Publications List

Publications List

Accepted/In Press

  • Yang, W., M. Lipsitch and J. Shaman: Inference of seasonal and pandemic influenza transmission dynamics using big surveillance data. Proceedings of the National Academy of Sciences.


  • Lofgren, E., M. E. Halloran, C. M. Rivers, J. M. Drake, T. C. Porco, B. Lewis, W. Yang, A. Vespignani, J. Shaman, J. N. S. Eisenberg, M. C. Eisenberg, M. Marathe, S. V. Scarpino, K. A. Alexander, R. Meza, M. J. Ferrari, J. M. Hyman, L. A. Meyers and S. Eubank, 2014: Opinion: Mathematical models: A key tool for outbreak response. Proceedings of the National Academy of Sciences, 111(51):18,095-18,096, doi:10.1073/pnas.1421551111.
  • Shaman, J., W. Yang and S. Kandula, 2014: Inference and Forecast of the Current West African Ebola Outbreak in Guinea, Sierra Leone and Liberia. PLOS Currents Outbreaks, 2014 Oct 31. Edition 1. doi: 10.1371/currents.outbreaks.3408774290b1a0f2dd7cae877c8b8ff6
  • Halloran, M. E., A. Vespignani, N. Bharti, L. R. Feldstein, K. A. Alexander, M. Ferrari, J. Shaman, J. M. Drake, T. Porco, J. N. S. Eisenberg, S. Y. Del Valle, E. Lofgren, S. V. Scarpino, M. C. Eisenberg, D. Gao, J. M. Hyman, S. Eubank, and I. M. Longini, 2014: Ebola: Mobility data. Science, 346(6208):443.
  • Shaman, J., 2014: Letter to the Editor: Caution needed when using gridded meteorological data products for analyses in Africa. Eurosurveillance, 19(41):pii=20930.
  • Yang, W., and J. Shaman, 2014: Does exposure to poultry and wild fowl confer immunity to H5N1? Chinese Medical Journal, 127(18):3335-3343.
  • Shaman, J., 2014: The Seasonal Effects of ENSO on European Precipitation: Observational Analysis. Journal of Climate, 27(17): 6423-6438.
  • Quinn, A., J. D. Tamerius, M. Perzanowski, J. S. Jacobson, I. Goldstein, L. Acosta and J. Shaman, 2014: Predicting indoor heat exposure risk during extreme heat events. Science of the Total Environment, 490: 686-693.
  • Gog, J. R., S. Ballesteros, C. Viboud, L. Simonsen, O. N. Bjornstad, J. Shaman, D. L. Chao, F. Khan, B. T. Grenfell, 2014: Spatial transmission of 2009 pandemic influenza in the US. PLOS Computational Biology, 10(6): e1003635, doi:10.1371/journal.pcbi.1003635
  • Yang, W., A. Karspeck and J. Shaman, 2014: Comparison of filtering methods for the modeling and retrospective forecasting of influenza epidemics. PLOS Computational Biology, 10(4): e1003583, doi:10.1371/journal.pcbi.1003583
  • Chretien, J.-P., D. George, J. Shaman, R. A. Chitale and F. E. McKenzie, 2014: Influenza forecasting in human populations: a scoping review. PLOS ONE, 9(4): e94130, doi:10.1371/journal.pone.0094130
  • Yang, W., E. Petkova and J. Shaman, 2014: Examination of mortality during the 1918 pandemic in New York City. Influenza and Other Respiratory Viruses, 8(2):177-188.
  • Huang, K. E., M. Lipsitch, J. Shaman and E. Goldstein, 2014: Quantifying the impact of school openings on the reproductive number of the 2009 A/H1N1 influenza epidemic in the United States. Epidemiology, 25(2):203-206.
  • Shaman, J., 2014: The Seasonal Effects of ENSO on Atmospheric Conditions Associated with European Precipitation: Model Simulations of Seasonal Teleconnections. Journal of Climate, 27(3):1010-1028.


  • Shaman, J, A. Karspeck, W. Yang, J. Tamerius, and M. Lipsitch, 2013: Real-Time Influenza Forecasts during the 2012-2013 Season. Nature Communications, 4: Article Number 2837, doi:10.1038/ncomms3837.
  • Kerr, D. C. R., J. Shaman, I. J. Washburn, S. Vuchinich, T. Neppl, D. Capaldi, R. Conger, 2013: Two Longterm Studies of Seasonal Variation in Depressive Symptoms among Community Participants. Journal of Affective Disorders, 151(3):837-842.
  • Shaman, J., S. Solomon, R. R. Colwell and C. B. Field, 2013: Reply to Rice and Henderson-Sellers: Survival of the fittest is not always the best option Proceedings of the National Academy of Sciences, 110(29):E2663, doi:10.1073/pnas.1307874110.
  • Rydbeck, A., E. D. Maloney, S.-P. Xie, J. Hafner and J. Shaman, 2013: Remote Forcing versus Local Feedback of East Pacific Intraseasonal Variability. Journal of Climate, 26(11):3575-3596.
  • Tamerius, J. D., L. M. Acosta, J. S. Jacobson, I. F. Goldstein, J. W. Quinn, A. G. Rundle, M. S. Perzanowski and J. Shaman, 2013: Socioeconomic and Outdoor Meteorological Determinants of Indoor Temperature and Humidity in New York City Households. Weather, Climate and Society, 5(2):168-179, doi:10.1175/WCAS-D-12-00030.1.
  • Gatton, M., N. Chitnis, T. Churcher, M. Donnely, A. Ghani, C. Godfray, F. Gould, I. Hastings, J. Marshall, H. Ranson, M. Rowland, J. Shaman, L. White, and S. Lindsay, 2013: The Importance of Mosquito Behavioural Adaptations to Malaria Control in Africa. Evolution, 67(4):1218-1230.
  • Tamerius, J. D., J. Shaman, W. Alonso, K. Bloom-Feshbach, C. Uejio, A. Comrie and C. Viboud, 2013: Environmental Predictors of Seasonal Influenza Epidemics across Temperate and Tropical Climates. PLoS Pathogens, 9(3): e1003194. doi:10.1371/journal.ppat.1003194.
  • Shaman, J. and M. Lipsitch, 2013: The ENSO-Pandemic Influenza Connection: Coincident or Causal? Proceedings of the National Academy of Sciences, 110(Supplement 1): 3689-3691, doi:10.1073/pnas.1107485109.
  • Shaman, J., S. Solomon, R. R. Colwell and C. B. Field, 2013: Fostering Advances in Interdisciplinary Climate Science. Proceedings of the National Academy of Sciences, 110(Supplement 1): 3653-3656, doi:10.1073/pnas.1301104110.
  • Koep, T. H., F. T. Enders, C. Pierret, S. C. Ekker, D. Krageschmidt, N. L. Kevin, M. Lipsitch, J. Shaman and C. Huskins, 2013: Predictors of Indoor Absolute Humidity and Estimated Effects on Influenza Virus Survival in Grade Schools. BMC Infectious Diseases, 13: 71, doi:10.1186/1471-2334-13-71.


  • Shaman, J. and A. Karspeck, 2012: Forecasting Seasonal Outbreaks of Influenza. Proceedings of the National Academy of Sciences, 109(50): 20425-20430, doi:10.1073/pnas.1208772109.
  • Shaman, J., R. M. Samelson and E. Tziperman, 2012: Complex wavenumber Rossby wave ray tracing. Journal of the Atmospheric Sciences, 69(7): 2112-2133.
  • Shaman, J. and E. Maloney, 2012: Shortcomings in Climate Model Simulations of the ENSO-Atlantic Hurricane Teleconnection. Climate Dynamics, 38(9-10): 1973-1988, doi:10.1007/s00382-011-1075-4.


  • Shaman, J., 2011: Strategies for Controlling the Enzootic Amplification of Arboviruses. Journal of Medical Entomology, 48(6): 1189-1196.
  • Shaman, J., K. Harding, and S. R. Campbell, 2011: Meteorological and Hydrological Influences on the Spatial and Temporal Prevalence of WNV in Culex Mosquitoes, Suffolk County New York. Journal of Medical Entomology, 48(4): 867-875.
  • Shaman, J., C. Y. Jeon, E. Giovannucci and M. Lipsitch, 2011: Shortcoming of Vitamin D-Based Model Simulations of Seasonal Influenza. PLoS ONE, 6(6): e20743, doi:10.1371/journal.pone.0020743.
  • Shaman, J., E. Goldstein and M. Lipsitch, 2011: Absolute humidity and pandemic versus epidemic influenza. American Journal of Epidemiology, 173(2):127-135, doi:10.1093/aje/kwq347.
  • Shaman, J. and E. Tziperman, 2011: An Atmospheric Teleconnection Linking ENSO and Southwestern European Precipitation. Journal of Climate, 24(1):124-139.


  • Simmerman, J. M., P. Suntarattiwong, J. Levy, R. V. Gibbons, C. Cruz, J. Shaman, R. G. Jarman, and T. Chotpitayasunondh, 2010: Influenza virus contamination of common household surfaces during the 2009 influenza A (H1N1) pandemic in Bangkok, Thailand--implications for contact transmission. Clinical Infectious Diseases, 51(9):1053-1061.
  • Shaman, J., R. M. Samelson and E. Skyllingstad, 2010: Air-Sea Fluxes over the Gulf Stream Region: Atmospheric Controls and Trends. Journal of Climate, 23(10):2651-2670.
  • Shaman, J., V. E. Pitzer, C. Viboud, B. T. Grenfell and M. Lipsitch, 2010: Absolute Humidity and the Seasonal Onset of Influenza in the Continental US. PLoS Biology, 8(2):e1000316. doi:10.1371/journal.pbio.1000316
  • Shaman, J., J. F. Day and N. Komar, 2010: Hydrologic Conditions Describe West Nile Virus Risk in Colorado. International Journal of Environmental Research and Public Health, 7(2):494-508, doi:10.3390/ijerph7020494.


  • Day, J. F. and J. Shaman, 2009: Severe Winter Freezes Enhance St. Louis Encephalitis Virus Amplification and Epidemic Transmission in Peninsular Florida. Journal of Medical Entomology, 46(6):1498-1506.
  • Shakun, J. D. and J. Shaman, 2009: Tropical Origins of North and South Pacific Decadal Variability. Geophysical Research Letters, 36, L19711, doi:10.1029/2009GL040313.
  • Shaman, J., S. K. Esbensen and E. D. Maloney, 2009: The Dynamics of the ENSO-Atlantic Hurricane Teleconnection: ENSO-related changes to the North African-Asian Jet affect Atlantic Basin Tropical Cyclogenesis. Journal of Climate, 22(9):2458-2482.
  • Shaman, J. and M. Kohn, 2009: Absolute Humidity Modulates Influenza Survival, Transmission and Seasonality. Proceedings of the National Academy of Sciences, 106(9):3243-3248, doi:10.1073/pnas.0806852106


  • Maloney, E. D. and J. Shaman, 2008: Intraseasonal Variability of the West African Monsoon and Atlantic ITCZ. Journal of Climate, 21(12):2898-2918.
  • Day, J. F. and J. Shaman, 2008: Using hydrologic conditions to track the risk of focal and epidemic arboviral transmission in peninsular Florida. Journal of Medical Entomology, 45(3):458-465.


  • Shaman, J., and E. Tziperman, 2007: The Summertime ENSO-North African-Asian Jet Teleconnection and Implications for the Indian Monsoons. Geophysical Research Letters, 34, L11702, doi:10.1029/2006GL029143.
  • Shaman, J., 2007: Amplification due to spatial clustering in an individual-based model of mosquito-avian arbovirus transmission. Transactions of the Royal Society of Tropical Medicine and Hygiene, 101(5):469-483, doi:10.1016/j.trstmh.2006.11.007.
  • Shaman, J. and J. F. Day, 2007: Reproductive Phase Locking of Mosquito Populations in Response to Rainfall Frequency. PLoS ONE, 2(3):e331. doi:10.1371/journal.pone.0000331.


  • Shaman, J., J. F. Day, M. Stieglitz, S. Zebiak, and M. Cane, 2006: An Ensemble Seasonal Forecast of Human Cases of St. Louis Encephalitis in Florida Based on Seasonal Hydrologic Forecasts. Climatic Change, 75(4):495-511.
  • Warrach, K., M. Stieglitz, J. Shaman, V. C. Engel, and K. L. Griffin, 2006: Twentieth Century Climate in the New York Hudson Highlands and the Potential Impacts on Eco-Hydrological Processes. Climatic Change, 75(4):455-493.
  • Shaman, J., M. Spiegelman, M. Cane, and M. Stieglitz, 2006: A Hydrologically Driven Model of Swamp Water Mosquito Population Dynamics. Ecological Modelling, 194(4):395-404.


  • Shaman, J., M. Cane, and A. Kaplan, 2005: The Relationship between Tibetan Snow Depth, ENSO, River Discharge and the Monsoons of Bangladesh. International Journal of Remote Sensing, 26(17):3735-3748.
  • Shaman, J. and J. F. Day, 2005: Achieving Operational Hydrologic Monitoring of Mosquito-Borne Disease Transmission. Emerging Infectious Diseases, 11(9):1343-1350.
  • Shaman, J. and E. Tziperman, 2005: The Effect of ENSO Variability on Tibetan Plateau Snow Depth: A Stationary Wave Teleconnection Mechanism and Implications for the South Asian Monsoons. Journal of Climate, 18(12):2067-2079.
  • Shaman, J., J. F. Day, and M. Stieglitz, 2005: Drought-induced amplification and epidemic transmission of West Nile virus in South Florida. Journal of Medical Entomology, 42(2):134-141.


  • Shaman, J., M. Stieglitz, and D. Burns, 2004: Are Big Basins just the Sum of Small Catchments? Hydrological Processes, 18:3195-3206.
  • Shaman, J., J. F. Day, and M. Stieglitz, 2004: The Association of Drought, Wetting and Human Cases of St. Louis Encephalitis Virus in South-Central Florida. American Journal of Tropical Medicine and Hygiene, 71(3):251-261.
  • Shaman, J., J. F. Day, M. Stieglitz, S. Zebiak, and M. Cane, 2004: Seasonal Forecast of St. Louis Encephalitis Virus Transmission, Florida. Emerging Infectious Diseases, 10(5):802-809.


  • Stieglitz, M., J. Shaman, J. McNamara, V. Engel, J. Shanley, and G. Kling, 2003: An approach to understanding hydrologic connectivity on the hillslope and the implications for nutrient transport. Global Biogeochemical Cycles, 17(4), 1105, doi:10.1029/2003GB002041.
  • Shaman, J., J. F. Day, and M. Stieglitz, 2003: St. Louis Encephalitis Virus in Wild Birds During the 1990 South Florida Epidemic: The Importance of Drought, Wetting Conditions, and the Emergence of Culex nigripalpus to Arboviral Amplification and Transmission. Journal of Medical Entomology, 40(4):547-554.
  • Shaman, J., M. Stieglitz, S. Zebiak, and M. Cane, 2003: A Local Forecast of Land Surface Wetness Conditions Derived from Seasonal Climate Predictions. Journal of Hydrometeorology, 4(3):611-626.


  • Shaman, J., M. Stieglitz, V. Engel, R. Koster, and C. Stark, 2002: Representation of Stormflow and a More Responsive Water Table in a TOPMODEL-Based Hydrology Model. Water Resources Research, 38(8), 1156, doi:10.1029/2001WR000636.
  • Shaman, J., J. F. Day, and M. Stieglitz, 2002: Drought-induced amplification of St. Louis encephalitis virus, Florida. Emerging Infectious Diseases, 8(6):575-580.
  • Shaman, J., M. Stieglitz, C. Stark, S. Le Blancq, and M. Cane, 2002: Using a dynamic hydrology model to predict mosquito abundances in flood and swamp water. Emerging Infectious Diseases, 8(1):6-13.

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    Jeffrey Shaman
    Department of Environmental Health Sciences
    Mailman School of Public Health
    Columbia University
    722 West 168th Street
    Rosenfield Building
    Room 1104C
    New York, NY