Journal Articles

2017

Lloyd-Smith, J.O. (2017) Predictions of virus spillover across species. Nature. 546: 603-604. [News & Views] Online

Plowright, R.K., Parrish, C.R., McCallum, H., Hudson, P.J., Ko, A.I., Graham, A.L., Lloyd-Smith, J.O. (2017) Pathways to zoonotic spillover. Nature Reviews Microbiology. 15: 502-510. Online

Buhnerkempe, M.G., K. C. Prager, Strelioff, C.C., Greig, D.J., Laake, J.L., Melin, S.R., DeLong, R.L., Gulland, F.M.D., Lloyd-Smith, J.O. (2017) Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions as a case study. Journal of Animal Ecology. 86: 460-472. Online

Pepin, K.M., Kay, S.L., Golas, B.D., Shriner, S.S., Gilbert, A.T., Miller, R.S., Graham, A.L., Riley, S., Cross, P.C., Samuel, M.D., Hooten, M.B., Hoeting, J.A., Lloyd-Smith, J.O., Webb, C.T., Buhnerkempe, M.G. (2017) Inferring infection hazard in wildlife populations by linking data across individual and population scales. Ecology Letters. 20: 275-292 doi: 10.1111/ele.12732. Online

2016

Lipsitch, M., Barclay, W., Raman, R., Russell, C.J., Belser, J.A., Cobey, S., Kasson, P.M., Lloyd-Smith, J.O., Maurer-Stroh, S., Riley, S., Beauchemin, C.A.A., Bedford, T., Friedrich, T.C., Handel, A., Herfst, S., Murcia, P.R., Roche, B., Wilke, C., Russell, C.A. (2016) Viral factors in influenza pandemic risk assessment. eLife. 5:e18491. Online

Schakner, Z., Buhnerkempe, M.G., Tennis, M.J., van der Leeuw, B.K., Lloyd-Smith, J.O., Blumstein, D.T. (2016) Epidemiological models to control the spread of information in marine mammals. Proceedings of the Royal Society of London, B. 283: 20162037. Online

Gostic, K.M., Ambrose, M.R., Worobey, M, Lloyd-Smith, J.O. (2016) Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting. Science. 354: 722-726. Online   PDF

Wu, N.C., Dai, L., Olson, C.A., Lloyd-Smith, J.O., Sun, R. (2016) Adaptation in protein fitness landscapes is facilitated by indirect paths. eLife. 5:e16965. Online

Muthukrishnan, R., Lloyd-Smith, J.O., Fong, P. (2016) Mechanisms of resilience: Empirically quantified positive feedbacks produce alternate stable states dynamics in a model of a tropical reef. Journal of Ecology. 104: 1662-1672. Online

A. L. Graham, D. H. Nussey, J. O. Lloyd-Smith, M. Maley, J. M. Pemberton, J. G. Pilkington, K. C. Prager, L. Smith, K. A. Watt, K. Wilson, T. N. McNeilly & F. Brulisauer. (2016) Exposure to viral and bacterial infections among Soay sheep of the St. Kilda archipelago. Epidemiology and Infection. 144: 1879-1888. Online

2015

Buhnerkempe, M.G., Gostic, K.M., Park, M., Ahsan, P., Belser, J.A., Lloyd-Smith, J.O. (2015) Mapping influenza transmission in the ferret model to transmission in humans. eLife. 4:e07969. Online

Biek, R., Pybus, O.G., Lloyd-Smith, J.O., Didelot, X. (2015) Measurably evolving pathogens in the genomic era. Trends in Ecology and Evolution. DOI: http://dx.doi.org/10.1016/j.tree.2015.03.009. Online

Gostic, K.M., Kucharski, A.J., Lloyd-Smith, J.O. (2015) Effectiveness of traveller screening for emerging pathogens is shaped by epidemiology and natural history of infection. eLife 4:e05564. Online

Heesterbeek, H., Anderson, R., Andreasen, V., Bansal, S., De Angelis, D., Dye, C., Eames, K., Edmunds, J., Frost, S, Funk, S., Hollingsworth, D., House, T., Isham, V., Klepac, P., Lessler, J., Lloyd-Smith, J., Metcalf, J., Mollison, D., Pellis, L., Pulliam, J., Roberts, M., Viboud, C., Isaac Newton Institute IDD Collaboration (2015) Modeling infectious disease dynamics in the complex landscape of global health. Science 347: aaa439-1-10. Online

2014

Buhnerkempe, M.G., Roberts, M.G., Dobson, A.P., Heesterbeek, H., Hudson, P.J., Lloyd-Smith,J.O. (2014) Eight challenges in modelling disease ecology in systems with multiple host species and multiple infectious agents. Epidemics. DOI:10.1016/j.epidem.2014.10.001. Online

Metcalf, C.J.E., Birger, R., Funk, S., Kouyos, R.D., Lloyd-Smith, J.O., Jansen, V.A.A. (2014) Five challenges in evolution and infectious diseases. Epidemics. DOI:10.1016/j.epidem.2014.12.003 Online

Gog, J.R., Pellis, L., Wood, J.L.N., McLean, A.R., Arinaminpathy, N., Lloyd-Smith, J.O. (2014) Seven challenges in modelling pathogen dynamics within-host and across scales. Epidemics. DOI: 10.1016/j.epidem.2014.09.009. Online

Lloyd-Smith, J.O., Funk, S., McLean, A.R., Riley, S., Wood, J.L.N. (2014) Nine challenges in modelling the emergence of novel pathogens. Epidemics. DOI: 10.1016/j.epidem.2014.09.00. Online

Russell CA, Kasson PM, Donis RO, Riley S, Dunbar J, Rambaut A, Asher J, Burke S, Davis CT, Garten RJ, Gnanakaran S, Hay SI, Herfst S, Lewis NS, Lloyd-Smith JO, Macken CA, Maurer-Stroh S, Neuhaus E, Parrish CR, Pepin KM, Shepard S, Smith DL, Suarez DL, Trock SC, Widdowson M, George D, Lipsitch M, Bloom JD. (2014) Improving pandemic influenza risk assessment. eLife. 3:e03883. Online

Viana, M., Mancy, R., Biek, R., Cleaveland, S., Cross, P.C., Lloyd-Smith, J.O., Haydon, D.T. (2014) Assembling evidence for identifying disease reservoirs. Trends in Ecology and Evolution. 29: 270-279. Online

Wu, Q., Prager, K.C., Goldstein, T., Alt, D.P., Galloway, R.L., Zuerner, R.L., Lloyd-Smith, J.O., Schwacke , L. (2014) Development of a real-time PCR for the detection of pathogenic Leptospira spp. in California sea lions (Zalophus californianus). Diseases of Aquatic Organisms. 110: 165-172. Online

Qi, H., Olson, C.A., Wu, N.C., Ke, R., Loverdo, C., Remenyi, R., Chu, V., Truong, S., Chen, Z., Su, S.-Y., Al-Mawsawi, L.Q., Wu, T.-T., Chen, S.-W., Lin, C., Zhong, W., Lloyd-Smith, J.O., Sun, R. (2014) A quantitative high-resolution genetic profile rapidly identifies sequence determinants of viral fitness and drug sensitivity. PLoS Pathogens. 10:e1004064. Online

Blumberg, S., Enanoria, W.T., Lloyd-Smith, J.O., Lietman, T.M., Porco, T.C. (2014) Identifying post-elimination trends for the introduction and transmissibility of measles in the United States. American Journal of Epidemiology. 179: 1375-1382. Online

Barclay, V.C., Kennedy, D.,Weaver, V.C., Sim, D., Lloyd-Smith, J.O., Read, A.F. (2014) The effect of immunodeficiency on the evolution of virulence: an experimental test with the rodent malaria Plasmodium chabaudi. American Naturalist. 184: S47-S57. Online

2013

Ke, R., Loverdo, C., Qi, H., Olson, C.A., Wu, N.C., Sun, R., Lloyd-Smith, J.O. Modelling clinical data shows active tissue concentration of daclatasvir is ten-fold lower than its plasma concentration. (2013) Journal of Antimicrobial Chemotherapy. Online

Loverdo, C. and Lloyd-Smith, J.O. (2013) Evolutionary invasion and escape in the presence of deleterious mutations. PLoS ONE. 8: e68179. Online

Blumberg, S. and Lloyd-Smith, J.O. (2013) Comparing methods for estimating R0 from the size distribution of subcritical transmission chains. Epidemics. 5: 131-145. Online

Thomassen, H.A., Fuller, T., Asefi-Najafabady, S., Shiplacoff, J., Mulembakani, P.M., Johnston, S.C., Kisalu, N.K., Lutathe, T.K., Blumberg, S., Fair, J.N., Wolfe, N.D., Shongo, R.L., LeBreton, M., Meyer, H., Wright, L.L., Muyembe, J.-J., Buermann, W., Okitolonda, E., Hensley, L., Lloyd-Smith, J.O., Smith, T. B., Rimoin A.W. (2013) Pathogen-host associations and predicted range shifts of human monkeypox in response to climate change in central Africa. PLoS ONE. 8: e66071. Online

Strelioff, C.C., Vijaykrishna, D., Riley, S., Guan, Y., Peiris, J.S.M., Lloyd-Smith, J.O. Inferring patterns of influenza transmission in swine from multiple streams of surveillance data. (2013) Proceedings of the Royal Society of London, B. 280: 20130872. Online

Ke, R. and Lloyd-Smith, J.O. Coadaptive stability of interfering particles with HIV-1 when there is an evolutionary conflict. [letter] Journal of Virology. 87: 9959.

Lloyd-Smith, J.O. (2013) Vacated niches, competitive release and the community ecology of pathogen eradication. Philosophical Transactions of the Royal Society of London, B. 368: 20120150. Online

Blumberg, S. and Lloyd-Smith, J.O. (2013) Inference of R0 and transmission heterogeneity from the size distribution of stuttering chains. PLoS Computational Biology. 9: e1002993. Online

Ke, R., Aaskov, J., Holmes, E.C., Lloyd-Smith, J.O. (2013) Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses. PLoS Pathogens. 9: e1003193. Online

Prager, K.C., Greig, D.J., Alt, D.P., Galloway, R.L., Hornsby, R.L., Palmer, L.J., Soper, J., Zuerner, R.L., Gulland, F.M.D., Lloyd-Smith, J.O. (2013) Asymptomatic and chronic carriage of Leptospira interrogans serovar Pomona in California sea lions (Zalophus californianus). Veterinary Microbiology. 164: 177-183. Online

Loverdo, C. and Lloyd-Smith, J.O. (2013) Inter-generational phenotypic mixing in viral evolution. Evolution. 67: 1815-1822. Online

Bulterys, P.L., Le, T., Quang, V.M., Nelson, K.E., Lloyd-Smith, J.O. (2013) Environmental predictors and incubation period of AIDS-associated Penicillium marneffei infection in Ho Chi Minh City, Vietnam Clinical Infectious Diseases. 56: 1273-1279. Online

Park, M.H., Loverdo, C., Schreiber, S.J., Lloyd-Smith, J.O. (2013) Multiple scales of selection influence the evolutionary emergence of novel pathogens. Philosophical Transactions of the Royal Society of London, B. 368: 20120333. Online   PDF

2012

Karesh, W.B., Dobson, A.P., Lloyd-Smith, J.O., Lubroth, J., Dixon, M.A., Bennett, M., Aldrich, S., Harrington, T., Loh, E., Machalaba, C., Thomas, M.J., Heymann, D.L. (2012) Ecology of zoonoses: natural and unnatural histories. The Lancet. 380: 1936-1945. Online   PDF

Ke, R. and Lloyd-Smith, J.O. (2012) Evolutionary analysis of Human Immunodeficiency Virus type 1 therapies based on conditionally replicating vectors. PLoS Computational Biology. 8: e1002744. Online   PDF   SUPP

Loverdo, C., Park, M., Schreiber, S.J., Lloyd-Smith, J.O. (2012) Influence of viral replication mechanisms on within-host evolutionary dynamics. Evolution. 66: 3462-3471. Online   PDF   SUPP

2011

Raffel, T.R., Lloyd-Smith, J.O., Sessions, S.K., Hudson, P.J., Rohr, J.R. (2011) Does the early frog catch the worm? Disentangling potential drivers of a parasite age-intensity relationship in tadpoles. Oecologia. 165: 1031-1042. PDF  SUPP

Metzger, V., Lloyd-Smith, J.O., Weinberger, L.S. (2011) Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS Computational Biology. 7: e1002015. PDF  SUPP

2010

Pepin, K.M., Lass, S., Pulliam, J.R.C., Read, A.F., Lloyd-Smith, J.O. (2010) Identifying genetic markers for surveillance of viral host jumps. Nature Reviews Microbiology. 8: 802- 813. PDF  SUPP

Fuller, T., Thomassen, H.A., Mulembakani, P.M., Johnston, S.C., Lloyd-Smith, J.O., Kisalu, N.K., Lutete, T.K., Blumberg, S., Fair, J.N., Wolfe, N.D., Shongo, R.L., Formenty, P., Meyer, H., Wright, L.L., Muyembe, J.-J., Buermann, W., Saatchi, S.S., Okitolonda, E., Hensley, L., Smith, T. B., Rimoin A.W. (2010) Using remote sensing to map the risk of human monkeypox in the Congo basin. EcoHealth doi:10.1007/s10393-010-0355-5. PDF  SUPP

Rimoin A.W., Mulembakani, P.M., Johnston, S., Lloyd-Smith, J.O., Kisalu, N.K., Lutete, T.K., Blumberg, S., Thomassen, H.A., Pike, B.L., Fair, J.N., Wolfe, N.D., Shongo, R.L., Graham, B.S., Formenty, P., Okitolonda, E., Hensley, L., Meyer, H., Wright, L.L., Muyembe, J.-J. (2010) Major increase in human monkeypox incidence 30 years after smallpox vaccination campaigns cease in the Democratic Republic of Congo. Proceedings of the National Academy of Sciences. 107: 16262-16267. PDF  SUPP

Volkov, I., Pepin, K., Lloyd-Smith, J.O., Banavar, J., Grenfell, B. (2010) Synthesizing within- host and population level selective pressures on viral populations: the impact of adaptive immunity on viral immune escape. Journal of the Royal Society Interface. 7: 1311-1318. PDF  SUPP

Lloyd-Smith, J. O. (2010) Modeling density dependence in heterogeneous landscapes: dispersal as a case study. Journal of Theoretical Biology 265: 160-166. PDF  

Sanchez, M.S., Lloyd-Smith, J. O., Getz, W.M. (2010) Monitoring linked epidemics: the case of tuberculosis and HIV. PLoS ONE 5: e8796. PDF  

2009

Lloyd-Smith, J. O., George, D., Pepin, K.M., Pitzer, V.E., Pulliam, J., Dobson, A.P., Hudson, P.J., Grenfell, B.T. (2009) Epidemic dynamics at the human-animal interface. Science 326: 1362-1367. PDF  SUPP

Schreiber, S.J. and Lloyd-Smith, J. O. (2009) Invasion dynamics in spatially heterogeneous environments. American Naturalist 174: 490-505. PDF  SUPP

Polansky, L., de Valpine, P., Lloyd-Smith, J. O., Getz, W.M. (2009) Likelihood ridges and multimodality in population growth rate models. Ecology 90: 2313-2320. PDF  SUPP

Hahn, J.A., Wylie, D., Dill, J., Sanchez, M., Lloyd-Smith, J. O., Page-Shafer, K., Getz, W.M. (2009) Potential impact of vaccination on the hepatitis C virus epidemic in injecting drug users. Epidemics 1: 47-57. PDF  

Sanchez, M.S., Lloyd-Smith, J.O., Williams, B.G., Porco, T.C., Ryan, S. J., Borgdorff, M.W, Mansoer, J., Dye, C., Getz, W.M. (2009) Incongruent HIV and tuberculosis epidemics in Kenya: Interacting epidemics monitor each other. Epidemics 1: 14-20. PDF  SUPP

2008

Polansky, L., de Valpine, P., Lloyd-Smith, J.O., Getz, W.M. (2008) Parameter estimation in a generalized discrete-time model of density dependence. Theoretical Ecology 1:221-229. PDF  SUPP

Auvert, B., Marseille, E., Korenromp, E.L., Lloyd-Smith, J.O., Sitta, R., Taljaard, D., Pretorius, C., Williams, B., Kahn, J.G. (2008) Estimating the resources needed and savings anticipated from roll-out of adult male circumcision in sub-Saharan Africa. PLoS ONE 3: e2679. PDF  

Lloyd-Smith, J.O., Poss, M., Grenfell, B.T. (2008) HIV-1/parasite co-infection and the emergence of new parasite strains. Parasitology 135: 795-806. PDF  

Sanchez, M.S., Lloyd-Smith, J.O., Porco, T.C., Williams, B.G., Borgdorff, M.W, Mansoer, J., Salomon, J.A., Getz, W.M. (2008) Impact of HIV on novel strategies for tuberculosis control. AIDS 22: 963-972. PDF  

2007

Lloyd-Smith, J.O., Greig, D., Ghneim, G., Hietala, S., Palmer, L., St. Leger, J., Grenfell, B.T., Gulland, F.M.D. (2007) Cyclical changes in seroprevalence of leptospirosis in California sea lions: endemic and epidemic disease in one host species? BMC Infectious Diseases 7: 125. PDF  

Graham, A.L., Cattadori, I.M., Lloyd-Smith, J.O., Ferrari, M.J., Bjornstad, O.N. (2007) Transmission consequences of co-infection: cytokines writ large? Trends in Parasitology 23: 284-291. PDF  

Cross, P.C., Johnson, P.L., Lloyd-Smith, J.O., Getz, W.M. (2007) Utility of R0 as a predictor of disease invasion in structured populations. Journal of the Royal Society Interface 4: 315-324. PDF  

Lloyd-Smith, J.O. (2007) Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed datasets, with applications to infectious disease data. PLoS ONE 2: e180. PDF  

2006

Salomon, J.A., Lloyd-Smith, J.O., Getz, W.M., Resch, S., Sanchez, M.S., Porco, T.C., Borgdorff, M.W. (2006) Prospects for advancing tuberculosis control efforts through novel therapies. PLoS Medicine 3: 1302-1309. PDF  SUPP

Williams, B.G., Lloyd-Smith, J.O., Gouws, E., Hankins, C., Getz, W.M., Dye, C., Hargrove, J., de Zoysa, I., Auvert, B. (2006) The potential impact of male circumcision on HIV in sub- Saharan Africa. PLoS Medicine 3: 1032-1040. PDF  SUPP

Bar-David, S., Lloyd-Smith, J.O., Getz, W.M. (2006) Dynamics and management of infectious disease in colonizing populations. Ecology 87: 1215-1224. PDF  

Getz, W.M. and Lloyd-Smith, J.O. (2006) Comment on 'On the regulation of populations in mammals, birds, fish and insects' I. Science 311: 1100. PDF  

2005

Lloyd-Smith, J.O., Schreiber, S.J., Kopp, P.E., Getz, W.M. (2005) Superspreading and the effect of individual variation on disease emergence. Nature 438: 355-359. PDF  SUPP

Lloyd-Smith, J.O., Cross, P.C., Briggs, C.J., Daugherty, M., Getz, W.M., Latto, J., Sanchez, M.S., Smith, A.B., Swei, A. (2005) Should we expect population thresholds for wildlife disease? Trends in Ecology & Evolution 20: 511-519. PDF  

Cross, P.C., Lloyd-Smith, J.O., Johnson, P.L., Getz, W.M. (2005) Dueling time scales of host mixing and disease recovery determine invasion of disease in structured populations. Ecology Letters 8: 587-595. PDF  

Bauch, C.T., Lloyd-Smith, J.O., Coffee, M., Galvani, A.P. (2005) Dynamically modeling SARS and other newly emerging respiratory illnesses: past, present, future. Epidemiology 16: 791-801. PDF  

Cross, P.C., Lloyd-Smith, J.O., Getz, W.M. (2005) Disentangling association patterns in fission-fusion societies using African buffalo as an example. Animal Behaviour 69: 499-506. PDF  

Porco, T.C., Lloyd-Smith, J.O., Gross, K.L., Galvani, A.P. (2005) The effect of treatment on pathogen virulence. Journal of Theoretical Biology 233: 91-102. PDF  

2004

Lloyd-Smith, J.O., Getz, W.M., Westerhoff, H.V. (2004) Frequency-dependent incidence in sexually-transmitted disease models: portrayal of pair-based transmission and effects of illness on contact behaviour. Proceedings of the Royal Society of London, B 271: 625-634. PDF  

Cross, P.C., Lloyd-Smith, J.O., Bowers, J., Hay, C.T., Hofmeyr, M., Getz, W.M. (2004) Integrating association data and disease dynamics: an illustration using African Buffalo in Kruger National Park. Annales Zoologici Fennici 41: 879-892. PDF  

2003

Lloyd-Smith, J.O.*, Galvani, A.P.*, Getz, W.M. (2003) Curtailing transmission of severe acute respiratory syndrome within a community and its hospital. Proceedings of the Royal Society of London, B 270, 1979-1989. PDF  


Before 2000: Work In Other Fields

Crawford, M.A., Bloom, M., Broadhurst, C.L., Schmidt, W.F., Cunnane, S.C., Galli, C., Gehbremeskel, K., Linseisen, F., Lloyd-Smith, J., Parkington, J. (1999) Evidence for the unique function of DHA during the evolution of the modern hominid brain. Lipids 34 supp: S39-47.

Graham, S.J., Stanchev, P.L., Lloyd-Smith, J.O.A., Bronskill, M.J., Plewes, D.B. (1995) Changes in fibroglandular volume and water content of breast tissue during the menstrual cycle observed by MR imaging at 1.5 T. Journal of Magnetic Resonance Imaging 5: 695-701.

Bloom, M., Linseisen, F., Lloyd-Smith, J., Crawford, M.A. (1999) Insights from NMR on the functional role of polyunsaturated lipids in the brain. Proceedings of the 1998 Enrico Fermi International School of Physics, on Magnetic Resonance and Brain Function: Approaches from Physics, ed. B. Maraviglia, Italian Physical Society.


Book Chapters (Peer Reviewed)

Shrestha, S. and Lloyd-Smith, J.O. (2010) Introduction to mathematical modelling of infectious disease. In Modeling Paradigms and Analysis of Disease Transmission Models, ed. A. Gumel, S. Lenhart. AMS/DIMACS Vol. 75: 1-46.

Sanchez, M.S., Lloyd-Smith, J.O., Williams, B.G., Getz, W.M. (2010) Using mathematical models to monitor and evaluate the impact of public health interventions on epidemics: the case of the TB/HIV co-pandemic in Africa. In Modeling Paradigms and Analysis of Disease Transmission Models, ed. A. Gumel, S. Lenhart. AMS/DIMACS Vol. 75: 135-186.

Bar-David, S., Lloyd-Smith, J.O., Getz, W.M. (2006) Infectious disease in spatially expanding populations: a model for reintroduced species. In Conservation Biology in Asia, ed. McNeely, J.A., McCarthy, T. M., Smith, A., Olsvig-Whittaker, L., Wikramanayake, E.D., Society for Conservation Biology (Asia Section) and Resources Himalaya, Kathmandu, Nepal, 340-362.

Lloyd-Smith, J.O., Schreiber, S.J., Getz, W.M. (2006) Moving beyond averages: Individual- level variation in disease transmission. In Mathematical studies of human disease dynamics: Emerging paradigms and challenges, ed. Gumel, A.B., Castillo-Chavez, C., Mickens, R.E., Clemence, D.P., AMS Contemporary Mathematics Series, Vol. 410, 235-258.

Getz, W. M., and Lloyd-Smith, J. O. (2006) Basic methods for modeling the invasion and spread of contagious disease. In Disease evolution: Models, concepts and data analysis, ed. Feng, Z., Dieckmann, U., Levin, S.A. AMS/DIMACS Vol. 71: 87-109.

Getz, W.M., Lloyd-Smith, J.O, Cross, P.C., Bar-David, S., Johnson, P.L., Porco, T.C., Sanchez, M.S. (2006) Modeling the invasion and spread of contagious disease in heterogeneous populations. In Disease evolution: Models, concepts and data analysis, ed. Feng, Z., Dieckmann, U., Levin, S.A. AMS/DIMACS Vol. 71: 113-144.

*authors contributed equally