Predicting host taxonomic information from viral genomes: A comparison of feature representations
出版年份 2020 全文链接
标题
Predicting host taxonomic information from viral genomes: A comparison of feature representations
作者
关键词
Genomic signal processing, Host-pathogen interactions, Phylogenetics, Protein domains, Viral genomics, Viral taxonomy, Protein sequencing, Viral genome
出版物
PLoS Computational Biology
Volume 16, Issue 5, Pages e1007894
出版商
Public Library of Science (PLoS)
发表日期
2020-05-27
DOI
10.1371/journal.pcbi.1007894
参考文献
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- A Viral Ecogenomics Framework To Uncover the Secrets of Nature’s “Microbe Whisperers”
- (2019) Simon Roux mSystems
- Universal evolutionary selection for high dimensional silent patterns of information hidden in the redundancy of viral genetic code
- (2018) Eli Goz et al. BIOINFORMATICS
- The genomic underpinnings of eukaryotic virus taxonomy: creating a sequence-based framework for family-level virus classification
- (2018) Pakorn Aiewsakun et al. Microbiome
- Comparative studies of alignment, alignment-free and SVM based approaches for predicting the hosts of viruses based on viral sequences
- (2018) Han Li et al. Scientific Reports
- Minimum Information about an Uncultivated Virus Genome (MIUViG)
- (2018) Simon Roux et al. NATURE BIOTECHNOLOGY
- IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
- (2018) David Paez-Espino et al. NUCLEIC ACIDS RESEARCH
- Predicting reservoir hosts and arthropod vectors from evolutionary signatures in RNA virus genomes
- (2018) Simon A. Babayan et al. SCIENCE
- High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
- (2018) Chirag Jain et al. Nature Communications
- 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
- MVP: a microbe–phage interaction database
- (2017) Na L Gao et al. NUCLEIC ACIDS RESEARCH
- Structural host-microbiota interaction networks
- (2017) Emine Guven-Maiorov et al. PLoS Computational Biology
- Protein–Protein Interactions in Virus–Host Systems
- (2017) Anderson F. Brito et al. Frontiers in Microbiology
- ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data
- (2016) Jaime Huerta-Cepas et al. MOLECULAR BIOLOGY AND EVOLUTION
- Alignment-free $d_2^*$ oligonucleotide frequency dissimilarity measure improves prediction of hosts from metagenomically-derived viral sequences
- (2016) Nathan A. Ahlgren et al. NUCLEIC ACIDS RESEARCH
- Linking Virus Genomes with Host Taxonomy
- (2016) Tomoko Mihara et al. Viruses-Basel
- HostPhinder: A Phage Host Prediction Tool
- (2016) Julia Villarroel et al. Viruses-Basel
- Machine learning applications in genetics and genomics
- (2015) Maxwell W. Libbrecht et al. NATURE REVIEWS GENETICS
- Inferring the hosts of coronavirus using dual statistical models based on nucleotide composition
- (2015) Qin Tang et al. Scientific Reports
- Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity
- (2015) Welkin H Pope et al. eLife
- The influence of CpG and UpA dinucleotide frequencies on RNA virus replication and characterization of the innate cellular pathways underlying virus attenuation and enhanced replication
- (2014) Nicky J. Atkinson et al. NUCLEIC ACIDS RESEARCH
- NCBI Viral Genomes Resource
- (2014) J. Rodney Brister et al. NUCLEIC ACIDS RESEARCH
- A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes
- (2014) Bas E. Dutilh et al. Nature Communications
- Modelling mutational and selection pressures on dinucleotides in eukaryotic phyla –selection against CpG and UpA in cytoplasmically expressed RNA and in RNA viruses
- (2013) Peter Simmonds et al. BMC GENOMICS
- Rules of Engagement: Molecular Insights from Host-Virus Arms Races
- (2012) Matthew D. Daugherty et al. Annual Review of Genetics
- HMMER web server: interactive sequence similarity searching
- (2011) R. D. Finn et al. NUCLEIC ACIDS RESEARCH
- Structural principles within the human-virus protein-protein interaction network
- (2011) E. A. Franzosa et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Virus–host interactomes and global models of virus-infected cells
- (2011) Caroline C. Friedel et al. TRENDS IN MICROBIOLOGY
- Accelerated Profile HMM Searches
- (2011) Sean R. Eddy PLoS Computational Biology
- Use of Nucleotide Composition Analysis To Infer Hosts for Three Novel Picorna-Like Viruses
- (2010) A. Kapoor et al. JOURNAL OF VIROLOGY
- Host Phylogeny Constrains Cross-Species Emergence and Establishment of Rabies Virus in Bats
- (2010) D. G. Streicker et al. SCIENCE
- How viruses hijack cell regulation
- (2010) Norman E. Davey et al. TRENDS IN BIOCHEMICAL SCIENCES
- Codon Bias is a Major Factor Explaining Phage Evolution in Translationally Biased Hosts
- (2008) Alessandra Carbone JOURNAL OF MOLECULAR EVOLUTION
- The Microbial Engines That Drive Earth's Biogeochemical Cycles
- (2008) P. G. Falkowski et al. SCIENCE
- Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses
- (2008) Benjamin D. Greenbaum et al. PLoS Pathogens
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