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

[1]  Zhìhóng Hú,et al.  Evidence of Human Exposure to Tamdy Virus, Northwest China , 2021, Emerging infectious diseases.

[2]  M. Saijo,et al.  A novel nairovirus associated with acute febrile illness in Hokkaido, Japan , 2021, Nature Communications.

[3]  H. Drost,et al.  Sensitive protein alignments at tree-of-life scale using DIAMOND , 2021, Nature Methods.

[4]  E. Esteves,et al.  Tick Immune System: What Is Known, the Interconnections, the Gaps, and the Challenges , 2021, Frontiers in Immunology.

[5]  M. Masika,et al.  Viromes and surveys of RNA viruses in camel-derived ticks revealing transmission patterns of novel tick-borne viral pathogens in Kenya , 2021, Emerging microbes & infections.

[6]  Jia-Fu Jiang,et al.  Large-Scale Comparative Analyses of Tick Genomes Elucidate Their Genetic Diversity and Vector Capacities , 2020, Cell.

[7]  Jia-Fu Jiang,et al.  Distribution of Haemaphysalis longicornis and associated pathogens: analysis of pooled data from a China field survey and global published data. , 2020, The Lancet. Planetary health.

[8]  E. Koonin,et al.  Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome , 2020, Nature Microbiology.

[9]  E. Holmes,et al.  Circumpolar diversification of the Ixodes uriae tick virome , 2020, bioRxiv.

[10]  M. Shi,et al.  Sustained RNA virome diversity in Antarctic penguins and their ticks , 2020, The ISME Journal.

[11]  G. Machado,et al.  Nairobi Sheep Disease Virus: A Historical and Epidemiological Perspective , 2020, bioRxiv.

[12]  D. Streicker,et al.  Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts , 2020, Proceedings of the National Academy of Sciences.

[13]  O. Lund,et al.  Contaminating viral sequences in high-throughput sequencing viromics: a linkage study of 700 sequencing libraries. , 2019, Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases.

[14]  C. Carrington,et al.  Viral Diversity of Tick Species Parasitizing Cattle and Dogs in Trinidad and Tobago , 2019, Scientific Reports.

[15]  K. Vandegrift,et al.  The Ecology of New Constituents of the Tick Virome and Their Relevance to Public Health , 2019, Viruses.

[16]  Niema Moshiri,et al.  TreeCluster: Clustering biological sequences using phylogenetic trees , 2019, bioRxiv.

[17]  H. Klompen,et al.  Phylogeography of Ticks (Acari: Ixodida). , 2019, Annual review of entomology.

[18]  Richard J. Orton,et al.  Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes , 2018, Science.

[19]  E. Koonin,et al.  Origins and Evolution of the Global RNA Virome , 2018, mBio.

[20]  M. Shi,et al.  Extensive Diversity of RNA Viruses in Australian Ticks , 2018, Journal of Virology.

[21]  A. Fauci,et al.  Tickborne Diseases - Confronting a Growing Threat. , 2018, The New England journal of medicine.

[22]  W. Lipkin,et al.  Identification of Novel Viruses in Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks , 2018, mSphere.

[23]  Zhìhóng Hú,et al.  Tick-Borne Viruses , 2018, Virologica Sinica.

[24]  Å. Andreassen,et al.  Characterizing the virome of Ixodes ricinus ticks from northern Europe , 2017, Scientific Reports.

[25]  Thomas K. F. Wong,et al.  ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates , 2017, Nature Methods.

[26]  Guangchuang Yu,et al.  ggtree: an r package for visualization and annotation of phylogenetic trees with their covariates and other associated data , 2017 .

[27]  Edward C. Holmes,et al.  Redefining the invertebrate RNA virosphere , 2016, Nature.

[28]  G. Hartman,et al.  Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens , 2016, Journal of Virology.

[29]  P. Bork,et al.  ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data , 2016, Molecular biology and evolution.

[30]  Nikos Vasilakis,et al.  Divergent Viruses Discovered in Arthropods and Vertebrates Revise the Evolutionary History of the Flaviviridae and Related Viruses , 2015, Journal of Virology.

[31]  M. Shi,et al.  Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses , 2015, eLife.

[32]  L. Lambrechts,et al.  Vertical transmission of arboviruses in mosquitoes: a historical perspective. , 2014, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[33]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[34]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[35]  M. Sanchez Leon,et al.  Virome Analysis of Amblyomma americanum, Dermacentor variabilis, and Ixodes scapularis Ticks Reveals Novel Highly Divergent Vertebrate and Invertebrate Viruses , 2014, Journal of Virology.

[36]  L. Kramer,et al.  Consequences of in vitro host shift for St. Louis encephalitis virus. , 2014, The Journal of general virology.

[37]  M. Shi,et al.  A tick-borne segmented RNA virus contains genome segments derived from unsegmented viral ancestors , 2014, Proceedings of the National Academy of Sciences.

[38]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[39]  Colin N. Dewey,et al.  De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis , 2013, Nature Protocols.

[40]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[41]  R. Ostfeld,et al.  Effects of Host Diversity on Infectious Disease , 2012 .

[42]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[43]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[44]  Kate E. Jones,et al.  Impacts of biodiversity on the emergence and transmission of infectious diseases , 2010, Nature.

[45]  Thomas L. Madden,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[46]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[47]  Toni Gabaldón,et al.  trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..

[48]  A. Brault,et al.  Arbovirus evolution in vivo is constrained by host alternation , 2008, Proceedings of the National Academy of Sciences.

[49]  O. Pybus,et al.  Correlating viral phenotypes with phylogeny: accounting for phylogenetic uncertainty. , 2008, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[50]  S. Higgs,et al.  A Single Mutation in Chikungunya Virus Affects Vector Specificity and Epidemic Potential , 2007, PLoS pathogens.

[51]  E. Domingo,et al.  Effect of Alternating Passage on Adaptation of Sindbis Virus to Vertebrate and Invertebrate Cells , 2005, Journal of Virology.

[52]  F. Jongejan,et al.  The global importance of ticks , 2004, Parasitology.

[53]  John P. Huelsenbeck,et al.  MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..

[54]  E. Holmes,et al.  Reduced positive selection in vector-borne RNA viruses. , 2002, Molecular biology and evolution.

[55]  H. Klompen The Genus Rhipicephalus (Acari, Ixodidae). A Guide to the Brown Ticks of the World, , 2000 .

[56]  K. Markvart,et al.  Antibodies against some arboviruses in persons with various neuropathies. , 1980, Acta virologica.

[57]  OUP accepted manuscript , 2021, Virus Evolution.

[58]  N. Friedman,et al.  Trinity : reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2016 .

[59]  Geoffrey E. Hinton,et al.  Visualizing Data using t-SNE , 2008 .

[60]  T G Burland,et al.  DNASTAR's Lasergene sequence analysis software. , 2000, Methods in molecular biology.

[61]  C. Chastel [Erve and Eyach: two viruses isolated in France, neuropathogenic for man and widely distributed in Western Europe]. , 1998, Bulletin de l'Academie nationale de medecine.

[62]  Thomas Lengauer,et al.  Bioinformatics Original Paper Improved Scoring of Functional Groups from Gene Expression Data by Decorrelating Go Graph Structure , 2022 .