» Papers

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.

Third Period:

H. J. Herrmann, C. M. Schneider, A. A. Moreira, J. S. Andrade Jr, S. Havlin, Onion-like network topology enhances robustness against malicious attacks, J. Stat. Mech. 2011, 01027 (2011)
C. Lagorio, M. Dickison, F. Vazquez, L. A. Braunstein, P. A. Macri, M. V. Migueles, S. Havlin, H. E. Stanley, Quarantine-generated phase transition in epidemic spreading, Phys. Rev. E 83, 026102 (2011)
A. A. Moreira, J. S. Andrade Jr., S. Havlin, H. J. Herrmann, C. M. Schneider, Mitigation of malicious attacks on networks, PNAS 108, 3838 (2011)
D. Rybski , SV Buldyrev , S Havlin , F Liljeros, HA Makse, Communication activity in social networks: growth and correlations European Physical Journal B 84, 147-159 (2011)
C.M. Schneider , T. Mihaljev, S. Havlin ,H.J. Herrmann, Suppressing epidemics with a limited amount of immunization units Phys. Rev. E 84, (2011)
W. Li, F.Z. Wang , S. Havlin, H.E. Stanley Financial factor inﬂuence on scaling and memory of trading volume in stock market, Phys. Rev. E 84 046112 (2011)
X.Q. Huang, I. Vodenska, F.Z. Wang , S. Havlin , H.E. Stanley Identifying inﬂuential directors in the United States corporate governance network Phys. Rev. E 84, (2011)
FC Coelho, CT Codeço , MGM Gomes, A Bayesian framework for parameter estimation in dynamical models, PLoS ONE 6(5):e19616
SP van Noort ,R Aguas , S Ballesteros, MGM Gomes The role of weather on the relation between influenza and influenza-like illness, J Theor Biol 298C:131-137 (2012)
MGM Gomes, R. Aguas, JS Lopes, MC Nunes, C. Rebelo, P. Rodriguez, C.J. Struchiner, How host selection governs tuberculosis reinfection Proc. R. Soc. Lond. (2012) (in press)
R. Aguas, MU Ferreira, MGM Gomes Modeling the effects of relapse in the transmission dynamics of malaria parasites. J Parasitol Res:921715 (2012)
O. Givan, N. Schwartz, A. Cygelberg, L. Stone Predicting epidemic thresholds on complex networks: Limitations of mean-field approaches. J Theor Biol. 2011 Nov 7;288:21-8 (2012)
G. Katriel The size of epidemics in populations with heterogeneous susceptibility.J Math Biol. 2011 Aug (2011)
O. Barnea, R. Yaari , G. Katriel ,L. Stone Modelling seasonal influenza in Israel. Math Biosci Eng. 2011 Apr;8(2):561-73 (2011)
U. Roll, R. Yaari, G. Katriel, O. Barnea, L. Stone, E. Mendelson ,M. Mandelboim , A. Huppert Onset of a pandemic: characterizing the initial phase of the swine flu (H1N1) epidemic in Israel. BMC Infect Dis. 2011 Apr 14;11:92.
G. Katriel , R. Yaari ,A. Huppert ,U. Roll, L.Stone Modelling the initial phase of an epidemic using incidence and infection network data: 2009 H1N1 pandemic in Israel as a case study. J R Soc Interface. 2011 Jun 6;8(59):856-67.
G. Katriel Note on ‘Age, influenza pandemics and disease dynamics’ by Greer et al. (2010). Epidemiol Infect. 2011 Sep;139(9):1440-1 (2010);
L. Stone, F.Hilker, H. Katriel SIR Epidemic models Sourcebook in Theoretical Ecology, Alan Hastings and Louis Gross, Editors, University of California Press 2011.
G. Katriel, L.Stone, Attack rates of seasonal epidemics, Mathematical Biosciences 235 (2012) 56–65
L. Stone Waltz of the weevil. Nature. 2011 Feb 3;470(7332):47-9
K. T. D. Eames, N. L. Tilston, E. Brooks-Pollock,W. J. Edmunds, Measured Dynamic Social Contact Patterns Explain the Spread of H1N1v Influenza PLoS Comput Biol 8(3): e1002425. doi:10.1371/journal.pcbi.1002425
M. Aguiar , S. Ballesteros , B. W. Kooi, N. Stollenwerk , The role of seasonality and import in a minimalistic multi-strain dengue model capturing differences between primary and secondary infections: complex dynamics and its implications for data analysis, Journal of Theoretical Biology, 289, 181–196 (2011)
P. Ghaffari, V. Jansen , N. Stollenwerk, Evolution towards critical fluctuations in a system of accidental pathogens, (Numerical Analysis and AppliedMathematics ICNAAM 2011 AIP Conf. Proc. 1389, 1224-1227 (2011)
J. Martins, Aguiar, M. A. Pinto, N. Stollenwerk, On the series expansion of the spatial SIS evolution operator. Journal of Difference Equations and Applications, 17, 1107–1118 (2011).
M. Aguiar, N. Stollenwerk, W. B. Kooi, The stochastic multi-strain dengue model: analysis of the dynamics. AIP Conference Proceedings, 1389, 1224–1227 (2011)
M.Aguiar, S. Ballesteros, J.P. Boto, B.W. Kooi, L. Mateus, N. Stollenwerk . Parameter estimation in epidemiology: from simple to complex dynamics. AIP Conference Proceedings, 1389, 1248–1251 (2011)
P. Gerrish, P. Sniegowski. Adding Dynamical Sufficiency to Fishers Fundamental Theorem of Natural Selection. AIP Conference Proceedings, 1389, 1260–126 (2011)

Fourth Period:

T Emmerich, A Bunde, S Havlin, Diffusion, annihilation, and chemical reactions in complex networks with spatial constraints, Physical Review E 86, 046103 (2012)
AM Petersen, JN Tenenbaum, S Havlin, et al., Languages cool as they expand: Allometric scaling and the decreasing need for new words, Scientific Reports 2, 943 (2012)
A Garas, F Schweitzer, S Havlin, A k-shell decomposition method for weighted networks , New Journal of Physics 14, 083030 (2012)
LK Gallos, P Barttfeld, S Havlin, M Sigman, HA Maks, Collective behavior in the spatial spreading of obesity, Nature Scientific Reports 2, 454 (2012)
Mark Dickison, Shlomo Havlin, HE Stanley, Epidemics on interconnected networks, Phys. Rev. E 85, 066109 (2012)
Jianxi Gao, S.V. Buldyrev, S Havlin, H.E. Stanley, Robustness of a network formed by n interdependent networks with a one-to-one correspondence of dependent nodes, Phys. Rev. E 85, 066134 (2012)
Wei Li, Amir Bashan, Sergey V. Buldyrev, H. Eugene Stanley, and Shlomo Havlin, Cascading Failures in Interdependent Lattice Networks: The Critical Role of the Length of Dependency Links, Phys. Rev. Lett. 108, 228702 (2012)
Toshihiro Tanizawa, Shlomo Havlin, H. Eugene Stanley, Robustness of onionlike correlated networks against targeted attacks, Phys. Rev. E 85, 046109 (2012)
Jianxi Gao, Sergey V. Buldyrev, H. Eugene Stanley, S Havlin, Networks formed from interdependent networks, NATURE PHYSICS 8, 40-48 (2012)
Stollenwerk, N., Aguiar, M., Ballesteros, S., Boto, J., Kooi, W. B., Mateus, L. (2012), Dynamic noise, chaos and parameter estimation in population biology, Interface, Focus, 2, 156–169.
Aguiar, M., Stollenwerk, N. Kooi, W. B. (2012). Scaling of stochasticity in dengue hemorrhagic fever epidemics, Math. Model. Nat. Phenom., 7, 1–11.
Martins, J., Pinto, A., Stollenwerk, N. (2012). Stationarity in moment closure and quasi-stationarity of the SIS model, accepted for publication in Mathematical Biosciences
Kooi, W. B., Aguiar, M., Stollenwerk, N. (2012). Bifurcation analysis of a family of multi-strain epidemiology models, accepted for publication in Journal of Computational and Applied Mathematics, JCAM
Aguiar, M., Kooi, W. B., Rocha, F., Gaffari, P., Stollenwerk, N. (2012). How much complexity is needed to describe the fluctuations observed in dengue hemorrhagic fever incidence data? accepted submitted to Ecological Modelling
Rocha, F., Aguiar, M., Souza, M., \& Stollenwerk, N. (2012) Time-scale separation and center manifold analysis describing vector-borne disease dynamics, submitted for publication, 1. Aug. 2012
Mateus, L., Stollenwerk, N., Zambrini, J.C. (2012) Stochastic Models in Population Biology: From Dynamic Noise to Bayesian Description and Model Comparison for Given Data Sets, submitted for publication
Aguas R, Ferreira MU, Gomes MGM (2012) Modeling the effects of relapse in the transmission dynamics of malaria parasites. J Parasitol Res: 921715.
WHO-VMI Dengue Vaccine Modeling Group, Beatty M, Boni MF, Brown S,Buathong R, Burke D, Coudeville L, Cummings DA, Edelman R, Farrar J, Focks DA, Gomes MG, Guignard A, Halstead S, Hombach J, Knerer G, Koelle K, Lam FC, Lang J, Longini I, Medlock J, Namgyal P, Powell M, Recker M, Rohani P, Standaert B, Struchiner C, Teyssou R, Wearing H. (2012) Assessing the Potential of a Candidate Dengue Vaccine with Mathematical Modeling. PLoS Negl Trop Dis 6(3): e1450.
van Noort SP, Águas R, Ballesteros S, Gomes MGM (2012) The role of weather on the relation between influenza and influenza-like illness. J Theor Biol 298: 131-137.
Gomes MGM, Águas R, Lopes JS, Nunes MC, Rebelo C, Rodrigues P, Struchiner CJ (2012) How host selection governs tuberculosis reinfection. Proc R Soc Lond B 279: 2473-2478.
Mayer BT, Henry CJ, Gomes MGM, Ionides E, Eisenberg JN, Koopman JS (accepted) Successes and shortcoming of polio eradication: A transmission modeling analysis. Am J Epidemiol.
Parisi A, Parisi JS, Nunes A, Gomes MGM (accepted) Heterogeneity in antibody range and the antigenic drift of influenza viruses. Ecological Complexity

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.

Third Period:

Y. Hu, Y. Wang, D. Li, S. Havlin, Z. Di, Possible Origin of Efficient Navigation in Small-Worlds Phys. Rev. Lett. 106, 108701 (2011)
D. Li, G. Li, K. Kosmidis, H.E. Stanley, A. Bunde, S. Havlin, Percolation of spatially constraints networks Europhys. Lett. 93, 68004 (2011)
D. Li, K. Kosmidis, A. Bunde, S. Havlin, Dimension of spatially embedded networks Nature Physics 7, 481-484 (2011)
J. Shao, S. V. Buldyrev, S. Havlin, H. E. Stanley Cascade of failures in coupled network systems with multiple support-dependence relationsPhys. Rev. E 83, 036116 (2011)
A. Bashan, R. Parshani, S. Havlin, Percolation in networks composed of connectivity and dependency links Phys, Rev. E 83, 051127 (2011)
G. Jianxi, S. V. Buldyrev , H. E. Stanley, S. Havlin , Networks formed from interdependent networks, Nature Physics 8, 40-48 (2011)
A.Bashan, S.Havlin The Combined Effect of Connectivity and Dependency Links on Percolation of Networks J Stat Phys 145, (2011)
Y. Q. Hu, B. Ksherim ,R. Cohen , S. Havlin , Percolation in interdependent and interconnected networks: Abrupt change from second- to ﬁrst-order transitions Phys. Rev. E 84, (2011)
G. Guzzetta, M. Ajelli, Z. Yang, S. Merler, C. Furlanello, D. Kirschner, Modeling socio-demography to capture tuberculosis transmission dynamics in a low burden setting, Journal of Theoretical Biology 289: 197-205. 2011
D Grady, R. Brune, C. Thiemann, F. Theis and D. Brockmann
Modularity maximization and tree clustering: Novel ways to determine effective geographic borders
in Handbook of Optimization in Complex Networks, Thai, My T., Pardalos, Panos M(eds.), Springer (2012)
V. Belik, T. Geisel and D. Brockmann, Recurrent host mobility in spatial epidemics: beyond reaction-diffusion European Physical Journal B, 84, 579–587 (2011)
V. Belik, T. Geisel and D. Brockmann Natural human mobility patterns and spatial spread of infectious diseases Phys. Rev. X 1, 011001 (2011)
G. O’Danleyman, J. J. Lee, H. Seebens, B. Blasius and D. Brockmann Complexity in human transportation networks: A comparative analysis of worldwide air transportation and global cargo ship movements European Physical Journal B, 84, 589–600 (2011)

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.

Third Period:

C. Pesquita, F. Couto, Where GO is going and what it means for ontology extension, Proceedings of ICBO 2011, International Conference on Biomedical Ontology, July 2011
B. Tavares, H. Bastos, D. Faria, J. D. Ferreira, T. Grego, C. Pesquita, F. Couto, The Biomedical Ontology Applications (BOA) framework. Proceedings of ICBO 2011, International Conference on Biomedical Ontology, July 2011.
J. D. Ferreira, F. Couto, Generic semantic relatedness measure for biomedical ontologies. Proceedings of ICBO 2011, International Conference on Biomedical Ontology, July 2011.
F. Couto, M.J. Silva, Disjunctive Shared Information between Ontology Concepts: application to Gene Ontology. Journal of Biomedical Semantics. Vol 2(5). doi:10.1186/2041-1480-2-5.
J. Zamite, F. Silva, F. Couto, M. Silva, MED Collector: Multisource epidemic data collector. Transactions on Large-scale Data-and Knowledge- centered Systems IV: Special Issue on Database Systems for Biomedical Applications (6990), pp. 40-72. Springer-Verlag New York, Inc. ISBN 978-3-642-23739-3 (2011)

Fourth Period:

J. Ferreira, D. Paolotti, F. Couto, M. J. Silva, On the usefulness of ontologies in epidemiologic research and practice, Journal of Epidemiology and Community Health, 2012.
C. Pesquita, F. M. Couto, Predicting the Extension of Biomedical Ontologies, PLOS Computational Biology 9(8), e1002630, 2012.

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.

Third Period:

R. Parshani, C. Rozenblat, D. Ietri, C. Ducruet, S. Havlin, Inter-similarity between coupled networks, Europhys. Lett. 92, 68002 (2011)
S. Merler, M. Ajelli ,A. Pugliese , NM Ferguson, 2011 Determinants of the Spatiotemporal Dynamics of the 2009 H1N1 Pandemic in Europe: Implications for Real-Time Modelling. PLoS Comput Biol 7(9): e1002205. 2011.
P. Poletti et al, The effect of risk perception on the 2009 H1N1 pandemic influenza dynamics, PLoS ONE, 6(2): e16460, 2011
AC Singer, V Colizza, H Schmitt, J Andrews, D Balcan, WE Huang, VDJ Keller, A Vespignani, RJ Williams, Assessing the Ecotoxicologic Hazards of a Pandemic Influenza Medical Response. Environmental Health Perspectives 119, 1084 (2011)

Fourth Period:

P. Poletti, A. Melegaro, M. Ajelli, E. del Fava, G. Guzzetta, L. Faustini, G. Scalia Tomba, P. Lopalco, C. Rizzo, S. Merler, P. Manfredi. Perspectives on the impact of varicella immunization on herpes zoster. A model-based evaluation from three European countries. PLOS ONE, 2013, in press.
S. Merler, G. Jurman, A combinatorial model of malware diffusion via Bluetooth connections, PLOS ONE, 2013, in press.
P. Poletti, B. Caprile, M. Ajelli, S. Merler. Uncoordinated Human responses During Epidemic Outbreaks. In P. Manfredi, A. D’Onofrio (eds), Modeling the Interplay Between Human Behavior and the Spread of Infectious Diseases. Springer, 2013
M. Ajelli, S. Merler. Transmission Potential and Design of Adequate Control Measures for Marburg Hemorrhagic Fever. PLOS ONE, 7(12):e50948
G. Guzzetta, P. Poletti, E. Del Fava, M. Ajelli, G. Scalia Tomba, S. Merler, P. Manfredi. Hope-Simpson’s progressive immunity hypothesis may explain Herpes Zoster incidence data. American Journal of Epidemiology, 2013, in press.
L. Fumanelli, M. Ajelli, P. Manfredi, A. Vespignani, S. Merler. Inferring the Structure of Social Contacts from Demographic Data in the Analysis of Infectious Diseases Spread. PLoS Computational Biology, 8(9): e1002673, 2012.
P. Poletti, M. Ajelli, S. Merler. Risk perception and effectiveness of uncoordinated behavioral responses in an emerging epidemic. Mathematical Biosciences, 238(2):80-89, 2012.

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

E. Brooks-Pollock, N. Tilston, W.J. Edmunds and K.T.D. Eames, Using an online survey of healthcare-seeking behaviour to estimate the magnitude and severity of the 2009 H1N1v influenza epidemic in England, BMC Infectious Diseases 2011, 11:68

Third Period

I. Carreras, A. Matic, P. Saar, V. Osmani, Comm2Sense: Detecting Proximity Through Smartphones, in Proc. of perMoby – PERCOM Workshop 2012.
E Brooks-Pollock , N Tilston , WJ Edmunds, KT Eames, Using an online survey of healthcare-seeking behaviour to estimate the magnitude and severity of the 2009 H1N1v influenza epidemic in England. BMC Infect Dis. 2011 Mar 16;11:68 (2011)
Eames KT, Brooks-Pollock E, Paolotti D, Perosa M, Gioannini C, Edmunds WJ. Rapid assessment of influenza vaccine effectiveness: analysis of an internet-based cohort. Epidemiol Infect. 2011 Sep 12:1-7. DOI: 10.1017/S0950268811001804

Fourth Period:

Marit MA de Lange, Adam Meijer, Ingrid HM Friesema, Gé A. Donker, Carl E Koppeschaar, Mariëtte Hooiveld, Nel Ruigrok, Wim van der Hoek: Comparison of five influenza surveillance systems during the 2009 pandemic and their association with media attention. BMC Public Health (accepted).

WP6:
First Period: