Outbreak analytics: a developing data science for informing the response to emerging pathogens

Real-Time Modeling Should Be Routinely Integrated into Outbreak Response

(2018) Daniel G. Bausch et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Nextstrain: real-time tracking of pathogen evolution

(2018) James Hadfield et al.   BIOINFORMATICS

Genomic Insights into Zika Virus Emergence and Spread

(2018) Nathan D. Grubaugh et al.   CELL

Ebola virus disease: 11 323 deaths later, how far have we come?

(2018) Joseph A Lewnard   LANCET

Outbreak of Ebola virus disease in the Democratic Republic of the Congo, April–May, 2018: an epidemiological study

(2018) Ahmadou Barry et al.   LANCET

Risk factors for measles mortality and the importance of decentralized case management during an unusually large measles epidemic in eastern Democratic Republic of Congo in 2013

(2018) Etienne Gignoux et al.   PLoS One

A comparison of smartphone and paper data-collection tools in the Burden of Obstructive Lung Disease (BOLD) study in Gezira state, Sudan

(2018) Rana Ahmed et al.   PLoS One

The Global Virome Project

(2018) Dennis Carroll et al.   SCIENCE

Evidence Synthesis for Stochastic Epidemic Models

(2018) Paul J. Birrell et al.   STATISTICAL SCIENCE

A simple approach to measure transmissibility and forecast incidence

(2018) Pierre Nouvellet et al.   Epidemics

Real-time forecasting of infectious disease dynamics with a stochastic semi-mechanistic model

(2018) Sebastian Funk et al.   Epidemics

The RAPIDD ebola forecasting challenge: Synthesis and lessons learnt

(2018) Cécile Viboud et al.   Epidemics

When are pathogen genome sequences informative of transmission events?

(2018) Finlay Campbell et al.   PLoS Pathogens

Quality Assurance and Quality Control in the Global Trachoma Mapping Project

(2018) Anthony W. Solomon et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Pandemics: spend on surveillance, not prediction

(2018) Edward C. Holmes et al.   NATURE

Genomic Analysis of Lassa Virus during an Increase in Cases in Nigeria in 2018

(2018) Katherine J. Siddle et al.   NEW ENGLAND JOURNAL OF MEDICINE

International risk of yellow fever spread from the ongoing outbreak in Brazil, December 2016 to May 2017

(2017) Ilaria Dorigatti et al.   Eurosurveillance

Local, national, and regional viral haemorrhagic fever pandemic potential in Africa: a multistage analysis

(2017) David M Pigott et al.   LANCET

Spread of yellow fever virus outbreak in Angola and the Democratic Republic of the Congo 2015–16: a modelling study

(2017) Moritz U G Kraemer et al.   LANCET INFECTIOUS DISEASES

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

Contact tracing performance during the Ebola virus disease outbreak in Kenema district, Sierra Leone

(2017) Mikiko Senga et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Key data for outbreak evaluation: building on the Ebola experience

(2017) Anne Cori et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probabilistic forecasting in infectious disease epidemiology: the 13th Armitage lecture

(2017) Leonhard Held et al.   STATISTICS IN MEDICINE

Real-time dynamic modelling for the design of a cluster-randomized phase 3 Ebola vaccine trial in Sierra Leone

(2017) A. Camacho et al.   VACCINE

Targeted DNA sequencing and in situ mutation analysis using mobile phone microscopy

(2017) Malte Kühnemund et al.   Nature Communications

Simultaneous inference of phylogenetic and transmission trees in infectious disease outbreaks

(2017) Don Klinkenberg et al.   PLoS Computational Biology

Factors associated with high heterogeneity of malaria at fine spatial scale in the Western Kenyan highlands

(2016) Amrish Y. Baidjoe et al.   MALARIA JOURNAL

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Ebola Virus Disease among Male and Female Persons in West Africa

(2016)   NEW ENGLAND JOURNAL OF MEDICINE

Unraveling the drivers of MERS-CoV transmission

(2016) Simon Cauchemez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SCOTTI: Efficient Reconstruction of Transmission within Outbreaks with the Structured Coalescent

(2016) Nicola De Maio et al.   PLoS Computational Biology

Spatiotemporal Analysis of the 2014 Ebola Epidemic in West Africa

(2016) Jantien A. Backer et al.   PLoS Computational Biology

The Impact of Hotspot-Targeted Interventions on Malaria Transmission in Rachuonyo South District in the Western Kenyan Highlands: A Cluster-Randomized Controlled Trial

(2016) Teun Bousema et al.   PLOS MEDICINE

Exposure Patterns Driving Ebola Transmission in West Africa: A Retrospective Observational Study

(2016) et al.   PLOS MEDICINE

Mapping global environmental suitability for Zika virus

(2016) Jane P Messina et al.   eLife

Genomics and outbreak investigation: from sequence to consequence

(2016) Esther R Robinson et al.   Genome Medicine

Public Health Investigation of Two Outbreaks of Shiga Toxin-Producing Escherichia coli O157 Associated with Consumption of Watercress

(2015) Claire Jenkins et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Accounting for behavioral responses during a flu epidemic using home television viewing

(2015) Michael Springborn et al.   BMC INFECTIOUS DISEASES

Emergence and potential for spread of Chikungunya virus in Brazil

(2015) Marcio Roberto Teixeira Nunes et al.   BMC Medicine

Assessing the risk of observing multiple generations of Middle East respiratory syndrome (MERS) cases given an imported case

(2015) H Nishiura et al.   Eurosurveillance

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

Surveillance and Outbreak Response Management System (SORMAS) to support the control of the Ebola virus disease outbreak in West Africa

(2015) C Fähnrich et al.   Eurosurveillance

Ebola Virus: Sensationalism, Science, and Human Rights: Table 1.

(2015) Daniel G. Bausch et al.   JOURNAL OF INFECTIOUS DISEASES

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

Global, regional, and national incidence, prevalence, and years lived with disability for 301 acute and chronic diseases and injuries in 188 countries, 1990–2013: a systematic analysis for the Global Burden of Disease Study 2013

(2015) Theo Vos et al.   LANCET

The role of rapid diagnostics in managing Ebola epidemics

(2015) Pierre Nouvellet et al.   NATURE

Ebola Virus Disease among Children in West Africa

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

West African Ebola Epidemic after One Year — Slowing but Not Yet under Control

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

Measuring the impact of Ebola control measures in Sierra Leone

(2015) Adam J. Kucharski et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Avoidable errors in the modelling of outbreaks of emerging pathogens, with special reference to Ebola

(2015) A. A. King et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Estimating the probability of demonstrating vaccine efficacy in the declining Ebola epidemic: a Bayesian modelling approach

(2015) Anton Camacho et al.   BMJ Open

Extracting transmission networks from phylogeographic data for epidemic and endemic diseases: Ebola virus in Sierra Leone, 2009 H1N1 pandemic influenza and polio in Nigeria

(2015) Michael Famulare et al.   International Health

Geographic Distribution and Mortality Risk Factors during the Cholera Outbreak in a Rural Region of Haiti, 2010-2011

(2015) Anne-Laure Page et al.   PLoS Neglected Tropical Diseases

A review of epidemiological parameters from Ebola outbreaks to inform early public health decision-making

(2015) Maria D. Van Kerkhove et al.   Scientific Data

Tidy Data

(2015) Hadley Wickham   Journal of Statistical Software

Innovative Technological Approach to Ebola Virus Disease Outbreak Response in Nigeria Using the Open Data Kit and Form Hub Technology

(2015) Daniel Tom-Aba et al.   PLoS One

A comparison of smartphones to paper-based questionnaires for routine influenza sentinel surveillance, Kenya, 2011–2012

(2014) Henry N Njuguna et al.   BMC Medical Informatics and Decision Making

Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data

(2014) Xavier Didelot et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ebola Virus Disease in West Africa — The First 9 Months of the Epidemic and Forward Projections

(2014)   NEW ENGLAND JOURNAL OF MEDICINE

Descriptive Epidemiology of Typhoid Fever during an Epidemic in Harare, Zimbabwe, 2012

(2014) Jonathan A. Polonsky et al.   PLoS One

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

(2014) S. K. Gire et al.   SCIENCE

OutbreakTools: A new platform for disease outbreak analysis using the R software

(2014) Thibaut Jombart et al.   Epidemics

BEAST 2: A Software Platform for Bayesian Evolutionary Analysis

(2014) Remco Bouckaert et al.   PLoS Computational Biology

Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data

(2014) Thibaut Jombart et al.   PLoS Computational Biology

Yellow Fever in Africa: Estimating the Burden of Disease and Impact of Mass Vaccination from Outbreak and Serological Data

(2014) Tini Garske et al.   PLOS MEDICINE

Mapping the zoonotic niche of Ebola virus disease in Africa

(2014) David M Pigott et al.   eLife

A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics

(2013) Anne Cori et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Risk factors for cholera transmission in Haiti during inter-peak periods: insights to improve current control strategies from two case-control studies

(2013) F. GRANDESSO et al.   EPIDEMIOLOGY AND INFECTION

Relating Phylogenetic Trees to Transmission Trees of Infectious Disease Outbreaks

(2013) Rolf J. F. Ypma et al.   GENETICS

Transmission and evolution of the Middle East respiratory syndrome coronavirus in Saudi Arabia: a descriptive genomic study

(2013) Matthew Cotten et al.   LANCET

Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility

(2013) Simon Cauchemez et al.   LANCET INFECTIOUS DISEASES

A Novel Electronic Data Collection System for Large-Scale Surveys of Neglected Tropical Diseases

(2013) Jonathan D. King et al.   PLoS One

ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R

(2012) Andrei-Alin Popescu et al.   BIOINFORMATICS

The R0 package: a toolbox to estimate reproduction numbers for epidemic outbreaks

(2012) Thomas Obadia et al.   BMC Medical Informatics and Decision Making

Years lived with disability (YLDs) for 1160 sequelae of 289 diseases and injuries 1990–2010: a systematic analysis for the Global Burden of Disease Study 2010

(2012) Theo Vos et al.   LANCET

Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study

(2012) Simon R Harris et al.   LANCET INFECTIOUS DISEASES

The Impact of Infection on Population Health: Results of the Ontario Burden of Infectious Diseases Study

(2012) Jeffrey C. Kwong et al.   PLoS One

German Outbreak ofEscherichia coliO104:H4 Associated with Sprouts

(2011) Udo Buchholz et al.   NEW ENGLAND JOURNAL OF MEDICINE

Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza

(2011) S. Cauchemez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unravelling transmission trees of infectious diseases by combining genetic and epidemiological data

(2011) R. J. F. Ypma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

High-throughput sequencing and clinical microbiology: progress, opportunities and challenges

(2010) Mark J Pallen et al.   CURRENT OPINION IN MICROBIOLOGY

Reconstructing disease outbreaks from genetic data: a graph approach

(2010) T Jombart et al.   HEREDITY

Inference in Epidemic Models without Likelihoods

(2009) Trevelyan McKinley et al.  

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

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

EpiCollect: Linking Smartphones to Web Applications for Epidemiology, Ecology and Community Data Collection

(2009) David M. Aanensen et al.   PLoS One

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

(2009) C. Fraser et al.   SCIENCE

Modeling Infectious Diseases in Humans and Animals:Modeling Infectious Diseases in Humans and Animals

(2008) Matthew James Keeling et al.   CLINICAL INFECTIOUS DISEASES

Estimating the impact of school closure on influenza transmission from Sentinel data

(2008) Simon Cauchemez et al.   NATURE

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

HealthMap: Global Infectious Disease Monitoring through Automated Classification and Visualization of Internet Media Reports

(2007) C. C. Freifeld et al.   JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION

Time is of the essence: exploring a measles outbreak response vaccination in Niamey, Niger

(2007) R.F Grais et al.   Journal of the Royal Society Interface