Jeffrey Shaman
YOU?
Author Swipe
View article: Inferring asymptomatic carriers of antimicrobial-resistant organisms in hospitals using genomic, microbiological and patient mobility data
Inferring asymptomatic carriers of antimicrobial-resistant organisms in hospitals using genomic, microbiological and patient mobility data Open
Asymptomatic carriers of antimicrobial-resistant organisms (AMROs) can unwittingly transmit these pathogens in hospitals, contributing to the burden of healthcare-associated infections (HAIs). Surveillance in hospitals can involve differen…
View article: Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City
Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City Open
The COVID-19 pandemic in New York City (NYC) was characterized by marked disparities in disease burdens across neighborhoods. Accurate neighborhood-level forecasts are critical for planning more equitable resource allocation to reduce heal…
View article: Infectious disease forecasting to support public health: use of readily available methods to predict malaria and diarrhoeal diseases in Mozambique
Infectious disease forecasting to support public health: use of readily available methods to predict malaria and diarrhoeal diseases in Mozambique Open
This study highlights the potential of using a readily available tool for generating accurate disease forecasts. It represents a step toward scalable and accessible forecasting solutions that can enhance disease surveillance and public hea…
View article: Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter Open
The metapopulation structure enables rapid simulation at a large scale, and the data assimilation method makes the system responsive to changes in system dynamics. This model can serve as a versatile platform for modeling other infectious …
View article: Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data
Estimating nosocomial transmission of micro-organisms in hospital settings using patient records and culture data Open
Pathogenic bacteria are a major threat to patient health in hospitals. Here we leverage electronic health records from a major New York City hospital system collected during 2020-2021 to support simulation inference of nosocomial transmiss…
View article: SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first 3 years of the pandemic
SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first 3 years of the pandemic Open
The 2019 emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread created a public health emergency of international concern. However, the impact of the pandemic in Sub-Saharan Africa, as documented in…
View article: Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
View article: Internet Search Activity for Intentional Self-Harm Forums After a High-Profile News Publication: Interrupted Time Series Analysis
Internet Search Activity for Intentional Self-Harm Forums After a High-Profile News Publication: Interrupted Time Series Analysis Open
Searches for “pro-suicide” websites in the United States peaked during the week a high-profile news story was published and remained elevated for 6 months afterward, highlighting the need to avoid mentioning specific sources of explicit su…
View article: A two-variant model of SARS-COV-2 transmission: estimating the characteristics of a newly emerging strain
A two-variant model of SARS-COV-2 transmission: estimating the characteristics of a newly emerging strain Open
The study demonstrates the potential for this model-inference framework to provide real-time insights during the emergence of novel variants, aiding in timely public health responses.
View article: Challenges of COVID-19 Case Forecasting in the US, 2020–2021
Challenges of COVID-19 Case Forecasting in the US, 2020–2021 Open
During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities…
View article: Hydrometeorology and geography affect hospitalizations for waterborne infectious diseases in the United States: A retrospective analysis
Hydrometeorology and geography affect hospitalizations for waterborne infectious diseases in the United States: A retrospective analysis Open
Meteorology, hydroclimatology, and drinking water infrastructure influence the transmission of waterborne infectious diseases in the United States, but their roles are not well-understood and may vary by pathogen type or geographic region.…
View article: Quantifying suicide contagion at population scale
Quantifying suicide contagion at population scale Open
The spread of suicidal behavior among individuals is often described as a contagion; however, rigorous modeling of suicide as a dynamic, contagious process is minimal. Here, we develop and validate a model-inference system depicting suicid…
View article: Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021–22 and 2022–23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
View article: Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter
Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter Open
Summary Background Metapopulation models provide platforms for understanding infectious disease dynamics and predicting clinical outcomes across interconnected populations, particularly for large epidemics and pandemics like COVID-19. Meth…
View article: COVID-19 transmission dynamics in South Korea prior to vaccine distribution
COVID-19 transmission dynamics in South Korea prior to vaccine distribution Open
In early 2020, South Korea experienced a large coronavirus disease 2019 (COVID-19) outbreak. However, despite its proximity to China, where the virus had emerged, and the high population density of the Seoul metropolitan area, a major inte…
View article: SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the First Three Years of the Pandemic
SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the First Three Years of the Pandemic Open
The 2019 emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and its rapid spread created a public health emergency of international concern. However, the impact of the pandemic in Sub-Saharan Africa, as documented in…
View article: Challenges of COVID-19 Case Forecasting in the US, 2020–2021
Challenges of COVID-19 Case Forecasting in the US, 2020–2021 Open
During the COVID-19 pandemic, forecasting COVID-19 trends to support planning and response was a priority for scientists and decision makers alike. In the United States, COVID-19 forecasting was coordinated by a large group of universities…
View article: Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City
Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City Open
The COVID-19 pandemic in New York City (NYC) was characterized by marked disparities in disease burdens across neighborhoods. Accurate neighborhood-level forecasts are critical for planning more equitable resource allocation to reduce heal…
View article: Association Between Prosuicide Website Searches Through Google and Suicide Death in the United States From 2010 to 2021: Lagged Time-Series Analysis
Association Between Prosuicide Website Searches Through Google and Suicide Death in the United States From 2010 to 2021: Lagged Time-Series Analysis Open
Background The rate of suicide death has been increasing, making understanding risk factors of growing importance. While exposure to explicit suicide-related media, such as description of means in news reports or sensationalized fictional …
View article: Reconciling the efficacy and effectiveness of masking on epidemic outcomes
Reconciling the efficacy and effectiveness of masking on epidemic outcomes Open
During the COVID-19 pandemic, mask wearing in public settings has been a key control measure. However, the reported effectiveness of masking has been much lower than laboratory measures of efficacy, leading to doubts on the utility of mask…
View article: Evaluating completion rates of COVID-19 contact tracing surveys in New York City
Evaluating completion rates of COVID-19 contact tracing surveys in New York City Open
View article: Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic
Age-specific transmission dynamics of SARS-CoV-2 during the first 2 years of the pandemic Open
During its first 2 years, the SARS-CoV-2 pandemic manifested as multiple waves shaped by complex interactions between variants of concern, non-pharmaceutical interventions, and the immunological landscape of the population. Understanding h…
View article: System identifiability in a time-evolving agent-based model
System identifiability in a time-evolving agent-based model Open
Mathematical models are a valuable tool for studying and predicting the spread of infectious agents. The accuracy of model simulations and predictions invariably depends on the specification of model parameters. Estimation of these paramet…
View article: Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people
Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people Open
Viral respiratory infections are an important public health concern due to their prevalence, transmissibility, and potential to cause serious disease. Disease severity is the product of several factors beyond the presence of the infectious…
View article: Excess Mortality in the United States, 2020-21: County-level Estimates for Population Groups and Associations with Social Vulnerability
Excess Mortality in the United States, 2020-21: County-level Estimates for Population Groups and Associations with Social Vulnerability Open
To assess the excess mortality burden of Covid-19 in the United States, we estimated sex, age and race stratified all-cause excess deaths in each county of the US during 2020 and 2021. Using spatial Bayesian models trained on all recorded …
View article: Heterogeneity in deaths of despair: excess mortality in the US during the Covid-19 pandemic
Heterogeneity in deaths of despair: excess mortality in the US during the Covid-19 pandemic Open
The impact of Covid-19 on mortality includes both direct effects of the virus and indirect effects mediated through other causal pathways. In the United States, the indirect effects, particularly from suicides, overdoses and alcohol-induce…
View article: Spatial analysis of ischemic stroke in Spain: the roles of accessibility to healthcare and economic development
Spatial analysis of ischemic stroke in Spain: the roles of accessibility to healthcare and economic development Open
Ischemic stroke is a major cause of mortality worldwide; however, few studies have been conducted to measure the impact of the distribution of healthcare services on ischemic stroke fatality. This study aimed to explore the relationship be…
View article: Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations
Evaluation of FluSight influenza forecasting in the 2021-22 and 2022-23 seasons with a new target laboratory-confirmed influenza hospitalizations Open
Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. Forecasting teams were asked to provide national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza ho…
View article: Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty
Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty Open
Our ability to forecast epidemics far into the future is constrained by the many complexities of disease systems. Realistic longer-term projections may, however, be possible under well-defined scenarios that specify the future state of cri…
View article: Trends in Suicide Among Black Women in the United States, 1999–2020
Trends in Suicide Among Black Women in the United States, 1999–2020 Open
OBJECTIVE: Recent increases in suicide deaths among Black women in the US warrant further investigation. Our objective was to clarify the epidemiology of suicide among Black girls and women, by estimating age-period-cohort effects on suici…