Identifying and prioritizing potential human-infecting viruses from their genome sequences

How accurately can we assess zoonotic risk?

(2021) Michelle Wille et al.   PLOS BIOLOGY

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

(2020) Michael Letko et al.   Nature Microbiology

The species Severe acute respiratory syndrome-related coronavirus: classifying 2019-nCoV and naming it SARS-CoV-2

(2020)   Nature Microbiology

Viral zoonotic risk is homogenous among taxonomic orders of mammalian and avian reservoir hosts

(2020) Nardus Mollentze et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bat-borne virus diversity, spillover and emergence

(2020) Michael Letko et al.   NATURE REVIEWS MICROBIOLOGY

Rapid identification of human‐infecting viruses

(2019) Zheng Zhang et al.   Transboundary and Emerging Diseases

Species-Specific Host–Virus Interactions: Implications for Viral Host Range and Virulence

(2019) Stefan Rothenburg et al.   TRENDS IN MICROBIOLOGY

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

Epidemiological characteristics of human-infective RNA viruses

(2018) Mark E. J. Woolhouse et al.   Scientific Data

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Ensembl 2019

(2018) Fiona Cunningham 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

Taxonomic patterns in the zoonotic potential of mammalian viruses

(2018) Alex D. Washburne et al.   PeerJ

CG dinucleotide suppression enables antiviral defence targeting non-self RNA

(2017) Matthew A. Takata et al.   NATURE

Host and viral traits predict zoonotic spillover from mammals

(2017) Kevin J. Olival et al.   NATURE

Pathways to zoonotic spillover

(2017) Raina K. Plowright et al.   NATURE REVIEWS MICROBIOLOGY

Beyond sigmoids: How to obtain well-calibrated probabilities from binary classifiers with beta calibration

(2017) Meelis Kull et al.   Electronic Journal of Statistics

Virological factors that increase the transmissibility of emerging human viruses

(2016) Jemma L. Geoghegan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Synonymous Virus Genome Recoding as a Tool to Impact Viral Fitness

(2016) Miguel Angel Martínez et al.   TRENDS IN MICROBIOLOGY

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Building Predictive Models inRUsing thecaretPackage

(2015) Max Kuhn   Journal of Statistical Software

Fast Implementation of DeLong’s Algorithm for Comparing the Areas Under Correlated Receiver Operating Characteristic Curves

(2014) Xu Sun et al.   IEEE SIGNAL PROCESSING LETTERS

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Prediction and prevention of the next pandemic zoonosis

(2012) Stephen S Morse et al.   LANCET

APCluster: an R package for affinity propagation clustering

(2011) U. Bodenhofer et al.   BIOINFORMATICS

Ability to Replicate in the Cytoplasm Predicts Zoonotic Transmission of Livestock Viruses

(2009) Juliet R. C. Pulliam et al.   JOURNAL OF INFECTIOUS DISEASES

Virus Attenuation by Genome-Scale Changes in Codon Pair Bias

(2008) J. R. Coleman et al.   SCIENCE

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

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