Influenza Publications
2024
Mathis, S.,…, S. Kandula, S. Pei, J. Shaman, R. Yaari, T.K. Yamana ,…, R.K. Borchering, 2024: Evaluation of FluSight influenza in 2021-22 and 2022-23 seasons with a new forecasting target: laboratory-confirmed influenza hospitalizations . Nature Communication, 15 :6289, doi:10.1038/s41467-024-50601-9.
2023
Prasad, P.V., M.K. Steele, C. Reed, L.A. Meyers, Z. Du, R. Pasco, J.A. Alfaro-Murillo, B. Lewis, S. Venkatramanan, J. Schlitt, J. Chen, M. Orr, M.L. Wilson, S. Eubank, L. Wang, M. Chinazzi, A. Pastore y Piontti, J.T. Davis, M.E. Halloran, I. Longini, A. Vespignzni, S. Pei, M. Galanti, S. Kandula, J. Shaman, D.J. Haw, N. Arinaminpathy and M. Biggerstaff. Multimodeling approach to evaluating efficacy of layering pharmaceutical and non-pharmaceutical interventions for influenza pandemics . Proceedings of the National Academy of Sciences, 120(28) :e2300590120, doi:10.1073/pnas.2300590120.
2021
Qi, Y., J. Shaman and S. Pei , 2021: Quantifying the effects of COVID-19 non-pharmaceutical interventions on influenza transmission in the United States . The Journal of Infectious Diseases, 224(9) :1500-1508, doi:10.1093/infdis/jiab485.
Pei, S., X. Teng, P. Lewis and J. Shaman, 2021: Optimizing influenza surveillance networks using uncertainty propagation . Nature Communications , 12 : Article Number 222, doi:10.1038/s41467-020-20399-3.Matienzo, N., M.M. Youssef, D. Comito, B. Lane, C. Ligon, H. Morita, A. Winchester, M.E. Decker, P. Dayan, B. Shopsin and J. Shaman, 2021: Respiratory viruses in pediatric emergency department patients and their family members . Influenza and Other Respiratory Viruses, 15(1) :91-98, doi:10.1111/irv.12789.
2020
Pei, S. and J. Shaman. Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness . PLOS Computational Biology, 16(10) :e1008301, dos:10.1371/journal.pcbi.1008301.Kramer, S.C., S. Pei and J. Shaman. Forecasting influenza in Europe using a meta population model incorporating cross-border commuting and air travel . PLOS Computational Biology, 16(10) :e1008233, dos:10.1371/journal.pcbi.1008233.Galanti, M., D. Comito, C. Ligon, B Lane, N. Matienzo, S. Ibrahim, A. Shittu, E. Tagne, R. Birger, M. Ud-Dean, I. Filip, H. Morito, R. Rabadan, S Anthony, G.A. Freyer, P. Dayan, B. Shopsin and J. Shaman , 2020: Active surveillance documents rates of clinical care seeking due to respiratory illness . Influenza and Other Respiratory Illnesses 14(5) :499-506, doi:10.1111/irv.12753.
2019
Reich NG, C. McGowan, T. Yamana , A. Tushar, E. Ray, D. Osthus, S. Kandula , S. Fox, L. Brooks, W. Crawford-Crudell, G.C. Gibson, E. Moore, R. Silva, M. Biggerstaff, M.A. Johansson, R. Rosenfeld and J. Shaman , 2019: A collaborative multi-model ensemble for real-time influenza forecasting in the U.S.: Results from the 2017/2018 season. PLOS Computational Biology , 15(11) :e1007486, dos:10.1371/journal.pcbi.1007486.
Reich, N.G., D. Osthus, E. Ray, T. Yamana, M. Biggerstaff, M.A. Johansson, R. Rosenfeld and J. Shaman , 2019: Reply to Bracher: Scoring probabilistic forecasts to maximize public health interpretability. Proceedings of the National Academy of Sciences, 116(42) :20811-20812, doi:10.1073/pnas.1912694116.
Kandula, S. and J. Shaman Reappraising the utility of Google Flu Trends . PLOS Computational Biology, 15(8) :e1007258, doi:10.1371/journal.pcbi.1007258.Kandula, S., S. Pei and J. Shaman ,2019: Improved forecasts of influenza-associated hospitalization rates with Google search trends . Journal of the Royal Society Interface, 16 :20190080, doi:10.1098/rsif.2019.0080.Kandula, S. and J. Shaman Near-term forecasts of influenza-like illness: an evaluation of autoregressive time series approaches . Epidemics, 27 :41-51, doi:10.1016/j.epidem.2019.01.002.Li, X., B. Xu and J. Shaman , 2019: The impact of environmental transmission and epidemiological features on the geographical translocation of highly pathogenic avian influenza virus . International Journal of Environmental Research and Public Health, 16(11) :1890, doi:10.3390/ijerph16111890.Li, X., B. Xu and J. Shaman , 2019: Pathobiological features favoring the intercontinental dissemination of highly pathogenic avian influenza virus . Royal Society Open Science, 6 :190276, doi:10.1098/rsos.190276.Galanti, M., R. Birger, S.M.M. Ud-Dean, I. Filip, H. Morita, D. Comito, S. Anthony, G.A. Freyer, S. Ibrahim, B. Lane, N. Matienzo, C. Ligon, R. Rabadan, A. Shittu, E. Tagne and J. Shaman , 2019: Rates of asymptomatic respiratory virus infection across age groups . Epidemiology and Infection, 147 :e176, 1-6, doi:10.1017/S0950268819000505. Galanti, M., R. Birger, S.M.M. Ud-Dean, I. Filip, H. Morita, D. Comito, S. Anthony, G.A. Freyer, S. Ibrahim, B. Lane, C. Ligon, R. Rabadan, A. Shittu, E. Tagne and J. Shaman , 2019: Longitudinal active sampling for respiratory viral infections across age groups . Influenza and Other Respiratory Viruses, 13(3) :226-232, doi:10.1111/irv.12629.Kramer, S. and J. Shaman . Development and validation of influenza forecasting for 64 temperate and tropical countries . PLOS Computational Biology, 15(2) :e1006742, doi:10.1371/journal.pcbi.1006742.Pei, S., M. Cane and J. Shaman , 2019: Predictability in process-based ensemble forecast of influenza . PLOS Computational Biology, 15(2) :e1006783, doi:10.1371/journal.pcbi.1006783.Reich, N.G., L. Brooks, F. Spencer, S. Kandula, C. McGowan, E. Moore, D. Osthus, E. Ray, A. Tushar, T. Yamana, M. Biggerstaff, M.A. Johansson, R. Rosenfeld and J. Shaman , 2019: Forecasting seasonal influenza in the U.S.: a collaborative multi-year, multi-model assessment of forecast performance . Proceedings of the National Academy of Sciences, 116(8) :3146-3154, doi:10.1073/pnas.1812594116.
McGowan, C., M. Biggerstaff, M. Johansson, K.M. Apfeldorf, M. Ben-Nun, L. Brooks, M. Convertino, M. Erraguntla, D.C. Farrow, J. Freeze, S. Ghosh, S. Hyun, S. Kandula , J. Lega, Y. Liu, N. Michaud, H. Morita , J. Niemi, N. Ramakrishnan, E.L. Ray, N.G. Reich, P. Riley, J. Shaman , R. Tibshirani, A. Vespignani, Q. Zhang and C. Reed, 2019: Collaborative efforts to forecast seasonal influenza in the United States, 2015-2016 . Scientific Reports, 9 :683, doi:10.1038/s41598-018-36361-9.
2018
Morita, H., S. Kramer, A. Heaney , H. Gil and J. Shaman , 2018: Influenza forecast optimization when using different surveillance data types and geographic scales. Influenza and Other Respiratory Viruses, 12(6) :755-764, doi:10.1111/irv.12594.Yang, W. , M. J. Cummings, B. Bakamutumaho, J. Kayiwa, N. Owor, B. Namagambo, T. Byaruhanga, J. J. Lutwama, M. R. O’Donnell and J. Shaman , 2018: Transmission dynamics of influenza in two major cities of Uganda . Epidemics, 24 :43-48, doi:10.1016/j.epidem.2018.03.002.Biggerstaff, M., M. Johansson, D. Alper, L. C. Brooks, P. Chakraborty, D. C. Farrow, S. Hyun, S. Kandula , C. McGowan, N. Ramakrishnan, R. Rosenfeld, J. Shaman , R. Tibshirani, R. J. Tibshirani, A. Vespignani, W. Yang , Q. Zhang and C. Reed, 2018: Results from the second year of a collaborative effort to forecast influenza seasons in the United States. Epidemics, 24 :43-48, doi:10.1016/j.epidem.2018.02.003.
Doms, C., S. Kramer and J. Shaman , 2018. Assessing the use of influenza forecasts and epidemiological modeling in public health . Scientific Reports, 8 :12406, doi:1038/s41598-018-30378-w.Kandula, S., T. Yamana, S. Pei, W. Yang, H. Morita and J. Shaman , 2018. Evaluation of mechanistic and statistical methods in forecasting influenza-like illness . Journal of the Royal Society Interface, 15 :20180174, doi:10.1098/rsif.2018.0174.Birger R., H. Morita, D. Comito, I. Filip, M. Galanti, B. Lane, C. Ligon, D. Rosenbloom, A. Shittu, M. Ud-Dean, R. Desalle, P. Planet and J. Shaman , 2018. Asymptomatic shedding of respiratory virus among an ambulatory population across seasons . mSphere, 3 :e00249-18, doi:10.1128/mSphere.00249-18.Yang W. , M. J. Cummings, B. Bakamutumaho, J. Kayiwa, N. Owor, B. Namagambo, T. Byaruhanga, J. J. Lutwama, M. R. O’Donnell and J. Shaman , 2018. Dynamics of influenza in the tropical Africa: temperature, humidity and co-circulating (sub)types . Influenza and Other Respiratory Viruses, 12(4) :446-456, doi:10.1111/irv.12556.Chattopadhyay, I., E. Kiciman, J. W. Elliott, J. Shaman and A. Rzhetsky, 2018: Conjunction of factors triggering waves of seasonal influenza . eLife, 7 :e30756, doi:10.7554/eLife.30756.
Pei, S., S. Kandula, W. Yang and J. Shaman , 2018: Forecasting the spatial transmission of influenza in the United States . Proceedings of the National Academy of Sciences 115(11) :2752-2757, doi:10.1073/pnas.1708856115.Shaman, J., H. Morita, R. Birger, M. Boyle, D. Comito, B. Lane, C. Ligon, H. Smith , R. Desalle, and P. Planet, 2018: Asymptomatic summertime shedding of respiratory viruses . Journal of Infectious Diseases, 217 :1074-1077. doi:10.1093/infdis/jix685.Cummings, M. J., B. Barnabas, W. Yang , J. F. Wamala, J. Kayiwa, N. Owor, B. Namagambo, T. Byaruhanga, A. Wolf, J. J. Lutwama, J. Shaman , and M. R. O’Donnell, 2018: Emergence and early-phase transmission dynamics of 2009 pandemic A/H1N1 influenza in Kampala, Uganda, 2009-2010 . American Journal of Tropical Medicine and Hygiene, 98(1) :203-206. doi:10.4268/ajtmh.17-0524.
2017
Shaman, J., S. Kandula, W. Yang and A. Karspeck, 2017: The use of ambient humidity conditions to improve influenza forecast . PLOS Computational Biology, 13(11) : e1005844. doi:10.1371/journal.pcbi.1005844.Yamana, T., S. Kandula and J. Shaman , 2017: Individual versus superensemble forecasts of seasonal influenza outbreaks in the United States . PLOS Computational Biology , 13(11) :e1005801. doi:10.1371/journal.pcbi.1005801.Kandula , S., D. J. Hsu and J. Shaman , 2017: Sub-regional nowcasts of seasonal influenza using search trends . Journal of Medical Internet Research, 19(11) :e370, doi:10.2196/jmir.7486.Pei, S. and J. Shaman , 2017: Counteracting structural errors in ensemble forecast of influenza outbreaks . Nature Communications, 8 , Article Number 925, doi:10.1038/s41467-017-01033-1.Tamerius, J., S. Ojeda, C. K. Uejio, J. Shaman , B. Lopez, N. Sanchez and A. Gordon, 2017: Influenza transmission during extreme indoor conditions in a low-resource tropical setting . International Journal of Biometeorology, 61(4) :613-622, doi:10.1007/s00484-016-1238-4. Kandula, S., W. Yang, and J. Shaman , 2017: Type- and Subtype-Specific Influenza Forecast . American Journal of Epidemiology, 185(5) :395-402, doi:10.1093/aje/kww211.Li, R., A. Heaney, S. Kandula, J. Cai, X. Zhao, B. Xu and J. Shaman , 2017: Inference and forecast of H7N9 influenza in China, 2013 to 2015 . Eurosurveillance, 22(7) :pii=30462. DOI: http://dx.doi.org/10.2807/1560-7917.ES.2017.22.7.30462.
2016
Yang, W., J. Shaman , 2016: Forecasting influenza outbreaks in boroughs and neighborhoods of New York City . PLOS Computational Biology, 12(11) :e1005201. doi:10.1371/journal.pcbi.1005201.Biggerstaff M., D. Alper, M. Dredge, S. Fox, I.C.-H. Fung, K.S. Hickman, B. Leis, R. Rosenfield, J. Shaman Results from the Centers for Disease Control and Prevention’s Predict the 2013-2014 Influenza Season Challenge . BMC Infectious Diseases, 16 :357, doi:10.1186/S12879-016-1669-x.
Nguyen, J.L. , W. Yang , K. Ito, T. Matte, J. Shaman , and P. L. Kinney, 2016: The temporal association and prediction of cardiovascular disease mortality with increases in seasonal influenza infections. JAMA Cardiology, 1(3) :274-281.
2015
Shaman, J. and S. Kandula , 2015: Improved Discrimination of Influenza Forecast Accuracy using Consecutive Predictions . PLOS Currents Outbreaks, 2015 Oct 5 . Edition 1. doi: 10.1371/currents.outbreaks.8a6a3df285af7ca973fab4b22e10911e.Tamerius, J. D., C. Viboud, J. Shaman and G. Chowell: Regional variability of specific humidity and school vacation can explain multiple spatially-focused waves of 2009 pandemic influenza in Mexico . PLOS Computational Biology, 11(8) : e1004337, doi:10.1371/journal.pcbi.1004337
Yang W. , B. J. Cowling, E. H. Y. Lau and J. Shaman : Forecasting influenza epidemics in Hong Kong . PLOS Computational Biology, 11 (7) : e1004383, doi:10.1371/journal.pcbi.1004383Yang, W., M. Lipsitch and J. Shaman , 2015: Inference of seasonal and pandemic influenza transmission dynamics. Proceedings of the National Academy of Sciences, 112(9) :2723-2728, doi:10.1073/pnas.1415012112.
2014
Yang, W. and J. Shaman , 2014: Does exposure to poultry and wild fowl confer immunity to H5N1? Chinese Medical Journal , 127 (18) :3335-3343.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.1003583Chretien, 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.
2013
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.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.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.
2012
2011
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.
2010
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., 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
2009
