Doubling of the known set of RNA viruses by metagenomic analysis of an aquatic virome
暂无分享,去创建一个
E. Koonin | Y. Wolf | A. Fire | V. Dolja | M. Krupovic | D. Kazlauskas | Sukrit Silas | Yongjie Wang | Shu-Yin. Wu | M. Bocek | Darius Kazlauskas
[1] E. Koonin,et al. Deep Roots and Splendid Boughs of the Global Plant Virome. , 2020, Annual review of phytopathology.
[2] E. Koonin,et al. Global Organization and Proposed Megataxonomy of the Virus World , 2020, Microbiology and Molecular Biology Reviews.
[3] R. P. Ross,et al. Expansion of known ssRNA phage genomes: From tens to over a thousand , 2020, Science Advances.
[4] A. Gibbs,et al. The Potyviruses: An Evolutionary Synthesis Is Emerging , 2020, Viruses.
[5] J. Vinjé,et al. ICTV Virus Taxonomy Profile , 2019 .
[6] E. Holmes,et al. Expanding the RNA Virosphere by Unbiased Metagenomics. , 2019, Annual review of virology.
[7] S. Elena,et al. Evolution and ecology of plant viruses , 2019, Nature Reviews Microbiology.
[8] W. P. Biggs,et al. Silicon limitation facilitates virus infection and mortality of marine diatoms , 2019, Nature Microbiology.
[9] C. Suttle,et al. Application of a sequence-based taxonomic classification method to uncultured and unclassified marine single-stranded RNA viruses in the order Picornavirales , 2019, Virus evolution.
[10] G. Cochrane,et al. Marine DNA Viral Macro- and Microdiversity from Pole to Pole , 2019, Cell.
[11] C. Suttle,et al. Marine RNA Virus Quasispecies Are Distributed throughout the Oceans , 2019, mSphere.
[12] E. Koonin,et al. Classify viruses — the gain is worth the pain , 2019, Nature.
[13] R. Bartenschlager,et al. Discovery of highly divergent lineages of plant-associated astro-like viruses sheds light on the emergence of potyviruses. , 2019, Virus research.
[14] Thijs J. G. Ettema,et al. Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism , 2018, mBio.
[15] Lele Zhao,et al. Eukaryotic Circular Rep-Encoding Single-Stranded DNA (CRESS DNA) Viruses: Ubiquitous Viruses With Small Genomes and a Diverse Host Range. , 2019, Advances in virus research.
[16] M. Roossinck. Evolutionary and ecological links between plant and fungal viruses. , 2018, The New phytologist.
[17] E. Koonin,et al. Origins and Evolution of the Global RNA Virome , 2018, mBio.
[18] Randall J. Platt,et al. Transcriptional recording by CRISPR spacer acquisition from RNA , 2018, Nature.
[19] S. Wilhelm,et al. Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions , 2018, Viruses.
[20] Darren J Obbard. Expansion of the metazoan virosphere: progress, pitfalls, and prospects. , 2018, Current opinion in virology.
[21] M. Shi,et al. The evolutionary history of vertebrate RNA viruses , 2018, Nature.
[22] Darren J Obbard,et al. Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes , 2017, bioRxiv.
[23] Alexander I. Culley. New insight into the RNA aquatic virosphere via viromics. , 2018, Virus research.
[24] E. Koonin,et al. Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer , 2017, Virus Research.
[25] Robert D. Finn,et al. EBI Metagenomics in 2017: enriching the analysis of microbial communities, from sequence reads to assemblies , 2017, Nucleic Acids Res..
[26] A. Greninger. A decade of RNA virus metagenomics is (not) enough , 2017, Virus Research.
[27] I. Rogozin,et al. Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite Leishmania , 2017, Proceedings of the National Academy of Sciences.
[28] Robert A Edwards,et al. Discovery of an expansive bacteriophage family that includes the most abundant viruses from the human gut , 2017, Nature Microbiology.
[29] Johannes Söding,et al. MMseqs2: sensitive protein sequence searching for the analysis of massive data sets , 2017, bioRxiv.
[30] Kira S. Makarova,et al. The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes , 2017, mBio.
[31] M. Valle,et al. Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses , 2017, Science Advances.
[32] C. Gobler,et al. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics , 2017, Nature Communications.
[33] A. Firth,et al. ICTV Virus Taxonomy Profile: Dicistroviridae , 2017, The Journal of general virology.
[34] J. Brenchley,et al. Statoviruses, A novel taxon of RNA viruses present in the gastrointestinal tracts of diverse mammals , 2017, Virology.
[35] Andrew J. Davison,et al. Consensus statement: Virus taxonomy in the age of metagenomics , 2017, Nature Reviews Microbiology.
[36] R. Coutts,et al. Studies on the Virome of the Entomopathogenic Fungus Beauveria bassiana Reveal Novel dsRNA Elements and Mild Hypervirulence , 2017, PLoS pathogens.
[37] Maria Jesus Martin,et al. Uniclust databases of clustered and deeply annotated protein sequences and alignments , 2016, Nucleic Acids Res..
[38] E. Koonin,et al. Virus taxonomy in the age of metagenomics , 2017 .
[39] Edward C. Holmes,et al. Redefining the invertebrate RNA virosphere , 2016, Nature.
[40] Steven M. Lakin,et al. West African Anopheles gambiae mosquitoes harbor a taxonomically diverse virome including new insect-specific flaviviruses, mononegaviruses, and totiviruses. , 2016, Virology.
[41] G. Steward,et al. RNA viruses as major contributors to Antarctic virioplankton. , 2016, Environmental microbiology.
[42] G. Hartman,et al. Identification of Diverse Mycoviruses through Metatranscriptomics Characterization of the Viromes of Five Major Fungal Plant Pathogens , 2016, Journal of Virology.
[43] David Wang,et al. Hyperexpansion of RNA Bacteriophage Diversity , 2016, PLoS biology.
[44] F. Küpper,et al. Zoosporic parasites infecting marine diatoms - A black box that needs to be opened. , 2016, Fungal ecology.
[45] Mikel Valle,et al. The near-atomic cryoEM structure of a flexible filamentous plant virus shows homology of its coat protein with nucleoproteins of animal viruses , 2015, eLife.
[46] N. Verdaguer,et al. The Structure of the RNA-Dependent RNA Polymerase of a Permutotetravirus Suggests a Link between Primer-Dependent and Primer-Independent Polymerases , 2015, PLoS pathogens.
[47] E. Koonin,et al. A novel group of diverse Polinton-like viruses discovered by metagenome analysis , 2015, BMC Biology.
[48] C. Suttle,et al. Biogeography of Viruses in the Sea. , 2015, Annual review of virology.
[49] 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.
[50] R. Peiró,et al. Ecological connectivity shapes quasispecies structure of RNA viruses in an Antarctic lake. , 2015, Molecular ecology.
[51] J. Derisi,et al. Draft Genome Sequences of Ciliovirus and Brinovirus from San Francisco Wastewater , 2015, Genome Announcements.
[52] Claire L. Webster,et al. The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster , 2015, bioRxiv.
[53] E. Koonin,et al. Origins and evolution of viruses of eukaryotes: The ultimate modularity , 2015, Virology.
[54] Matthew B. Sullivan,et al. Rising to the challenge: accelerated pace of discovery transforms marine virology , 2015, Nature Reviews Microbiology.
[55] M. Shi,et al. Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses , 2015, eLife.
[56] Narmada Thanki,et al. CDD: NCBI's conserved domain database , 2014, Nucleic Acids Res..
[57] J. García,et al. Molecular biology of potyviruses. , 2015, Advances in virus research.
[58] Julia A Gustavsen,et al. High temporal and spatial diversity in marine RNA viruses implies that they have an important role in mortality and structuring plankton communities , 2014, Front. Microbiol..
[59] K. Kimura,et al. Discovery of Two Novel Viruses Expands the Diversity of Single-Stranded DNA and Single-Stranded RNA Viruses Infecting a Cosmopolitan Marine Diatom , 2014, Applied and Environmental Microbiology.
[60] Ying-jie Pan,et al. Efficient purification and concentration of viruses from a large body of high turbidity seawater , 2014, MethodsX.
[61] J. Florez,et al. Progress, pitfalls, and prospects , 2013 .
[62] G. Cai,et al. The family narnaviridae: simplest of RNA viruses. , 2013, Advances in virus research.
[63] Rachel L. Marine,et al. High Variety of Known and New RNA and DNA Viruses of Diverse Origins in Untreated Sewage , 2012, Journal of Virology.
[64] Steven L Salzberg,et al. Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.
[65] E. Koonin,et al. Identification of Novel Positive-Strand RNA Viruses by Metagenomic Analysis of Archaea-Dominated Yellowstone Hot Springs , 2012, Journal of Virology.
[66] A. Biegert,et al. HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment , 2011, Nature Methods.
[67] E. Koonin,et al. Common origins and host-dependent diversity of plant and animal viromes. , 2011, Current opinion in virology.
[68] Sean R. Eddy,et al. Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..
[69] Leonard D. Goldstein,et al. Natural and Experimental Infection of Caenorhabditis Nematodes by Novel Viruses Related to Nodaviruses , 2011, PLoS biology.
[70] O. Spring,et al. The nucleotide sequence and genome organization of Plasmopara halstedii virus , 2011, Virology Journal.
[71] Paramvir S. Dehal,et al. FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments , 2010, PloS one.
[72] Q. Zeng,et al. Analysis of High-Throughput Sequencing and Annotation Strategies for Phage Genomes , 2010, PloS one.
[73] Natalya Yutin,et al. Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution , 2009, Virology Journal.
[74] A. Gorbalenya,et al. Permutation of the active site of putative RNA-dependent RNA polymerase in a newly identified species of plant alpha-like virus. , 2009, Virology.
[75] Yan Wei Lim,et al. Metagenomic analysis of viruses in reclaimed water. , 2009, Environmental microbiology.
[76] K. Nagasaki,et al. Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Bloom-Forming Diatom Chaetoceros socialis , 2009, Applied and Environmental Microbiology.
[77] K. Nagasaki,et al. Dinoflagellates, diatoms, and their viruses , 2008, The Journal of Microbiology.
[78] K. Nagasaki,et al. Isolation and Characterization of a Single-Stranded RNA Virus Infecting the Marine Planktonic Diatom Chaetoceros tenuissimus Meunier , 2008, Applied and Environmental Microbiology.
[79] P. Tyler,et al. An improved molecular phylogeny of the Nematoda with special emphasis on marine taxa. , 2007, Molecular phylogenetics and evolution.
[80] K. Mise,et al. Complete nucleotide sequence and genome organization of a single-stranded RNA virus infecting the marine fungoid protist Schizochytrium sp. , 2006, The Journal of general virology.
[81] Johannes Söding,et al. Protein homology detection by HMM?CHMM comparison , 2005, Bioinform..
[82] Andrei N. Lupas,et al. CLANS: a Java application for visualizing protein families based on pairwise similarity , 2004, Bioinform..
[83] Robert C. Edgar,et al. MUSCLE: a multiple sequence alignment method with reduced time and space complexity , 2004, BMC Bioinformatics.
[84] C. Suttle,et al. Genome sequence and characterization of a virus (HaRNAV) related to picorna-like viruses that infects the marine toxic bloom-forming alga Heterosigma akashiwo. , 2004, Virology.
[85] T. Hibi,et al. The nucleotide sequence and genome organization of Sclerophthora macrospora virus A. , 2003, Virology.
[86] C. Cameron,et al. The Palm Subdomain-based Active Site is Internally Permuted in Viral RNA-dependent RNA Polymerases of an Ancient Lineage , 2002, Journal of Molecular Biology.
[87] M. Suzuki,et al. The nucleotide sequence and genome organization of Sclerophthora macrospora virus B. , 2003, Virology.
[88] E. Koonin,et al. Phylogeny of capsid proteins of rod-shaped and filamentous RNA plant viruses: two families with distinct patterns of sequence and probably structure conservation. , 1991, Virology.