All Group Publications
2026
Zhang, R., R. Deng, S. Liu, Q. Yao, J. Shaman , B.T. Grenfell, C. Viboud and S. Pei, 2026: Reconstructing the early spatial spread of pandemic respiratory viruses in the United States . Proceedings of the National Academy of Sciences , 123(2) :2518051123, doi:10.1073/pnas.2518051123.
2025
Wunrow, H.Y., S. Pei, J. Shaman and M.W. Spiegelman, 2025: Data assimilation for estimating time-varying reproduction numbers . Journal of the Royal Society Interface, 22 :20250131, doi:10.1098/rsif.2025.0131.Pei, S., D. Seeram, S. Blumberg, B. Shopsin, A.-C. Uhlemann and J. Shaman , 2025: Inferring asymptomatic carriers of antimicrobial-resistant organisms in hospitals using genomic, microbiological and patient mobility data . Nature Communications, 16 :10140, doi:10.1028/s41467-025-65241-w.
Jahandari, S. and J. Shaman , 2025: Estimation in networks with spatiotemporally correlated noise . IEEE Transactions on Automatic Control, 70(10) :6885-6892, doi:10.1109/TAC.2025.30565015.Zhang, R., J. Tai, Q. Yao, W. Yang, K. Ruggeri, J. Shaman and S. Pei, 2025: Behavior-driven forecasts of neighborhood-level COVID-19 spread in New York City . PLOS Computational Biology , 21(4) :e1012979, doi:10.1371/journal.pcbi.1012979.
Yaari, R., M. Galanti, R. Zepeda Tello, S. Chicumbe, I. Jani, A. Cassy, I Macicame, N. Manafe, S.M. Farley, W.M. El-Sadr and J. Shaman , 2025: Infectious disease forecasting to support public health: Use of readily available methods to predict malaria and diarrheal diseases in Mozambique . Journal of Global Health, 15 :04114, doi:10.7189/jogh.15.04114. Perini, M., T.K. Yamana, M. Galanti, J. Suh, R. Kaondera-Shava and J. Shaman , 2025: Modelling COVID-19 in the North American region with a metapopulation network and Kalman filter . Epidemics, 50 :100817, doi:10.1016.jepidem.2025.100817.Cascante-Vega, J., T. Robin, L. Wen, J. Zucker, A.-C. Uhlemann, S. Pei and J. Shaman , 2025: Estimating importation and nosocomial transmission of micro-organisms in hospital settings using patient records and culture data . Epidemics, 50 :100818, doi:10.1016.jepidem.2025.100818. Kaondera-Shava, R., M. Galanti, M. Perini, J. Suh J. Shaman , 2025: SARS-CoV-2 transmission dynamics in Mozambique and Zimbabwe during the first three years of the pandemic . Royal Society Open Science, 12 :241275, doi:10.1098/rsos.241275.
2024
Kelsall, N.C., C. Gimbrone, M. Olfson, M.S. Gould, J. Shaman and K.M. Keyes, 2024: Internet search activity for intentional self-harm forums after a high-profile news publication: Interrupted time series analysis . Journal of Medical Internet Research, 26 :e52354, doi:10.2196/52354
Yamana, T.K. , S. Rajagopal, D.C. Hall Jr, A.M. Moustafa, A. Feder, A. Ahmed, C. Bianco, R. Harris, S. Coffin, A.E. Campbell, S. Pei S, J. Chang Mell, P.J. Planet and J. Shaman , 2024: A two-variant model of SARS-COV-2 transmission: Estimating the characteristics of a newly emerging strain . BMC Infectious Diseases, 24 :938, doi:10.1186/s12879-024-09823-x.Leveau, C., J. Riancho, J. Shaman and A. Santurtún, 2024: Accessibility to healthcare and ischemic stroke: a spatial analysis in Spanish provinces . Cadernos de Sade Publica, 40(9) :e00212923, doi:10.1590/0102-311XEN212923.
Lynch, V.D. and J. Shaman , 2024: Hydrometeorology and geography affect hospitalizations for waterborne infectious diseases in the United States: A retrospective analysis . PLOS Water, 3(8) :e0000206, doi:10.1371/journal.pwat.0000206.Shaman, J., S. Kandula , S. Pei, M. Galanti, M. Olfson, M. Gould and K. Keyes, 2024: Quantifying suicide contagion at population scale . Science Advances, 10 :eadq4074, doi:10.1126/sciadv.adq4074.Kelsall, N.C., C. Gimbrone, M. Olfson, M.S. Gould, J. Shaman and K.M. Keyes, 2024: Association between pro-suicide website searches through Google and suicide death in the United States from 2010-2021 . Journal of Medical Internet Research, 26 :e53404, doi:10.2196/53404.
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.
Lopez, V.,…, S. Pei, J. Shaman, T.K. Yamana ,…, M.A. Johansson, 2024: Challenges of COVID-19 case forecasting in the US, 2020-2021 . PLOS Computational Biology, 20(5) :e1011200, doi:10.1371/journal.pcbi.1011200.
Yang, W. and J. Shaman , 2024: Reconciling the efficacy and effectiveness of masking on epidemic outcomes . Journal of the Royal Society Interface, 21(212) :20230666, doi:10.1098/rsif.2023.0666.
He, K., S. Foerster, N.M. Vora, K. Blaney, C. Keeley, L. Hendricks, J.K. Varma, T. Long, J. Shaman and S. Pei, 2024: Evaluating completion rates of COVID-19 contact tracing surveys in New York City . BMC Public Health, 24 :414, doi:10.1186/s12889-024-17920-4.
Keyes, K.M., S. Kandula, G. Martinez-Ales, C. Gimbrone, V. Joseph, S. Monnat, C. Rutherford, M. Olfson, M.S. Gould and J. Shaman , 2024: Geographic Variation, Economic Activity, and Labor Market Characteristics in Traje ctories of Suicide in the United States, 2008 to 2020 . American Journal of Epidemiology, 193(2) :256-266, doi:10.1093/aje/kwad205.
Boldea, O., A. Alipoor, S. Pei, J. Shaman and G. Rozhnova, 2024: Age-specific transmission dynamics of SARS-CoV-2 during the first two years of the pandemic . PNAS Nexus, 3 :1-14, doi:10.1093/pnasnexus/pgae024.
Robin, T.T., J. Cascante-Vega, J. Shaman and S. Pei, 2024: System identifiability in a time-evolving agent-based model . PLOS ONE , 19(1) :0290821, doi:10.1371/journal/pone.0290821.Galanti, M., J.A Patino-Galindo, I. Filip, H. Morita , A. Galianese, M. Youssef, D. Comito, C. Ligon, B. Lane, N. Matienzo, S. Ibrahim, E. Tagne, A. Shittu , O. Elliott, T. Perea-Chamblee, S. Natesan, D.S. Rosenbloom, J. Shaman and R. Rabadan, 2024: Virome Data Explorer: A web resource to longitudinally explore respiratory viral infections, their interactions with other pathogens and host transcriptomic changes in over 100 people . PLOS Biology, 22(1) :e3002089, doi:10.1371/journal.pbio.3002089.
2023
Ward, M.J., M. Sorek-Hamer, J. Henke, E. Little, A. Patel, J. Shaman , K. Vamuri and N. DeFelice, 2023: A spatially resolved and environmentally informed forecast model of West Nile virus in Coachella Valley, California . GeoHealth, 7(12) :e2023GH000855, doi:10.1029/2023GH000855.
Joseph, V.A., G. Martinez-Ales, M. Olfson, J. Shaman , M. Gould, C. Gimbrone, K.M. Keyes, 2023: Trends in suicide among black women in the US, 1999-2020 . American Journal of Psychiatry , 180(12) :914-917, doi:10.1176/appi.ajp.20230254.
Howerton, E.,…, M. Galanti, T. Yamana, S. Pei, J. Shaman, …, J. Lessler, 2023: Evaluation of the US COVID-19 Scenario Modeling Hub for informing pandemic response under uncertainty . Nature Communications, 14(1) :7260, doi:10.1028/s41467-023-42680-x.
Cascante-Vega, J., M. Galanti, K. Schley, S. Pei, and J. Shaman, 2023: Inference of transmission dynamics and retrospective forecast of invasive meningococcal disease . PLOS Computational Biology, 19(10) :e1011564, doi:10.1371/journal.pcbi.1011564.Dai, K. , S. Foerster, N.M. Vora, K. Blaney, C. Keeley, L. Hendricks, J.K. Varma, T. Long, J. Shaman and S. Pei, 2023: Community transmission of SARS-CoV-2 during the Delta wave in New York City . BMC Infectious Diseases, 23: 753, doi:10.1186/s12879-023-08735-6.Toomre, D., S. Kandula and J. Shaman , 2023: Longitudinal association of COVID hospitalization and death with online search for loss of smell or taste . Emerging Infectious Diseases, 29(8) :1711-1713, doi:10.3201/eid2908.230071.
Lynch, V.D. and J. Shaman , 2023: Waterborne infectious diseases associated with exposure to tropical cyclonic storms, United States, 1996-2018 . Emerging Infectious Diseases, 29(8) :1548-1558, doi:10.3201/eid2908.221906.Yang, W. and J. Shaman , 2023: Development of accurate long-lead COVID-19 forecast . PLOS Computational Biology, 19(7) :e1011278, doi:10.1371/journal.pcbi.1011278.
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. Vespignani, S. Pei, M. Galanti, S. Kandula, J. Shaman, D.J. Haw, N. Arinaminpathy and M. Biggerstaff, 2023: 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.
Yamana, T.K., M. Galanti, S. Pei, M. Di Fusco, F.J. Angulo, M.M. Moran, F. Khan, D.L. Swerdlow and J. Shaman , 2023: The impact of COVID-19 vaccination in the US: averted burden of SARS-CoV-2 related cases, hospitalizations and deaths . PLOS ONE, 18(4) :e1010945, doi:10.1371/journal.pone.0275699.Pei, S., S. Blumberg, J. Cascante Vega, T. Robin, J. Shaman , 2023: Challenges in forecasting antimicrobial resistance . Emerging Infectious Diseases, 29(4) :679-685, doi:10.3201/eid2904.221552.
Kandula, S., J. Shaman , 2023: Hindcasts and forecasts of suicide mortality in the US: a modeling study . PLOS Computational Biology, 19(3): e1010945, doi:10.1371/journal.pcbi.1010945.Kandula, S., J. Shaman , 2023: Trends in crisis hotline call rates and suicide mortality in the United States . Psychiatric Services, app. ps. 20220199, doi:10.1176/appi.ps.20220199.Santurtún, A. and J. Shaman , 2023: Work accidents, climate change and COVID-19 . Science of the Total Environment, 871 :162129, doi:10.1016/j.scitotenv.2023.162129.Kandula, S., J. Shaman , 2023: County-level estimates of suicide mortality in the USA: a modeling study . The Lancet Public Health, 8(3) :e184-e193, doi:10.1016/S2468-2667(22)00290-0.Borchering, R.K.,…, M. Galanti, T. Yamana, S. Pei, J. Shaman ,…, J. Lessler, 2023: Impact of SARS-CoV-2 vaccination of children ages 5-11 years on COVID-19 disease burden and resilience to new variants in the United States, November 2021-March 2022: a multi-model study . The Lancet Regional Health – Americas, 17 :100398, doi:10.1016/j.lana.2022.100398.
2022
Lewandowski, S.A. , M.A. Kioumourtzoglou and J.L. Shaman , 2022: Heat stress illness outcomes and annual indices of outdoor heat at U.S. Army installations . PLOS ONE, 17(11) :e0263803, doi:10.1371/journal/pone.0263803.Kessler, D., A. Dessie, P. Kanjanauptom, M. Vindas, L. Ng, M.M. Youssef, R. Birger, J. Shaman and P. Dayan, 2022: Lack of association between a quantified lung ultrasound score and illness severity in pediatric emergency department patients with acute respiratory infections . Journal of Ultrasound in Medicin e, 41(12) :3013-3022, doi:10.1002/jum.16023.
Casey, J.A., M.A. Kioumourtzoglou, E. Ogburn, A. Melamed, J. Shaman, S. Kandula , A. Neophytou, K. Darwin, J. Sheffield and C. Gyamfi-Bannerman: 2022. Long-term fine particulate matter concentrations and prevalence of severe acute respiratory syndrome coronavirus 2: differential relationships by socioeconomic status among pregnant individuals in New York City . American Journal of Epidemiology, 191(11) :1897-1905, doi:10.1093/aje/kwac139.
Pei, S., S. Kandula, J.C. Vega , W. Yang, S. Foerster, C. Thompson, J. Baumgartner, S.D. Ahuja, K. Blakey, J.K. Varma, T. Long and J. Shaman : 2022. Contact tracing reveals community transmission of COVID-19 in New York City . Nature Communications, 13 :6307, doi:10.1038/s41467-022-34130-x.
Joseph V.A., G. Martinez-Ales, M. Olfson, J. Shaman , M.S. Gould and K.M. Keyes. Temporal trends in suicide methods among adolescents in the US , 2022: JAMA Network Open, 5(10) :e2236049, doi:10.1001/jamanetworkopen.2022.36049.
Platt, J.M., J.R. Pamplin II, C. Gimbrone, C. Rutherford, S. Kandula , M. Olfson, M. Gould, G. Martinez-Ales, J. Shaman and K.M. Keyes, 2022: Racial disparities in spatial and temporal youth suicide clusters . Journal of the American Academy of Child and Adolescent Psychiatry, 61(9) :1131-1140, dot:10.1016/jaac.2021.12.012.
Yang, W. and J. Shaman, 2022: COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron) . eLife, 11: e78933, doi:10.7554/eLife.78933.
Truelove S,…, M. Galanti, T.K. Yamana, S. Pei, J. Shaman ,…, Viboud C, 2022: Projected resurgence of COVID-19 in the United States in July-December 2021 resulting from the increased transmissibility of the Delta variant and faltering vaccination . eLife, 11: e73584, doi:10.7554/eLife.73584.
Schneider, T., O.R.A. Dunbar, J. Wu, L. Boettcher, D. Burov, A. Garbuno-Inigo, G.L. Wagner, S. Pei, C. Daraio, R. Ferrari and J. Shaman, 2022: Epidemic management and control through risk-dependent individual contact interventions . PLOS Computational Biology , 18(6): e1010171, doi:10.1371/journal.pcbi.1010171.
Lynch, V.D. and J. Shaman, 2022: The effect of seasonal and extreme floods on hospitalizations for Legionnaires’ disease in the United States, 2000-2011 . BMC Infectious Diseases, 22: 550, doi.10.1186/s12879-022-07489-x.Yang, W. and J. Shaman, 2022: COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant, and implications for vaccination . Journal of the Royal Society Interface, 19(191): 20210900, doi:10.1098/rsif.2021.0900.
Ukawuba, I. and J.Shaman, 2022: Inference and dynamic simulation of malaria using a simple climate-driven entomological model of malaria transmission . PLOS Computational Biology, 18(6): e1010161, doi:10.1371/journal.pcbi.1010161.Lewandowski, S.A. and J. Shaman, 2022: Heat stress morbidity among United States military personnel: daily exposure and lagged response (1998-2019) . International Journal of Biometeorology, 66(6): 1199-1208, doi:10.1007/s00484-022-02269-3. Correction to: Heat stress morbidity among United States military personnel: daily exposure and lagged response (1998-2019) . International Journal of Biometeorology, 66(6): 1209-1217, doi:10.1007/s00484-022-02291-5.Cramer, E.Y.,…,T.K. Yamana, S. Pei, J. Shaman, …, N.G. Reich, 2022: Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the US . Proceedings of the National Academy of Sciences, 119(15): e2113561119, doi:10.1073/pnas.2113561119.
Keyes, K.M. and J. Shaman, 2022: Contagion and psychiatric disorders: the social epidemiology of risk (Comment on “The epidemic of mental disorders in business”). Administrative Science Quarterly, 67(1): 49-55, doi:10.1177/00018392211067693.
Yang, W. and J. Shaman , 2022: Viral replication dynamics could critically modulate vaccine effectiveness and should be accounted for when assessing new SARS-CoV-2 variants . Influenza and Other Respiratory Viruses , 16(2) :366-367, doi:10.1111/irv.12961.
Kannoth, S., S. Kandula and J. Shaman, 2022: The association between early country-level COVID-19 testing capacity and later COVID-19 mortality outcomes . Influenza and Other Respiratory Viruses, 16(1) :56-62, doi:10.1111/irv.12906
2021
Gimbrone, C., C. Rutherford, S. Kandula, G. Martinez-Ales, J. Shaman , M. Olfson, M. Gould, S. Pei, M. Galanti and K.M. Keyes, 2021: Associations between COVID-19 mobility restrictions and economic, mental health, and suicide-related concerns in the US using cellular phone GPS and Google search volume data . PLOS ONE, 16(12) :e0260931, doi:10.1371/journal/pone.0260931.
Lieberman-Cribbin, W., M. Galanti and J. Shaman, 2021: Socioeconomic disparities in SARS-CoV-2 serological testing and positivities in New York City . Open Forum Infectious Diseases, 8(12) :ofab534, doi:10.1093/ofid/ofab534
Martinez-Ales, G., C. Gimbrone, C. Rutherford, S. Kandula, M. Olfson, M. Gould, J. Shaman and K.M. Keyes, 2021: Role of firearm ownership on 2001-2016 trends in U.S. firearm suicide rates . American Journal of Preventive Medicine, 61(6) :795-803, doi:10.1016/j.amepre.2021.05.026.
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.
Galanti, M., S. Pei, T.K. Yamana, F.J. Angulo, A. Charos, F. Khan, K. Shea, D. Swerdlow and J. Shaman, 2021: Non-pharmaceutical interventions and inoculation rate shape SARS-CoV-2 vaccination campaign success . Epidemiology and Infection, 149 :e222, doi:10.1017/S095026882100217X.Pei, S., T.K. Yamana, S. Kandula, M. Galanti and J. Shaman, 2021: Burden and characteristics of COVID-19 in the United States during 2020 . Nature, 598 :338-341, doi:10.1038/s41586-021-03914-4.Yang, W. and J. Shaman , 2021: Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern . Nature Communications, 12 :5573, doi:10.1038/s41467-021-25913-9.
Pei, S., F. Liljeros and J. Shaman, 2021: Identifying asymptomatic spreaders of antimicrobial resistant pathogens in hospital settings . Proceedings of the National Academy of Sciences, 118(37) :e2111190118, doi:10.1073/pnas.2111190118.Kandula, S. and J. Shaman, 2021: Investigating associations between COVID-19 mortality and population level health and socioeconomic indicators in the United States: A modeling study. PLOS Medicine, 18(7) :e1003693, doi:10.1371/journal.pmed.1003693.Ma, Y., S. Pei, J. Shaman, R. Dubrow and K. Chen, 2021: Role of meteorological factors in the transmission of SARS-CoV-2 in the United States . Nature Communications, 12 :3602, doi:10.1038/s41467-021-23866-7.
Martinez-Ales, G., J. Pamplin II, C. Rutherford, C. Gimbrone, S. Kandula, M. Olfson, M. Gould, J. Shaman and K.M. Keyes, 2021: Age, period, and cohort effects on suicide death in the United States from 1999 to 2018: moderation by sex, race, and firearm involvement . Molecular Psychology, doi:10.1038/s41380-021-01078-1.
Zebrowski, A., A. Rundle, S. Pei , T. Yaman, W. Yang, B.G. Carr, S. Sims, R. Doorley, N. Schluger, J. Shaman and C. Branas, 2021: A spatiotemporal tool to project hospital critical care capacity and mortality from COVID-19 in US counties . American Journal of Public Health, 111 :1113-1122, doi:10.2105/AJPH.2021.306220.
Keyes, K.M., S. Kandula , M. Olfson, M.S. Gould, G. Martinez-Ales, C. Rutherford and J. Shaman, 2021: Suicide and the agent-host-environment triad: leveraging surveillance sources to inform prevention . Psychological Medicine, 51(4) :529-537, doi:10.1017/S003329172000536X.
Yang, W., J. Shaff and J. Shaman, 2021: COVID-19 transmission dynamics and effectiveness of public health interventions in New York City during the 2020 spring pandemic wave . Journal of the Royal Society Interface, 18(175) :20200691, doi:10.1098/rsif.2020.0822.
Lamb, M. R., S. Kandula and J. Shaman, 2021: Differential COVID-19 case positivity in New York City neighborhoods: socioeconomic factors and mobility . Influenza and Other Respiratory Viruses, 15(2) :209-217, doi:10.1111/irv.12816.
Rader, B., L.F. White, M.R. Burns, J. Chen, J. Brilliant, J. Cohen, J. Shaman , L. Brilliant, M.U.G. Kraemer, J.B. Hawkins, S.V. Scarpino, C.M. Astley and J.S. Brownstein, 2021: Mask wearing and control of SARS-CoV-2 transmission in the United States . Lancet Digital Health, 3(3) :e148-e157, doi:10.1016/S2589-7500(20)30293-4.
Galanti, M. and J. Shaman, 2021: Direct observations of repeated infections with endemic coronaviruses . The Journal of Infectious Diseases, 223(3) :409-415, doi:10.1093/infdis/jiaa392.Shaman, J., 2021: An estimation of undetected COVID cases in France. Nature, 590 :38-39, doi:10.1038/d41586-020-03513-9.Galanti, M., S. Pei, T.K. Yamana, F.J. Angulo, A. Charos, D. Swerdlow and J. Shaman, 2021: Social distancing remains key during vaccinations . Science, 371(6528) : 473-474, doi:10.1126/science.abg2326.Yang, W., S. Kandula , M. Huynh, S. K. Greene, G. Van Wye, W. Li, H T. Chan, E. McGibbon, A. Yeung, D. Olson, A. Fine and J. Shaman, 2021: Estimating the infection fatality risk of COVID-19 in New York City during the spring 2020 pandemic wave: a model-based analysis . Lancet Infectious Diseases, 21(2) :203-212, doi:10.1016/S1473-3099(20)30769-6.
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., S. Kandula and J. Shaman, 2020: Differential Effects of Intervention Timing on COVID-19 Spread in the United States . Science Advances, 6(49) :eabd6370, doi:10.1126/sciadv.abd6370.Pei, S., K. Dahl, T.K. Yamana, R. Licker and J. Shaman, 2020: Compound risks of hurricane evacuation amid the COVID-19 pandemic in the United States . GeoHealth, 4(12) :e2020GH000319, doi:10.1029/2020GH000319.Cruz, A. T., J. Shaman and P. Dayan, 2020: The challenge of clearly counting COVID-19 in children . Pediatrics, 146(6) :e2020031682, doi:10.1542/peds.2020-027425.
Bomfim, R., S. Pei, J. Shaman, T. Yamana , H. A. Makse, J. S. Andrade Jr., A. S. Lima Neto and V. Furtado, 2020: Predicting dengue outbreaks at neighborhood level using human mobility in urban areas . Journal of the Royal Society Interface, 17(171) :20200691, doi:10.1098/rsif.2020.0691.
Shaman, J. and M. Galanti, 2020: Will SARS-CoV-2 become endemic? Science, 370(6516) :527-529, doi:10.1126/science.abe5960.Pei, S. and J. Shaman , 2020: Aggregating forecasts of multiple respiratory pathogens supports more accurate forecasting of influenza-like illness . PLOS Computational Biology, 16(10) :e1008301, doi:10.1371/journal.pcbi.1008301.Kramer, S.C., S. Pei and J. Shaman , 2020: Forecasting influenza in Europe using a meta population model incorporating cross-border commuting and air travel . PLOS Computational Biology, 16(10) :e1008233, doi: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.Emeruwa, U.N., S. Ona, J. Shaman , A. Turitz, J. D. Wright, C. Gyamfi-Bannerman and A. Melamed, 2020: Associations between built environment, neighborhood socioeconomic status and SARS-CoV-2 infection among pregnant women in New York City . JAMA, 324(4) :390-392, doi:10.1001/jama.2020.11370.
Shea, B., K. Knowlton and J. Shaman , 2020: Assessment of climate-health curricula at international health professions schools . JAMA Open Network, 3(5) :e206609, doi:10.1001/jamanetworkopen.2020.6609.Li, R., S. Pei , B. Chen, Y. Song, T. Zhang, W. Yang and J. Shaman , 2020: Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-CoV2) . Science, 368(6490) :489-493, doi:10.1126/science.abb3221. Full text . Reprint .
Gervais, M., J. Shaman and Y. Kushnir, 2020: Impacts of the North Atlantic warming hole on sensible weather . Journal of Climate . 33(10) :4255-4271, doi:10.1175/JCLI-D-1909636.1.
Heaney, A.K., K. Alexander and J. Shaman , 2020: Ensemble Forecast and Parameter Inference of Childhood Diarrhea in Chobe District, Botswana . Epidemics, 30 :100372, doi:10.1016.jepidem.2019.100372.Yamana, T. and J. Shaman , 2020: A framework for evaluating the effects observational type and quality on vector-borne disease forecast . Epidemics, 30 :100359, doi:10.1016.jepidem.2019.100359.Krasna, H., K. Czabanowska, S. Jiang, S. Khadka, H. Morita , J. Kornfeld and J. Shaman , 2020: The future of careers at the intersection of climate change and public health: What can job postings and an employer survey tell us? International Journal of Environmental Research and Public Health, 17(4) :1310, doi:10.3390/ijerph17041310.
Shaman, J., M. Galanti , 2020: Direct measurement of rates of asymptomatic infection and clinical care-seeking for seasonal coronavirus . medRxiv, 19612, doi:10.1101/2020.01.30.20019612.Orenbuch, R., I. Filip, D. Comito, J. Shaman , I. Pe’er and R. Rabadan, 2020: arcasHLA: high resolution HLA typing from RNAseq . Bioinformatics, 36(1) :33-40, doi:10.1093/bioinformatics/btz474.
2019
Heaney, A.K., J. Shaman and K. Alexander, 2019: El Niño-Southern Oscillation and under-5 diarrhea in Botswana . Nature Communications , 10 : Article Number 5798, doi:10.1038/s41467-019-13584-6.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.
Johansson, M.A., …, T. Yamana, J. Shaman , … et al., 2019: Advancing probabilistic epidemic forecasting through an open challenge: The Dengue Forecasting Project . Proceedings of the National Academy of Sciences, 116(48) :24268-24274, doi:10.1073/pnas.1909865116.
Sy, K.T.L., J. Shaman, S. Kandula, S. Pei, M. Gould and K.M. Keyes, 2019: Spatial temporal clustering of suicide deaths from 1999 to 2016: a spatial epidemiological approach . Social Psychiatry and Psychiatric Epidemiology, 54 :1471-1482, doi:10.1007/s00127-019001736-4.
Lipsitch, M. and J. Shaman , 2019: Comment on: ‘Antibiotic footprint’ as a communication tool to aid reduction of antibiotic consumption . Journal of Antimicrobial Chemotherapy, 74(11) :3404-3406, doi:10.1093/jac/dkz320.
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.
George D., W. Taylor, J. Shaman , C. Rivers, B. Paul, T. O’Toole, M.A. Johansson, L. Hirschman, M. Biggerstaff, J. Asher and N. Reich, 2019: Technology to advance infectious disease forecasting for outbreak management . Nature Communications, 10 : Article Number 3932, doi:10.1038/s41467-019-11901-7.
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.Gervais, M., J. Shaman and Y. Kushnir, 2019: Impacts of the North Atlantic Warming Hole in Future Climate Projections: Mean Atmospheric Circulation and the North Atlantic jet . Journal of Climate, 32(10): 2673-2689, doi:10.1175/JCLI-D-18-0647.1.
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. DeFelice, N.B. , R. Birger, N. DeFelice, A. Gagner, S.R. Campbell, C. Romano, M. Santoriello, J. Henke, J. Wittie, B. Cole, C. Kaiser and J. Shaman , 2019: Real time 2017 West Nile virus forecast: operational challenges . JAMA Network Open, 2(4) :e193175, doi:10.1001/jamanetworkopen.2019.3175.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.Reis, J., T. Yamana, S. Kandula and J. Shaman , 2019: Superensemble forecast of respiratory syncytial virus outbreaks at regional, state and municipal levels. Epidemics, 26 :1-8, doi:10.1016/j.epidem.2018.07.001.Kramer, S. and J. Shaman , 2019: 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.
Yang, W., J. Li and J. Shaman , 2019: Characteristics of Measles Epidemics in China (1951-2004) and Implications for Elimination: A Case Study of Three Key Locations . PLOS Computational Biology, 15(2) :e1006806, doi:10.1371/journal.pcbi.1006806.
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
Pei, S. , F. Morone, F. Liljeros, H.A. Makse and J. Shaman , 2018: Inference of the nosocomial transmission dynamics of methicillin-resistant Staphylococcus aureus. eLife, 7 :e40977, doi:10.7554/eLife.40977.Alexander, K.A., A. Heaney and J. Shaman , 2018: Hydrometeorology and flood pulse dynamics drive diarrheal disease outbreaks and increase vulnerability to climate change in surface-water dependent populations: a retrospective analysis . PLOS Medicine, 15(11) :e1002688, doi:10.1371/journal.pmed.1002688.
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.Fu, C., Z. Dong, J. Shen, Z. Yang, Y. Liao, W. Hu, S. Pei and J. Shaman , 2018: Rotavirus gastroenteritis infection among children vaccinated and unvaccinated with rotavirus vaccine in southern China: A population-based assessment. JAMA Network Open, 1(4) , e181382, doi:10.1001/jamanetworkopen.2018.1381.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.Shea, B., K. Knowlton and J. Shaman , 2018. The Need for Informed Climate-Health Governance . International Journal of Health Governance, 23(3) :196-204, doi:10.1108/IJHG-01-2018-0001.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.Gervais, M. , J. Shaman and Y. Kushnir, 2018. Mechanisms Governing the Development of the North Atlantic Warming Hole in the CESM-LE Future Climate Simulations . Journal of Climate, 31(15) :5927-5946, doi:10.1175/JCLI-D-17-0635.1.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.Shaman, J. and K. M. Knowlton, 2018: The need for climate and health education . American Journal of Public Health, 108(S2) :S66-S67.Ukawuba, I. and J. Shaman , 2018: Association of spring-summer hydrology and meteorology and human West Nile virus infection in West Texas, USA, 2002-2016 . Parasites & Vectors , 11 :224, doi:10.1186/s13071-018-2781-0.Reis, J. and J. Shaman , 2018: Simulation of four respiratory viruses and inference of epidemiological parameters . Infectious Disease Modeling, 3 :23-34, doi:10.1016/j.idm.2018.03.006.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.
DeFelice, N. B., Z. D. Schneider, E. Little , C. Barker, K. A. Callout, S. R. Campbell, D. Damian, P. Irwin, H. M. P. Jones, J. Townsend and J. Shaman , 2018: Use of temperature to improve West Nile virus forecasts . PLOS Computational Biology, 14(3) :e1006047, doi:10.1371/journal.pcbi.1006047.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.Shaman, J. , 2018: Pandemic preparedness and forecast . Nature Microbiology, 3 :265-267. doi:10.1038/s41564-018-0117-7.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.Little , E., W. Bajwa and J. Shaman , 2017: Local environmental and meteorological conditions influencing the invasive mosquito Aedes albopictus and arbovirus transmission risk in New York City . PLOS Neglected Tropical Diseases, 11(8) :e0005828, doi:1371/journal.pntd.0005828.Quinn, A., P. L. Kinney and J. Shaman , 2017: Predictors of summertime heat index levels in New York City apartments . Indoor Air, 27(4) :840-851, doi:10.1111/ina.12367.Quinn, A. and J. Shaman , 2017: Health symptoms in relation to temperature, humidity, and self-reported perceptions of climate in New York City residential environments . International Journal of Biometeorology , 61(7) :1209-1220, doi:10.1007/s00484-016-1299-4.Fu, C., S. Pei , Z. Yang, Q. Guo, and J. Shaman , 2017: Pre-Vaccination Evolution of Antibodies among Infants 0, 3 and 6 Months of Age: a Longitudinal Analysis of Measles, Enterovirus 71 and Coxsackievirus 16 . Vaccine, 35(31) :3817-3822, doi:10.1016/j.vaccine.2017.06.002.Yang, W., L. Wen, S.-L. Li, K. Chen, W.-Y. Zhang, and J. Shaman , 2017 : Geospatial characteristics of measles transmission in China during 2005-2014 . PLOS Computational Biology, 13(4) :e1005474. doi:10.1371/journal.pcbi.1005474.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.
Pei, S., X. Teng, J. Shaman , F. Morone and H.A. Efficient collective influence maximization in cascading processes with first-order transitions . Scientific Reports, 7 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.DeFelice, N. B., E. Little, S.R. Campbell and J. Shaman , 2017: Ensemble forecast of human West Nile virus cases and mosquito infection rates . Nature Communications, 8 , Article number 14592, doi:10.1038/ncomms14592.DeBlander, E. and J. Shaman , 2017: Teleconnection between the South Atlantic Convergence Zone and the Southern Indian Ocean: Implications for Tropical Cyclone Steering . Journal of Geophysical Research Atmospheres, 122 :728-740, doi:10.1002/2016JD025373.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.Quinn, A. and J. Shaman , 2017: Indoor temperature and humidity in New York City apartments during winter . Science of the Total Environment, 583 :29:45, doi:10.1016/j.scitotenv.2016.12.183.Lee, W. V. and J. Shaman , 2017: Heat-coping strategies and bedroom thermal satisfaction in New York City . Science of the Total Environment , 574 :1217-1231, doi:10.1016/j.scitotenv.2016.07.006.
2016
F u, C., L. Lu, H. Wu, J. Shaman , Y. Cao, F. Fang, Q. Yang, Q. He, Z. Yang, and M. Wang, 2016: Placental antibody transfer efficiency and maternal levels: specific for measles, coxsackievirus A16, enterovirus 71, poliomyelitis I-III and HIV-1 antibodies . Scientific Reports, 6 :38874. doi:10.1038/srep38874.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.Heaney, A., E. Little, J. Shaman , 2016: Meteorological variability and infectious disease in Central Africa: A review of meteorological data quality. Annals of the New York Academy of Sciences, 1382(1) :31-43. doi:10.1111/nyas.13090.Yamana, T., S. Kandula J. Shaman Superensemble forecasts of dengue outbreaks . Journal of the Royal Society Interface, 13 :20160410. doi:10.1098/rsif.2016.0410.Reis, J. J. Shaman Retrospective parameter estimation and forecast of respiratory syncytial virus in the United States. PLOS Computational Biology, 12(10) : e1005133. doi:10.1371/journal.pcbi.1005133.Shaman, J. The Superposition of Eastward and Westward Rossby Waves in Response to Localized Forcing . Journal of Climate, 29 (20):7547-7557, doi:10.1175/JCLI-D-16-0119.1Little, E., S.R. Campbell and J. Shaman , 2016: Development and validation of a climate-based ensemble prediction model for West Nile virus infection rates in Culex mosquitoes, Suffolk County, New York . Parasites & Vectors, 9 :443, doi: 10.1186/s13071-016-1720-1.Biggerstaff M., D. Alper, M. Dredge, S. Fox, I.C.-H. Fung, K.S. Hickman, B. Leis, R. Rosenfield, J. Shaman , M.-H. Tsou, P. Velardi, A. Vespignani, and L. Finelli for the Influenza Forecasting Contest Working Group, 2016: 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.Sobel, A., S. Camargo, W. Debucquoy, G. Deodatis, M. Gerrard, T. Hall, R. Hallman, J. Keenan, U. Lall, M. Levy, B. Orlove, C. Rosenzweig, R. Seager, J. Shaman , and M. Tippet, 2016: Extreme Weather and Climate: Workshop Report . Journal of Extreme Events, 3(1) :167001, doi:10.1142/S2345737616710019.
2015
Seager, R., J. C. H. Chiang and J. Shaman : Do the tropics rule? Assessing the state of tropical climate science . Bulletin of the American Meteorological Society, 96 , ES211-ES214; doi: 10.1175/BAMS-D-15-00043.1
Yang W. , W. Zhang, D. Kargbo, R. Yang, Y. Chen, Z. Chen, A. Kamara, B. Kargbo, S. Kandula , A. Karspeck, C. Liu and J. Shaman , 2015: Transmission network of the 2014-2015 Ebola epidemic in Sierra Leone . Journal of the Royal Society Interface , 12 20150536; doi: 10.1098/rsif.2015.0536. 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, 2015: 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 , 2015: Forecasting influenza epidemics in Hong Kong . PLOS Computational Biology, 11 (7) : e1004383, doi:10.1371/journal.pcbi.1004383Alexander K. A., C. E. Sanderson, M. Marathe, B. L. Lewis, C. M. Rivers, J. Shaman , J. M. Drake, E. Lofgren, V. M. Dato, M. C. Eisenberg, and S. Eubank, 2015: What factors might have led to the emergence of Ebola in West Africa? . PLOS Neglected Tropical Diseases, 9(6) : e0003652, doi:10.1371/journal.pntd.0003652
Yang, 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
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.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.
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.
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.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.
2012
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.
2011
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.
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., 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.1000316Shaman, 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.
2009
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
2008
2007
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.
2006
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.
2005
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.
2004
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.
2003
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.
2002
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.
