2025

Friant, J. Mistrick, A.D. Luis, C. Harden, D. Simons, E. Fichet-Calvet, R. Gibb, N. Grube, H. Henttonen, N. Imirizian, L. Moses, G.H. Perry, D. Redding, N. Chr Stenseth, K. Vandegrift, O.N. Bjornstad, A. Dobson, J.O. Lloyd-Smith, P.J. Hudson. (2025) Reducing the threats of rodent-borne diseases requires understanding and leveraging three key pillars: ecology, synanthropy, and rodentation. The Lancet Planetary Health Online

F. D’Azeredo Torres, M.E. Martinez, M. Rivard, P. Duignan, K.C. Prager, J.O. Lloyd-Smith, M.I. Nogueira Di Azevedo, W. Lilenbaum. (2025) Leptospirosis in marine mammals: an in-depth look at an underexplored ecosystem. Research in Veterinary Science, 193: 105760. Online

S.A. Sura, J.O. Lloyd-Smith*, P. Fong*. (2025) Herbivore community function shapes resilience and bistability of coral reefs. PLOS Computational Biology, 21: e1013221. Online

F. Kaiser, S. Cardenas, K.C. Yinda, R. Mukesh, M. Ochwoto, S. Gallogly, A. Wickenhagen, K. Bibby, E. de Wit, D. Morris, J.O. Lloyd-Smith, Vincent Munster. (2025) Highly Pathogenic Avian Influenza A(H5N1) virus stability in irradiated raw milk and wastewater and on surfaces, United States. Emerging Infectious Diseases, 31:833-837. Online

D.R. Daversa, J.O. Lloyd-Smith, G.M. Bucciarelli, H.B. Shaffer, D.T. Blumstein. (2025) The non-lethal effects of climate change and infectious disease on individuals and populations. Functional Ecology, 39: 916-928. Online

T. Peacock, L. Moncla, G. Dudas, D. VanInsberghe, K. Sukhova, J.O. Lloyd-Smith, M. Worobey, A.C. Lowen, M.I. Nelson (2025). The global H5N1 influenza panzootic in mammals. Nature 637: 304-313. Online

2024

E.N. Blackmore, J.O. Lloyd-Smith (2024) Reply to Uzoigwe: Modeling and the historic record. PNAS, 121: e2417598121. Online

R. Mummah, A.C.R. Gomez, A.H. Guglielmino, B. Borremans, R.L. Galloway, K.C. Prager, J.O. Lloyd-Smith (2024) Navigating cross-reactivity and host species effects in a serological assay: A case study of the microscopic agglutination test for Leptospira serology. PLOS Neglected Tropical Diseases. 18:e0012042. Online

B. Borremans, C.A. Falvo, D.E. Crowley, A. Hoegh, J.O. Lloyd-Smith, A.J. Peel, O. Restif, M. Ruiz-Aravena, R.K. Plowright (2024) Reconstructing prevalence dynamics of wildlife pathogens from pooled and individual samples. Peer Community Journal, 4: e80. Online

F. Kaiser, D.H. Morris, A. Wickenhagen, R. Mukesh, S. Gallogly, K.C. Yinda, E. de Wit, J.O. Lloyd-Smith, V.J. Munster (2024) Inactivation of avian influenza A (H5N1) virus in raw milk at 63°C and 72°C. New England Journal of Medicine, 391: 90-92. Online

K.C. Prager, K. Danil, E. Wurster, K.M. Colegrove, R. Galloway, N. Kettler, R. Mani, R.F. McDonough, J.W. Sahl, N.E. Stone, D.M. Wagner, J.O. Lloyd-Smith (2024) Detection of Leptospira kirschneri in a short-beaked common dolphin (Delphinus delphis delphis) stranded off the coast of southern California, USA. BMC Veterinary Research 20: 266. Online

E.N. Blackmore, J.O. Lloyd-Smith (2024) Transoceanic pathogen circulation in the age of sail and steam. PNAS, 121: e2400425121. Online

C.E. Snedden, J.O. Lloyd-Smith (2024) Predicting the presence of infectious virus from PCR data: A meta-analysis of SARS-CoV-2 in non-human primates. PLOS Pathogens 20: e1012171.  Online

The Lancet-PPATS Commission on Prevention of Viral Spillover, T.C. Mettenleiter, A.S. Winkler (2024). Draft of WHO Pandemic Agreement plays down primary prevention [Correspondence]. The Lancet 403: 525-526.  Online

J.R. Port, D.H. Morris, J.C. Riopelle, C.K. Yinda, V.A. Avanzato, M.G. Holbrook, T. Bushmaker, J.E. Schulz, T.A. Saturday, K. Barbian, C.A. Russell, R. Perry-Gottschalk, C.I. Shaia, C. Martens, J.O. Lloyd-Smith, R.J. Fischer, V.J. Munster. (2024) Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster. eLife. 12:RP87094. Online

2023

A.D. Rosen, M. Javanbakht, S.J. Shoptaw, M.J. Seamans, J.O. Lloyd-Smith*, P.M. Gorbach* (2023) Association of current substance use treatment with future reduced methamphetamine use in an observational cohort of men who have sex with men in Los Angeles. Journal of Substance Use and Addiction Treatment 157: 209228. Online

C.K. Yinda*, D.H. Morris*, R.J. Fischer, S. Gallogly, Z.A. Weishampel, J.R. Port, T. Bushmaker, J.E. Schulz, K. Bibby, N. van Doremalen, J.O. Lloyd-Smith, V.J. Munster. (2023) Stability of monkeypox virus in body fluids and wastewater. Emerging Infectious Diseases 29: 2065-2072. Online

S.K. Helman, A.F.N. Tokuyama, R.O. Mummah, Nathan E. Stone, M.W. Gamble, C.E. Snedden, B. Borremans, A.C.R. Gomez, C. Cox†, J. Nussbaum†, I. Tweedt†, D.A. Haake, R.L. Galloway, J. Monzón, S.P.D. Riley, J.A. Sikich, J. Brown, A. Friscia, Jason W. Sahl, David M. Wagner, J.W. Lynch, K.C. Prager, J.O. Lloyd-Smith. (2023) Pathogenic Leptospira are widespread in the urban wildlife of southern California. Scientific Reports 13: 14368. Online

B. Borremans, R.O. Mummah, A.H. Guglielmino, R.L. Galloway, N. Hens, K.C. Prager, J.O. Lloyd-Smith. (2023) Inferring time of infection from field data using dynamic models of antibody decay. Methods in Ecology and Evolution 14: 2654-2667. Online

Z. Qian *, D.H. Morris*, A. Avery, K.A. Kormuth, M.M. Myerburg, J.O. Lloyd-Smith, L.C. Marr, S.S. Lakdawala. (2023) Variability in donor lung culture and relative humidity impact the stability of 2009 pandemic H1N1 influenza virus on nonporous surfaces. Applied and Environmental Microbiology 89: e00633-23. Online

T. Bushmaker*, C.K. Yinda*, D.H. Morris*, M.G. Holbrook, A. Gamble, D. Adney, C. Bushmaker, N. van Doremalen, R.J. Fischer, R.K. Plowright, J.O. Lloyd-Smith, V.J. Munster (2023) Comparative aerosol and surface stability of SARS-CoV-2 Variants of Concern. Emerging Infectious Diseases 29: 1033-1036. Online

J.C. Taube, E.C. Rest, J.O. Lloyd-Smith, S. Bansal. (2023) The global landscape of smallpox vaccination history and implications for current and future orthopoxvirus susceptibility: a modelling study. The Lancet Infectious Diseases, 23: 454-462. Online

2022

S. Blumberg, P. Lu, A.T. Kwan, C.M. Hoover, J.O. Lloyd-Smith, D. Sears, S.M. Bertozzi, L. Worden. (2022) Modeling scenarios for mitigating outbreaks in congregate settings. PLOS Computational Biology. 18:e1010308. Online

C.A. Whittier, F.B. Nutter, P.L.F. Johnson, P. Cross, J.O. Lloyd-Smith, B.D. Slenning, M.K. Stoskopf. (2022) Population structure, intergroup interaction, and human contact govern infectious disease impacts in mountain gorilla populations. American Journal of Primatology. 84:e23291. Online

2021

M. Ruiz-Aravena*, C. McKee*, A. Gamble, T. Lunn, A. Morris, C.E. Snedden, C.K. Yinda, J.R. Port, D.W. Buchholz, Y.Y. Yeo, C. Faust, E. Jax, L. Dee, C. Falvo, D. Jones, M. Kessler, C. Falvo, D. Crowley, N. Bharti, C.E. Brook, H.C. Aguilar, A.J. Peel, O. Restif, T. Schountz, C.R. Parrish, E.S. Gurley, J.O. Lloyd-Smith, P. Hudson, V.J. Munster, R.K. Plowright. (2022) Ecology, evolution and spillover of coronaviruses from bats. Nature Reviews Microbiology. 20:299-314. Online

L. Muylaert, B. Davidson, A. Ngabirano, G. Kalema-Zikusoka, H. MacGregor, J.O. Lloyd-Smith, A. Fayaz, M.A. Knox, D.T.S. Hayman. (2021) Community health and human-animal contacts on the edges of Bwindi Impenetrable National Park, Uganda. PLOS ONE. 16:e0254467. https://doi.org/10.1371/journal.pone.0254467

Gamble A., Yeo Y.Y.*, Butler A.A.*, Tang H., Snedden C.E., Mason C.T., Buchholz D.W., Bingham J., Aguilar H.C. and Lloyd-Smith J.O. (2021). Drivers and distribution of henipavirus-induced syncytia: what do we know? Viruses 13:1755. Online

Gamble A.*, Fischer R.J.*, Morris D.H., Yinda K.C., Munster V.J. and Lloyd-Smith J.O. (2021). Heat-treated virus inactivation rate depends strongly on treatment procedure: illustration with SARS-CoV-2. Applied and Environmental Microbiology 87:e00314-21. Online

Snedden, C.E.*, Makanani, S.K.*, Schwartz, S.T., Gamble, A., Blakey, R.V., Borremans, B., Helman, S.K., Espericueta, L., Valencia, A., Endo, A., Alfaro, M.E., Lloyd-Smith, J.O. (2021). SARS-CoV-2: cross-scale insights from ecology and evolution. Trends in Microbiology 29:593-605. Online

Morris, D.H.*, Yinda, K.C.*, Gamble, A.*, Rossine, F.W., Huang, Q., Bushmaker, T., Fischer, R.J., Matson, M.J., van Doremalen, N., Vikesland, P.J., Marr, L.C., Munster, V.J., Lloyd-Smith, J.O. (2021). Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses. eLife 10:e65902. Online

Du, Y.*, Dai, L.*, Qi, H., Huber, C., Chen, D., Zhang, T., Wu, N.C., Wang, E., Lloyd‐Smith,
J.O., Sun, R. (2021). Quantifying the evolutionary constraints and potential of HCV NS5A protein.
mSystems. mSystems, in press. Online

Whitmer, E.R., Borremans, B., Duignan, P.J., Johnson, S.P., Lloyd-Smith, J.O., McClain, A.M., Field, C.L., Prager, K.C. (2021). Classification and regression tree (CART) analysis for predicting prognosis in wildlife rehabilitation: a case study of leptospirosis in California sea lions (Zalophus californianus). Journal of Zoo and Wildlife Medicine 52:38-48. Online

Schreiber, S.J., Ke, R., Loverdo, C., Park, M., Ahsan, P., Lloyd-Smith, J.O. (2021). Cross-scale dynamics and the evolutionary emergence of infectious diseases. Virus Evolution 7:veaa105. Online

2020

Mummah, R.O., Hoff, N.A., Rimoin, A.W., Lloyd-Smith, J.O. (2020). Controlling emerging zoonoses at the animal-human interface. One Health Outlook 2:1-15. Online

Zhang, T.H., Dai, L., Barton, J.P., Du, Y., Tan, Y., Pang, W., … Sun, R. (2020). Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease. PLoS Genetics 16:e1009009. Online

Matson, M.J., Yinda, C.K., Seifert, S.N., Bushmaker, T., Fischer, R.J., van Doremalen, N., …, Munster, V.J. (2020). Effect of environmental conditions on SARS-CoV-2 stability in human nasal mucus and sputum. Emerging Infectious Diseases 26:2276. Online

Fischer, R.J.*, Morris, D.H.*, van Doremalen, N., Sarchette, S., Matson, J., Bushmaker, T., Yinda, C.K., Seifert, S., Gamble, A., Williamson, B., Judson, S., de Wit, E., Lloyd-Smith, J.O., Munster, V.J. (2020). Effectiveness of N95 respirator decontamination and reuse against SARS-CoV-2 virus. Emerging Infectious Diseases 26:2253. Online

Vespignani, A., Tian, H., Dye, C., Lloyd-Smith, J.O., Eggo, R.M., Shrestha, M., … Leung, G.M. (2020). Modelling covid-19. Nature Reviews Physics 2:279-281. Online

Borremans, B., Gamble, A., Prager, K.C., Helman, S.K., McClain, A.M., Cox, C., Savage, V., Lloyd-Smith, J.O. (2020). Quantifying antibody kinetics and RNA shedding during early-phase SARS-CoV-2 infection. eLife 9:e60122. Online

van Doremalen, N.*, Bushmaker, T.*, Morris, D.H.*, Holbrook, M.G., Gamble, A., Williamson, B.N., Tamin, A., Harcourt, J.L., Thornburg, N.J., Gerber, S.I., Lloyd-Smith, J.O., de Wit, E., Munster, V.J. (2020). Aerosol and surface stability of SARS-CoV-2 as compared with SARS-CoV-1. New England Journal of Medicine 382:1564-1567. Online

Prager, K.C., Buhnerkempe, M.G., Greig, D.J., Orr, A.J., Jensen, E.D., Gomez, F., Galloway, R.L., Wu, Q., Gulland, F.M.D., Lloyd-Smith, J.O. (2020). Linking longitudinal and cross-sectional biomarker data to understand host-pathogen dynamics: Leptospira in California sea lions (Zalophus californianus) as a Case Study. PLoS Neglected Tropical Diseases 6:e0008407. Online

Helman, S., Mummah, R., Gostic, K.M., Buhnerkempe, M., Prager, K.C., Lloyd-Smith, J.O. (2020). Estimating prevalence and test accuracy in disease ecology: how Bayesian latent class analysis can boost or bias imperfect test results. Ecology and Evolution 14:7221-7232. Online

Gostic, K., Gomez, A. C., Mummah, R. O., Kucharski, A. J., Lloyd-Smith, J. O. (2020). Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19. eLife 9:e55570. Online

Schreiber, S.J., Ke, R., Loverdo, C., Park, M., Ahsan, P., Lloyd-Smith, J.O. (2019). Cross-scale dynamics and the evolutionary emergence of infectious diseases. Virus Evolution in press. Online

2019

Gostic, K.M., Wunder Jr, E.A., Bisht, V., Hamond, C., Julian, T.R., Ko, A.I., Lloyd-Smith, J.O. (2019). Mechanistic dose–response modelling of animal challenge data shows that intact skin is a crucial barrier to leptospiral infection. Philosophical Transactions of The Royal Society B 374:20190367. Online

Wasik, B. R., de Wit, E., Munster, V., Lloyd-Smith, J. O., Martinez-Sobrido, L., & Parrish, C. R. (2019). Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover? Philosophical Transactions of The Royal Society B 374:20190017. Online

Borremans, B., Faust, C., Manlove, K.R., Sokolow, S.S., Lloyd-Smith, J.O. (2019). Cross-species pathogen spillover across ecosystem boundaries: mechanisms and theory.
Philosophical Transactions of The Royal Society B 374:20180344. Online

Becker, D.J., Washburne, A.D., Faust, C.L., Pulliam, J.R., Mordecai, E.A., Lloyd-Smith, J.O., Plowright, R.K. (2019). Dynamic and integrative approaches to understanding pathogen spillover. Philosophical Transactions of the Royal Society B 374:20190014 Online

Pepin, K.M., Hopken, M.W., Shriner, S.A., Spackman, E., Abdo, Z., Parrish, C., … & Piaggio, A.J. (2019). Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance. Philosophical Transactions of the Royal Society B 374, 20180346. Online

Sura, S.A., Smith, L.L., Ambrose, M.R., Amorim, C.E.G., Beichman, A.C., Gomez, A.C., … Lloyd-Smith, J.O. (2019). Ten simple rules for giving an effective academic job talk. PLoS Computational Biology 15:e1007163. Online

Nelson, M.I., Lloyd-Smith, J.O., Simonsen, L., Rambaut, A., Holmes, E.C., Chowell, G., … Viboud, C. (2019). Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building. Epidemics 26, 116-127. Online

Ambrose, M.R., Kucharski, A.J., Formenty, P., Muyembe-Tamfum, J.J., Rimoin, A.W., Lloyd-Smith, J.O. (2019). Quantifying transmission of emerging zoonoses: using mathematical models to maximize the value of surveillance data. BioRxiv 677021. Online

Gostic, K.M., Bridge, R., Brady, S., Viboud, C., Worobey, M., Lloyd-Smith, J.O. (2019). Childhood immune imprinting to influenza A shapes birth year-specific risk during seasonal H1N1 and H3N2 epidemics. PLoS pathogens 15, e1008109. Online

2018

Nelson, M. I., Lloyd-Smith, J. O., Simonsen, L., Rambaut, A., Holmes, E. C., Chowell, G., … Viboud, C. (2018). Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building. Epidemics 26:116-127. Online

Whitaker, D., Reichly, S., Griffin, M., Prager, K. C., Richey, C., Kenelty, K., Stevens, B., Lloyd-Smith, J. O., Kreuder Johnson, C., Duignan, P., Johnson, S., Rios, C., DeLong, R., Halaska, B., Rust, L., Byrne, B., Struve, C., Mapes, S., Soto., E. (2018) Hypermucoviscous Klebsiella pneumoniae isolates from stranded and wild-caught marine mammals of the United States Pacific Coast: prevalence, phenotype and genotype. Journal of Wildlife Diseases, 54(4), 659–670. Online

2017

Gostic, K. M., Ambrose, M., Worobey, M., & Lloyd-Smith, J. O. (2017). Do maternal antibodies facilitate hemagglutinin imprinting to influenza A viruses encountered early in childhood? BioRxiv, 110981. Online

Hoff, N. A., Morier, D. S., Kisalu, N. K., Johnston, S. C., Doshi, R. H., Hensley, L. E., … Rimoin, A. W. (2017). Varicella Coinfection in Patients with Active Monkeypox in the Democratic Republic of the Congo. EcoHealth, 14(3), 564–574. Online

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

Laake, J. L., S. R. Melin, A. J. Orr, D. J. Greig, K. C. Prager, R. L. DeLong, and J. D. Harris. 2016. California sea lion sex and age specific morphometry. Page 21 in N. T. M. U.S. Dep. Commer., editor.
Burge, C. A., C. S. Friedman, R. Getchell, M. House, K. D. Lafferty, L. D. Mydlarz, K. C. Prager, K. P. Sutherland, T. Renault, I. Kiryu, and R. Vega-Thurber. (2016) Complementary approaches to diagnosing marine diseases: a union of the modern and the classic. Philosophical Transactions of the Royal Society of London B: Biological Sciences 371.

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

Prager KC, Alt DP, Buhnerkempe MG, Greig DJ, Galloway RL, Wu Q, Gulland FMD, & Lloyd-Smith JO. (2015). Antibiotic efficacy in eliminating leptospiruria in California sea lions (Zalophus californianus) stranding with leptospirosis stranding with leptospirosis: 14 cases (2010-2011). Aquatic Mammals 41(2): 203-212. DOI: 10.1578/AM.41.2.2015.203.

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

Burge, C. A., C. M. Eakin, C. S. Friedman, B. Froelich, P. K. Hershberger, E. E. Hofmann, L. E. Petes, K. C. Prager, E. Weil, B. L. Willis, S. E. Ford, and C. D. Harvell. 2013. Climate Change Influences on Marine Infectious Diseases: Implications for Management and Society. Annual review of marine science 6:249-277.

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
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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
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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
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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
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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.
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Metzger, V., Lloyd-Smith, J.O., Weinberger, L.S. (2011) Autonomous targeting of infectious superspreaders using engineered transmissible therapies. PLoS Computational Biology. 7:
e1002015.
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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.
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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.
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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.
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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.
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Lloyd-Smith, J. O. (2010) Modeling density dependence in heterogeneous landscapes:
dispersal as a case study. Journal of Theoretical Biology 265: 160-166.
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Sanchez, M.S., Lloyd-Smith, J. O., Getz, W.M. (2010) Monitoring linked epidemics: the case of tuberculosis and HIV. PLoS ONE 5: e8796.
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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.
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Schreiber, S.J. and Lloyd-Smith, J. O. (2009) Invasion dynamics in spatially heterogeneous environments. American Naturalist 174: 490-505.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Bar-David, S., Lloyd-Smith, J.O., Getz, W.M. (2006) Dynamics and management of
infectious disease in colonizing populations. Ecology 87: 1215-1224.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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