Predicting host taxonomic information from viral genomes: A comparison of feature representations

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