James Lloyd-Smith

James O Lloyd-Smith

Professor, Ecology And Evolutionary Biology, University of California Los Angeles

Professor, Computational Medicine, University of California Los Angeles

UC Profile

Publications

  1. Blackmore EN, Lloyd-Smith JO. Reply to Uzoigwe: Modeling and the historical record.. Proceedings of the National Academy of Sciences of the United States of America, 2024.
  2. Mummah RO, Gomez ACR, Guglielmino AH, Borremans B, Galloway RL, Prager KC, Lloyd-Smith JO. 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, 2024.
  3. Peacock TP, Moncla L, Dudas G, VanInsberghe D, Sukhova K, Lloyd-Smith JO, Worobey M, Lowen AC, Nelson MI. The global H5N1 influenza panzootic in mammals.. Nature, 2024.
  4. Blackmore EN, Lloyd-Smith JO. Transoceanic pathogen transfer in the age of sail and steam.. Proceedings of the National Academy of Sciences of the United States of America, 2024.
  5. Prager KC, Danil K, Wurster E, Colegrove KM, Galloway R, Kettler N, Mani R, McDonough RF, Sahl JW, Stone NE, Wagner DM, Lloyd-Smith JO. Detection of Leptospira kirschneri in a short-beaked common dolphin (Delphinus delphis delphis) stranded off the coast of southern California, USA.. BMC veterinary research, 2024.
  6. Kaiser F, Morris DH, Wickenhagen A, Mukesh R, Gallogly S, Yinda KC, de Wit E, Lloyd-Smith JO, Munster VJ. Inactivation of Avian Influenza A(H5N1) Virus in Raw Milk at 63°C and 72°C.. The New England journal of medicine, 2024.
  7. Snedden CE, Lloyd-Smith JO. Predicting the presence of infectious virus from PCR data: A meta-analysis of SARS-CoV-2 in non-human primates.. PLoS pathogens, 2024.
  8. Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia C, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster.. eLife, 2024.
  9. Rosen AD, Javanbakht M, Shoptaw SJ, Seamans MJ, Lloyd-Smith JO, Gorbach PM. 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, 2023.
  10. Port JR, Morris DH, Riopelle JC, Yinda CK, Avanzato VA, Holbrook MG, Bushmaker T, Schulz JE, Saturday TA, Barbian K, Russell CA, Perry-Gottschalk R, Shaia CI, Martens C, Lloyd-Smith JO, Fischer RJ, Munster VJ. Host and viral determinants of airborne transmission of SARS-CoV-2 in the Syrian hamster.. bioRxiv : the preprint server for biology, 2023.
  11. Yinda CK, Morris DH, Fischer RJ, Gallogly S, Weishampel ZA, Port JR, Bushmaker T, Schulz JE, Bibby K, van Doremalen N, Lloyd-Smith JO, Munster VJ. Stability of Monkeypox Virus in Body Fluids and Wastewater.. Emerging infectious diseases, 2023.
  12. Helman SK, Tokuyama AFN, Mummah RO, Stone NE, Gamble MW, Snedden CE, Borremans B, Gomez ACR, Cox C, Nussbaum J, Tweedt I, Haake DA, Galloway RL, Monzón J, Riley SPD, Sikich JA, Brown J, Friscia A, Sahl JW, Wagner DM, Lynch JW, Prager KC, Lloyd-Smith JO. Pathogenic Leptospira are widespread in the urban wildlife of southern California.. Scientific reports, 2023.
  13. Qian Z, Morris DH, Avery A, Kormuth KA, Le Sage V, Myerburg MM, Lloyd-Smith JO, Marr LC, Lakdawala SS. Variability in Donor Lung Culture and Relative Humidity Impact the Stability of 2009 Pandemic H1N1 Influenza Virus on Nonporous Surfaces.. Applied and environmental microbiology, 2023.
  14. Bushmaker T, Yinda CK, Morris DH, Holbrook MG, Gamble A, Adney D, Bushmaker C, van Doremalen N, Fischer RJ, Plowright RK, Lloyd-Smith JO, Munster VJ. Comparative Aerosol and Surface Stability of SARS-CoV-2 Variants of Concern.. Emerging infectious diseases, 2023.
  15. Taube JC, Rest EC, Lloyd-Smith JO, Bansal S. The global landscape of smallpox vaccination history and implications for current and future orthopoxvirus susceptibility: a modelling study.. The Lancet. Infectious diseases, 2022.
  16. Bushmaker T, Yinda CK, Morris DH, Holbrook MG, Gamble A, Adney D, Bushmaker C, van Doremalen N, Fischer RJ, Plowright RK, Lloyd-Smith JO, Munster VJ. Comparative aerosol and surface stability of SARS-CoV-2 Variants of Concern.. bioRxiv : the preprint server for biology, 2022.
  17. Blumberg S, Lu P, Kwan AT, Hoover CM, Lloyd-Smith JO, Sears D, Bertozzi SM, Worden L. Modeling scenarios for mitigating outbreaks in congregate settings.. PLoS computational biology, 2022.
  18. Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Author Correction: Ecology, evolution and spillover of coronaviruses from bats.. Nature reviews. Microbiology, 2022.
  19. Whittier CA, Nutter FB, Johnson PLF, Cross P, Lloyd-Smith JO, Slenning BD, Stoskopf MK. Population structure, intergroup interaction, and human contact govern infectious disease impacts in mountain gorilla populations.. American journal of primatology, 2021.
  20. Muylaert RL, Davidson B, Ngabirano A, Kalema-Zikusoka G, MacGregor H, Lloyd-Smith JO, Fayaz A, Knox MA, Hayman DTS. Community health and human-animal contacts on the edges of Bwindi Impenetrable National Park, Uganda.. PloS one, 2021.
  21. Ruiz-Aravena M, McKee C, Gamble A, Lunn T, Morris A, Snedden CE, Yinda CK, Port JR, Buchholz DW, Yeo YY, Faust C, Jax E, Dee L, Jones DN, Kessler MK, Falvo C, Crowley D, Bharti N, Brook CE, Aguilar HC, Peel AJ, Restif O, Schountz T, Parrish CR, Gurley ES, Lloyd-Smith JO, Hudson PJ, Munster VJ, Plowright RK. Ecology, evolution and spillover of coronaviruses from bats.. Nature reviews. Microbiology, 2021.
  22. Gamble A, Yeo YY, Butler AA, Tang H, Snedden CE, Mason CT, Buchholz DW, Bingham J, Aguilar HC, Lloyd-Smith JO. Drivers and Distribution of Henipavirus-Induced Syncytia: What Do We Know?. Viruses, 2021.
  23. Gamble A, Fischer RJ, Morris DH, Yinda CK, Munster VJ, Lloyd-Smith JO. Heat-Treated Virus Inactivation Rate Depends Strongly on Treatment Procedure: Illustration with SARS-CoV-2.. Applied and environmental microbiology, 2021.
  24. Morris DH, Yinda KC, Gamble A, Rossine FW, Huang Q, Bushmaker T, Fischer RJ, Matson MJ, Van Doremalen N, Vikesland PJ, Marr LC, Munster VJ, Lloyd-Smith JO. Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses.. eLife, 2021.
  25. Gamble A, Fischer RJ, Morris DH, Yinda KC, Munster VJ, Lloyd-Smith JO. Heat-treated virus inactivation rate depends strongly on treatment procedure: illustration with SARS-CoV-2.. bioRxiv : the preprint server for biology, 2021.
  26. Blumberg S, Lu P, Hoover CM, Lloyd-Smith JO, Kwan AT, Sears D, Bertozzi SM, Worden L. Mitigating outbreaks in congregate settings by decreasing the size of the susceptible population.. medRxiv : the preprint server for health sciences, 2021.
  27. Schreiber SJ, Ke R, Loverdo C, Park M, Ahsan P, Lloyd-Smith JO. Cross-scale dynamics and the evolutionary emergence of infectious diseases.. Virus evolution, 2021.
  28. Dai L, Du Y, Qi H, Huber CD, Chen D, Zhang TH, Wu NC, Wang E, Lloyd-Smith JO, Sun R. Quantifying the Evolutionary Constraints and Potential of Hepatitis C Virus NS5A Protein.. mSystems, 2021.
  29. Whitmer ER, Borremans B, Duignan PJ, Johnson SP, Lloyd-Smith JO, McClain AM, Field CL, Prager KC. CLASSIFICATION AND REGRESSION TREE ANALYSIS FOR PREDICTING PROGNOSIS IN WILDLIFE REHABILITATION: A CASE STUDY OF LEPTOSPIROSIS IN CALIFORNIA SEA LIONS (ZALOPHUS CALIFORNIANUS).. Journal of zoo and wildlife medicine : official publication of the American Association of Zoo Veterinarians, 2021.
  30. Snedden CE, Makanani SK, Schwartz ST, Gamble A, Blakey RV, Borremans B, Helman SK, Espericueta L, Valencia A, Endo A, Alfaro ME, Lloyd-Smith JO. SARS-CoV-2: Cross-scale Insights from Ecology and Evolution.. Trends in microbiology, 2021.
  31. Morris DH, Yinda KC, Gamble A, Rossine FW, Huang Q, Bushmaker T, Fischer RJ, Matson MJ, van Doremalen N, Vikesland PJ, Marr LC, Munster VJ, Lloyd-Smith JO. Mechanistic theory predicts the effects of temperature and humidity on inactivation of SARS-CoV-2 and other enveloped viruses.. bioRxiv : the preprint server for biology, 2020.
  32. Zhang TH, Dai L, Barton JP, Du Y, Tan Y, Pang W, Chakraborty AK, Lloyd-Smith JO, Sun R. Predominance of positive epistasis among drug resistance-associated mutations in HIV-1 protease.. PLoS genetics, 2020.
  33. Mummah RO, Hoff NA, Rimoin AW, Lloyd-Smith JO. Controlling emerging zoonoses at the animal-human interface.. One health outlook, 2020.
  34. Borremans B, Gamble A, Prager KC, Helman SK, McClain AM, Cox C, Savage V, Lloyd-Smith JO. Quantifying antibody kinetics and RNA detection during early-phase SARS-CoV-2 infection by time since symptom onset.. eLife, 2020.
  35. Prager KC, Buhnerkempe MG, Greig DJ, Orr AJ, Jensen ED, Gomez F, Galloway RL, Wu Q, Gulland FMD, Lloyd-Smith JO. 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, 2020.
  36. Helman SK, Mummah RO, Gostic KM, Buhnerkempe MG, Prager KC, Lloyd-Smith JO. Estimating prevalence and test accuracy in disease ecology: How Bayesian latent class analysis can boost or bias imperfect test results.. Ecology and evolution, 2020.
  37. Matson MJ, Yinda CK, Seifert SN, Bushmaker T, Fischer RJ, van Doremalen N, Lloyd-Smith JO, Munster VJ. Effect of Environmental Conditions on SARS-CoV-2 Stability in Human Nasal Mucus and Sputum.. Emerging infectious diseases, 2020.
  38. Fischer RJ, Morris DH, van Doremalen N, Sarchette S, Matson MJ, Bushmaker T, Yinda CK, Seifert SN, Gamble A, Williamson BN, Judson SD, de Wit E, Lloyd-Smith JO, Munster VJ. Effectiveness of N95 Respirator Decontamination and Reuse against SARS-CoV-2 Virus.. Emerging infectious diseases, 2020.
  39. Vespignani A, Tian H, Dye C, Lloyd-Smith JO, Eggo RM, Shrestha M, Scarpino SV, Gutierrez B, Kraemer MUG, Wu J, Leung K, Leung GM. Modelling COVID-19.. Nature reviews. Physics, 2020.
  40. Fischer RJ, Morris DH, van Doremalen N, Sarchette S, Matson MJ, Bushmaker T, Yinda CK, Seifert SN, Gamble A, Williamson BN, Judson SD, de Wit E, Lloyd-Smith JO, Munster VJ. Assessment of N95 respirator decontamination and re-use for SARS-CoV-2.. medRxiv : the preprint server for health sciences, 2020.
  41. van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, Tamin A, Harcourt JL, Thornburg NJ, Gerber SI, Lloyd-Smith JO, de Wit E, Munster VJ. Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1.. The New England journal of medicine, 2020.
  42. van Doremalen N, Bushmaker T, Morris DH, Holbrook MG, Gamble A, Williamson BN, Tamin A, Harcourt JL, Thornburg NJ, Gerber SI, Lloyd-Smith JO, de Wit E, Munster VJ. Aerosol and surface stability of HCoV-19 (SARS-CoV-2) compared to SARS-CoV-1.. medRxiv : the preprint server for health sciences, 2020.
  43. Gostic K, Gomez AC, Mummah RO, Kucharski AJ, Lloyd-Smith JO. Estimated effectiveness of symptom and risk screening to prevent the spread of COVID-19.. eLife, 2020.
  44. Gostic KM, Gomez ACR, Mummah RO, Kucharski AJ, Lloyd-Smith JO. Estimated effectiveness of traveller screening to prevent international spread of 2019 novel coronavirus (2019-nCoV).. medRxiv : the preprint server for health sciences, 2020.
  45. Gostic KM, Bridge R, Brady S, Viboud C, Worobey M, Lloyd-Smith JO. Childhood immune imprinting to influenza A shapes birth year-specific risk during seasonal H1N1 and H3N2 epidemics.. PLoS pathogens, 2019.
  46. Borremans B, Faust C, Manlove KR, Sokolow SH, Lloyd-Smith JO. Cross-species pathogen spillover across ecosystem boundaries: mechanisms and theory.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019.
  47. Becker DJ, Washburne AD, Faust CL, Pulliam JRC, Mordecai EA, Lloyd-Smith JO, Plowright RK. Dynamic and integrative approaches to understanding pathogen spillover.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019.
  48. Pepin KM, Hopken MW, Shriner SA, Spackman E, Abdo Z, Parrish C, Riley S, Lloyd-Smith JO, Piaggio AJ. Improving risk assessment of the emergence of novel influenza A viruses by incorporating environmental surveillance.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019.
  49. Gostic KM, Wunder EA, Bisht V, Hamond C, Julian TR, Ko AI, Lloyd-Smith JO. 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 of London. Series B, Biological sciences, 2019.
  50. Wasik BR, de Wit E, Munster V, Lloyd-Smith JO, Martinez-Sobrido L, Parrish CR. Onward transmission of viruses: how do viruses emerge to cause epidemics after spillover?. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019.
  51. Sura SA, Smith LL, Ambrose MR, Amorim CEG, Beichman AC, Gomez ACR, Juhn M, Kandlikar GS, Miller JS, Mooney J, Mummah RO, Lohmueller KE, Lloyd-Smith JO. Ten simple rules for giving an effective academic job talk.. PLoS computational biology, 2019.
  52. Nelson MI, Lloyd-Smith JO, Simonsen L, Rambaut A, Holmes EC, Chowell G, Miller MA, Spiro DJ, Grenfell B, Viboud C. Fogarty International Center collaborative networks in infectious disease modeling: Lessons learnt in research and capacity building.. Epidemics, 2018.
  53. Whitaker DM, Reichley SR, Griffin MJ, Prager K, Richey CA, Kenelty KV, Stevens BN, Lloyd-Smith JO, Johnson CK, Duignan P, Johnson S, Rios C, DeLong R, Halaska B, Rust L, Byrne BA, Struve C, Barnum S, Soto E. HYPERMUCOVISCOUS KLEBSIELLA PNEUMONIAE ISOLATES FROM STRANDED AND WILD-CAUGHT MARINE MAMMALS OF THE US PACIFIC COAST: PREVALENCE, PHENOTYPE, AND GENOTYPE.. Journal of wildlife diseases, 2018.
  54. Hoff NA, Morier DS, Kisalu NK, Johnston SC, Doshi RH, Hensley LE, Okitolonda-Wemakoy E, Muyembe-Tamfum JJ, Lloyd-Smith JO, Rimoin AW. Varicella Coinfection in Patients with Active Monkeypox in the Democratic Republic of the Congo.. EcoHealth, 2017.
  55. Lloyd-Smith JO. Infectious diseases: Predictions of virus spillover across species.. Nature, 2017.
  56. Plowright RK, Parrish CR, McCallum H, Hudson PJ, Ko AI, Graham AL, Lloyd-Smith JO. Pathways to zoonotic spillover.. Nature reviews. Microbiology, 2017.
  57. Buhnerkempe MG, Prager KC, Strelioff CC, Greig DJ, Laake JL, Melin SR, DeLong RL, Gulland FM, Lloyd-Smith JO. Detecting signals of chronic shedding to explain pathogen persistence: Leptospira interrogans in California sea lions.. The Journal of animal ecology, 2017.
  58. Gostic KM, Ambrose M, Worobey M, Lloyd-Smith JO. Maternal antibodies' role in immunity-Response.. Science (New York, N.Y.), 2017.
  59. Pepin KM, Kay SL, Golas BD, Shriner SS, Gilbert AT, Miller RS, Graham AL, Riley S, Cross PC, Samuel MD, Hooten MB, Hoeting JA, Lloyd-Smith JO, Webb CT, Buhnerkempe MG. Inferring infection hazard in wildlife populations by linking data across individual and population scales.. Ecology letters, 2017.
  60. Schakner ZA, Buhnerkempe MG, Tennis MJ, Stansell RJ, van der Leeuw BK, Lloyd-Smith JO, Blumstein DT. Epidemiological models to control the spread of information in marine mammals.. Proceedings. Biological sciences, 2016.
  61. Gostic KM, Ambrose M, Worobey M, Lloyd-Smith JO. Potent protection against H5N1 and H7N9 influenza via childhood hemagglutinin imprinting.. Science (New York, N.Y.), 2016.
  62. Lipsitch M, Barclay W, Raman R, Russell CJ, Belser JA, Cobey S, Kasson PM, Lloyd-Smith JO, Maurer-Stroh S, Riley S, Beauchemin CA, Bedford T, Friedrich TC, Handel A, Herfst S, Murcia PR, Roche B, Wilke CO, Russell CA. Viral factors in influenza pandemic risk assessment.. eLife, 2016.
  63. Wu NC, Dai L, Olson CA, Lloyd-Smith JO, Sun R. Adaptation in protein fitness landscapes is facilitated by indirect paths.. eLife, 2016.
  64. Graham AL, Nussey DH, Lloyd-Smith JO, Longbottom D, Maley M, Pemberton JM, Pilkington JG, Prager KC, Smith L, Watt KA, Wilson K, McNEILLY TN, Brülisauer F. Exposure to viral and bacterial pathogens among Soay sheep (Ovis aries) of the St Kilda archipelago.. Epidemiology and infection, 2016.
  65. Buhnerkempe MG, Gostic K, Park M, Ahsan P, Belser JA, Lloyd-Smith JO. Mapping influenza transmission in the ferret model to transmission in humans.. eLife, 2015.
  66. Ke R, Loverdo C, Qi H, Sun R, Lloyd-Smith JO. Rational Design and Adaptive Management of Combination Therapies for Hepatitis C Virus Infection.. PLoS computational biology, 2015.
  67. Prager KC, Alt DP, Buhnerkempe MG, Greig DJ, Galloway RL, Wu Q, Gulland FMD, Lloyd-Smith JO. Antibiotic Efficacy in Eliminating Leptospiruria in California Sea Lions (Zalophus californianus) Stranding with Leptospirosis.. Aquatic mammals, 2015.
  68. Biek R, Pybus OG, Lloyd-Smith JO, Didelot X. Measurably evolving pathogens in the genomic era.. Trends in ecology & evolution, 2015.
  69. Heesterbeek H, Anderson RM, Andreasen V, Bansal S, De Angelis D, Dye C, Eames KT, Edmunds WJ, Frost SD, Funk S, Hollingsworth TD, House T, Isham V, Klepac P, Lessler J, Lloyd-Smith JO, Metcalf CJ, Mollison D, Pellis L, Pulliam JR, Roberts MG, Viboud C, Isaac Newton Institute IDD Collaboration. Modeling infectious disease dynamics in the complex landscape of global health.. Science (New York, N.Y.), 2015.
  70. Gostic KM, Kucharski AJ, Lloyd-Smith JO. Effectiveness of traveller screening for emerging pathogens is shaped by epidemiology and natural history of infection.. eLife, 2015.
  71. Lloyd-Smith JO, Mollison D, Metcalf CJ, Klepac P, Heesterbeek JA. Challenges in modelling infectious disease dynamics: preface.. Epidemics, 2015.
  72. Metcalf CJ, Birger RB, Funk S, Kouyos RD, Lloyd-Smith JO, Jansen VA. Five challenges in evolution and infectious diseases.. Epidemics, 2014.
  73. Buhnerkempe MG, Roberts MG, Dobson AP, Heesterbeek H, Hudson PJ, Lloyd-Smith JO. Eight challenges in modelling disease ecology in multi-host, multi-agent systems.. Epidemics, 2014.
  74. 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 SS, Smith DL, Suarez DL, Trock SC, Widdowson MA, George DB, Lipsitch M, Bloom JD. Improving pandemic influenza risk assessment.. eLife, 2014.
  75. Gog JR, Pellis L, Wood JL, McLean AR, Arinaminpathy N, Lloyd-Smith JO. Seven challenges in modeling pathogen dynamics within-host and across scales.. Epidemics, 2014.
  76. Lloyd-Smith JO, Funk S, McLean AR, Riley S, Wood JL. Nine challenges in modelling the emergence of novel pathogens.. Epidemics, 2014.
  77. Wu Q, Prager KC, Goldstein T, Alt DP, Galloway RL, Zuerner RL, Lloyd-Smith JO, Schwacke L. Development of a real-time PCR for the detection of pathogenic Leptospira spp. in California sea lions.. Diseases of aquatic organisms, 2014.
  78. Barclay VC, Kennedy DA, Weaver VC, Sim D, Lloyd-Smith JO, Read AF. The effect of immunodeficiency on the evolution of virulence: an experimental test with the rodent malaria Plasmodium chabaudi.. The American naturalist, 2014.
  79. Blumberg S, Enanoria WT, Lloyd-Smith JO, Lietman TM, Porco TC. Identifying postelimination trends for the introduction and transmissibility of measles in the United States.. American journal of epidemiology, 2014.
  80. Viana M, Mancy R, Biek R, Cleaveland S, Cross PC, Lloyd-Smith JO, Haydon DT. Assembling evidence for identifying reservoirs of infection.. Trends in ecology & evolution, 2014.
  81. Qi H, Olson CA, Wu NC, Ke R, Loverdo C, Chu V, Truong S, Remenyi R, Chen Z, Du Y, Su SY, Al-Mawsawi LQ, Wu TT, Chen SH, Lin CY, Zhong W, Lloyd-Smith JO, Sun R. A quantitative high-resolution genetic profile rapidly identifies sequence determinants of hepatitis C viral fitness and drug sensitivity.. PLoS pathogens, 2014.
  82. Pepin KM, Lloyd-Smith JO, Webb CT, Holcomb K, Zhu H, Guan Y, Riley S. Minimizing the threat of pandemic emergence from avian influenza in poultry systems.. BMC infectious diseases, 2013.
  83. Ke R, Loverdo C, Qi H, Olson CA, Wu NC, Sun R, Lloyd-Smith JO. Modelling clinical data shows active tissue concentration of daclatasvir is 10-fold lower than its plasma concentration.. The Journal of antimicrobial chemotherapy, 2013.
  84. Ke R, Lloyd-Smith JO. Coadaptive stability of interfering particles with HIV-1 when there is an evolutionary conflict.. Journal of virology, 2013.
  85. Thomassen HA, Fuller T, Asefi-Najafabady S, Shiplacoff JA, Mulembakani PM, Blumberg S, Johnston SC, Kisalu NK, Kinkela TL, Fair JN, Wolfe ND, Shongo RL, LeBreton M, Meyer H, Wright LL, Muyembe JJ, Buermann W, Okitolonda E, Hensley LE, Lloyd-Smith JO, Smith TB, Rimoin AW. Pathogen-host associations and predicted range shifts of human monkeypox in response to climate change in central Africa.. PloS one, 2013.
  86. Loverdo C, Lloyd-Smith JO. Evolutionary invasion and escape in the presence of deleterious mutations.. PloS one, 2013.
  87. Lloyd-Smith JO. Vacated niches, competitive release and the community ecology of pathogen eradication.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013.
  88. Blumberg S, Lloyd-Smith JO. Comparing methods for estimating R0 from the size distribution of subcritical transmission chains.. Epidemics, 2013.
  89. Strelioff CC, Vijaykrishna D, Riley S, Guan Y, Peiris JS, Lloyd-Smith JO. Inferring patterns of influenza transmission in swine from multiple streams of surveillance data.. Proceedings. Biological sciences, 2013.
  90. Blumberg S, Lloyd-Smith JO. Inference of R(0) and transmission heterogeneity from the size distribution of stuttering chains.. PLoS computational biology, 2013.
  91. Ke R, Aaskov J, Holmes EC, Lloyd-Smith JO. Phylodynamic analysis of the emergence and epidemiological impact of transmissible defective dengue viruses.. PLoS pathogens, 2013.
  92. Bulterys PL, Le T, Quang VM, Nelson KE, Lloyd-Smith JO. Environmental predictors and incubation period of AIDS-associated penicillium marneffei infection in Ho Chi Minh City, Vietnam.. Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2013.
  93. Prager KC, Greig DJ, Alt DP, Galloway RL, Hornsby RL, Palmer LJ, Soper J, Wu Q, Zuerner RL, Gulland FM, Lloyd-Smith JO. Asymptomatic and chronic carriage of Leptospira interrogans serovar Pomona in California sea lions (Zalophus californianus).. Veterinary microbiology, 2013.
  94. Loverdo C, Lloyd-Smith JO. Intergenerational phenotypic mixing in viral evolution.. Evolution; international journal of organic evolution, 2013.
  95. Park M, Loverdo C, Schreiber SJ, Lloyd-Smith JO. Multiple scales of selection influence the evolutionary emergence of novel pathogens.. Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2013.
  96. Karesh WB, Dobson A, Lloyd-Smith JO, Lubroth J, Dixon MA, Bennett M, Aldrich S, Harrington T, Formenty P, Loh EH, Machalaba CC, Thomas MJ, Heymann DL. Ecology of zoonoses: natural and unnatural histories.. Lancet (London, England), 2012.
  97. Ke R, Lloyd-Smith JO. Evolutionary analysis of human immunodeficiency virus type 1 therapies based on conditionally replicating vectors.. PLoS computational biology, 2012.
  98. Loverdo C, Park M, Schreiber SJ, Lloyd-Smith JO. Influence of viral replication mechanisms on within-host evolutionary dynamics.. Evolution; international journal of organic evolution, 2012.
  99. Metzger VT, Lloyd-Smith JO, Weinberger LS. Autonomous targeting of infectious superspreaders using engineered transmissible therapies.. PLoS computational biology, 2011.
  100. Fuller T, Thomassen HA, Mulembakani PM, Johnston SC, Lloyd-Smith JO, Kisalu NK, Lutete TK, Blumberg S, Fair JN, Wolfe ND, Shongo RL, Formenty P, Meyer H, Wright LL, Muyembe JJ, Buermann W, Saatchi SS, Okitolonda E, Hensley L, Smith TB, Rimoin AW. Using remote sensing to map the risk of human monkeypox virus in the Congo Basin.. EcoHealth, 2010.
  101. Pepin KM, Lass S, Pulliam JR, Read AF, Lloyd-Smith JO. Identifying genetic markers of adaptation for surveillance of viral host jumps.. Nature reviews. Microbiology, 2010.
  102. Raffel TR, Lloyd-Smith JO, Sessions SK, Hudson PJ, Rohr JR. Does the early frog catch the worm? Disentangling potential drivers of a parasite age-intensity relationship in tadpoles.. Oecologia, 2010.
  103. Lloyd-Smith JO. Modeling density dependence in heterogeneous landscapes: dispersal as a case study.. Journal of theoretical biology, 2010.
  104. Volkov I, Pepin KM, Lloyd-Smith JO, Banavar JR, Grenfell BT. 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, 2010.
  105. Sánchez MS, Lloyd-Smith JO, Getz WM. Monitoring linked epidemics: the case of tuberculosis and HIV.. PloS one, 2010.
  106. Lloyd-Smith JO, George D, Pepin KM, Pitzer VE, Pulliam JR, Dobson AP, Hudson PJ, Grenfell BT. Epidemic dynamics at the human-animal interface.. Science (New York, N.Y.), 2009.
  107. Schreiber SJ, Lloyd-Smith JO. Invasion dynamics in spatially heterogeneous environments.. The American naturalist, 2009.
  108. Polansky L, de Valpine P, Lloyd-Smith JO, Getz WM. Likelihood ridges and multimodality in population growth rate models.. Ecology, 2009.
  109. Hahn JA, Wylie D, Dill J, Sanchez MS, Lloyd-Smith JO, Page-Shafer K, Getz WM. Potential impact of vaccination on the hepatitis C virus epidemic in injection drug users.. Epidemics, 2009.
  110. Sánchez MS, Lloyd-Smith JO, Williams BG, Porco TC, Ryan SJ, Borgdorff MW, Mansoer J, Dye C, Getz WM. Incongruent HIV and tuberculosis co-dynamics in Kenya: interacting epidemics monitor each other.. Epidemics, 2008.
  111. Auvert B, Marseille E, Korenromp EL, Lloyd-Smith J, Sitta R, Taljaard D, Pretorius C, Williams B, Kahn JG. Estimating the resources needed and savings anticipated from roll-out of adult male circumcision in Sub-Saharan Africa.. PloS one, 2008.
  112. Sánchez MS, Lloyd-Smith JO, Porco TC, Williams BG, Borgdorff MW, Mansoer J, Salomon JA, Getz WM. Impact of HIV on novel therapies for tuberculosis control.. AIDS (London, England), 2008.
  113. Lloyd-Smith JO, Poss M, Grenfell BT. HIV-1/parasite co-infection and the emergence of new parasite strains.. Parasitology, 2008.
  114. Lloyd-Smith JO, Greig DJ, Hietala S, Ghneim GS, Palmer L, St Leger J, Grenfell BT, Gulland FM. Cyclical changes in seroprevalence of leptospirosis in California sea lions: endemic and epidemic disease in one host species?. BMC infectious diseases, 2007.
  115. Graham AL, Cattadori IM, Lloyd-Smith JO, Ferrari MJ, Bjørnstad ON. Transmission consequences of coinfection: cytokines writ large?. Trends in parasitology, 2007.
  116. Cross PC, Johnson PL, Lloyd-Smith JO, Getz WM. Utility of R0 as a predictor of disease invasion in structured populations.. Journal of the Royal Society, Interface, 2007.
  117. Lloyd-Smith JO. Maximum likelihood estimation of the negative binomial dispersion parameter for highly overdispersed data, with applications to infectious diseases.. PloS one, 2007.
  118. Salomon JA, Lloyd-Smith JO, Getz WM, Resch S, Sánchez MS, Porco TC, Borgdorff MW. Prospects for advancing tuberculosis control efforts through novel therapies.. PLoS medicine, 2006.
  119. Williams BG, Lloyd-Smith JO, Gouws E, Hankins C, Getz WM, Hargrove J, de Zoysa I, Dye C, Auvert B. The potential impact of male circumcision on HIV in Sub-Saharan Africa.. PLoS medicine, 2006.
  120. Bar-David S, Lloyd-Smith JO, Getz WM. Dynamics and management of infectious disease in colonizing populations.. Ecology, 2006.
  121. Getz WM, Lloyd-Smith JO. Comment on "On the regulation of populations of mammals, birds, fish, and insects" I.. Science (New York, N.Y.), 2006.
  122. Lloyd-Smith JO, Schreiber SJ, Kopp PE, Getz WM. Superspreading and the effect of individual variation on disease emergence.. Nature, 2005.
  123. Bauch CT, Lloyd-Smith JO, Coffee MP, Galvani AP. Dynamically modeling SARS and other newly emerging respiratory illnesses: past, present, and future.. Epidemiology (Cambridge, Mass.), 2005.
  124. Lloyd-Smith JO, Cross PC, Briggs CJ, Daugherty M, Getz WM, Latto J, Sanchez MS, Smith AB, Swei A. Should we expect population thresholds for wildlife disease?. Trends in ecology & evolution, 2005.
  125. Porco TC, Lloyd-Smith JO, Gross KL, Galvani AP. The effect of treatment on pathogen virulence.. Journal of theoretical biology, 2004.
  126. Lloyd-Smith JO, Getz WM, Westerhoff HV. Frequency-dependent incidence in models of sexually transmitted diseases: portrayal of pair-based transmission and effects of illness on contact behaviour.. Proceedings. Biological sciences, 2004.
  127. Lloyd-Smith JO, Galvani AP, Getz WM. Curtailing transmission of severe acute respiratory syndrome within a community and its hospital.. Proceedings. Biological sciences, 2003.
  128. Crawford MA, Bloom M, Broadhurst CL, Schmidt WF, Cunnane SC, Galli C, Gehbremeskel K, Linseisen F, Lloyd-Smith J, Parkington J. Evidence for the unique function of docosahexaenoic acid during the evolution of the modern hominid brain.. Lipids, 1999.
  129. Graham SJ, Stanchev PL, Lloyd-Smith JO, Bronskill MJ, Plewes DB. 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 : JMRI, 1995.