Weekly and Daily Projections of COVID19 Epidemic Outcomes and Healthcare Demands for New York City (NYC)


57. Chen J, Terry MB, Dalerba P, Hur C, Hu J, Yang W. Environmental drivers of the rising incidence of early-onset colorectal cancer in the United States. International Journal of Cancer. First published: 10 February 2024. doi:

56. Chen K, Ma Y, Bell ML, Yang W. Canadian Wildfire Smoke and Asthma Syndrome Emergency Department Visits in New York City. JAMA. 2023. doi: 10.1001/jama.2023.18768.

55. Chen J, Zhang W, Wang Y, Yang W. Determinants of measles persistence in Beijing, China: A modelling study. Epidemiology and infection. 2023;151:e144.

54. Yang W, Shaman J. Reconciling the efficacy and effectiveness of masking on epidemic outcomes. pre-print: medRxiv. 2023:2023.05.10.23289803. doi: 10.1101/2023.05.10.23289803.

53. Yang W, Shaman J. Development of Accurate Long-lead COVID-19 Forecast. PLoS Comput Biol 2023. 19(7): e1011278.

52. Wiemken TL, Khan F, Puzniak L, Yang W, Simmering J, Polgreen P, Nguyen JL, Jodar L, McLaughlin JM. Seasonal trends in COVID-19 cases, hospitalizations, and mortality in the United States and Europe. Scientific Reports. 2023;13(1):3886. doi: 10.1038/s41598-023-31057-1.

51. Jianjiu Chen, Isabella L. Zhang, Mary Beth Terry, Wan Yang. Dietary Factors and Early-Onset Colorectal Cancer in the United States—an Ecologic Analysis. Cancer Epidemiol Biomarkers Prev 2022;

50. Yang W & Shaman J. 2022 COVID-19 pandemic dynamics in South Africa and epidemiological characteristics of three variants of concern (Beta, Delta, and Omicron) eLife 11:e78933.

49. Yang W & Shaman J. COVID-19 pandemic dynamics in India, the SARS-CoV-2 Delta variant, and implications for vaccination. J R Soc Interface. 2022;19(191):20210900. doi: doi:10.1098/rsif.2021.0900.

48. Yuan H, Yeung A, Yang W. Interactions among common non-SARS-CoV-2 respiratory viruses and influence of the COVID-19 pandemic on their circulation in New York City. Influenza and other respiratory viruses. 2022.

47. Yuan H, Reynolds C, Ng S, Yang W. Factors affecting the transmission of SARS-CoV-2 in school settings. Influenza and other respiratory viruses. 2022.

46. Yang W, Greene SK, Peterson ER, Li W, Mathes R, Graf L, Lall R, Hughes S, Wang J, Fine A. Epidemiological characteristics of the B.1.526 SARS-CoV-2 variant. Science Advances. 2022; 8, eabm0300. 

45. W. Yang, J. Shaman, 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,  2022.

44. Yang W, Shaman J. Development of a model-inference system for estimating epidemiological characteristics of SARS-CoV-2 variants of concern. Nature Communications. 2021;12:5573. doi:

43. Yuan H, Kramer SC, Lau EHY, Cowling BJ, Yang W. Modeling influenza seasonality in the tropics and subtropics. PLoS Comput Biol. 2021 Jun;17(6):e1009050. doi: 10.1371/journal.pcbi.1009050. eCollection 2021 Jun. PubMed PMID: 34106917; PubMed Central PMCID: PMC8216520

42. Kehm RD, Lima SM, Swett K, Mueller L, Yang W, Gonsalves L, Terry MB. Age-specific Trends in Colorectal Cancer Incidence for Women and Men, 1935-2017. Gastroenterology. 2021 Sep;161(3):1060-1062.e3. doi: 10.1053/j.gastro.2021.05.050. Epub 2021 May 28. PubMed PMID: 34058214

41. Yang W, Shaff J, Shaman J. Effectiveness of non-pharmaceutical interventions to contain COVID-19: a case study of the 2020 spring pandemic wave in New York City. Journal of The Royal Society Interface. 2021;18(175):20200822. doi:10.1098/rsif.2020.0822.

40. Zebrowski A, Rundle A, Pei S, Yaman T, Yang W, Carr BG, Sims S, Doorley R, Schluger N, Quinn JW, Shaman J, Branas CC. A spatiotemporal tool to project hospital critical care capacity and mortality from COVID-19 in US counties. American Journal of Public Health, 2021 Jun;111(6):1113-1122.doi: 10.2105/AJPH.2021.306220. Epub 2021 Apr 15.

39. Yang W, Kandula S, Huynh M, Greene SK, Van Wye G, Li W, Chan HT, McGibbon E, Yeung A, Olson D, Fine A, Shaman J. Estimating the infection-fatality risk of SARS-CoV-2 in New York City during the spring 2020 pandemic wave: a model-based analysis. The Lancet Infectious Diseases. doi: 10.1016/S1473-3099(20)30769-6.

38. Yang W. Transmission Dynamics of and Insights from the 2018-2019 Measles Outbreak in New York City: A Modeling Study. Science Advances. 2020; 6(22): eaaz4037. doi: 10.1126/sciadv.aaz4037.

37. Li R, Pei S, Chen B, Song Y, Zhang T, Yang W, Shaman J. Substantial undocumented infection facilitates the rapid dissemination of novel coronavirus (SARS-Cov2). Science 16 Mar 2020: eabb3221. doi: 10.1126/science.abb3221

36. Yang W, Terry MB. Do temporal trends in cancer incidence reveal organ system connections for cancer etiology? Epidemiology. 2020 Mar 25. doi: 10.1097/EDE.0000000000001192. [Epub ahead of print].

35. Yang W, Kehm RD, Terry MB. Survival model methods for analyses of cancer incidence trends in young adults. Statistics in Medicine. 2020;1–14.

34. Kehm RD, Yang W, Tehranifar P, Terry MB. 40 years of change in age- and stage-specific cancer incidence rates in US women and men. JNCI Cancer Spectrum. 2019.

33. Yang W, Li J, and Shaman J. Characteristics of Measles Epidemics in China (1951-2004) and Implications for Elimination: A Case Study of Three Key Locations. PLoS Computational Biology 2019; 15(2):e1006806.

32. Kandula S, Yamana T, Pei S, Yang W, Morita H, and Shaman J. Evaluation of mechanistic and statistical methods in forecasting influenza-like illness. Journal of the Royal Society Interface. 2018 Jul;15(144). pii: 20180174. doi: 10.1098/rsif.2018.0174.

31. Yang W, Cummings MJ, Bakamutumaho B, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Lutwama JJ, O’Donnell MR, and Shaman J. Dynamics of influenza in Tropical Africa: temperature, humidity, and co-circulating (sub)types. Influenza and Other Respiratory Viruses. 2018;12(4):446-56.

30. Yang W, Cummings MJ, Bakamutumaho B, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Lutwama JJ, O’Donnell MR, and Shaman J. Transmission Dynamics of Influenza in Two Major Cities of Uganda. Epidemics. 2018.

39. Biggerstaff M, Johansson M, Alper D, Brooks L, Chakraborty P, Farrow D, Hyun S, Kandula S, McGowan C, Ramakrishnan N, Rosenfeld R, Shaman J, Tibshirani R, Tibshirani RJ, Vespignani A, Yang W, Zhang Q, Reed C. Results from the second year of a collaborative effort to forecast influenza seasons in the United States. Epidemics. 2018; Available online 24 February 2018.

28. Pei S., Kandula S., Yang W, Shaman J. Forecasting the spatial transmission of influenza in the United States. Proceedings of the National Academy of Sciences of the United States of America. 2018; published ahead of print February 26, 2018,

27. Cummings MJ, Bakamutumaho B, Yang W, Wamala JF, Kayiwa J, Owor N, Namagambo B, Byaruhanga T, Wolf A, Lutwama JJ, Shaman J, O’Donnell MR. Emergence, epidemiology, and transmission dynamics of 2009 pandemic A/H1N1 influenza in Kampala, Uganda, 2009-2015. The American Journal of Tropical Medicine and Hygiene. 2018;98(1):203-6.

26. Shaman J, Kandula S, Yang W, Karspeck A. 2017. The use of ambient humidity conditions to improve influenza forecast. PLOS Computational Biology 13(11): e1005844. doi: 10.1371/journal.pcbi.1005844

25. Yang W, Wen L, Li SL, Chen K, Zhang WY, Shaman J. 2017. Geospatial characteristics of measles transmission in China during 2005-2014. PLOS Computational Biology 13(4):e1005474. doi: 10.1371/journal.pcbi.1005474

24. Kandula S, Yang W, Shaman J. 2017. Type- and subtype-specific influenza forecast. American Journal of Epidemiology 185 (5): 395-402

23. Yang W, Olson DR, Shaman J. 2016. Forecasting Influenza Outbreaks in Boroughs and Neighborhoods of New York City. PLOS Computational Biology 12(11): e1005201. doi:10.1371/journal. pcbi.1005201.

22. Nguyen J, Yang W, Ito K, Matte T, Shaman J, Kinney P. 2016. Seasonal influenza infections and cardiovascular disease mortality. JAMA Cardiology. 1(3):274-81.

21. Yang W, Zhang W, Kargbo D, Yang R, Chen Y, Chen Z, Kamara A, Kargbo B, Kandula S, Karspeck A, Liu C, Shaman J. 2015. Transmission network of the 2014-2015Ebola epidemic in Sierra Leone. Journal of the Royal Society Interface. Published 11 November 2015. DOI: 10.1098/rsif.2015.0536.

20. Yang W, Lipsitch M, Shaman J. 2015. Inference of seasonal and pandemic influenza transmission dynamics. Proceedings of the National Academy of Sciences 112: 2723-2728.

19. Yang W, Cowling BJ, Lau EHY, Shaman J. 2015. Forecasting influenza epidemics in Hong Kong. PLoS Computational Biology 11: e1004383.

18. Hong A, Schweitzer L, Yang W, Marr LC. 2015. The impact of temporary freeway closure onregional air quality: A lesson from Carmageddon in Los Angeles, United States. Environmental Science & Technology 49: 3211–3218.

17. Lofgren E, Halloran ME, Rivers CM, Drake JM, Porco TC, Lewis B, Yang W, Vespignani A, Shaman J, Eisenberg JNS, Eisenberg MC, Marathe M, Scarpino SV, Alexander KA, Meza R, Ferrari MJ, Hyman JM, Meyers LA, Eubank S. 2014. Opinion:Mathematical models: A key tool for outbreak response. Proceedings of the National Academy of Sciences 111: 18095-18096.

16. Shaman J, Yang W, Kandula S. 2014. Inference and forecast of the current West African Ebola outbreak in Guinea, Sierra Leone and Liberia. PLoS Currents Outbreaks. 2014 Oct 28. Edition 1. doi: 10.1371/currents.outbreaks.3408774290b1a0f2dd7cae877c8b8ff6.

15. Yang W, Shaman J. 2014. Does exposure to poultry and wild fowl confer immunity to H5N1? Chinese Medical Journal 127: 3335-3343.

14. Yang W, Karspeck A, Shaman J. 2014. Comparison of filtering methods for the modeling and retrospective forecasting of influenza epidemics. PLoS Computational Biology 10: e1003583.

13. Yang W, Shaman J. 2014. A simple modification to improving inference for non-linear dynamical systems. arXiv: 1403.6804.

12. Yang W, Petkova E, Shaman J. 2014. The 1918 influenza pandemic in New York City: age-specific timing, mortality, and transmission dynamics. Influenza and Other Respiratory Viruses 8: 177-188.

11. Shaman J, Karspeck A, Yang W, Tamerius J, Lipsitch M. 2013. Real-time influenza forecasts during the 2012-2013 season. Nature Communications 4: 2837.

10. Yang W, Elankumaran S, Marr LC. 2012. Relationship between humidity and influenza A viability in droplets and implications for influenza’s seasonality. PLoS ONE 7: e46789.

9. Yang W, Marr LC. 2012. Mechanisms by which ambient humidity may affect viruses in aerosols. Applied and Environmental Microbiology 78: 6781-6788.

8. Yang W, Marr LC. 2011. Dynamics of airborne influenza A viruses indoors and dependence on humidity. PLoS ONE 6: e21481.

7. Yang W, Elankumaran S, Marr LC. 2011. Concentrations and size distributions of airborne influenza A viruses measured indoors at a health centre, a day-care centre, and on aeroplanes. Journal of The Royal Society Interface 8: 1176-1184.

6. Yang W, Gu AZ, Zeng SY, Li D, He M, Shi HC. 2011. Development of a combined immunomagnetic separation and quantitative reverse transcription-PCR assay for sensitive detection of infectious rotavirus in water samples. Journal of Microbiological Methods 84: 447-453.

5. Li D, Gu AZ, Zeng SY, Yang W, He M, Shi HC. 2011. Monitoring and evaluation of infectious rotaviruses in various wastewater effluents and receiving waters revealed correlation and seasonal pattern of occurrences. Journal of Applied Microbiology 110:1129-1137.

4. Li D, Gu AZ, Zeng S, Yang W, He M, Shi HC. 2011. Evaluation of the infectivity, gene and antigenicity persistence of rotaviruses by free chlorine disinfection. Journal of Environmental Sciences 23: 1691-1698.

3. Li D, Gu AZ, Yang W, He M, Hu XH, Shi HC. 2010. An integrated cell culture and reverse transcription quantitative PCR assay for detection of infectious rotaviruses in environmental waters. Journal of Microbiological Methods 82: 59-63.

2. Yang L, Zeng S, Chen J, He M, Yang W. 2010. Operational energy performance assessment system of municipal wastewater treatment plants. Water Science & Technology 62:1361-70.

1. Li D, Gu AZ, He M, Shi HC, Yang W. 2009. UV inactivation and resistance of rotavirus evaluated by integrated cell culture and real-time RT-PCR assay. Water Research 43: 3261-3269.


Airborne Transmission of Influenza A Virus in Indoor Environments (VT 2012)