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Papers

WP1:
First Period:

Guy Katriel and Lewi Stone. Pandemic influenza dynamics and the breakdown of herd immunity. PLoS Curr Influenza. 2009 October 1: RRN1046.
Santhakumaran, S., O’Brien; K, Bakker, R., Ealden, T., Shafer, LA., Daniel, RM., Chapman, R., Hayes, RJ., White, RG. The potential impact of polygyny on long-duration STI prevalence using simulated sexual networks (Submitted to the journal STI)
Martins, J., Pinto, A., Stollenwerk, N. (2009). A scaling analysis in the SIRI epidemiological model, Journal of Biological Dynamics, 479–496.
Martins, J., Aguiar, M., Pinto, A., Stollenwerk, N. (2009). On the series expansion of the spatial SIS evolution operator, accepted for publication in Journal of Difference Equations and Applications.
M. Aguiar, N. Stollenwerk, B. Kooi, Torus bifurcation, isolas and chaotic attractors in a simple dengue fever model with ADE and temporary cross immunity, Intern. Journal of Computer Mathematics. In press.
S. Ballesteros, A. Camacho and B. Cazelles, Introducing gradual antigenic drift in co-circulating cross reactive antigenic cluster models, Proceedings of the 9th Conference on Computational and Mathematical Methods in Science and Engineering, 2009, edited by Jesus Vigo Auiar et al., Salamanca, 2009, pp. 1471-1482
Y. Berchenko, Y. Artzy-Randrop, M. Teicher, L. Stone, Emergence and size of the giant component in clustered random graphs with a given degree distribution, Physical Review Letters. Vol. 102 (13) 138701.
J.P. Boto and N. Stollenwerk (2009). Fractional calculus and Levy flights: modelling spatial epidemic spreading, Proceedings of 9^th Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2009, edited by Jesus Vigo Aguiar et al., Salamanca, pp. 177—188.
Nico Stollenwerk, J.P. Boto, (2009). Reaction-superdiffusion systems in epidemiology, an application of fractional calculus, Proceedings of the International Conference on Numerical Analysis and Applied Mathematics, ICNAAM, Simos, Theodore E.; Psihoyios, George; Tsitouras, Ch., (eds.)
A. Huppert, G. Katriel, R. Yaari, U. Roll, R. Balicer, L. Stone, Mathematical models as a tool for facing the influenza pandemic, HaRefuah (Hebrew) 149, p 4-8
Bacaër N, Gomes MGM (2009) On the final size of epidemics with seasonality. Bulletin of Mathematical Biology 71:1954-66.
van Noort SP, Stollenwerk N, Stone L (2009) Analytic likelihood function for data analysis in the starting phase of an influenza outbreak Proceedings of CMMSE 2009, ISBN 978-84-612-9727-6.
Rodrigues P, Margheri A, Rebelo C, Gomes MGM (2009) Heterogeneity in susceptibility to infection can explain high reinfection rates. J Theor Biol 259:280-90.

Second period:

van Noort SP, Nunes MC, Weedall GD, Hviid L, Gomes MGM (2010) Immune selection and within-host competition can structure the repertoire of variant surface antigens in Plasmodium falciparum – A mathematical model. PLoS One 5(3): e9778.

Kretzschmar M, Gomes MGM, Coutinho RA, Koopman JS (2010), Unlocking pathogen genotyping information for public health by mathematical modelling. Trends Ecol Evol 18: 406-412.

Stollenwerk N, van Noort SP, Martins J, Aguiar M, Hilker FM, Pinto A, Gomes MGM (2010) A spatially stochastic epidemic model with partial immunization shows in mean field approximation the reinfection threshold. Journal of Biological Dynamics 4: 634-649.

Barnea O., Rami Y., Katriel G. & Stone L. Modelling seasonal influenza in Israel, Mathematical BioSciences and Engineering 2011.

Katriel G. (2011) Epidemics with partial immunity to reinfection. Mathematical BioSciences (in press)

G. Katriel, R. Yaari, A. Huppert, U. Roll and L. Stone. Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study. Interface 2011.

Sieber M, Hilker FM (2011) Prey, predators, parasites: intraguild predation or simpler community modules in disguise? Journal of Animal Ecology 80, 414-421.

Stone L, Hilker FM, Katriel G (accepted) SIR models. In Sourcebook in Theoretical Ecology (Hastings A, Gross L, eds.). University of California Press, Berkeley. 2011.

Brooks-Pollock E, Eames KTD. Pigs didn’t fly, but swine flu. Mathematics Today, 2011 47(1).

M. Kitsak, L. K. Gallos, S. Havlin, F. Liljeros, L. Muchnik, H. E. Stanley and H.A. Makse, Identification of influential spreaders in complex networks, , Nature Physics 6, 888 (2010)

R. Parshani, M. Dickison, R. Cohen, H. E. Stanley and S. Havlin, Dynamic networks and directed percolation, EPL 90(3), 38004 (2010);

Parshani, R., Carmi, S. and Shlomo Havlin (2010). Epidemic Threshold for the Susceptible-Infectious-Susceptible Model on Random Networks. Physics Review Letters 104:258701

D. Miorandi and F. De Pellegrini, k-Shell Decomposition for Dynamic Complex Networks, appeared in the Proc. of WiOpt (WDN Workshop), Avignon, June 2010.

M. Aguiar, S. Ballesteros and N. Stollenwerk, The influence of seasonality on dengue epidemiology, modelling and data analysis, Proceedings of 10th Conference on Computational and Mathematical Methods in Science and Engineering, CMMSE 2010, ISBN 978-84-613-5510-5, edited byJesus V.A., Almeria, 2010, pp. 25–35.

M. Aguiar, S. Ballesteros and N. Stollenwerk, Two strain dengue model with temporary cross immunity and seasonality, AIP Conference Proceedings 1168 volume 2, of 8^th International Conference of Numerical Analysis and Applied Mathematics, ICNAAM 2010, ISBN 978-0-7354-0831-9, edited by Theodore E. Simos, Greece, 2010, pp.732–735.

M. Aguiar, S. Ballesteros and N. Stollenwerk, Dynamic noise and its role in understanding epidemiological processes, AIP Conference Proceedings 1168 volume 2, of 8^th International Conference of Numerical Analysis and Applied Mathematics, ICNAAM 2010, ISBN 978-0-7354-0831-9, edited by Theodore E. Simos, Greece, 2010, pp.736–40.

WP2:

First Period:

D. Brockmann, V. David and A. Morales Gallardo, in Diffusion Fundamentals III, C. Chmelik, N. Kanellopoulos, J. Kärger and D. Theodorou (eds.), Leipziger Universitätsverlag (2009)
D. Brockmann, Human Mobility and Spatial Disease Dynamics, Reviews of Nonlinear Dynamics and Complexity, H. G. Schuster (ed.), Wiley-VCH (2009)
D.Balcan, V. Colizza, B. Gonçalves, H. Hu, J. J. Ramasco, A. Vespignani Multiscale mobility networks and the spatial spreading of infectious diseases Proc Natl Acad Sci U S A 106, 21484-21489 (2009).

Second period:

G. Li, S. D. S. Reis, A. A. Moreira, S. Havlin, H. E. Stanley and J. S. Andrade, Towards Design Principles for Optimal Transport Networks, , Jr., Phys. Rev. Lett. 104, 018701 (2010)
S. V. Buldyrev, R. Parshani, G. Paul, H. E. Stanley and S. Havlin, Catastrophic cascade of failures in interdependent networks, , Nature 465, 08932 (2010);
R. Parshani, S. V. Buldyrev and S. Havlin, Interdependent Networks: Reducing the Coupling Strength Leads to a Change from a First to Second Order Percolation Transition, Phys. Rev. Lett. 105(4), 048701 (2010);
C. Thiemann, F. Theis, D. Grady, R. Brune and D. Brockmann, The Structure of Borders in a Small World, PLoS ONE 5(11): e15422.

WP3:

First Period

M. J. Silva, F. A. B. da Silva, L. F. Lopes, F. M. Couto, Building a Digital Library for Epidemic Modelling, Proceedings of ICDL 2010 – The International Conference on Digital Libraries New Delhi, India, February, 2010.
L. F. Lopes, J. Zamite, B. Tavares, F. Couto, F. Silva, M. J. Silva, Automated Social Network Epidemic Data Collector, INForum – Simpósio de Informática September, 2009.
Fabrício A.B. Silva, Mário J. Silva, Francisco Couto 2010: Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis, ERCIM News 82 – Special Theme: Computational Biology, July 2010.

João Zamite, Fabrício A.B. Silva, Francisco Couto, Mário J. Silva, MEDCollector: Multisource Epidemic Data Collector, Proceedings of ITBAM’10 – 1st International Conference on Information Technology in Bio- and Medical Informatics – DEXA 2010, August, 2010.

Luis Filipe Lopes, Fabrício A.B. Silva, Francisco Couto, João Zamite, Hugo Ferreira, Carla Sousa, Mário J. Silva, Epidemic Marketplace: An Information Management System for Epidemiological Data, Proceedings of the ITBAM – DEXA 2010, August 2010.

Second period:

F. A.B. Silva, M. J. Silva, F. Couto 2010: Epidemic Marketplace: an e-Science Platform for Epidemic Modelling and Analysis. ERCIM News 82 – Special Theme: Computational Biology.

L. F. Lopes, F. A.B. Silva, F. Couto, J. Zamite, H. Ferreira, C. Sousa, M. J. Silva, Epidemic Marketplace: An Information Management System for Epidemiological Data. Presented at ITBAM’10 – 1st International Conference on Information Technology in Bio- and Medical Informatics – DEXA 2010 – August, 2010.

J. Zamite, F. A.B. Silva, F. Couto, M. J. Silva, MEDCollector: Multisource Epidemic Data Collector. Presented at ITBAM’10 – 1st International Conference on Information Technology in Bio- and Medical Informatics – DEXA 2010 – August, 2010.

M. J. Silva, F. A.B. Silva, L. F. Lopes, F. Couto, Building a Digital Library for Epidemic Modelling. Proceedings of ICDL 2010 – The International Conference on Digital Libraries 1, p. 447–459, New Delhi, India, 23–27 February, 2010. TERI Press — New Delhi, India. Presentation of invited paper.

WP4:
First Period:

S. Merler and M. Ajelli, The role of population heterogeneity and human mobility in the spread of pandemic influenza, Proceeding of the Royal Society B, 277:557-565, 2010
M. Ajelli and S. Merler, An individual-based model of hepatitis A transmission, Journal of Theoretical Biology, 259(3):478-488, 2009.
P. Bajardi, C. Poletto, D. Balcan, H. Hu, B. Goncalves, J. Ramasco, D. Paolotti, N. Perra, M. Tizzoni, W. Van den Broeck, V. Colizza and A. Vespignani, Modeling vaccination campaigns and the Fall/Winter 2009 activity of the new A(H1N1) influenza in the Northern Hemisphere, Emerging Health Threats Journal, 2009 2:e11
D. Balcan, H. Hu, B. Goncalves, P. Bajardi, C. Poletto, J.J. Ramasco, D. Paolotti, N. Perra, M. Tizzoni, W. Van den Broeck, V. Colizza, A. Vespignani, Seasonal transmission potential and activity peaks of the new influenza A(H1N1): a Monte Carlo likelihood analysis based on human mobility, BMC Medicine 2009 7:45
D. Balcan, V. Colizza, A. Singer, C. Chouaid, H. Hu, B. Gonçalves, P. Bajardi, C. Poletto, J.J. Ramasco, N. Perra, M. Tizzoni, D. Paolotti, W. Van den Broeck, A.J. Valleron, A. Vespignani, Modeling the critical care demand and antibiotics resources needed during the Fall 2009 wave of influenza A(H1N1) pandemic, PLoS Currents: Influenza, 2009 Dec 7:RRN1133.
V. Colizza, A. Vespignani, N. Perra, C. Poletto, B. Goncalves, H. Hu, D. Balcan, D. Paolotti, W. Van den Broeck, M.Tizzoni, P. Bajardi, J.J.Ramasco, Estimate of Novel Influenza H1N1 cases in Mexico at the early stage of the pandemic with a spatially structured epidemic model, PLoS Currents Influenza, 2009 Nov 18:RRN1129.
M. Ajelli, B. Gonçalves, D. Balcan, V. Colizza, H. Hu, J. J. Ramasco, S. Merler and A. Vespignani, Comparing large-scale computational approaches to epidemic modeling: agent-based versus structured metapopulation models, BMC Infectious Diseases 2010, 10:190.
P. Bajardi, C. Poletto, J.J. Ramasco, M. Tizzoni, V. Colizza and A. Vespignani, Human Mobility Networks, Travel restrictions, and the Global Spread of 2009 H1N1 Pandemic, PLoS ONE 6(1): e16591. doi:10.1371/journal.pone.0016591

Second period:

W. Van den Broeck, C. Gioannini, B. Gonçalves, M. Quaggiotto, V. Colizza, A. Vespignani The GLEaMviz computational tool, a publicly available software to explore realistic epidemic spreading scenarios at the global scale BMC Infectious Diseases 11, 37 (2011).

P Bajardi, C Poletto, J J Ramasco, M Tizzoni, V Colizza, A Vespignani, Human Mobility Networks, Travel Restrictions, and the Global Spread of 2009 H1N1 Pandemic
PLoS ONE 6(1): e16591 (2011).

D Balcan, B Goncalves, H Hu, JJ Ramasco, V Colizza, A Vespignani.,
Modeling the spatial spread of infectious diseases: The GLobal Epidemic and Mobility computational model, Journal of Computational Sciences 1, 132 (2010).

M Ajelli, B Goncalves, D Balcan, V Colizza, H Hu, JJ Ramasco, S Merler, A Vespignani, Comparing large-scale computational approaches to epidemic modeling: agent-based versus structured metapopulation models
BMC Infectious Diseases 10, 190 (2010).

P. Poletti, M. Ajelli, S. Merler, The effect of risk perception on the 2009 H1N1 pandemic influenza dynamics, PLoS ONE, 6(2): e16460, 2011.

M. Ajelli , L. Fumanelli, P. Manfredi, S. Merler, Spatiotemporal dynamics of viral hepatitis A in Italy. Theoretical Population Biology, 79:1-11, 2011.

F. Iozzi, F. Trusiano, M. Chinazzi, F. C. Billari, E. Zagheni, S. Merler, Marco Ajelli, E. Del Fava, P. Manfredi, Little Italy: an agent-based approach to the estimation of contact patterns. Fitting predicted matrices to serological data. PLoS Computational Biology, 6(12): e1001021, 2010.
S. Merler and M. Ajelli. Human mobility and population heterogeneity in the spread of an epidemic. Procedia Computer Science, 1(1):2231-2238, 2010.

WP5:
First Period:

I.H.M. Friesema, C.E. Koppeschaar, G.A. Donker, F. Dijkstra, S.P. van Noort, R. Smallenburg, W. van der Hoek, M.A.B. van der Sande “Internet-based monitoring of influenza-like illness in the general population: Experience of five influenza seasons in the Netherlands“, Vaccine 27 (2009) 6353–6357

Baguelin M, Hoek AJ, Jit, Flasche S, White PJ, Vaccination against pandemic influenza A/H1N1v in England: a real-time economic evaluation, Vaccine 28 (2010) 2370-2384
N.L Tilston, K.T.D. Eames, D. Paolotti, T. Ealden, W. J. Edmunds, Internet-based surveillance of Influenza-like-illness in the UK during the 2009 H1N1 influenza pandemic, BMC Public Health 2010, 10:650 (2010)

Second period:

Tilston NL, Eames KTD, Paolotti D, Ealden T, Edmunds WJ. Internet-based surveillance of Influenza-like-illness in the UK during the 2009 H1N1 influenza pandemic. BMC Public Health. 2010 Oct 27;10:650.

D. Paolotti, C. Gioannini, V. Colizza, A. Vespignani, Internet-based monitoring system for influenza-like illness: H1N1 surveillance in Italy, proceedings of the 3^rd International ICST Conference on Electronic Healthcare for the 21^st century, Casablanca 13-15 December 2010.

R. Quax, D.A. Bader and P.M.A. Sloot: SEECN: Simulating Complex Systems using Dynamic Complex Networks, International Journal for Multiscale Computational Engineering, accepted March 23, 2010