Tracking virus outbreaks in the twenty-first century

Novel graphene-based biosensor for early detection of Zika virus infection

(2018) Savannah Afsahi et al.   BIOSENSORS & BIOELECTRONICS

Genomic Insights into Zika Virus Emergence and Spread

(2018) Nathan D. Grubaugh et al.   CELL

Impact of the tree prior on estimating clock rates during epidemic outbreaks

(2018) Simon Möller et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Field-deployable viral diagnostics using CRISPR-Cas13

(2018) Cameron Myhrvold et al.   SCIENCE

CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity

(2018) Janice S. Chen et al.   SCIENCE

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

(2018) Jonathan S. Gootenberg et al.   SCIENCE

Active Ebola Virus Replication and Heterogeneous Evolutionary Rates in EVD Survivors

(2018) Shannon L.M. Whitmer et al.   Cell Reports

Preprints: An underutilized mechanism to accelerate outbreak science

(2018) Michael A. Johansson et al.   PLOS MEDICINE

When are pathogen genome sequences informative of transmission events?

(2018) Finlay Campbell et al.   PLoS Pathogens

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

The Structured Coalescent and Its Approximations

(2017) Nicola F. Müller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

Virus genomes reveal factors that spread and sustained the Ebola epidemic

(2017) Gytis Dudas et al.   NATURE

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Towards a genomics-informed, real-time, global pathogen surveillance system

(2017) Jennifer L. Gardy et al.   NATURE REVIEWS GENETICS

Nucleic acid detection with CRISPR-Cas13a/C2c2

(2017) Jonathan S. Gootenberg et al.   SCIENCE

Rapid and specific detection of Asian- and African-lineage Zika viruses

(2017) Nunya Chotiwan et al.   Science Translational Medicine

Ebola Virus Glycoprotein with Increased Infectivity Dominated the 2013–2016 Epidemic

(2016) William E. Diehl et al.   CELL

Roots, Not Parachutes: Research Collaborations Combat Outbreaks

(2016) Nathan L. Yozwiak et al.   CELL

Human Adaptation of Ebola Virus during the West African Outbreak

(2016) Richard A. Urbanowicz et al.   CELL

Resurgence of Ebola Virus Disease in Guinea Linked to a Survivor With Virus Persistence in Seminal Fluid for More Than 500 Days

(2016) Boubacar Diallo et al.   CLINICAL INFECTIOUS DISEASES

Field Validation of the ReEBOV Antigen Rapid Test for Point-of-Care Diagnosis of Ebola Virus Infection

(2016) Matthew L. Boisen et al.   JOURNAL OF INFECTIOUS DISEASES

Functional Characterization of Adaptive Mutations during the West African Ebola Virus Outbreak

(2016) Erik Dietzel et al.   JOURNAL OF VIROLOGY

Phylodynamics with Migration: A Computational Framework to Quantify Population Structure from Genomic Data

(2016) Denise Kühnert et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of Ebola virus: Insights from the 2013–2016 epidemic

(2016) Edward C. Holmes et al.   NATURE

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Prediction, dynamics, and visualization of antigenic phenotypes of seasonal influenza viruses

(2016) Richard A. Neher et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using genomics data to reconstruct transmission trees during disease outbreaks

(2016) M.D. HALL et al.   REVUE SCIENTIFIQUE ET TECHNIQUE-OFFICE INTERNATIONAL DES EPIZOOTIES

Comment on "Mutation rate and genotype variation of Ebola virus from Mali case sequences"

(2016) A. Rambaut et al.   SCIENCE

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Origins of the 2009 H1N1 influenza pandemic in swine in Mexico

(2016) Ignacio Mena et al.   eLife

Reduced evolutionary rate in reemerged Ebola virus transmission chains

(2016) D. J. Blackley et al.   Science Advances

Clinical Sequencing Uncovers Origins and Evolution of Lassa Virus

(2015) Kristian G. Andersen et al.   CELL

Puzzling Origins of the Ebola Outbreak in the Democratic Republic of the Congo, 2014

(2015) Tommy Tsan-Yuk Lam et al.   JOURNAL OF VIROLOGY

ReEBOV Antigen Rapid Test kit for point-of-care and laboratory-based testing for Ebola virus disease: a field validation study

(2015) Mara Jana Broadhurst et al.   LANCET

Data sharing: Make outbreak research open access

(2015) Nathan L. Yozwiak et al.   NATURE

Bayesian molecular clock dating of species divergences in the genomics era

(2015) Mario dos Reis et al.   NATURE REVIEWS GENETICS

Molecular Evidence of Sexual Transmission of Ebola Virus

(2015) Suzanne E. Mate et al.   NEW ENGLAND JOURNAL OF MEDICINE

Co-circulation of three camel coronavirus species and recombination of MERS-CoVs in Saudi Arabia

(2015) J. S. M. Sabir et al.   SCIENCE

Measurably evolving pathogens in the genomic era

(2015) Roman Biek et al.   TRENDS IN ECOLOGY & EVOLUTION

New Routes to Phylogeography: A Bayesian Structured Coalescent Approximation

(2015) Nicola De Maio et al.   PLoS Genetics

Efficient Bayesian inference under the structured coalescent

(2014) Timothy G. Vaughan et al.   BIOINFORMATICS

Paper-Based Synthetic Gene Networks

(2014) Keith Pardee et al.   CELL

Simultaneous reconstruction of evolutionary history and epidemiological dynamics from viral sequences with the birth-death SIR model

(2014) D. Kuhnert et al.   Journal of the Royal Society Interface

A predictive fitness model for influenza

(2014) Marta Łuksza et al.   NATURE

Analyses of evolutionary dynamics in viruses are hindered by a time-dependent bias in rate estimates

(2014) S. Duchene et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Genomic surveillance elucidates Ebola virus origin and transmission during the 2014 outbreak

(2014) S. K. Gire et al.   SCIENCE

Unifying Viral Genetics and Human Transportation Data to Predict the Global Transmission Dynamics of Human Influenza H3N2

(2014) Philippe Lemey et al.   PLoS Pathogens

Molecular Evolution of Viruses of the Family Filoviridae Based on 97 Whole-Genome Sequences

(2012) S. A. Carroll 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

A Bayesian Inference Framework to Reconstruct Transmission Trees Using Epidemiological and Genetic Data

(2012) Marco J. Morelli et al.   PLoS Computational Biology

Estimating the Basic Reproductive Number from Viral Sequence Data

(2011) Tanja Stadler et al.   MOLECULAR BIOLOGY AND EVOLUTION

Toward a quantitative understanding of viral phylogeography

(2011) Nuno Rodrigues Faria et al.   Current Opinion in Virology

Inference for Nonlinear Epidemiological Models Using Genealogies and Time Series

(2011) David A. Rasmussen et al.   PLoS Computational Biology

Phylodynamics of Infectious Disease Epidemics

(2009) Erik M. Volz et al.   GENETICS

Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic

(2009) Gavin J. D. Smith et al.   NATURE

Emergence of a Novel Swine-Origin Influenza A (H1N1) Virus in Humans

(2009)   NEW ENGLAND JOURNAL OF MEDICINE

Pandemic Potential of a Strain of Influenza A (H1N1): Early Findings

(2009) C. Fraser et al.   SCIENCE

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

(2009) Thomas Briese et al.   PLoS Pathogens

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Rates of evolutionary change in viruses: patterns and determinants

(2008) Siobain Duffy et al.   NATURE REVIEWS GENETICS

Integrating genetic and epidemiological data to determine transmission pathways of foot-and-mouth disease virus

(2008) E. M Cottam et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES