Characterization of a Novel Mitovirus of the Sand Fly Lutzomyia longipalpis Using Genomic and Virus–Host Interaction Signatures

A single unidirectional piRNA cluster similar to the flamenco locus is the major source of EVE-derived transcription and small RNAs in Aedes aegypti mosquitoes

(2020) Eric R G R Aguiar et al.   RNA

Dissimilation of synonymous codon usage bias in virus–host coevolution due to translational selection

(2020) Feng Chen et al.   Nature Ecology & Evolution

Broader Geographical Distribution of Toscana Virus in the Mediterranean Region Suggests the Existence of Larger Varieties of Sand Fly Vectors

(2020) Nazli Ayhan et al.   Microorganisms

A novel narnavirus from the plant-pathogenic fungus Magnaporthe oryzae

(2020) Yuan Lin et al.   ARCHIVES OF VIROLOGY

Narnaviruses: novel players in fungal–bacterial symbioses

(2020) Astrid N. Espino-Vázquez et al.   ISME Journal

Comparative Analysis of RNA Virome Composition in Rabbits and Associated Ectoparasites

(2020) Jackie E. Mahar et al.   JOURNAL OF VIROLOGY

Domain-centric database to uncover structure of minimally characterized viral genomes

(2020) John C. Bramley et al.   Scientific Data

Increased resolution of African Swine Fever Virus genome patterns based on profile HMMs of protein domains

(2020) Charles Masembe et al.   Virus Evolution

Analysis of the virome associated to grapevine downy mildew lesions reveals new mycovirus lineages

(2020) M Chiapello et al.   Virus Evolution

Analysis of the codon usage pattern of the RdRP gene of mycovirus infecting Aspergillus spp.

(2019) Mikyung Je et al.   Virology Journal

Mosquito Small RNA Responses to West Nile and Insect-Specific Virus Infections in Aedes and Culex Mosquito Cells

(2019) Giel Göertz et al.   Viruses-Basel

Three ourmia-like viruses and their associated RNAs in Pyricularia oryzae

(2019) Shuhei Ohkita et al.   VIROLOGY

Codon Usage Bias Analysis of Citrus tristeza Virus: Higher Codon Adaptation to Citrus reticulata Host

(2019) Kajal Biswas et al.   Viruses-Basel

Mitovirus and Mitochondrial Coding Sequences from Basal Fungus Entomophthora muscae

(2019) Max Nibert et al.   Viruses-Basel

Antiviral RNAi in Insects and Mammals: Parallels and Differences

(2019) Susan Schuster et al.   Viruses-Basel

Vertical transmission in Caenorhabditis nematodes of RNA molecules encoding a viral RNA-dependent RNA polymerase

(2019) Aurélien Richaud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An exploration of ambigrammatic sequences in narnaviruses

(2019) Joseph L. DeRisi et al.   Scientific Reports

The Discovery of Arthropod-Specific Viruses in Hematophagous Arthropods: An Open Door to Understanding the Mechanisms of Arbovirus and Arthropod Evolution?

(2018) Charles H. Calisher et al.   Annual Review of Entomology

Using Metagenomics to Characterize an Expanding Virosphere

(2018) Yong-Zhen Zhang et al.   CELL

Complexities of Viral Mutation Rates

(2018) Kayla M. Peck et al.   JOURNAL OF VIROLOGY

Evidence for contemporary plant mitoviruses

(2018) Max L. Nibert et al.   VIROLOGY

Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer

(2018) Valerian V. Dolja et al.   VIRUS RESEARCH

The small non-coding RNA response to virus infection in the Leishmania vector Lutzomyia longipalpis

(2018) Flávia Viana Ferreira et al.   PLoS Neglected Tropical Diseases

Discovery and characterization of novel Aspergillus fumigatus mycoviruses

(2018) Jan Zoll et al.   PLoS One

Mitochondrial genome of the entomophthoroid fungus Conidiobolus heterosporus provides insights into evolution of basal fungi

(2018) Yong Nie et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Novel Mitoviruses and a Unique Tymo-Like Virus in Hypovirulent and Virulent Strains of the Fusarium Head Blight Fungus, Fusarium boothii

(2018) Yukiyoshi Mizutani et al.   Viruses-Basel

High-Resolution Metatranscriptomics Reveals the Ecological Dynamics of Mosquito-Associated RNA Viruses in Western Australia

(2017) Mang Shi et al.   JOURNAL OF VIROLOGY

Dinucleotide Composition in Animal RNA Viruses Is Shaped More by Virus Family than by Host Species

(2017) Francesca Di Giallonardo et al.   JOURNAL OF VIROLOGY

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Mitovirus UGA(Trp) codon usage parallels that of host mitochondria

(2017) Max L. Nibert   VIROLOGY

Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics

(2017) Simon Roux et al.   Nature Communications

Of phlebotomines (sandflies) and viruses: a comprehensive perspective on a complex situation

(2017) Nazli Ayhan et al.   Current Opinion in Insect Science

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Selective Factors Associated with the Evolution of Codon Usage in Natural Populations of Arboviruses

(2016) Lauro Velazquez-Salinas et al.   PLoS One

Virus-derived small RNAs: molecular footprints of host-pathogen interactions

(2016) Eric Roberto Guimarães Rocha Aguiar et al.   Wiley Interdisciplinary Reviews-RNA

GenSeed-HMM: A Tool for Progressive Assembly Using Profile HMMs as Seeds and its Application in Alpavirinae Viral Discovery from Metagenomic Data

(2016) João M. P. Alves et al.   Frontiers in Microbiology

A 454 sequencing approach to dipteran mitochondrial genome research

(2015) Meganathan P. Ramakodi et al.   GENOMICS

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host

(2015) Eric Roberto Guimarães Rocha Aguiar et al.   NUCLEIC ACIDS RESEARCH

Endogenous viruses: Connecting recent and ancient viral evolution

(2015) Pakorn Aiewsakun et al.   VIROLOGY

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

(2015) Claire L. Webster et al.   PLOS BIOLOGY

RNA shotgun metagenomic sequencing of northern California (USA) mosquitoes uncovers viruses, bacteria, and fungi

(2015) James Angus Chandler et al.   Frontiers in Microbiology

Widespread mitovirus sequences in plant genomes

(2015) Jeremy A. Bruenn et al.   PeerJ

Impact of transposable elements on insect genomes and biology

(2015) Florian Maumus et al.   Current Opinion in Insect Science

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements

(2014) Eugene V. Koonin et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Diagnostic metagenomics: potential applications to bacterial, viral and parasitic infections

(2014) M. J. PALLEN   PARASITOLOGY

ClassyFlu: Classification of Influenza A Viruses with Discriminatively Trained Profile-HMMs

(2014) Sandra Van der Auwera et al.   PLoS One

Profile Hidden Markov Models for the Detection of Viruses within Metagenomic Sequence Data

(2014) Peter Skewes-Cox et al.   PLoS One

Standards for Sequencing Viral Genomes in the Era of High-Throughput Sequencing

(2014) J. T. Ladner et al.   mBio

Sandfly-borne phleboviruses of Eurasia and Africa: Epidemiology, genetic diversity, geographic range, control measures

(2013) Cigdem Alkan et al.   ANTIVIRAL RESEARCH

Viral pathogen discovery

(2013) Charles Y Chiu   CURRENT OPINION IN MICROBIOLOGY

Diversity and function of bacterial microbiota in the mosquito holobiont

(2013) Guillaume Minard et al.   Parasites & Vectors

Causes and Implications of Codon Usage Bias in RNA Viruses

(2013) Ilya S. Belalov et al.   PLoS One

Novel Virus Discovery and Genome Reconstruction from Field RNA Samples Reveals Highly Divergent Viruses in Dipteran Hosts

(2013) Shelley Cook et al.   PLoS One

Functional Specialization of the Small Interfering RNA Pathway in Response to Virus Infection

(2013) Joao Trindade Marques et al.   PLoS Pathogens

Phylogeny, integration and expression of sigma virus-like genes in Drosophila

(2012) Matthew J. Ballinger et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Computational tools for viral metagenomics and their application in clinical research

(2012) L. Fancello et al.   VIROLOGY

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

Malaria and other vector-borne infection surveillance in the U.S. Department of Defense Armed Forces Health Surveillance Center-Global Emerging Infections Surveillance program: review of 2009 accomplishments

(2011) Mark M Fukuda et al.   BMC PUBLIC HEALTH

Microsatellite is an important component of complete Hepatitis C virus genomes

(2011) Ming Chen et al.   INFECTION GENETICS AND EVOLUTION

Broad Surveys of DNA Viral Diversity Obtained through Viral Metagenomics of Mosquitoes

(2011) Terry Fei Fan Ng et al.   PLoS One

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Comprehensive Analysis of Simple Sequence Repeats in Pre-miRNAs

(2010) Ming Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Virus-Host Coevolution: Common Patterns of Nucleotide Motif Usage in Flaviviridae and Their Hosts

(2009) Francisco P. Lobo et al.   PLoS One

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

The role of alternative genetic codes in viral evolution and emergence

(2008) Laura A. Shackelton et al.   JOURNAL OF THEORETICAL BIOLOGY

Mycoviruses of filamentous fungi and their relevance to plant pathology

(2008) MICHAEL N. PEARSON et al.   MOLECULAR PLANT PATHOLOGY

The evolution of RNAi as a defence against viruses and transposable elements

(2008) D. J Obbard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES