CSE 8803 EPI, Fall 2025
Data Science for Epidemiology
Data Science for Epidemiology
Lectures and Readings
- Tina Rosenberg. Stopping Pandemics Before they Start, New York Times, June 2017.
- Ed Young. The next plauge is coming: Is America ready?, The Atlantic, July/Aug 2018.
- H. Hethcote. Sections 1-2.4. The mathematics of infectious diseases, SIAM Review, 2000.
- Ina Holmdahl and Caroline Buckee. Wrong but Useful — What Covid-19 Epidemiologic Models Can and Cannot Tell Us, The New England Journal of Medicine, July 2020.
- Simon Frost, Epidemiological Models Interactive Example (try it out!): SIR in Python using scipy, Accessed Aug 2020.
- Another Interactive COVID-19 SEIR model (try it out!): Modeling COVID-19 Spread vs Healthcare Capacity, Accessed Aug 2020.
- (Details about Bernoulli's model) M. Glomski and E. Ohanian. Eradicating a Disease: Lessons from Mathematical Epidemiology. College Mathematics Journal. 2012.
- Chapter 21 from Easley and Kleinberg: Epidemics.
- Stephen Eubank, Hasan Guclu, V.S. Anil Kumar, Madhav Marathe, Aravind Srinivasan, Zoltan Toroczkai and Nan Wang. Modeling disease outbreaks in realistic urban social networks. Nature. 2004.
- D. Balcan, V. Colizza, B. Goncalves, H. Hu, J. Ramasco and A. Vespignani. Multiscale mobility networks and the spatial spreading of infectious diseases. PNAS 2009.
- L. Pellis, F. Ball, S. Bansal, K. Eames, T. House, V. Isham and P. Trapman. Eight challenges for network epidemic models. Epidemics 2015
- C. T. Kelley. Iterative methods for Optimization. SIAM 1999.
- David Kempe, Jon Kleinberg, and Eva Tardos. Maximizing the spread of influence through a social network. SIGKDD 2003.
- L. Pelley. Why COVID-19 and flu could be in a 'tug of war' in the years ahead. CBC 2022.
- Joao Gama Oliveira and Albert-Lazlo Barabasi. Darwin and Einstein correspondence patterns . Nature, 2005.
- P. S. Dodds and D. J. Watts. Universal behavior in a generalized model of contagion. PRL 2004.
- Y. Matsubara, Y. Sakurai, B. A. Prakash, L. Li, C. Faloutsos. Rise and Fall Patterns of Information Diffusion: Model and Implications. SIGKDD, 2012.
- D. Romero, B. Meeder, J. Kleinberg. Differences in the Mechanics of Information Diffusion Across Topics: Idioms, Political Hashtags, and Complex Contagion on Twitter. WWW, 2011.
- The Lotka-Volterra Model. Wikipedia.
- A. Beutel, B. A. Prakash, R. Rosenfeld and C. Faloutsos. Interacting Viruses in Networks: Can Both Survive?. SIGKDD 2012.
- S. Nickbakhsh et al. Virus–virus interactions impact the population dynamics of influenza and the common cold. PNAS 2019.
- R. Baker et al. The impact of COVID-19 nonpharmaceutical interventions on the future dynamics of endemic infections. PNAS 2020.
- B. A. Prakash et al. Threshold Conditions for Arbitrary Cascade Models on Arbitrary Networks. ICDM 2011.
- R. Pastor-Santorras and A. Vespignani. Epidemic spreading in scale-free networks. Physical Review Letters 86, 14, 2001.
- A. Ganesh et al. The effect of network topology on the spread of epidemics , INFOCOM 2005.
- B. Grenfell et al. Travelling waves and spatial hierarchies in measles epidemics. Nature 2001.
- N. C. Grassly et al. Host immunity and synchronized epidemics of syphilis across the United States Nature 2005
- B. A. Prakash et al. Winner-takes-all: Competing Viruses on fair-play networks. WWW 2012
- Chapter 21 from Easley and Kleinberg: Epidemics. (See Sec 21.5)
- Madhav Marathe and Anil Vullikanti. Computational Epidemiology, CACM 2013
- N. Dimitrov and L. Meyers. Section 5. Mathematical Approaches to Infectious Disease Prediction and Control, INFORMS 2010.
- V. Das Swain, J. Xie et al. WiFi mobility models for COVID-19 enable less burdensome and more localized interventions for university campuses. Frontiers Public Health, 2023.
- S. Pai et al. Spatiotemporal clustering of in-hospital Clostridioides difficile infection. Infection Control and Hospital Epi. 2020
- A. Aleta et al. Modelling the impact of testing, contact tracing and household quarantine on second waves of COVID-19. Nature Human Behavior 2020.
- K. Eames, S. Bansal, S. Frost and S. Riley. Six challenges in measuring contact networks for use in modelling. Epidemics, 2015.
- P. S. Bearman, J. Moody, and K. Stoval. Chains of affection: The structure of adolescent romantic and sexual networks AJS 2004.
- P. Sapiezynski, A. Stopczynski, D. D. Lassen, and S. Lehmann Interaction data from the copenhagen networks study. Nature Scientific Data, 2019.
- A. Hess, K. A. Hummel, W. N. Gansterer, G. Haring. Data-driven Human Mobility Modeling: A Survey and Engineering Guidance for Mobile Networking. ACM Computing Surveys, 2016.