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List of works by Jonathan Dushoff

A conceptual guide to measuring species diversity

scientific article published on 9 February 2021

A double-edged sword: does highly active antiretroviral therapy contribute to syphilis incidence by impairing immunity to Treponema pallidum?

scientific article

A mixability theory for the role of sex in evolution

scholarly article

A non-negative matrix factorization framework for identifying modular patterns in metagenomic profile data

scientific article

A practical generation-interval-based approach to inferring the strength of epidemics from their speed

scientific article published on 10 January 2019

A shift from science to politics : a content analysis of COVID-19 Videos on YouTube (Preprint)

scientific article published on 14 October 2021

A simulation model of African Anopheles ecology and population dynamics for the analysis of malaria transmission

scientific article

Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses.

scientific article published in February 2009

Acceleration of plague outbreaks in the second pandemic

scientific article published on 19 October 2020

Age-dependence of healthcare interventions for SARS-CoV-2 infection in Ontario, Canada

scientific article published on 3 September 2020

Age-specific mortality risk from pandemic influenza

scientific article

Agricultural antibiotics and human health

scientific article

Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis

scientific article published on June 2011

Alternative stable states in host–phage dynamics

scientific article published in 2007

An extended catalytic model to assess changes in risk for multiple reinfections with SARS-CoV-2

scientific article published on 28 September 2023

Analytic calculation of finite-population reproductive numbers for direct- and vector-transmitted diseases with homogeneous mixing.

scientific article published on 23 April 2014

Assessing influenza-related mortality: comment on Zucs et al

scientific article

Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations

scientific article published on 22 December 2020

Bounding the levels of transmissibility & immune evasion of the Omicron variant in South Africa

scientific article published on 21 December 2021

Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites

scholarly article

Calibration of individual-based models to epidemiological data: A systematic review

scientific article published on 11 May 2020

Carrying capacity and demographic stochasticity: scaling behavior of the stochastic logistic model.

scientific article

Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus ⬇️

scientific article published on May 14, 2003

Codon usage and selection on proteins

scientific article published on 14 October 2006

Comment on "Metapopulation persistence with age-dependent disturbance or succession"

scientific article published on 01 April 2004

Community assembly and the emergence of ecosystem pattern

scientific article published in 2001

Correction to ‘Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier’.

scientific article published on 13 June 2018

Correction: Estimating the global burden of endemic canine rabies

scientific article

Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology.

scientific article published on 27 April 2018

Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study

scientific article (publication date: 2013)

Detecting selection using a single genome sequence of M. tuberculosis and P. falciparum

scientific article published in April 2004

Directionality in the evolution of influenza A haemagglutinin

scientific article published on 01 November 2008

Directionality in the evolution of influenza A haemagglutinin.

scientific article

Does Counting Different Life Stages Impact Estimates for Extinction Probabilities for Tsetse (Glossina spp)?

scientific article published in 2021

Dynamical resonance can account for seasonality of influenza epidemics

scientific article

Ebola control: effect of asymptomatic infection and acquired immunity

scientific article published on 15 October 2014

Ebola virus vaccine trials: the ethical mandate for a therapeutic safety net.

scientific article published on 10 December 2014

Eco-Evolutionary Theory and Insect Outbreaks

scientific article

Ecology and evolution of the flu

article published in 2002

Effects of mixing in threshold models of social behavior.

scientific article published on 25 July 2013

Effects of school closure on incidence of pandemic influenza in Alberta, Canada

scientific article

Equivalence of the Erlang Seir Epidemic Model and the Renewal Equation

scientific article published on 11 May 2018

Estimating finite-population reproductive numbers in heterogeneous populations

scientific article

Estimating initial epidemic growth rates

scientific article published on 23 November 2013

Estimating selection pressures from limited comparative data

scientific article published on 05 June 2006

Estimating the global burden of endemic canine rabies

scientific article published in April 2015

Evaluating Ebola vaccine trials: insights from simulation

scientific article published on 20 September 2015

Evidence that promotion of male circumcision did not lead to sexual risk compensation in prioritized Sub-Saharan countries

scientific article

Evolution and persistence of influenza A and other diseases

scientific article published in March 2004

Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus

scientific article published on 4 September 2023

Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm

scientific article published on 25 October 2013

Exploring reservoir dynamics: a case study of rabies in the Serengeti ecosystem

scientific article published in August 2008

Extra-couple HIV transmission in sub-Saharan Africa: a mathematical modelling study of survey data

scientific article

Finding Attractors on a Folding Energy Landscape

scientific article published in 2011

Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches

article by Michael Li et al published July 2018 in Statistical Methods in Medical Research

Fitting mechanistic epidemic models to data: a comparison of simple Markov chain Monte Carlo approaches

scientific article published on 22 February 2017

Fluctuation domains in adaptive evolution

scientific article published on 18 October 2009

Forward-looking serial intervals correctly link epidemic growth to reproduction numbers

scientific article published on 01 January 2021

From science to politics: COVID-19 information fatigue on YouTube

scientific article published on 23 April 2022

Functional biogeography of ocean microbes revealed through non-negative matrix factorization

scientific article (publication date: 2012)

Genomic Dynamics of Transposable Elements in the Western Clawed Frog (Silurana tropicalis) ⬇️

scientific article published on January 1, 2013

HIV sexual transmission is predominantly driven by single individuals rather than discordant couples: a model-based approach

scientific article

Healthcare Resource Uses and Out-of-Pocket Expenses Associated with Pulmonary TB Treatment in Thailand

article

Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus

scientific article

Host heterogeneity and disease endemicity: a moment-based approach

scientific article published on 01 December 1999

Host-pathogen interactions, insect outbreaks, and natural selection for disease resistance.

scientific article published on December 2008

How to Make Epidemiological Training Infectious ⬇️

scientific article published on April 3, 2012

Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models

article published in the Proceedings of the National Academy of Sciences of the United States of America

I can see clearly now: Reinterpreting statistical significance

scientific article published on 27 February 2019

Immune boosting bridges leaky and polarized vaccination models

scientific article published on 18 July 2023

Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

scientific article published on 6 May 2022

Increased risk of SARS-CoV-2 reinfection associated with emergence of Omicron in South Africa

scientific article published on 11 November 2021

Incubation-period estimates of Omicron (BA.1) variant from Taiwan, December 2021–January 2022, and its comparison to other SARS-CoV-2 variants: a statistical modeling, systematic search and meta-analysis

scientific article published on 24 July 2023

Inferring generation-interval distributions from contact-tracing data

scientific article published on 24 June 2020

Inferring generation-interval distributions from contact-tracing data

scientific article published on 27 June 2019

Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales

scientific article published on 7 September 2013

Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

scientific article published on 30 May 2023

Inferring the differences in incubation-period and generation-interval distributions of the Delta and Omicron variants of SARS-CoV-2

scientific article published on 5 July 2022

Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.

scientific article

Intermediate levels of asymptomatic transmission can lead to the highest epidemic fatalities

Intervention Serology and Interaction Substitution: Modeling the Role of 'Shield Immunity' in Reducing COVID-19 Epidemic Spread

scientific article published on 03 April 2020

Intimate partner violence is associated with HIV infection in women in Kenya: A cross-sectional analysis ⬇️

scientific article published on May 28, 2013

Intraspecific Variation and Species Coexistence

scientific article

Intraspecific variation and species coexistence

scientific article published in December 2007

Intrinsic and realized generation intervals in infectious-disease transmission

scientific article

Kaiso is highly expressed in TNBC tissues of women of African ancestry compared to Caucasian women

scientific article published on 8 September 2017

Lysis, lysogeny and virus-microbe ratios

scientific article published on September 2017

MARINE RESERVE DESIGN AND THE EVOLUTION OF SIZE AT MATURATION IN HARVESTED FISH

scholarly article by Marissa L. Baskett et al published June 2005 in Ecological Applications

Male and female bees show large differences in floral preference

scientific article published on 24 April 2019

Male and female bees show large differences in floral preference

scientific article published on 3 October 2018

Mangrove filtration of anthropogenic nutrients in the Rio Coco Solo, Panama

scientific article published in April 2004

Metapopulations, community assembly, and scale invariance in aspect space.

scientific article

Modeling post-death transmission of Ebola: challenges for inference and opportunities for control

scientific article published on 4 March 2015

Modeling shield immunity to reduce COVID-19 epidemic spread

scientific article published on 07 May 2020

Modeling the Population-Level Effects of Male Circumcision as an HIV-Preventive Measure: A Gendered Perspective ⬇️

scientific article published on December 20, 2011

Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus

scientific article published on 27 April 2015

Modelling of OGTT curve identifies 1 h plasma glucose level as a strong predictor of incident type 2 diabetes: results from two prospective cohorts

scientific article published on 8 October 2014

Mortality due to influenza in the United States--an annualized regression approach using multiple-cause mortality data

scientific article

Moving Beyond a Peak Mentality: Plateaus, Shoulders, Oscillations and Other 'Anomalous' Behavior-Driven Shapes in COVID-19 Outbreaks

scientific article published on 08 May 2020

Multi-stability and multi-instability phenomena in a mathematical model of tumor-immune-virus interactions

scientific article published on 8 April 2011

Native bees provide insurance against ongoing honey bee losses

scientific article

Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes

scientific article published on 5 March 2008

Network metrics reveal differences in social organization between two fission-fusion species, Grevy's zebra and onager.

scientific article published on 9 September 2006

On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A

scientific article published on 22 June 2007

On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A.

scientific article

On the accessibility of adaptive phenotypes of a bacterial metabolic network

scientific article

On the use of hemagglutination-inhibition for influenza surveillance: surveillance data are predictive of influenza vaccine effectiveness

scientific article

Out-of-Pocket Expenditures, Indirect Costs and Health-Related Quality of Life of Patients with Pulmonary Tuberculosis in Thailand

article

Partner age differences and associated sexual risk behaviours among adolescent girls and young women in a cash transfer programme for schooling in Malawi.

scientific article

Patterns of influenza vaccination coverage in the United States from 2009 to 2015.

scientific article published on 14 October 2017

Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada

scientific article published on 06 September 2019

Patterns of spread of influenza A in Canada

scientific article published on 11 September 2013

Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: resistance is a regional problem

scholarly article

Population-level effects of clinical immunity to malaria

scientific article

Potential Role of Social Distancing in Mitigating Spread of Coronavirus Disease, South Korea

scientific article published on 14 August 2020

Potential roles of social distancing in mitigating the spread of coronavirus disease 2019 (COVID-19) in South Korea

scientific article published on 30 March 2020

Prevalence of epistasis in the evolution of influenza A surface proteins

scientific article

Quantifying ethical tradeoffs for vaccine efficacy trials during severe epidemics

Rabies exposures, post-exposure prophylaxis and deaths in a region of endemic canine rabies

scientific article

Re: "The 'case-chaos study' L adjunct or alternative to conventional case-control study methodology".

scientific article published on 14 October 2013

Reassessment of HIV-1 acute phase infectivity: accounting for heterogeneity and study design with simulated cohorts

scientific article

Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak

scientific article published on 22 July 2020

Reconciling early-outbreak preliminary estimates of the basic reproductive number and its uncertainty: a new framework and applications to the novel coronavirus (2019-nCoV) outbreak

scientific article published on 2 February 2020

Reconstructing influenza incidence by deconvolution of daily mortality time series

scholarly article

Reevaluating Cumulative HIV-1 Viral Load as a Prognostic Predictor: Predicting Opportunistic Infection Incidence and Mortality in a Ugandan Cohort

scientific article published on 04 May 2016

Relatedness of the incidence decay with exponential adjustment (IDEA) model, "Farr's law" and SIR compartmental difference equation models

scientific article published on 09 March 2018

Robust estimation of microbial diversity in theory and in practice.

scientific article

Roles of generation-interval distributions in shaping relative epidemic strength, speed, and control of new SARS-CoV-2 variants

scientific article published on 5 May 2021

SCALING FROM TREES TO FORESTS: TRACTABLE MACROSCOPIC EQUATIONS FOR FOREST DYNAMICS

scientific article

Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier

scientific article

Species abundance, not diet breadth, drives the persistence of the most linked pollinators as plant-pollinator networks disassemble

scientific article

Speed and strength of an epidemic intervention

scientific article published on 04 March 2020

Speed and strength of an epidemic intervention

scientific article published on 31 March 2021

Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis

scientific article

Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach.

scientific article published on 21 November 2017

Stochasticity and the limits to confidence when estimating R0 of Ebola and other emerging infectious diseases

scientific article published on 11 August 2016

Surveillance to Establish Elimination of Transmission and Freedom from Dog-mediated Rabies

article

Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts

scholarly article

Testing and Isolation Efficacy: Insights from a Simple Epidemic Model

scientific article published in 2022

Testing simple indices of habitat proximity

scientific article published on 30 March 2005

The Hayflick Limit May Determine the Effective Clonal Diversity of Naive T Cells

scientific article

The combined effects of pathogens and predators on insect outbreaks

scientific article published in July 2004

The effect of sexually transmitted co-infections on HIV viral load amongst individuals on antiretroviral therapy: a systematic review and meta-analysis

scientific article published on 30 June 2015

The effects of population heterogeneity on disease invasion ⬇️

scientific article published on July 1, 1995

The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance

scientific article

The importance of the generation interval in investigating dynamics and control of new SARS-CoV-2 variants

scientific article published in June 2022

The odds of duplicate gene persistence after polyploidization.

scientific article

The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic

scientific article published in 2021

The risk of a mosquito-borne infection in a heterogeneous environment

scientific article

The risk of incomplete personal protection coverage in vector-borne disease

scientific article published on February 2016

The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

scientific article (preprint)

The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak

scientific article published on 11 May 2020

The unmitigated profile of COVID-19 infectiousness

scientific article published in August 2022

Traditional Male Circumcision is Associated with Sexual Risk Behaviors in Sub-Saharan Countries Prioritized for Male Circumcision

scientific article published on 01 March 2020

Transmission dynamics and prospects for the elimination of canine rabies

scientific article

Transmission dynamics are crucial to COVID-19 vaccination policy

scientific article published on 6 July 2021

Two approaches to forecast Ebola synthetic epidemics.

scientific article published on 24 February 2017

US flu mortality estimates are based on solid science

scientific article published in January 2006

Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors

scientific article

Unsupervised statistical clustering of environmental shotgun sequences.

scientific article

Vaccinating to protect a vulnerable subpopulation

scientific article

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