Metavirome of 31 tick species provides a compendium of 1,801 RNA virus genomes

Tick Immune System: What Is Known, the Interconnections, the Gaps, and the Challenges

(2021) Andréa C. Fogaça et al.   Frontiers in Immunology

Sensitive protein alignments at tree-of-life scale using DIAMOND

(2021) Benjamin Buchfink et al.   NATURE METHODS

A novel nairovirus associated with acute febrile illness in Hokkaido, Japan

(2021) Fumihiro Kodama et al.   Nature Communications

Tick virome diversity in Hubei Province, China, and the influence of host ecology

(2021) Lin Xu et al.   Virus Evolution

Sustained RNA virome diversity in Antarctic penguins and their ticks

(2020) Michelle Wille et al.   ISME Journal

Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts

(2020) Nardus Mollentze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circumpolar diversification of the Ixodes uriae tick virome

(2020) John H.-O. Pettersson et al.   PLoS Pathogens

Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome

(2020) Yuri I. Wolf et al.   Nature Microbiology

Nairobi Sheep Disease Virus: A Historical and Epidemiological Perspective

(2020) Stephanie Krasteva et al.   Frontiers in Veterinary Science

Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities

(2020) Na Jia et al.   CELL

Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries

(2019) Maria Asplund et al.   CLINICAL MICROBIOLOGY AND INFECTION

The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health

(2019) Kurt J. Vandegrift et al.   Viruses-Basel

Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago

(2019) Stephen Sameroff et al.   Scientific Reports

TreeCluster: Clustering biological sequences using phylogenetic trees

(2019) Metin Balaban et al.   PLoS One

Identification of Novel Viruses in Amblyomma americanum , Dermacentor variabilis , and Ixodes scapularis Ticks

(2018) Rafal Tokarz et al.   mSphere

Tick-Borne Viruses

(2018) Junming Shi et al.   VIROLOGICA SINICA

Tickborne Diseases — Confronting a Growing Threat

(2018) Catharine I. Paules et al.   NEW ENGLAND JOURNAL OF MEDICINE

Phylogeography of Ticks (Acari: Ixodida)

(2018) Lorenza Beati et al.   Annual Review of Entomology

Extensive Diversity of RNA Viruses in Australian Ticks

(2018) Erin Harvey et al.   JOURNAL OF VIROLOGY

Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes

(2018) Simon A. Babayan et al.   SCIENCE

Origins and Evolution of the Global RNA Virome

(2018) Yuri I. Wolf et al.   mBio

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Characterizing the virome of Ixodes ricinus ticks from northern Europe

(2017) John H.-O. Pettersson et al.   Scientific Reports

Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens

(2016) Shin-Yi Lee Marzano et al.   JOURNAL OF VIROLOGY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses

(2015) Mang Shi et al.   JOURNAL OF VIROLOGY

Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses

(2015) Ci-Xiu Li et al.   eLife

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Vertical transmission of arboviruses in mosquitoes: A historical perspective

(2014) Sebastian Lequime et al.   INFECTION GENETICS AND EVOLUTION

Consequences of in vitro host shift for St. Louis encephalitis virus

(2014) A. T. Ciota et al.   JOURNAL OF GENERAL VIROLOGY

Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses

(2014) R. Tokarz et al.   JOURNAL OF VIROLOGY

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

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

A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors

(2014) X.-C. Qin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Effects of Host Diversity on Infectious Disease

(2011) Richard S. Ostfeld et al.   Annual Review of Ecology Evolution and Systematics

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Impacts of biodiversity on the emergence and transmission of infectious diseases

(2010) Felicia Keesing et al.   NATURE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Arbovirus evolution in vivo is constrained by host alternation

(2008) L. L. Coffey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Correlating viral phenotypes with phylogeny: Accounting for phylogenetic uncertainty

(2007) Joe Parker et al.   INFECTION GENETICS AND EVOLUTION