses. PMID:24109214
Distribution of mosquitoes in the south east of Argentina and first report on the analysis based on 18S rDNA and COI sequences. PMID:24098700
DIRS and Ngaro Retrotransposons in Fungi. PMID:24086727
PPR proteins of green algae. PMID:24021981
Bacteria mediate oviposition by the black soldier fly, Hermetia illucens (L.), (Diptera: Stratiomyidae). PMID:23995019
Insights into the evolution of cotton diploids and polyploids from whole-genome re-sequencing. PMID:23979935
Badger--an accessible genome exploration environment. PMID:23940251
Transcriptional response of bathypelagic marine bacterioplankton to the Deepwater Horizon oil spill. PMID:23902988
Utilization of heme as an iron source by marine Alphaproteobacteria in the Roseobacter clade. PMID:23872569
Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA. PMID:23756462
CoPAP: Coevolution of presence-absence patterns. PMID:23748951
Topographic diversity of fungal and bacterial communities in human skin. PMID:23698366
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. PMID:23677614
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient. PMID:23668630
Assembly-driven community genomics of a hypersaline microbial ecosystem. PMID:23637883
The evolutionary rewiring of the ribosomal protein transcription pathway modifies the interaction of transcription factor heteromer Ifh1-Fhl1 (interacts with forkhead 1-forkhead-like 1) with the DNA-binding specificity element. PMID:23625919
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. PMID:23575371
EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats. PMID:23479348
Variations in the rhythms of respiration and nitrogen fixation in members of the unicellular diazotrophic cyanobacterial genus Cyanothece. PMID:23274238
Multiple inter-kingdom horizontal gene transfers in the evolution of the phosphoenolpyruvate carboxylase gene family. PMID:23251445
Evolution of general transcription factors. PMID:23229069
Virus pathogen database and analysis resource (ViPR): a comprehensive bioinformatics database and analysis resource for the coronavirus research community. PMID:23202522
PeroxiBase: a database for large-scale evolutionary analysis of peroxidases. PMID:23180785
This Déjà vu feeling--analysis of multidomain protein evolution in eukaryotic genomes. PMID:23166479
PICKLE is a CHD subfamily II ATP-dependent chromatin remodeling factor. PMID:23128324
Sharing and re-use of phylogenetic trees (and associated data) to facilitate synthesis. PMID:23088596
The hexameric structure of a conjugative VirB4 protein ATPase provides new insights for a functional and phylogenetic relationship with DNA translocases. PMID:23035111
Characterization of a viral synergism in the monocot Brachypodium distachyon reveals distinctly altered host molecular processes associated with disease. PMID:22961132
Dynamics of bacterial communities in two unpolluted soils after spiking with phenanthrene: soil type specific and common responders. PMID:22934091
HSPIR: a manually annotated heat shock protein information resource. PMID:22923302
Bio.Phylo: a unified toolkit for processing, analyzing and visualizing phylogenetic trees in Biopython. PMID:22909249
Origin, diversity, and maturation of human antiviral antibodies analyzed by high-throughput sequencing. PMID:22876240
The cervical microbiome over 7 years and a comparison of methodologies for its characterization. PMID:22792313
The mitochondrial genomes of Euphausia pacifica and Thysanoessa raschii sequenced using 454 next-generation sequencing, with a phylogenetic analysis of their position in the Malacostracan family tree. PMID:22733485
Novel bacterial taxa in the human microbiome. PMID:22719826
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. PMID:22695796
Diversity patterns and activity of uncultured marine heterotrophic flagellates unveiled with pyrosequencing. PMID:22534609
Very small embryonic-like stem cells purified from umbilical cord blood lack stem cell characteristics. PMID:22509366
Identification and characterization of a bacterial hydrosulphide ion channel. PMID:22407320
CRDB: database of chemosensory receptor gene families in vertebrate. PMID:22393364
NeXML: rich, extensible, and verifiable representation of comparative data and metadata. PMID:22357728
Comparative metatranscriptomics identifies molecular bases for the physiological responses of phytoplankton to varying iron availability. PMID:22308424
Barcoding and border biosecurity: identifying cyprinid fishes in the aquarium trade. PMID:22276096
IMG: the Integrated Microbial Genomes database and comparative analysis system. PMID:22194640
LegumeIP: an integrative database for comparative genomics and transcriptomics of model legumes. PMID:22110036
Niche adaptation by expansion and reprogramming of general transcription factors. PMID:22108796
DBETH: a Database of Bacterial Exotoxins for Human. PMID:22102573
Cellulosomics, a gene-centric approach to investigating the intraspecific diversity and adaptation of Ruminococcus flavefaciens within the rumen. PMID:22043282
Characterization of partial and near full-length genomes of HIV-1 strains sampled from recently infected individuals in São Paulo, Brazil. PMID:22022460
ViPR: an open bioinformatics database and analysis resource for virology research. PMID:22006842
Novel metabolic attributes of the genus cyanothece, comprising a group of unicellular nitrogen-fixing Cyanothece. PMID:21972240
Mycobacterium tuberculosis Rv0899 defines a family of membrane proteins widespread in nitrogen-fixing bacteria. PMID:21905117
TreeRipper web application: towards a fully automated optical tree recognition software. PMID:21599881
Rebooting the human mitochondrial phylogeny: an automated and scalable methodology with expert knowledge. PMID:21595926
Wolbachia prophage DNA adenine methyltransferase genes in different Drosophila-Wolbachia associations. PMID:21573076
PhyleasProg: a user-oriented web server for wide evolutionary analyses. PMID:21531699
CDAO-store: ontology-driven data integration for phylogenetic analysis. PMID:21496247
Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy. PMID:21470960
Performance, accuracy, and Web server for evolutionary placement of short sequence reads under maximum likelihood. PMID:21436105
iPhy: an integrated phylogenetic workbench for supermatrix analyses. PMID:21261969
Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. PMID:21248859
Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires. PMID:21241503
pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. PMID:21034504
Comparative genomics of Gardnerella vaginalis strains reveals substantial differences in metabolic and virulence potential. PMID:20865041
GreenPhylDB v2.0: comparative and functional genomics in plants. PMID:20864446
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PMID:20838655
BioXSD: the common data-exchange format for everyday bioinformatics web services. PMID:20823319
jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PMID:20805892
BioRuby: bioinformatics software for the Ruby programming language. PMID:20739307
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. PMID:20727200
HyperCAT: an extension of the SuperCAT database for global multi-scheme and multi-datatype phylogenetic analysis of the Bacillus cereus group population. PMID:20651034
TreeGraph 2: combining and visualizing evidence from different phylogenetic analyses. PMID:20051126
Initial implementation of a comparative data analysis ontology. PMID:19812726
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