Samit Bhattacharyya: Research

I study  how complexities at host and pathogen level scale up to population level dynamics. 

Pathogen interference often plays an important role in shaping out the disease outbreak. In this lab, I am specifically studying (in collaboration with Ottar BjornstadWhooping cough strains (pertussis andparapertussis) and investigating mechanisms that underlie the out-of-phase dynamical pattern of these two pathogens. I blend both mathematical theories and computational techniques to address these problems. 

I am also working on transient dynamics of resurgent Measles outbreaks. Measles are still fairly common in developing countries, even after years of apparent control. Recent re-emergence of measles in many places characterizes unpredictable features that indicate a clear shift in the disease epidemiology. I am exploring several hypotheses by developing mechanistic models that can explain the epidemiological shift in measles dynamics.

Samit Bhattacharyya: Papers

  1. Bhattacharyya S, and Ferrari MJ. 2016. Age-specific mixing generates transient outbreak risk following critical-level vaccination. Epidemiology and Infection 145 (1): 12-22.
  2. Bauch C. T. and Bhattacharyya S. (2012).  Social learning and evolutionary game dynamics determine how vaccine scares unfold. PLoS Comput. Biol., 8(4): e1002452. doi:10.1371/journal.pcbi.1002452.
  3. Bhattacharyya S. and Bauch C. T. (2011). “Wait and see” vaccinating behavior during a pandemic: a game theoretic analysis, Vaccine, 29(33), 5519-5525.
  4. Ghosh S. and Bhattacharyya S. (2011).  A two-patch prey-predator model with food-gathering activity, J. Applied Mathematics and Computating, 37(1-2), 497-521.
  5. Bauch C.T. and Bhattacharyya S. and Ball B. (2010). Rapid Emergence of Free-Riding Behavior in New Pediatric Immunization Programs, PLoS ONE 5(9): e12594. doi:10.1371/journal.pone.0012594.
  6. Bhattacharyya S. and Bauch C. T. (2010). A game dynamic model for delayer strategies in vaccinating behaviour for pediatric infectious diseases, J. Theoretical Biology 267, 276-282.
  7. Bhattacharyya S. and Ghosh S. (2010).Optimal control of vertically transmitted disease: an integrated approach, Computational and Mathematical Methods in Medicine, 11(4), 369-387.

Spencer Carran: About

My research focuses on how demographic patterns determine the build-up of epidemic risk, particularly for measles.

Previously I came from an applied math background and worked on the dynamics of insurgent warfare with Neil Johnson at the University of Miami.

Spencer Carran: PAPERS

  1. Pattern in Escalations in Insurgent and Terrorist Activity, 2011, Science 333 no. 6038 pp. 81-84.
  2. Afghanistan Casualty Timeline (2008 - 2010) Science 331, 1256 (2011).
  3. Financial black swans driven by ultrafast machine ecology (2012)
  4. Suma Ghosh: About

       I am interested in developing biologically motivated models to understand the ecology and evolution of infectious diseases. 

         My current research focuses in determining how the biological effects – direct such as competition for host resources or indirect such as host-mediated immunity – influence the parasite dynamics within a host. Working in this lab I am also collaborating with Dr. Cattadori’s group to integrate the theory with empirical work of rabbit/worm model in understanding the impact of interactions between helminth life-history traits and host immune responses on the transmission at the population level. I combine theories from mathematical and statistical modeling and analysis together with computational techniques to achieve this goal. I am also eager to extend my research in understanding the effect of other key determinants like host heterogeneity and polyparasitism, underlying the epidemiology of helminth infection. 

          My other interests are: to see how the higher order interactions among the species in a pathogen-vector-host system play a key role in shaping vector-borne disease transmission, to study the effects of immune memory in the individual and the population for directly transmitted diseases.

Suma Ghosh: Papers

  1. Suma Ghosh, Jessica L Waite, Dale H Clayton and Fredrick R Adler (2013). Can antibodies against flies alter malaria transmission by changing vector behavior? – Submitted
  2. Suma Ghosh and Samit Bhattacharyya (2013). Spatiotemporal dynamics of insect pest population under viral infection, Mathematical Biosciences, 244(1):13–21.
  3. Ghosh S. and Heffernan J.M. (2010). Influenza Pandemic Waves under Various Mitigation Strategies with 2009 H1N1 as a case study. PLoS ONE. 5(12):e14307.
  4. Ghosh S., Rangarajan G. and Sinha S. (2010). Stability of synchronization in a multi-cellular system. Europhysics Letters, 92:40012. doi:10.1209/0295-5075/92/40012.
  5. Ghosh S. and Bhattacharya D.K. (2010). Optimization in microbial pest control: An integrated approach, Applied Mathematical Modelling, 34:1382–1395.

Sheng Li: RESEARCH  

The goals of my current research are to understand the fundamental process of human infectious disease ecology, and eventually to help improve public health practice in field.  My public health/medical background motivates me carry out both theoretical and practical researches using multidisciplinary approaches.  

Specifically, I apply both statistical and mathematical modeling methods to understand human infectious diseases dynamics.  Collaboration with national and global health organizations, we analyze long term measles data sets and explore the spatio-temporal patterns of morbidity.

We study the interaction of vaccination and demographic transition on the dynamics of measles transmission in 6 focal provinces in China

Sheng Li: PAPERS

  1. Li S, Ma C, Hao L, Su Q, An Z, Ma F, Xie S, Xu A, Zhang Y, Ding Z, Li H, Cairns L, Wang H, Luo H, Wang N, Li L, Ferrari MJ. 2017. Demographic transition and the dynamics of measles in six provinces in China: A modeling study. PLoS Medicine
  2. S. Li, J.S.N Eisenberg et al.  (2010) Dynamics and control of infections transmitted from person to person through the environment. American Journal of Epidemiology.  170(2):257-265; doi:10.1093/aje/kwp116.
  3. J. Zhao, J.S.N Eisenberg, I.H. Spicknall, S. Li, J.S. Koopman.  (2012) Model Analysis of Fomite Mediated Influenza Transmission. Plos One Volume 7 ,Issue 12 e51984.
  4.   I.H. Spicknall, J.S. Koopman, M. Nicas, J.M. Pujol, S. Li, J.N.S. Eisenberg. (2010)  Informing Optimal Environmental Influenza Interventions: How the Host, Agent, and Environment Alter Dominant Routes of Transmission. PLoS Comput Biol  6(10): e1000969. doi:10.1371/journal.pcbi.1000969.

Amalie McKee: About

I study disease ecology under Professors Katriona Shea and Matthew Ferrari through the Department of Biology at Pennsylvania State University.

My research focuses on the interactions between population parameters such as age structure and maternal immunity waning and vaccine policy, with the goal of better targeting vaccine policy to specific populations.

I am also hugely involved with the Center for Infectious Disease Dynamics Graduate Student Association (CGSA).  More about me can be found on the CIDD page or the CGSA page.

My undergraduate degree is in Applied Math from Case Western Reserve University.

aMalie McKee: Papers

  1. Winter AK, Martinez ME, Cutts FJ, Moss WJ, Ferrari MJ, McKee A, Lessler JT, Hayford K, Wallinga J, Metcalf CJE. 2018. Benefits and challenges in using sero-prevalence data to inform models for measles and rubella elimination. The Journal of Infectious Diseases, jiy137,
  2. McKee A, Shea K, Ferrari MJ. 2018. Correlation between measles vaccine doses: Implications for the maintenance of elimination.Epidemiology and Infection 146: 468-475.
  3. McKee A, Shea K, Ferrari MJ. 2017. Optimal vaccine schedules to maintain measles elimination with a two-dose routine policy. Epidemiology and Infection 145(1): 227. 
  4. McKee A, Ferrari MJ, Shea K. 2015. The effects of maternal immunity and age distribution on population immunity to measles. Theoretical Ecology 10.1007/s12080-014-0250-8 

Will Probert: RESEARCH  

My research focuses on the development of models of spread of foot and mouth disease (FMD) in the United States, and associated mathematical optimization methods for the control of an FMD outbreak. 

I was previously based in Toulouse, France, working with collaborators at INRA-Toulouse. We developed tools from the optimization and decision-theoretic literature for use in the conservation of biodiversity and natural resource management. 

My PhD supervisors were Hugh Possingham, Peter Baxter, and Anthony Richardson at the Centre of Excellence for Environmental Decisions, Brisbane. 


Will Probert: PAPERS

  1. Higginson, A., Haynes, M., Probert, W.J.M. and Boreham, P. (2011) Interrelationships and Social Determinants of Residential Location Moves and Unemployment Duration in Australia.Proceedings of the 2011 HILDA conference, Melbourne, Australia.
  2. Probert, W.J.M. , Drechsler, M., Baxter, P.W.J. and Possingham, H.P. (2011) Resource allocation in two species systems: Is it worth acknowledging species interactions?Ecological Modelling, 222, 1781-1789. 
  3. Probert, W.J.M. , Hauser, C. E., McDonald-Madden, E., Runge, M.C., Baxter, P.W.J, Possingham, H.P. (2010) Managing and learning with multiple models: Objectives and optimization algorithms. Biological Conservation. 144: 1237-1245. 
  4. Bode, M., Probert, W. , Turner, W., Wilson, K. A., Venter, O. (2010) Conservation planning with multiple organizations and objectives. Conservation Biology. 25, 295-304 (listed in Faculty of 1000). 
  5. McDonald-Madden, E., Probert, W.J.M. , Hauser, C.E., Runge, M.C., Possingham, H.P., Jones, M.E., Moore, J.L., Rout, T.M., Vesk, P.A., Wintle, B.A. (2010) Active adaptive conservation of threatened species in the face of uncertainty. Ecological Applications. 20 (5) pp. 1476-1489. 


I am a post-doctoral researcher in the Center for Infectious Disease Dynamics. My work consists of developing behavioral models of vaccination strategies for the management of foot-and-mouth disease (FMD) in the United States.

I completed my PhD with Alan Hastings in theoretical ecology at the University of California, Davis. My research interests combine animal behavior, population ecology, and epidemiology, with a focus on predicting the emergence of complex spatiotemporal patterns stemming from movement patterns. 

My past experience also includes modeling metapopulation dynamics at the University of Helsinki with Otso Ovaskainen and Ilkka Hanski. I am currently in collaboration with researchers at EcoHealth Alliance to investigate the risks and management options of Rift Valley Fever based on the seasonal home range patterns of wild and domestic ungulates.


  1. Tao, Y., L. Borger, and A. Hastings. Dynamic Range Size Analysis of Territorial Animals: An Optimality Approach. In revision.
  2. Epstein, J., S. Anthony, A. Kilpatrick, A. Islam, S. Khan, M. Hossein, K. Olival, M. Sanchez, J. Barr, I. Smith, Y. Tao, C., Zambrana-Torrelio, P. Quan, E. Gurley, M. Fielder, T. Briese, G. Crameri, L. Wang, W. Lipkin, S. Luby, and P. Daszak. Human activities, more than bat host viral dynamics, drive Nipah Virus Encephalitis outbreaks in Bangladesh. submitted
  3. Tao, Y., L. Borger, M. Lewis, and A. Hastings. Review: Embracing Transient Dynamics in Movement Ecology. Ecology Letters. Pre-submission accepted.
  4. Tao, Y., and A. Hastings. Departing from Steady-State: Transient Home Range Analysis via FiPy. in prep.
  5. Tao, Y., M. Rostal, A. Kemp, and P. Hosseni. Transient Movement Effects of Ungulate Rift Valley Fever Dynamics: Method and Analysis. in prep.
  6. Tao, Y., O. Ovaskainen, and I. Hanski. Numerical Correspondence between Individual-Based and Metapopulation Models under Environmental Stochasticity. in prep.
  7. Tao, Y., C. Zambrana-Torrelio, and K. Lee. On Integrations of Movement, Economics, and Disease Modelings in Ecological Systems. in prep.