Other Infectious Diseases

Accepted/In Press/Early Release

Cascante-Vega, J., T. Robin, L. Wen, J. Zucker, A.-C. Uhlemann, S. Pei and J. Shaman. Estimating importation and nosocomial transmission of micro-organisms in hospital settings using patient records and culture data. Epidemics.

2024

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.
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

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.
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.
Pei, S., S. Blumberg, J. Cascante Vega, T. Robin, Y. Zhang, R.J. Medford, B. Adhikari and J. Shaman, 2023: Challenges in forecasting antimicrobial resistance. Emerging Infectious Diseases, 29(4):679-685, doi:10.3201/eid2904.221552.

2022

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.

2021

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.
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.
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.
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.
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.
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.
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.

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.
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.
Reis, J., T. Yamana, S. Kandula and J. Shaman. 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.
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.

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.
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.
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.

2016

Reis, J. and J. Shaman, 2016: 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.

2015

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.
Alexander 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: 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

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.