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

Digital disease detection: A systematic review of event-based internet biosurveillance systems

(2017) Jesse O'Shea   INTERNATIONAL JOURNAL OF MEDICAL INFORMATICS

Application of next generation sequencing in clinical microbiology and infection prevention

(2017) Ruud H. Deurenberg et al.   JOURNAL OF BIOTECHNOLOGY

Epidemiology: Molecular mapping of Zika spread

(2017) Michael Worobey   NATURE

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

(2017) N. R. Faria et al.   NATURE

Genomic epidemiology reveals multiple introductions of Zika virus into the United States

(2017) Nathan D. Grubaugh 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

Clinical and biological insights from viral genome sequencing

(2017) Charlotte J. Houldcroft et al.   NATURE REVIEWS MICROBIOLOGY

One Health proof of concept: Bringing a transdisciplinary approach to surveillance for zoonotic viruses at the human-wild animal interface

(2017) Terra R. Kelly et al.   PREVENTIVE VETERINARY MEDICINE

Our Shared Vulnerability to Dangerous Pathogens

(2017) Lawrence O. Gostin   Medical Law Review

Whole Genome Sequencing—Implications for Infection Prevention and Outbreak Investigations

(2017) Kyle J. Popovich et al.   Current Infectious Disease Reports

Precision Public Health for the Era of Precision Medicine

(2016) Muin J. Khoury et al.   AMERICAN JOURNAL OF PREVENTIVE MEDICINE

A brief primer on genomic epidemiology: lessons learned fromMycobacterium tuberculosis

(2016) Jennifer L. Guthrie et al.   Annals of the New York Academy of Sciences

Known unknowns: building an ethics of uncertainty into genomic medicine

(2016) Ainsley J. Newson et al.   BMC Medical Genomics

Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

(2016) Brendan R. Jackson et al.   CLINICAL INFECTIOUS DISEASES

Environmental surveillance of viruses by tangential flow filtration and metagenomic reconstruction

(2016) Vyacheslav Furtak et al.   Eurosurveillance

Traditional and syndromic surveillance of infectious diseases and pathogens

(2016) Cédric Abat et al.   INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Expansion of Microbial Forensics

(2016) Sarah E. Schmedes et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Democratic databases: science on GitHub

(2016) Jeffrey Perkel   NATURE

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

Redefining the invertebrate RNA virosphere

(2016) Mang Shi et al.   NATURE

Using genomics data to reconstruct transmission trees during disease outbreaks

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

Zika virus in the Americas: Early epidemiological and genetic findings

(2016) N. R. Faria et al.   SCIENCE

Genomics reveals historic and contemporary transmission dynamics of a bacterial disease among wildlife and livestock

(2016) Pauline L. Kamath et al.   Nature Communications

Illuminating uveitis: metagenomic deep sequencing identifies common and rare pathogens

(2016) Thuy Doan et al.   Genome Medicine

Next-generation sequencing diagnostics of bacteremia in septic patients

(2016) Silke Grumaz et al.   Genome Medicine

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Make Data Sharing Routine to Prepare for Public Health Emergencies

(2016) Jean-Paul Chretien et al.   PLOS MEDICINE

Real-Time Sharing of Zika Virus Data in an Interconnected World

(2016) Esper G. Kallas et al.   JAMA Pediatrics

The structure and diversity of human, animal and environmental resistomes

(2016) Chandan Pal et al.   Microbiome

Reduced evolutionary rate in reemerged Ebola virus transmission chains

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

Nanopore sequencing in microgravity

(2016) Alexa B R McIntyre et al.   NPJ Microgravity

Flu Near You: Crowdsourced Symptom Reporting Spanning 2 Influenza Seasons

(2015) Mark S. Smolinski et al.   AMERICAN JOURNAL OF PUBLIC HEALTH

DiagnosingBalamuthia mandrillarisEncephalitis With Metagenomic Deep Sequencing

(2015) Michael R. Wilson et al.   ANNALS OF NEUROLOGY

nextflu: real-time tracking of seasonal influenza virus evolution in humans

(2015) Richard A. Neher et al.   BIOINFORMATICS

A multi-country Salmonella Enteritidis phage type 14b outbreak associated with eggs from a German producer: ‘near real-time’ application of whole genome sequencing and food chain investigations, United Kingdom, May to September 2014

(2015) T Inns et al.   Eurosurveillance

Best Practices for Ethical Sharing of Individual-Level Health Research Data From Low- and Middle-Income Settings

(2015) Susan Bull et al.   Journal of Empirical Research on Human Research Ethics

West African Ebola crisis and orphans

(2015) David K Evans et al.   LANCET

Will Ebola change the game? Ten essential reforms before the next pandemic. The report of the Harvard-LSHTM Independent Panel on the Global Response to Ebola

(2015) Suerie Moon et al.   LANCET

Data sharing: Make outbreak research open access

(2015) Nathan L. Yozwiak et al.   NATURE

Molecular Evidence of Sexual Transmission of Ebola Virus

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

A Delphi Technology Foresight Study: Mapping Social Construction of Scientific Evidence on Metagenomics Tests for Water Safety

(2015) Stanislav Birko et al.   PLoS One

Global biogeography of human infectious diseases

(2015) Kris A. Murray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Germline genome-editing research and its socioethical implications

(2015) Tetsuya Ishii   TRENDS IN MOLECULAR MEDICINE

Social and Economic Aspects of the Transmission of Pathogenic Bacteria between Wildlife and Food Animals: A Thematic Analysis of Published Research Knowledge

(2015) A. Fournier et al.   Zoonoses and Public Health

Non-random patterns in viral diversity

(2015) Simon J. Anthony et al.   Nature Communications

Optimization of a Novel Non-invasive Oral Sampling Technique for Zoonotic Pathogen Surveillance in Nonhuman Primates

(2015) Tierra Smiley Evans et al.   PLoS Neglected Tropical Diseases

Detecting the emergence of novel, zoonotic viruses pathogenic to humans

(2014) Ronald Rosenberg   CELLULAR AND MOLECULAR LIFE SCIENCES

Real-time investigation of a Legionella pneumophila outbreak using whole genome sequencing

(2014) R. M. A. GRAHAM et al.   EPIDEMIOLOGY AND INFECTION

Inferring Epidemiological Dynamics with Bayesian Coalescent Inference: The Merits of Deterministic and Stochastic Models

(2014) Alex Popinga et al.   GENETICS

Viral Metagenomics on Animals as a Tool for the Detection of Zoonoses Prior to Human Infection?

(2014) Sarah Temmam et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli

(2014) K. G. Joensen et al.   JOURNAL OF CLINICAL MICROBIOLOGY

The Reliability of Tweets as a Supplementary Method of Seasonal Influenza Surveillance

(2014) Anoshé A Aslam et al.   JOURNAL OF MEDICAL INTERNET RESEARCH

Emergence of Zaire Ebola Virus Disease in Guinea

(2014) Sylvain Baize et al.   NEW ENGLAND JOURNAL OF MEDICINE

Actionable Diagnosis of Neuroleptospirosis by Next-Generation Sequencing

(2014) Michael R. Wilson et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evaluation of Local Media Surveillance for Improved Disease Recognition and Monitoring in Global Hotspot Regions

(2014) Jessica S. Schwind et al.   PLoS One

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

(2014) S. K. Gire et al.   SCIENCE

Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice

(2014) Gail Geller et al.   Genome Medicine

An overview of Internet biosurveillance

(2013) D.M. Hartley et al.   CLINICAL MICROBIOLOGY AND INFECTION

Search strategy has influenced the discovery rate of human viruses

(2013) Ronald Rosenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ethical Introduction of Genome-Based Information and Technologies into Public Health

(2013) H.C. Howard et al.   Public Health Genomics

A Strategy To Estimate Unknown Viral Diversity in Mammals

(2013) S. J. Anthony et al.   mBio

Prediction and prevention of the next pandemic zoonosis

(2012) Stephen S Morse et al.   LANCET

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Performance comparison of benchtop high-throughput sequencing platforms

(2012) Nicholas J Loman et al.   NATURE BIOTECHNOLOGY

Preventing Pandemics Via International Development: A Systems Approach

(2012) Tiffany L. Bogich et al.   PLOS MEDICINE

Assessing Google Flu Trends Performance in the United States during the 2009 Influenza Virus A (H1N1) Pandemic

(2011) Samantha Cook et al.   PLoS One

Grand challenges in global health governance

(2009) L. O. Gostin et al.   BRITISH MEDICAL BULLETIN

Google Trends: A Web‐Based Tool for Real‐Time Surveillance of Disease Outbreaks

(2009) Herman Anthony Carneiro et al.   CLINICAL INFECTIOUS DISEASES

A Call for “Smart Surveillance”: A Lesson Learned from H1N1

(2009) Peter Daszak   EcoHealth

Digital Disease Detection — Harnessing the Web for Public Health Surveillance

(2009) John S. Brownstein et al.   NEW ENGLAND JOURNAL OF MEDICINE

Web Queries as a Source for Syndromic Surveillance

(2009) Anette Hulth et al.   PLoS One

Criteria for Validation of Methods in Microbial Forensics

(2008) B. Budowle et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE