A selected list of publications:

• Plowright Raina K, Parrish Colin R, McCallum Hamish, Hudson Peter J, Ko Albert I, Graham Andrea L, Lloyd-Smith James O   Pathways to zoonotic spillover Nature reviews. Microbiology, 2017; 15(8): 502-510.
• Lloyd-Smith James O   Infectious diseases: Predictions of virus spillover across species Nature, 2017; 546(7660): 603-604.
• Buhnerkempe Michael G, Prager Katherine C, Strelioff Christopher C, Greig Denise J, Laake Jeff L, Melin Sharon R, DeLong Robert L, Gulland Frances M D, Lloyd-Smith James O   Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions The Journal of animal ecology, 2017; 86(3): 460-472.
• Gostic Katelyn M, Ambrose Monique, Worobey Michael, Lloyd-Smith James O   Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting Science (New York, N.Y.), 2016; 354(6313): 722-726.
• Wu Nicholas C, Dai Lei, Olson C Anders, Lloyd-Smith James O, Sun Ren   Adaptation in protein fitness landscapes is facilitated by indirect paths eLife, 2016; 5(6313): 722-726.
• Buhnerkempe Michael G, Gostic Katelyn, Park Miran, Ahsan Prianna, Belser Jessica A, Lloyd-Smith James O   Mapping influenza transmission in the ferret model to transmission in humans eLife, 2015; 4(6313): 722-726.
• Biek Roman, Pybus Oliver G, Lloyd-Smith James O, Didelot Xavier   Measurably evolving pathogens in the genomic era Trends in ecology & evolution, 2015; 30(6): 306-13.
• Ke Ruian, Loverdo Claude, Qi Hangfei, Sun Ren, Lloyd-Smith James O   Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection PLoS computational biology, 2015; 11(6): e1004040.
• Heesterbeek Hans, Anderson Roy M, Andreasen Viggo, Bansal Shweta, De Angelis Daniela, Dye Chris, Eames Ken T D, Edmunds W John, Frost Simon D W, Funk Sebastian, Hollingsworth T Deirdre, House Thomas, Isham Valerie, Klepac Petra, Lessler Justin, Lloyd-Smith James O, Metcalf C Jessica E, Mollison Denis, Pellis Lorenzo, Pulliam Juliet R C, Roberts Mick G, Viboud Cecile, Viboud Cecile   Modeling infectious disease dynamics in the complex landscape of global health Science (New York, N.Y.), 2015; 347(6227): aaa4339.
• Lloyd-Smith James O, Funk Sebastian, McLean Angela R, Riley Steven, Wood James L N   Nine challenges in modelling the emergence of novel pathogens Epidemics, 2015; 10(6227): 35-9.
• Gog Julia R, Pellis Lorenzo, Wood James L N, McLean Angela R, Arinaminpathy Nimalan, Lloyd-Smith James O   Seven challenges in modeling pathogen dynamics within-host and across scales Epidemics, 2015; 10(6227): 45-8.
• Gostic Katelyn M, Kucharski Adam J, Lloyd-Smith James O   Effectiveness of traveller screening for emerging pathogens is shaped by epidemiology and natural history of infection eLife, 2015; 4(6227): 26-30.
• Russell Colin A, Kasson Peter M, Donis Ruben O, Riley Steven, Dunbar John, Rambaut Andrew, Asher Jason, Burke Stephen, Davis C Todd, Garten Rebecca J, Gnanakaran Sandrasegaram, Hay Simon I, Herfst Sander, Lewis Nicola S, Lloyd-Smith James O, Macken Catherine A, Maurer-Stroh Sebastian, Neuhaus Elizabeth, Parrish Colin R, Pepin Kim M, Shepard Samuel S, Smith David L, Suarez David L, Trock Susan C, Widdowson Marc-Alain, George Dylan B, Lipsitch Marc, Bloom Jesse D   Improving pandemic influenza risk assessment eLife, 2014; 3(6227): e03883.
• Viana Mafalda, Mancy Rebecca, Biek Roman, Cleaveland Sarah, Cross Paul C, Lloyd-Smith James O, Haydon Daniel T   Assembling evidence for identifying reservoirs of infection Trends in ecology & evolution, 2014; 29(5): 270-9.
• Qi Hangfei, Olson C Anders, Wu Nicholas C, Ke Ruian, Loverdo Claude, Chu Virginia, Truong Shawna, Remenyi Roland, Chen Zugen, Du Yushen, Su Sheng-Yao, Al-Mawsawi Laith Q, Wu Ting-Ting, Chen Shu-Hua, Lin Chung-Yen, Zhong Weidong, Lloyd-Smith James O, Sun Ren   A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity PLoS pathogens, 2014; 10(4): e1004064.
• Lloyd-Smith James O   Vacated niches, competitive release and the community ecology of pathogen eradication Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013; 368(1623): 20120150.
• Strelioff Christopher C, Vijaykrishna Dhanasekaran, Riley Steven, Guan Yi, Peiris J S Malik, Lloyd-Smith James O   Inferring patterns of influenza transmission in swine from multiple streams of surveillance data Proceedings. Biological sciences, 2013; 280(1762): 20130872.
• Loverdo Claude, Lloyd-Smith James O   Intergenerational phenotypic mixing in viral evolution Evolution; international journal of organic evolution, 2013; 67(6): 1815-22.
• Prager K C, Greig Denise J, Alt David P, Galloway Renee L, Hornsby Richard L, Palmer Lauren J, Soper Jennifer, Wu Qingzhong, Zuerner Richard L, Gulland Frances M D, Lloyd-Smith James O   Asymptomatic and chronic carriage of Leptospira interrogans serovar Pomona in California sea lions (Zalophus californianus) Veterinary microbiology, 2013; 164(1-2): 177-83.
• Park Miran, Loverdo Claude, Schreiber Sebastian J, Lloyd-Smith James O   Multiple scales of selection influence the evolutionary emergence of novel pathogens Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013; 368(1614): 20120333.
• Blumberg Seth, Lloyd-Smith James O   Inference of R(0) and transmission heterogeneity from the size distribution of stuttering chains PLoS computational biology, 2013; 9(5): e1002993.
• Ke Ruian, Aaskov John, Holmes Edward C, Lloyd-Smith James O   Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses PLoS pathogens, 2013; 9(2): e1003193.
• Karesh William B, Dobson Andy, Lloyd-Smith James O, Lubroth Juan, Dixon Matthew A, Bennett Malcolm, Aldrich Stephen, Harrington Todd, Formenty Pierre, Loh Elizabeth H, Machalaba Catherine C, Thomas Mathew Jason, Heymann David L   Ecology of zoonoses: natural and unnatural histories Lancet (London, England), 2012; 380(9857): 1936-45.
• Ke Ruian, Lloyd-Smith James O   Evolutionary analysis of human immunodeficiency virus type 1 therapies based on conditionally replicating vectors PLoS computational biology, 2012; 8(10): e1002744.
• Loverdo Claude, Park Miran, Schreiber Sebastian J, Lloyd-Smith James O   Influence of viral replication mechanisms on within-host evolutionary dynamics Evolution; international journal of organic evolution, 2012; 66(11): 3462-71.
• Pepin Kim M, Lass Sandra, Pulliam Juliet R C, Read Andrew F, Lloyd-Smith James O   Identifying genetic markers of adaptation for surveillance of viral host jumps Nature reviews. Microbiology, 2010; 8(11): 802-13.
• Fuller Trevon, Thomassen Henri A, Mulembakani Prime M, Johnston Sara C, Lloyd-Smith James O, Kisalu Neville K, Lutete Timothee K, Blumberg Seth, Fair Joseph N, Wolfe Nathan D, Shongo Robert L, Formenty Pierre, Meyer Hermann, Wright Linda L, Muyembe Jean-Jacques, Buermann Wolfgang, Saatchi Sassan S, Okitolonda Emile, Hensley Lisa, Smith Thomas B, Rimoin Anne W   Using Remote Sensing to Map the Risk of Human Monkeypox Virus in the Congo Basin EcoHealth, 2010; .
• Volkov Igor, Pepin Kim M, Lloyd-Smith James O, Banavar Jayanth R, Grenfell Bryan T   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 / the Royal Society, 2010; 7(50): 1311-8.
• Lloyd-Smith James O   Modeling density dependence in heterogeneous landscapes: dispersal as a case study Journal of theoretical biology, 2010; 265(2): 160-6.
• Sánchez María S, Lloyd-Smith James O, Getz Wayne M   Monitoring linked epidemics: the case of tuberculosis and HIV PloS one, 2010; 5(1): e8796.
• Lloyd-Smith James O, George Dylan, Pepin Kim M, Pitzer Virginia E, Pulliam Juliet R C, Dobson Andrew P, Hudson Peter J, Grenfell Bryan T   Epidemic dynamics at the human-animal interface Science (New York, N.Y.), 2009; 326(5958): 1362-7.
• Schreiber Sebastian J, Lloyd-Smith James O   Invasion dynamics in spatially heterogeneous environments The American naturalist, 2009; 174(4): 490-505.
• Polansky Leo, de Valpine Perry, Lloyd-Smith James O, Getz Wayne M   Likelihood ridges and multimodality in population growth rate models Ecology, 2009; 90(8): 2313-20.
• Hahn Judith A, Wylie Dennis, Dill Jesse, Sanchez Maria S, Lloyd-Smith James O, Page-Shafer Kimberly, Getz Wayne M   Potential impact of vaccination on the hepatitis C virus epidemic in injection drug users Epidemics, 2009; 1(1): 47-57.
• Lloyd-Smith James O, Poss Mary, Grenfell Bryan T   HIV-1/parasite co-infection and the emergence of new parasite strains Parasitology, 2008; 135(7): 795-806.
• Sánchez María S, Lloyd-Smith James O, Porco Travis C, Williams Brian G, Borgdorff Martien W, Mansoer John, Salomon Joshua A, Getz Wayne M   Impact of HIV on novel therapies for tuberculosis control AIDS (London, England), 2008; 22(8): 963-72.
• Lloyd-Smith James O   Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed data, with applications to infectious diseases PloS one, 2007; 2(2): e180.
• Cross Paul C, Johnson Philip L F, Lloyd-Smith James O, Getz Wayne M   Utility of R0 as a predictor of disease invasion in structured populations Journal of the Royal Society, Interface / the Royal Society, 2007; 4(13): 315-24.
• Salomon Joshua A, Lloyd-Smith James O, Getz Wayne M, Resch Stephen, Sánchez María S, Porco Travis C, Borgdorff Martien W   Prospects for advancing tuberculosis control efforts through novel therapies PLoS medicine, 2006; 3(8): e273.
• Williams Brian G, Lloyd-Smith James O, Gouws Eleanor, Hankins Catherine, Getz Wayne M, Hargrove John, de Zoysa Isabelle, Dye Christopher, Auvert Bertran   The potential impact of male circumcision on HIV in Sub-Saharan Africa PLoS medicine, 2006; 3(7): e262.
• Bar-David Shirli, Lloyd-Smith James O, Getz Wayne M   Dynamics and management of infectious disease in colonizing populations Ecology, 2006; 87(5): 1215-24.
• Getz Wayne M, Lloyd-Smith James O   Comment on “On the regulation of populations of mammals, birds, fish, and insects” I Science (New York, N.Y.), 2006; 311(5764): 1100; author reply 1100.
• Lloyd-Smith James O, Cross Paul C, Briggs Cheryl J, Daugherty Matt, Getz Wayne M, Latto John, Sanchez Maria S, Smith Adam B, Swei Andrea   Should we expect population thresholds for wildlife disease? Trends in ecology & evolution, 2005; 20(9): 511-9.
• Lloyd-Smith James O, Getz Wayne M, Westerhoff Hans V   Frequency-dependent incidence in models of sexually transmitted diseases: portrayal of pair-based transmission and effects of illness on contact behaviour Proceedings. Biological sciences / The Royal Society, 2004; 271(1539): 625-34.
• Lloyd-Smith James O, Galvani Alison P, Getz Wayne M   Curtailing transmission of severe acute respiratory syndrome within a community and its hospital Proceedings. Biological sciences / The Royal Society, 2003; 270(1528): 1979-89.