Machine learning using intrinsic genomic signatures for rapid classification of novel pathogens: COVID-19 case study

The continuing 2019-nCoV epidemic threat of novel coronaviruses to global health — The latest 2019 novel coronavirus outbreak in Wuhan, China

(2020) David S. Hui et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Preliminary estimation of the basic reproduction number of novel coronavirus (2019-nCoV) in China, from 2019 to 2020: A data-driven analysis in the early phase of the outbreak

(2020) Shi Zhao et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Potential inhibitors against 2019-nCoV coronavirus M protease from clinically approved medicines

(2020) Xin Liu et al.   Journal of Genetics and Genomics

A new coronavirus associated with human respiratory disease in China

(2020) Fan Wu et al.   NATURE

A pneumonia outbreak associated with a new coronavirus of probable bat origin

(2020) Peng Zhou et al.   NATURE

Return of the Coronavirus: 2019-nCoV

(2020) Lisa E. Gralinski et al.   Viruses-Basel

Functional assessment of cell entry and receptor usage for SARS-CoV-2 and other lineage B betacoronaviruses

(2020) Michael Letko et al.   Nature Microbiology

Full-genome evolutionary analysis of the novel corona virus (2019-nCoV) rejects the hypothesis of emergence as a result of a recent recombination event

(2020) D. Paraskevis et al.   INFECTION GENETICS AND EVOLUTION

Global Epidemiology of Bat Coronaviruses

(2019) Antonio Wong et al.   Viruses-Basel

Codon stabilization coefficient as a metric to gain insights into mRNA stability and codon bias and their relationships with translation

(2019) Rodolfo L Carneiro et al.   NUCLEIC ACIDS RESEARCH

ML-DSP: Machine Learning with Digital Signal Processing for ultrafast, accurate, and scalable genome classification at all taxonomic levels

(2019) Gurjit S. Randhawa et al.   BMC GENOMICS

Coronavirus envelope protein: current knowledge

(2019) Dewald Schoeman et al.   Virology Journal

Molecular epidemiology, evolution and phylogeny of SARS coronavirus

(2019) Hayes K.H. Luk et al.   INFECTION GENETICS AND EVOLUTION

Differential Evolution of Antiretroviral Restriction Factors in Pteropid Bats as Revealed by APOBEC3 Gene Complexity

(2018) Joshua A Hayward et al.   MOLECULAR BIOLOGY AND EVOLUTION

APOBEC3-mediated restriction of RNA virus replication

(2018) Aleksandra Milewska et al.   Scientific Reports

Origin and evolution of pathogenic coronaviruses

(2018) Jie Cui et al.   NATURE REVIEWS MICROBIOLOGY

An open-source k-mer based machine learning tool for fast and accurate subtyping of HIV-1 genomes

(2018) Stephen Solis-Reyes et al.   PLoS One

Genetic diversity of coronaviruses in bats in Lao PDR and Cambodia

(2017) Audrey Lacroix et al.   INFECTION GENETICS AND EVOLUTION

DNA helix: the importance of being AT-rich

(2017) A. E. Vinogradov et al.   MAMMALIAN GENOME

CG dinucleotide suppression enables antiviral defence targeting non-self RNA

(2017) Matthew A. Takata et al.   NATURE

Epidemiology, Genetic Recombination, and Pathogenesis of Coronaviruses

(2016) Shuo Su et al.   TRENDS IN MICROBIOLOGY

An investigation into inter- and intragenomic variations of graphic genomic signatures

(2015) Rallis Karamichalis et al.   BMC BIOINFORMATICS

Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus

(2015) Xing-Lou Yang et al.   JOURNAL OF VIROLOGY

Mapping the Space of Genomic Signatures

(2015) Lila Kari et al.   PLoS One

Diversity of coronavirus in bats from Eastern Thailand

(2015) Supaporn Wacharapluesadee et al.   Virology Journal

On the biased nucleotide composition of the human coronavirus RNA genome

(2015) Ben Berkhout et al.   VIRUS RESEARCH

To sense or not to sense viral RNA—essentials of coronavirus innate immune evasion

(2014) Eveline Kindler et al.   CURRENT OPINION IN MICROBIOLOGY

Identification of Diverse Alphacoronaviruses and Genomic Characterization of a Novel Severe Acute Respiratory Syndrome-Like Coronavirus from Bats in China

(2014) B. He et al.   JOURNAL OF VIROLOGY

Middle East Respiratory Syndrome Coronavirus Infection in Dromedary Camels in Saudi Arabia

(2014) A. N. Alagaili et al.   mBio

A Case for the Ancient Origin of Coronaviruses

(2013) J. O. Wertheim et al.   JOURNAL OF VIROLOGY

Genetic Characterization of Betacoronavirus Lineage C Viruses in Bats Reveals Marked Sequence Divergence in the Spike Protein of Pipistrellus Bat Coronavirus HKU5 in Japanese Pipistrelle: Implications for the Origin of the Novel Middle East Respiratory Syndrome Coronavirus

(2013) S. K. P. Lau et al.   JOURNAL OF VIROLOGY

Identification of diverse full-length endogenous betaretroviruses in megabats and microbats

(2013) Joshua A Hayward et al.   Retrovirology

Recent Transmission of a Novel Alphacoronavirus, Bat Coronavirus HKU10, from Leschenault's Rousettes to Pomona Leaf-Nosed Bats: First Evidence of Interspecies Transmission of Coronavirus between Bats of Different Suborders

(2012) S. K. P. Lau et al.   JOURNAL OF VIROLOGY

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

(2012) Ali M. Zaki et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of SARS-like coronaviruses in horseshoe bats (Rhinolophus hipposideros) in Slovenia

(2010) Danijela Rihtarič et al.   ARCHIVES OF VIROLOGY

Genomic Characterization of Severe Acute Respiratory Syndrome-Related Coronavirus in European Bats and Classification of Coronaviruses Based on Partial RNA-Dependent RNA Polymerase Gene Sequences

(2010) J. F. Drexler et al.   JOURNAL OF VIROLOGY

Coronavirus Genomics and Bioinformatics Analysis

(2010) Patrick C. Y. Woo et al.   Viruses-Basel

Coronavirus Diversity, Phylogeny and Interspecies Jumping

(2009) Patrick C. Y. Woo et al.   EXPERIMENTAL BIOLOGY AND MEDICINE

Molecular dynamic simulations analysis of ritronavir and lopinavir as SARS-CoV 3CLpro inhibitors

(2008) Veena Nukoolkarn et al.   JOURNAL OF THEORETICAL BIOLOGY

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Patterns of Evolution and Host Gene Mimicry in Influenza and Other RNA Viruses

(2008) Benjamin D. Greenbaum et al.   PLoS Pathogens