Jonathan Dushoff – MIDAS

Jonathan Dushoff

Professor

Education

Affiliations

Department of Biology, Faculty of Science, McMaster University

Projects

INTEGRATIVE MODELING OF STUDY DESIGN AND TRANSMISSION DYNAMICS TO INFER EPIDEMIC DRIVERS AND INFORM DECISION-MAKING: APPLICATIONS TO HIV AND OTHER EMERGING PATHOGENS

National Institutes of Health, National Institute of Allergy and Infectious Diseases
People: Steven Bellan, Jonathan Dushoff
2016 – 2022

MODELING CONTACT INVESTIGATION AND RAPID RESPONSE

National Institutes of Health, National Institute of General Medical Sciences
People: Wayne Getz, Travis Porco, James (Mac) Hyman, Lee Worden, Sarah Rae Wannier, Jonathan Dushoff
2011 – 2016

DYNAMIC DATA-DRIVEN DECISION MODELS FOR INFECTIOUS DISEASE CONTROL

National Institutes of Health, National Institute of General Medical Sciences
People: Alison Galvani, Wayne Getz, Meagan Fitzpatrick, Jonathan Dushoff, Zhanwei Du, Lauren Meyers
2009 – 2020

Papers

Otto SP, Day T, Arino J, Colijn C, Dushoff J, Li M, Mechai S, Van Domselaar G, Wu J, Earn DJD, Ogden NH. (2021). The origins and potential future of SARS-CoV-2 variants of concern in the evolving COVID-19 pandemic. Current biology : CB, 31(14)

Dushoff J, Park SW. (2021). Speed and strength of an epidemic intervention. Proceedings. Biological sciences, 288(1947)

Papst I, Li M, Champredon D, Bolker BM, Dushoff J, D Earn DJ. (2021). Age-dependence of healthcare interventions for COVID-19 in Ontario, Canada. BMC public health, 21(1)

Dushoff J, Colijn C, Earn DJD, Bolker BM. (2021). Transmission dynamics are crucial to COVID-19 vaccination policy. Proceedings of the National Academy of Sciences of the United States of America, 118(29)

Park SW, Champredon D, Dushoff J. (2020). Inferring generation-interval distributions from contact-tracing data. Journal of the Royal Society, Interface, 17(167)

Park SW, Bolker BM, Champredon D, Earn DJD, Li M, Weitz JS, Grenfell BT, Dushoff J. (2020). Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: framework and applications to the novel coronavirus (SARS-CoV-2) outbreak. Journal of the Royal Society, Interface, 17(168)

Weitz JS, Park SW, Eksin C, Dushoff J. (2020). Awareness-driven behavior changes can shift the shape of epidemics away from peaks and toward plateaus, shoulders, and oscillations. Proceedings of the National Academy of Sciences of the United States of America

Park SW, Sun K, Viboud C, Grenfell BT, Dushoff J. (2020). Potential roles of social distancing in mitigating the spread of coronavirus disease 2019 (COVID-19) in South Korea. medRxiv : the preprint server for health sciences

Park SW, Sun K, Champredon D, Li M, Bolker BM, Earn DJD, Weitz JS, Grenfell BT, Dushoff J. (2021). Forward-looking serial intervals correctly link epidemic growth to reproduction numbers. Proceedings of the National Academy of Sciences of the United States of America, 118(2)

Earn DJD, Ma J, Poinar H, Dushoff J, Bolker BM. (2020). Acceleration of plague outbreaks in the second pandemic. Proceedings of the National Academy of Sciences of the United States of America

Park SW, Cornforth DM, Dushoff J, Weitz JS. (2020). The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak. medRxiv : the preprint server for health sciences

Park SW, Cornforth DM, Dushoff J, Weitz JS. (2020). The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak. Epidemics, (31)

Hazelbag CM, Dushoff J, Dominic EM, Mthombothi ZE, Delva W. (2020). Calibration of individual-based models to epidemiological data: A systematic review. PLoS computational biology, 16(5)

Weitz JS, Park SW, Eksin C, Dusho J. (2020). Moving Beyond a Peak Mentality: Plateaus, Shoulders, Oscillations and Other 'Anomalous' Behavior-Driven Shapes in COVID-19 Outbreaks. medRxiv : the preprint server for health sciences

Weitz JS, Beckett SJ, Coenen AR, Demory D, Dominguez-Mirazo M, Dushoff J, Leung CY, Li G, Măgălie A, Park SW, Rodriguez-Gonzalez R, Shivam S, Zhao CY. (2020). Modeling shield immunity to reduce COVID-19 epidemic spread. Nature medicine

Park Sang Woo, Bolker Benjamin M., Champredon David, Earn David J.D., Li Michael, Weitz Joshua S., Grenfell Bryan T., Dushoff Jonathan. (2019). Reconciling early-outbreak estimates of the basic reproductive number and its uncertainty: a new framework and applications to the novel coronavirus (2019-nCoV) outbreak. Cold Spring Harbor Laboratory Press

Park SW, Champredon D, Weitz JS, Dushoff J. (2019). A practical generation-interval-based approach to inferring the strength of epidemics from their speed. Epidemics, (27)

Roswell M, Dushoff J, Winfree R. (2019). Male and female bees show large differences in floral preference. PloS one, 14(4)

Shi C, Li M, Dushoff J. (2020). Traditional Male Circumcision is Associated with Sexual Risk Behaviors in Sub-Saharan Countries Prioritized for Male Circumcision. AIDS and behavior, 24(3)

Li M, Bolker BM, Dushoff J, Ma J, Earn DJD. (2019). Patterns of seasonal and pandemic influenza-associated health care and mortality in Ontario, Canada. BMC public health, 19(1)

Li M, Dushoff J, Bolker BM. (2018). Fitting mechanistic epidemic models to data: A comparison of simple Markov chain Monte Carlo approaches. Statistical methods in medical research, 27(7)

Beauclair R, Dushoff J, Delva W. (2018). Partner age differences and associated sexual risk behaviours among adolescent girls and young women in a cash transfer programme for schooling in Malawi. BMC public health, 18(1)

Bellan SE, Champredon D, Dushoff J, Meyers LA. (2018). Couple serostatus patterns in sub-Saharan Africa illuminate the relative roles of transmission rates and sexual network characteristics in HIV epidemiology. Scientific reports, 8(1)

Tanvejsilp P, Loeb M, Dushoff J, Xie F. (2018). Out-of-Pocket Expenditures, Indirect Costs and Health-Related Quality of Life of Patients with Pulmonary Tuberculosis in Thailand. PharmacoEconomics - open, 2(3)

Tanvejsilp P, Loeb M, Dushoff J, Xie F. (2018). Healthcare Resource Uses and Out-of-Pocket Expenses Associated with Pulmonary TB Treatment in Thailand. PharmacoEconomics - open, 2(3)

Park SW, Dushoff J, Earn DJD, Poinar H, Bolker BM. (2018). Human ectoparasite transmission of the plague during the Second Pandemic is only weakly supported by proposed mathematical models. Proceedings of the National Academy of Sciences of the United States of America, 115(34)

Evans BJ, Tosi AJ, Zeng K, Dushoff J, Corvelo A, Melnick DJ. (2017). Speciation over the edge: gene flow among non-human primate species across a formidable biogeographic barrier. Royal Society open science, 4(10)

Perez-Acle T, Fuenzalida I, Martin AJM, Santibañez R, Avaria R, Bernardin A, Bustos AM, Garrido D, Dushoff J, Liu JH. (2018). Stochastic simulation of multiscale complex systems with PISKaS: A rule-based approach. Biochemical and biophysical research communications, 498(2)

Champredon D, Li M, Bolker BM, Dushoff J. (2018). Two approaches to forecast Ebola synthetic epidemics. Epidemics, (22)

Weitz JS, Beckett SJ, Brum JR, Cael BB, Dushoff J. (2017). Lysis, lysogeny and virus-microbe ratios. Nature, 549(7672)

Chiu APY, Dushoff J, Yu D, He D. (2017). Patterns of influenza vaccination coverage in the United States from 2009 to 2015. International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases, (65)

Páez DJ, Dukic V, Dushoff J, Fleming-Davies A, Dwyer G. (2017). Eco-Evolutionary Theory and Insect Outbreaks. The American naturalist, 189(6)

Rekart ML, Ndifon W, Brunham RC, Dushoff J, Park SW, Rawat S, Cameron CE. (2017). ?. Sexually transmitted infections, 93(5)

Miller E, Dushoff J, Huppert A. (2016). The risk of incomplete personal protection coverage in vector-borne disease. Journal of the Royal Society, Interface, 13(115)

Keegan LT, Dushoff J. (2016). Estimating finite-population reproductive numbers in heterogeneous populations. Journal of theoretical biology, (397)

Sempa JB, Dushoff J, Daniels MJ, Castelnuovo B, Kiragga AN, Nieuwoudt M, Bellan SE. (2016). Reevaluating Cumulative HIV-1 Viral Load as a Prognostic Predictor: Predicting Opportunistic Infection Incidence and Mortality in a Ugandan Cohort. American journal of epidemiology, 184(1)

Birger R, Kouyos R, Dushoff J, Grenfell B. (2015). Modeling the effect of HIV coinfection on clearance and sustained virologic response during treatment for hepatitis C virus. Epidemics, (12)

Hampson K, Coudeville L, Lembo T, Sambo M, Kieffer A, Attlan M, Barrat J, Blanton JD, Briggs DJ, Cleaveland S, Costa P, Freuling CM, Hiby E, Knopf L, Leanes F, Meslin FX, Metlin A, Miranda ME, Müller T, Nel LH, Recuenco S, Rupprecht CE, Schumacher C, Taylor L, Vigilato MA, Zinsstag J, Dushoff J, . (2015). Estimating the global burden of endemic canine rabies. PLoS neglected tropical diseases, 9(4)

Pulliam JRC, Bellan SE, Gambhir M, Meyers LA, Dushoff J. (2015). Evaluating Ebola vaccine trials: insights from simulation. The Lancet. Infectious diseases, 15(10)

Hampson K, Coudeville L, Lembo T, Sambo M, Kieffer A, Attlan M, Barrat J, Blanton JD, Briggs DJ, Cleaveland S, Costa P, Freuling CM, Hiby E, Knopf L, Leanes F, Meslin FX, Metlin A, Miranda ME, Müller T, Nel LH, Recuenco S, Rupprecht CE, Schumacher C, Taylor L, Antonio M, Vigilato N, Zinsstag J, Dushoff J, . (2015). Correction: Estimating the global burden of endemic canine rabies. PLoS neglected tropical diseases, 9(5)

Champredon D, Bellan SE, Delva W, Hunt S, Shi CF, Smieja M, Dushoff J. (2015). The effect of sexually transmitted co-infections on HIV viral load amongst individuals on antiretroviral therapy: a systematic review and meta-analysis. BMC infectious diseases, (15)

Bellan SE, Dushoff J, Galvani AP, Meyers LA. (2015). Reassessment of HIV-1 acute phase infectivity: accounting for heterogeneity and study design with simulated cohorts. PLoS medicine, 12(3)

Bellan SE, Pulliam JR, Pearson CA, Champredon D, Fox SJ, Skrip L, Galvani AP, Gambhir M, Lopman BA, Porco TC, Meyers LA, Dushoff J. (2015). Statistical power and validity of Ebola vaccine trials in Sierra Leone: a simulation study of trial design and analysis. The Lancet. Infectious diseases, 15(6)

Champredon D, Dushoff J. (2015). Intrinsic and realized generation intervals in infectious-disease transmission. Proceedings. Biological sciences, 282(1821)

Weitz JS, Dushoff J. (2015). Modeling post-death transmission of Ebola: challenges for inference and opportunities for control. Scientific reports, (5)

Bellan SE, Pulliam JR, Dushoff J, Meyers LA. (2014). Ebola control: effect of asymptomatic infection and acquired immunity. Lancet, 384(9953)

Keegan L, Dushoff J. (2014). Analytic calculation of finite-population reproductive numbers for direct- and vector-transmitted diseases with homogeneous mixing. Bulletin of mathematical biology, 76(5)

Bellan SE, Pulliam JR, Dushoff J, Meyers LA. (2014). Ebola virus vaccine trials: the ethical mandate for a therapeutic safety net. BMJ (Clinical research ed.), (349)

Alyass A, Almgren P, Akerlund M, Dushoff J, Isomaa B, Nilsson P, Tuomi T, Lyssenko V, Groop L, Meyre D. (2014). Modelling of OGTT curve identifies 1 h plasma glucose level as a strong predictor of incident type 2 diabetes: results from two prospective cohorts. Diabetologia, 58(1)

Akhmetzhanov AR, Worden L, Dushoff J. (2013). Effects of mixing in threshold models of social behavior. Physical review. E, Statistical, nonlinear, and soft matter physics, 88(1)

Shi CF, Kouyoumdjian FG, Dushoff J. (2013). Intimate partner violence is associated with HIV infection in women in Kenya: a cross-sectional analysis. BMC public health, (13)

Ma J, Dushoff J, Bolker BM, Earn DJ. (2013). Estimating initial epidemic growth rates. Bulletin of mathematical biology, 76(1)

Townsend SE, Sumantra IP, Pudjiatmoko, Bagus GN, Brum E, Cleaveland S, Crafter S, Dewi AP, Dharma DM, Dushoff J, Girardi J, Gunata IK, Hiby EF, Kalalo C, Knobel DL, Mardiana IW, Putra AA, Schoonman L, Scott-Orr H, Shand M, Sukanadi IW, Suseno PP, Haydon DT, Hampson K. (2013). Designing programs for eliminating canine rabies from islands: Bali, Indonesia as a case study. PLoS neglected tropical diseases, 7(8)

Champredon D, Bellan S, Dushoff J. (2013). HIV sexual transmission is predominantly driven by single individuals rather than discordant couples: a model-based approach. PloS one, 8(12)

Pulliam JR, Dushoff J. (2014). Re: "The 'case-chaos study' L adjunct or alternative to conventional case-control study methodology". American journal of epidemiology, 179(2)

Haegeman B, Hamelin J, Moriarty J, Neal P, Dushoff J, Weitz JS. (2013). Robust estimation of microbial diversity in theory and in practice. The ISME journal, 7(6)

Bartram AK, Jiang X, Lynch MD, Masella AP, Nicol GW, Dushoff J, Neufeld JD. (2014). Exploring links between pH and bacterial community composition in soils from the Craibstone Experimental Farm. FEMS microbiology ecology, 87(2)

He D, Dushoff J, Eftimie R, Earn DJ. (2013). Patterns of spread of influenza A in Canada. Proceedings. Biological sciences, 280(1770)

He D, Dushoff J, Day T, Ma J, Earn DJ. (2013). Inferring the causes of the three waves of the 1918 influenza pandemic in England and Wales. Proceedings. Biological sciences, 280(1766)

Bellan SE, Fiorella KJ, Melesse DY, Getz WM, Williams BG, Dushoff J. (2013). Extra-couple HIV transmission in sub-Saharan Africa: a mathematical modelling study of survey data. Lancet, 381(9877)

Jiang X, Langille MG, Neches RY, Elliot M, Levin SA, Eisen JA, Weitz JS, Dushoff J. (2012). Functional biogeography of ocean microbes revealed through non-negative matrix factorization. PloS one, 7(9)

Earn DJ, He D, Loeb MB, Fonseca K, Lee BE, Dushoff J. (2012). Effects of school closure on incidence of pandemic influenza in Alberta, Canada. Annals of internal medicine, 156(3)

Bellan SE, Pulliam JR, Scott JC, Dushoff J, . (2012). How to make epidemiological training infectious. PLoS biology, 10(4)

Ma J, Dushoff J, Earn DJ. (2011). Age-specific mortality risk from pandemic influenza. Journal of theoretical biology, (288)

Dushoff J, Patocs A, Shi CF. (2011). Modeling the population-level effects of male circumcision as an HIV-preventive measure: a gendered perspective. PloS one, 6(12)

Chain FJ, Dushoff J, Evans BJ. (2011). The odds of duplicate gene persistence after polyploidization. BMC genomics, (12)

Pulliam JR, Epstein JH, Dushoff J, Rahman SA, Bunning M, Jamaluddin AA, Hyatt AD, Field HE, Dobson AP, Daszak P, . (2012). Agricultural intensification, priming for persistence and the emergence of Nipah virus: a lethal bat-borne zoonosis. Journal of the Royal Society, Interface, 9(66)

Lichstein JW, Dushoff J, Ogle K, Chen A, Purves DW, Caspersen JP, Pacala SW. (2010). Unlocking the forest inventory data: relating individual tree performance to unmeasured environmental factors. Ecological applications : a publication of the Ecological Society of America, 20(3)

Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, Villaseñor I, Galván F, Cravioto P, Earn DJ, Dushoff J, Fisman D, Edmunds WJ, Hupert N, Scarpino SV, Trujillo J, Lutzow M, Morales J, Contreras A, Chávez C, Patrick DM, Brunham RC. (2009). Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America. Influenza and other respiratory viruses, 3(5)

Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M. (2009). Reconstructing influenza incidence by deconvolution of daily mortality time series. Proceedings of the National Academy of Sciences of the United States of America, 106(51)

Boettiger C, Dushoff J, Weitz JS. (2010). Fluctuation domains in adaptive evolution. Theoretical population biology, 77(1)

Ndifon W, Dushoff J, Levin SA. (2009). On the use of hemagglutination-inhibition for influenza surveillance: surveillance data are predictive of influenza vaccine effectiveness. Vaccine, 27(18)

Pulliam JR, Dushoff J. (2009). Ability to replicate in the cytoplasm predicts zoonotic transmission of livestock viruses. The Journal of infectious diseases, 199(4)

Hampson K, Dushoff J, Cleaveland S, Haydon DT, Kaare M, Packer C, Dobson A. (2009). Transmission dynamics and prospects for the elimination of canine rabies. PLoS biology, 7(3)

Hampson K, Dobson A, Kaare M, Dushoff J, Magoto M, Sindoya E, Cleaveland S. (2008). Rabies exposures, post-exposure prophylaxis and deaths in a region of endemic canine rabies. PLoS neglected tropical diseases, 2(11)

Kryazhimskiy S, Bazykin GA, Plotkin JB, Plotkin J, Dushoff J. (2008). Directionality in the evolution of influenza A haemagglutinin. Proceedings. Biological sciences, 275(1650)

Kryazhimskiy S, Bazykin GA, Dushoff J. (2008). Natural selection for nucleotide usage at synonymous and nonsynonymous sites in influenza A virus genes. Journal of virology, 82(10)

Elderd BD, Dushoff J, Dwyer G. (2008). Host-pathogen interactions, insect outbreaks, and natural selection for disease resistance. The American naturalist, 172(6)

Kryazhimskiy S, Dieckmann U, Levin SA, Dushoff J. (2007). On state-space reduction in multi-strain pathogen models, with an application to antigenic drift in influenza A. PLoS computational biology, 3(8)

Dushoff J, Plotkin JB, Viboud C, Simonsen L, Miller M, Loeb M, Earn DJ. (2007). Vaccinating to protect a vulnerable subpopulation. PLoS medicine, 4(5)

Lichstein JW, Dushoff J, Levin SA, Pacala SW. (2007). Intraspecific variation and species coexistence. The American naturalist, 170(6)

Simonsen L, Viboud C, Grenfell BT, Dushoff J, Jennings L, Smit M, Macken C, Hata M, Gog J, Miller MA, Holmes EC. (2007). The genesis and spread of reassortment human influenza A/H3N2 viruses conferring adamantane resistance. Molecular biology and evolution, 24(8)

Hampson K, Dushoff J, Bingham J, Brückner G, Ali YH, Dobson A. (2007). Synchronous cycles of domestic dog rabies in sub-Saharan Africa and the impact of control efforts. Proceedings of the National Academy of Sciences of the United States of America, 104(18)

Winfree R, Williams NM, Dushoff J, Kremen C. (2007). Native bees provide insurance against ongoing honey bee losses. Ecology letters, 10(11)

Bazykin GA, Dushoff J, Levin SA, Kondrashov AS. (2006). Bursts of nonsynonymous substitutions in HIV-1 evolution reveal instances of positive selection at conservative protein sites. Proceedings of the National Academy of Sciences of the United States of America, 103(51)

Plotkin JB, Dushoff J, Desai MM, Fraser HB. (2006). Estimating selection pressures from limited comparative data. Molecular biology and evolution, 23(8)

Winfree R, Dushoff J, Crone EE, Schultz CB, Budny RV, Williams NM, Kremen C. (2005). Testing simple indices of habitat proximity. The American naturalist, 165(6)

Dushoff J. (2005). Assessing influenza-related mortality: comment on Zucs et al. Emerging themes in epidemiology, (2)

Dushoff J, Plotkin JB, Viboud C, Earn DJ, Simonsen L. (2006). Mortality due to influenza in the United States--an annualized regression approach using multiple-cause mortality data. American journal of epidemiology, 163(2)

Smith DL, Dushoff J, McKenzie FE. (2004). The risk of a mosquito-borne infection in a heterogeneous environment. PLoS biology, 2(11)

Smith DL, Dushoff J, Perencevich EN, Harris AD, Levin SA. (2004). Persistent colonization and the spread of antibiotic resistance in nosocomial pathogens: resistance is a regional problem. Proceedings of the National Academy of Sciences of the United States of America, 101(10)

Dushoff J, Plotkin JB, Levin SA, Earn DJ. (2004). Dynamical resonance can account for seasonality of influenza epidemics. Proceedings of the National Academy of Sciences of the United States of America, 101(48)

Levin SA, Dushoff J, Plotkin JB. Evolution and persistence of influenza A and other diseases. Mathematical biosciences, (188)

Plotkin JB, Dushoff J. (2003). Codon bias and frequency-dependent selection on the hemagglutinin epitopes of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America, 100(12)

Plotkin JB, Dushoff J, Levin SA. (2002). Hemagglutinin sequence clusters and the antigenic evolution of influenza A virus. Proceedings of the National Academy of Sciences of the United States of America, 99(9)

Dushoff J, Worden L, Keymer J, Levin S. (2002). Metapopulations, community assembly, and scale invariance in aspect space. Theoretical population biology, 62(4)

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