F. Castiglione and F. Celada. Immune System Modeling and Simulation. CRC Press, Boca Raton (2015), p. 274.

ISBN 978-1-4665-9748-8

Marilda Sotomayor, David Perez-Castrillo and F. Castiglione (Eds.). Complex Social and Behavioral Systems Game Theory and Agent-Based Models. Springer US, Aug 21, 2020

ISBN 978-1-07-160367-3


P. Stolfi, F. Castiglione. Emulating complex simulations by machine learning methods. BMC Bioinformatics 22, 483 (2021).

D. Deb, S. Basak, T. Kar, U. Narsaria, F. Castiglione, A. Paul, A. Pandey, A. P. Srivastava. Immunoinformatics based designing a multi-epitope vaccine against pathogenic Chandipura Vesiculovirus. Journal of Cellular Biochemistry, 3(2):322-346 (2021)

F. Castiglione, D. Deb, A.P. Srivastava, P. Lio`, A. Liso. From infection to immunity: understanding the response to SARS-CoV2 through in-silico modeling. Frontiers in Immunology, 12:3433-3449 (2021)

S. Basak, D. Deb, U. Narsaria, T. Kar, F. Castiglione, I. Sanyal, P. D. Bade, A. P. Srivastava. In silico designing of vaccine candidate against Clostridium difficile. Nature Scientific Reports, 11: 14215 (2021)

C. Ragone, C. Manolio, B. Cavalluzzo, A. Petrizzo,  A. Mauriello, M-L. Tornesello, F. M. Buonaguro, F. Castiglione, L. Vitagliano, M. Ruvo, M. Tagliamonte, L. Buonaguro. Identification and validation of viral antigens sharing sequence and structural homology with tumor associated antigens (TAAs). Journal for ImmunoTherapy of Cancer. 9:e002694 (2021)

M. Zanin, N. Atiya, J. Basilio, J. Baumbach, A. Benis, C. Behera, M. Bucholc, F. Castiglione, I. Chouvarda, B. Comte, T-T., Dao, X. Ding, E. Pujos-Guillot, N. Filipovic, D. Finn, D.H. Glass,  N. Harel, T. Iesmantas, I. Ivanoska, A. Joshi, K. Boudjeltia, B. Kaoui, D. Kaur, L. Maguire, P. McClean, N. McCombe, J. Luis de Miranda, M. Moisescu, F. Pappalardo, A. Polster, G. Prasad, D. Rozman, I. Sacala, J. S. Bornot, J. Schmid, T. Sharp, J. Solé-Casals, V. Spiwok, G. Spyrou, E. Stalidzans, B. Stres, T. Sustersic, I. Symeonidis, P. Tieri, S. Todd, K. van Steen, M. Veneva, D. Wang, H./HY Wang, H. Wang, S. Watterson, S. Yang, X. Zou, K. Wong-Lin, H.H.W. Schmidt. An Early Stage Researcher's Primer on Systems Medicine Terminology. Network and Systems Medicine, 4(1):1-50. doi: 10.1089/nsm.2020.0003 (2021)

H. Wang, E. Pujos-Guillot, B. Comte, J. Luis de Miranda, V. Spiwok, I. Chorbev, F. Castiglione, P. Tieri, S. Watterson, R. McAllister, T. de Melo Malaquias, M. Zanin, T. Singh Rai, H. Zheng. Deep learning in systems medicine. Briefings in Bioinformatics. bbaa237 (2020),

T. Kar, U. Narsaria, S. Basak, D. Deb, F. Castiglione, D. Mueller, A. Srivastava. A candidate multi-epitope vaccine against SARS-CoV-2. Nature Scientific Reports. 10:10895 (2020)

E. Stalidzans, M. Zanin, P. Tieri, F. Castiglione, A. Polster, S. Scheiner, J. Pahle, B. Stres, M. List, J. Baumbach, M. Lautizi, K. Van Steen, H. H.H.W. Schmidt  Mechanistic Modeling and Multiscale Applications for Precision Medicine: Theory and Practice. Network and Systems Medicine. 3(1): 36-56 (2020)

doi 10.1089/nsm.2020.0002

F. Castiglione, D. Ghersi, F. Celada. Computer modeling of clonal dominance: Memory-Anti-Naiïve and its curbing by Atrition. Frontiers in Immunology 10:1513 (2019)

doi: 10.3389/fimmu.2019.01513

A. Presbitero, E. Mancini, F. Castiglione, V. V. Krzhizhanovskaya, R. Quax. The Game of Neutrophils: Modeling the Balance Between Apoptosis and Necrosis. BMC Bioinformatics 20, 475 (2019)

V. Prana, P. Tieri, M-C. Palumbo, E. Mancini and F. Castiglione. Modeling the Effect of High Calorie Diet on the Interplay between Adipose Tissue, Inflammation, and Diabetes. Computational and Mathematical Methods in Medicine 2019, Article ID 7525834 (2019)

A. Palma,  A. S Jarrah,  P. Tieri,  G. Cesareni and  F. Castiglione. Gene regulatory network modeling of macrophage differentiation corroborates the continuum hypothesis of polarization states. Front. Physiol. 9: 1659 (2018)

M-C.Palumbo, M. Morettini, P. Tieri, F. Diele, M. Sacchetti, F. Castiglione. Personalizing physical exercise in a computational model of fuel homeostasis. PLOS Computational Biology 14(4): e1006073 (2018)

M. Zanin, aI. Chorbev, B. Stres, E. Stalidzans, J. Vera, P. Tieri, F. Castiglione,  D. Groen, H. Zheng, J. Baumbach, J. Schmid, J. Basilio, P. Klimek, N. Debeljak, D. Rozman, H. Schmidt. Community effort endorsing multiscale modeling, multiscale data science and multiscale computing for systems medicine. Briefings in Bioinformatics, bbx160 (2017)

H. De Assis Lopes Ribeiro, T. Uceli Maioli, L. Martins Freitas, Paolo Tieri, F. Castiglione. Modeling immune response to Leishmania sp. indicates adenosine as an important inhibitor of Th-cell activation.

Frontiers Cell Infect Microbiol, 7:309 (2017)


M. Morettini, M-C. Palumbo, M. Sacchetti, F. Castiglione, C. Mazza'. A system model of the effects of exercise on plasma Interleukin-6 dynamics in healthy individuals: role of skeletal muscle and adipose tissue. PLoS ONE, 12(7): e0181224 (2017)

A. Madonia, C. Melchiorri, S. Bonamano, M. Marcelli, C. Bulfon, F. Castiglione, M. Galeotti, D. Volpatti, F. Mosca, P-G. Tiscar and N. Romano. Computational modeling of immune system of the fish for a more effective vaccination in aquaculture. Bioinformatics, (2017) btx341.

doi: 10.1093/bioinformatics/btx341

A. Liso, Castellani, F. Massenzio, A. Pucciarini, B. Bigerna, P. De Luca, P. Zoppoli, F. Castiglione, M-C. Palumbo, M. Conese, S. Castellani, F. Stracci, M. Landriscina, G. Specchia and B. Falini. Human monocyte-derived den- dritic cells exposed to hyperthermia show a distinct gene expression profile and selective upregulation of IGFBP6. Oncotarget (2017)

J-F. Moreau, T. Pradeu, A. GRignolio, C. Nardini, F. Castiglione, P. Tieri, M. Capri, S. Salvioli, J-L. Taupin,

P. Garagnani, C. Franceschi. The emerging role of ECM crosslinking in T cell mobility as a hallmark of immunosenescence in humans. Ageing Research Reviews, Available online 19 November 2016,

F. Castiglione, P. Tieri, A. Palma, A.S. Jarrah. Statistical ensemble of gene regulatory networks of macrophage  differentiation. BMC Bioinformatics 17(Suppl 19):1363 (2016)

doi: 10.1186/s12859-016-1363-4

A-R. Garbuglia, U. Visco-Comandini, R. Lionetti, D. Lapa, F. Castiglione, G. D'Offizi, C. Taibi, M. Montalbano, M-R. Capobianchi, P. Paci. Ultrasensitive HCV-RNA quantification in antiviral triple therapy: new insight on viral

clearance dynamic and treatment outcome predictors. PLoS ONE, 11(8):e0158989 (2016)

doi: 10.1371/journal.pone.0158989

C. Sansom, F. Castiglione, P. Lio`. Metabolic disorders: how can systems modelling help? The Lancet Diabetes and Endocrinology, 4(4):305-6  (2016)


A-R. Garbuglia, R. Lionetti; D. Lapa, C. Taibi, U. Visco Comandini, M. Montalbano, G. D'Offizi, F. Castiglione, M. Capobianchi, P. Paci. The clinical significance of  HCV core antigen  detection during Telaprevir/Peg-Interferon/Ribavirin

therapy in patients with HCV 1 genotype infection. Journal of Clinical Virology, 69:68-73 (2015)

E. Galeota, C. Gavrila, F. Castiglione, M. Bernaschi and G. Cesareni. The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. BMC Systems Biology, 9(3)}:S3 (2015) doi:10.1186/1752-0509-9-S3-S3

A. Cappuccio, P. Tieri, and F. Castiglione. Multiscale modelling in immunology: a review. Briefings in Bioinformatics 17(3): 408-418 (2015)  doi:10.1093/bib/bbv012

M-C. Palumbo, L. Farina, F. Castiglione, M. Fasoli, S. Zenoni, M. Pezzotti and P. Paci. Integrated network analysis identifies key switch genes that control major transcriptome reprogramming during grapevine development.

The Plant Cell. 26(12): 4617-4635 (2014),

A.S. Jarrah, F. Castiglione,  N.P. Evans,  R.W. Grange, R. Laubenbacher. A mathematical model of skeletal muscle disease and immune response in the mdx mouse. BioMed Research International, 2014, 871810, (2014) doi:10.1155/2014/871810

F. Castiglione, F. Pappalardo, C. Bianca and S. Motta. Modeling biology spanning different scales: An open challenge. BioMed Research International, 2014, 902545, (2014) doi:10.1155/2014/902545

F. Castiglione, P. Tieri, A. De Graaf, C. Franceschi, P. Lio' , B. Van Ommen, C. Mazza' , A. Tuchel, M. Bernaschi, C. Samson, T. Colombo, G. Castellani, M. Capri, P. Garagnani, S. Salvioli, V. Anh Nguyen, I. Bobeldijk-Pastorova, S. Krishnan, A. Cappozzo, M. Sacchetti, M. Morettini, M. Ernst. The Onset of Type 2 Diabetes: Proposal for a Multi-Scale Model. JMIR research protocols, 01/2013 2(2):e44 (2013) doi:10.2196/resprot.2854

J. von Eichborn, A-L. Woelke, F. Castiglione, R. Preissner. VaccImm: Simulating peptide vaccination in cancer therapy. BMC Bioinformatics 14:127  (2013) doi:10.1186/1471-2105-14-127

D. Santoni, F. Castiglione, P. Paci. Identifying Correlations between Chromosomal Proximity of Genes and Distance of Their Products in Protein-Protein Interaction Networks of Yeast. PLoS ONE. 8(3): e57707 (2013) doi:10.1371/journal.pone.0057707

F. Castiglione, V. Diaz, A. Gaggioli, P. Lio' , C. Mazza' , E. Merelli, C.G.M. Meskers, F. Pappalardo and R. von Ammon. Physio-environmental sensing and live modeling. Interact J Med Res. 2(1): e3 (2013) doi:10.2196/ijmr.2092

B. Ribba, H. El Garch, S. Brunet, E. Grenier, F. Castiglione, H. Poulet and P. Vanhems. Time-course analysis of main markers of primary infection in cats with the feline immunodeficiency virus.  Comp. Math. Methods Med. 2012: 342602 (2012) doi:10.1155/2012/342602

F. Castiglione, F. Mantile, P. De Berardinis, A. Prisco. How the interval between prime and boost injection affects the immune response in a computational model of the immune system. Comp. Math. Methods Med., 2012: 842329 (2012)


E. Mancini, F. Castiglione, M. Bernaschi, A. de Luca, P.M.A. Sloot. HIV reservoirs and immune surveillance evasion cause the failure of structured treatment interruptions: A computational study. PLoS ONE. 7(4): e36108 (2012) doi:10.1371/journal.pone.0036108  

N. Arrigo, P. Paci, L. Di Paola, D. Santoni, M. De Ruvo, A. Giuliani, F. Castiglione. Characterizing protein shape by a volume distribution asymmetry index. The Open Bionformatics Journal, 6: 20-27 (2012) doi:10.2174/1875036201206010020

F. Castiglione, S. Motta, F. Pappalardo and M. Pennisi. A modeling framework for immune-related diseases. Math. Model. Nat. Phenom., 7(3): 40-48 (2012)

F. Castiglione, A. Palladini, M. Pennisi, F. Castiglione, S. Motta. Mathematical and computational models in tumor immunology. Math. Model. Nat. Phenom., 7(3): 186-203 (2012)

A-L. Woelke, J. von Eichborn, M.S. Murgueitio, C.L. Worth, F. Castiglione, R. Preissner. Development of Immune-Specific Interaction Potentials and Their Application in the Multi-Agent-System VaccImm. PLoS ONE 6(8): e23257 (2011) doi:10.1371/journal.pone.0023257

N. Rapin, O. Lund and F. Castiglione. Immune System Simulation Online. Bioinformatics, Application note. 27(14):2013-2014 (2011) doi: 10.1093/bioinformatics/btr335

T. Clancy, M. Pedicini, F. Castiglione, D. Santoni, V. Nygaard, T. J. Lavelle, M. Benson and E. Hovig. Immunological network signatures of cancer progression and survival. BMC Medical Genomics 4:28 (2011) doi:10.1186/1755-8794-4-28

P. Paci, F. Martini, M. Bernaschi, G. D'Offizi and F. Castiglione. Earlier is better: a timely HAART initiation may pave the way for best controllers. BMC Infectious Diseases 11:56 (2011) doi:10.1186/1471-2334-11-56

F. Castiglione, D. Santoni, N. Rapin. CTLs  repertoire shaping in the thymus: a Montecarlo simulation. Autoimmunity 44(4): 1 10 (2011) doi:10.3109/08916934.2011.523272

M. Pedicini, F. Barrenas, T. Clancy, F. Castiglione, E. Hovig, K. Kanduri, D. Santoni and M. Benson. Combining network modeling and gene expression microarray analysis to explore the dynamics of Th1 and Th2 cell regulation. PLoS Comput Biol 6(12): e1001032 (2010). doi:10.1371/journal.pcbi.1001032

F. Castiglione and P. Paci. Criticality of timing for anti-HIV therapy initiation. PLoS ONE 5(12): e15294 (2010)


M. Halling-Brown, F. Pappalardo, N. Rapin, P. Zhang, D. Alemani, A. Emerson, F. Castiglione, P. Doroux,

M. Penisi, O. Miotto, D. Churchill, E. Rossi, D. S. Moss, C. E. Sansom, M. Bernaschi, M-P. Lefranc, S. Brunak, S. Motta,

P-L. Lollini, K. E. Basford, V. Brusic, A.J. Shepherd. ImmunoGrid: towards agent-based simulations of the human immune system at a natural scale. Phil. Trans. R. Soc. A. 368: 2799 2815 (2010) doi:10.1098/rsta.2010.0067

N. Rapin, O. Lund, M. Bernaschi and F. Castiglione. Computational immunology meets bioinformatics: the use of prediction tools for molecular binding in the simulation of the immune system. PLoS ONE. 5(4): e9862 (2010)


F. Pappalardo, M. Pennisi, F. Castiglione, S. Motta. Vaccine protocols optimization: in silico  experiences. Biotechnology Advances. 28: 82 93 (2010) doi:10.1016/j.biotechadv.2009.10.001

T. Avitabile, Francesco Castiglione, V. Bonfiglio, F. Castiglione. Transconjunctival suture-less 25-gauge versus 20-gauge standard vitrectomy: correlation between corneal topography and ultrasound biomicroscopy measurements of sclerotomy sites. Cornea. 29(1):19-25 (2010) doi:10.1097/ICO.0b013e3181ab98ae

V. Baldazzi, P. Paci, M. Bernaschi and F. Castiglione. Modeling lymphocytes homing and encounters in lymph nodes. BMC Bioinformatics. 10: 387 (2009) doi:10.1186/1471-2105-10-387

P. Paci, R. Carello, M. Bernaschi, G. D'Offizi and F. Castiglione. Immune control of HIV-1 infection after therapy interruption: immediate versus deferred antiretroviral therapy. BMC Infectious Diseases. 9: 172 (2009)

doi:10.1186/1471-2334-9-172. Highly Accessed.

G. Dell'Acqua and F. Castiglione. Stability and phase transitions in a mathematical model of Duchenne muscular dystrophy.  J Theor Biol. 260(2): 283-9 (2009) doi:10.1016/j.jtbi.2009.05.037

D. Vergni, F. Castiglione, M. Briani, S. Middei, E. Alberdi, K. G. Reymann, R. Natalini, C. Volonte', C. Matute, F. Cavaliere.  A Model of Ischemia-Induced Neuroblast Activation in the Adult Subventricular Zone. PLoS ONE. 4(4): e5278 (2009) doi:10.1371/journal.pone.0005278.

F. Pappalardo, M. D. Halling-Brown, N. Rapin, P. Zhang, D. Alemani, A. Emerson, P. Paci, P. Duroux, M. Pennisi, A. Palladini, O. Miotto, D. Churchill, E. Rossi, A. J. Shepherd, D. S. Moss, F. Castiglione, M. Bernaschi, M-P. Lefranc, S. Brunak, S. Motta, P-L. Lollini, K. E. Basford and V. Brusic. ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design, and optimization. Briefing in Bioinformatics.10(3):330-40 (2009) doi:10.1093/bib/bbp014

A. Cappuccio, F. Castiglione, B. Piccoli and V. Tozzi. Evaluation of HIV/CD4+ T cell dynamic parameters in patients treated with genotypic resistance testing-guided HAART. Curr HIV Res. 6(4): 363-9 (2008)

A. Liso, F. Castiglione, A. Cappuccio, F. Stracci, R. Schlenk, S. Amadori, C. Thiede, S. Schnittger, P. J.M. Valk, K. D hner, M. F. Martelli, M. Schaich, J. Krauter, A. Ganser, M. P. Martelli, N. Bolli, B. L wenberg, T. Haferlach, G. Ehninger, F. Mandelli, H. D hner, F. Michor, and B. Falini. A one-mutation mathematical model can explain the age incidence of AML with mutated nucleophosmin (NPM1). Haematologica/The Hematology Journal, 93(8): 1219-26 (2008)

D. Santoni, M.Pedicini, F. Castiglione. Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hyper-sensitivity reactions.  Bioinformatics, 24(11):1374-1380 (2008).


V. Tozzi, R. Bellagamba, F. Castiglione, A. Amendola, J. Ivanovic, E. Nicastri, R. Libertone, G. D'Offizi, G. Liuzzi, C. Gori, F. Forbici, R. D'Arrigo, A. Bertoli, M-F. Salvatori, M-R. Capobianchi, A. Antinori, C-F. Perno, P. Narciso. Plasma HIV RNA decline and drug resistance evolution among patients with multiple virologic failures receiving resistance testing-guided HAART. AIDS Res Hum Retrovirus, 24(6): 787-796 (2008)


M. Bernaschi and F. Castiglione. A comment to  Optimization and parallelisation strategies for Monte Carlo simulation of HIV infection   by D. Hecqueta , H.J. Ruskinb , M. Crane. Computers in Biol and Medicine, 38: 281 (2008)

F. Castiglione, F. Pappalardo, M. Bernaschi and S. Motta. Optimization of HAART with genetic algorithms and agent based models of HIV infection. Bioinformatics, 23(24): 3350-3355 (2007)

doi: 10.1093/bioinformatics/btm408

F. Castiglione and B. Piccoli. Cancer immunotherapy, mathematical modeling and optimal control. J Theo Biol, 247(4): 723-732 (2007)


F. Castiglione, K.A. Duca, A. Jarrah, R. Laubenbacher, K. Luzuriaga, D. Hochberg and D.A. Thorley-Lawson. Simulating Epstein Barr Virus Infection with C-ImmSim.  Bioinformatics, 23: 1371-1377 (2007)  

doi: 10.1093/bioinformatics/btm044

A. Cappuccio, F. Castiglione and B. Piccoli. Determination of the optimal therapeutic protocol in cancer immunotherapy. Math Biosci, 209(1): 1-13 (2007)


M. Bernaschi, F. Castiglione, A. Ferranti, C. Gavrila, and G. Cesareni. Protnet: a stochastic tool for dynamic simulation of protein interaction networks. BMC Bioinformatics, 8(Suppl 1):S4 (2007)


F. Castiglione, A. Liso, M. Bernaschi and S. Succi.  Microscopic simulation in biology and medicine. Current Medicinal Chemistry, 14(6): 625-637 (2007)

B. Piccoli and F. Castiglione. Optimal vaccine scheduling in cancer immunotherapy. Physica A, 370(2): 672-680 (2006)

V. Baldazzi, F. Castiglione and M. Bernaschi An Enhanced Agent Based Model of the Immune System Response. Cellular Immunol, 244: 77-79 (2006)

F. Castiglione and B. Piccoli. Optimal control in a model of dendritic cell transfection cancer immunotherapy. Bull Math Biol, 68: 255 274 (2006). Online version: ISSN: 0092-8240 (Paper) 1522-9602. doi: 10.1007/s11538-005-9014-3

F. Massaioli, F. Castiglione and M. Bernaschi. OpenMP parallelization of agent-based models. Parallel Computing, 31(10-12): 1066-1081 (2006)

F. Castiglione and Bernaschi M. HIV-1 strategies of immune evasion. Int J Mod Phys C, 16(12):1869-1879 (2006)

S. Motta, F. Castiglione, P.-L. Lollini, F. Pappalardo. Modelling vaccination schedules for a cancer immunoprevention vaccine. Immunome Research, 1:5, 2005.


F. Castiglione and A. Liso. The role of computational models in designing vaccination strategies. Immunopharmacology and Immunotoxicology, 27(3): 417-432, 2005

F. Pappalardo, P.-L. Lollini, F. Castiglione, S. Motta. Modelling and Simulation of Cancer Immunoprevention Vaccine. Bioinformatics, 2005 Jun 15;21(12): 2891-7.


F. Castiglione, F. Toschi, M. Bernaschi, S. Succi, R. Benedetti, B. Falini and A. Liso. Computational modeling of the immune response to tumor antigens: implications for vaccination. J Theo Biol, 237(4):390-400 (2005)

F. Castiglione and S. Succi. Simulating the G-protein cAMP pathway with a two-compartment reactive lattice gas. Theory in Biosci, 123: 413-429 (2005)

M. Bernaschi and F. Castiglione. Computational features of agent-based models. Int J Comp Methods, 2(1): 33-48 (2005)

F. Castiglione, F. Poccia, G. D'Offizi and M. Bernaschi. Mutation, fitness, viral diversity and predictive markers of disease progression in a computational model of HIV-1 infection. AIDS Res Hum Retrovirus, 20(12): 1316-1325 (2004)

T. Avitabile, L. Franco, E. Ortisi, Francesco Castiglione, M. Pulvirenti, B. Torrisi, F. Castiglione, A Reibaldi. Keratoconus Staging: A Computer-Assisted Ultrabiomicroscopic Method Compared With Videokeratographic Analysis. Cornea. 23(7): 655-660, (2004).

F. Castiglione, M. Bernaschi, S. Succi R. Heinrich, and M.W. Kirschner. Intracellular signal propagation in a two-dimensional auto-catalytic reaction model. Phys Rev E 66: 031905 (2002)

M. Bernaschi and F. Castiglione. Selection of escape mutants from immune recognition during HIV infection, Immunol and Cell Biol, 80: 307-313 (2002)

F. Castiglione and D. Stauffer. Multi-scaling in the Cont-Bouchaud microscopic stock market model. Physica A, 300(3-4): 531-538 (2001)

K.E. K rten and F. Castiglione. A dynamical model of B-T cell regulation. Int J Mod Phys C, 12(3):367-375 (2001)

M. Bernaschi and F. Castiglione. Design and implementation of an Immune System Simulator. Comp in Biol and Med, 31(5): 303-331 (2001)

F. Castiglione, S. Motta and G. Nicosia. Pattern Recognition by primary and secondary response of an Artificial Immune System. Theory in Biosci, 120(2): 93-106 (2001)

F. Castiglione, RB Pandey and D Stauffer. Effect of Trading Momentum and Price Resistance on Stock Market Dynamics: A Glauber Monte Carlo Simulation. Physica A, 289(1-2): 223-228 (2001)

F. Castiglione. Forecasting price increments using an artificial Neural Network, in Complex Dynamics in Economics, a Special Issue of Advances in Complex Systems, 4(1): 45-56, Hermes-Oxford (2001)

M Bernaschi and F. Castiglione. Effect of technical traders in a synthetic Stock Market. Int J Mod Phys C 11(7): 1437 (2000)

Filippo Castiglione and F. Castiglione. Estimating the Keratoconus Index from ultrasound images of the human cornea. IEEE Transaction on Medical Imaging, 19(12): 1268-1227 (2000)

F. Castiglione. Diffusion and Aggregation in an Agent Based Model of Stock Market Fluctuations. Int J Mod Phys C, 11(5): 865-880 (2000)

M. Bernaschi, S. Succi and F. Castiglione. Large-scale Cellular Automata simulations of the Immune System response. Phys Rev E 61(2): 1851-1854 (2000)

F. Castiglione, G Mannella, S Motta and G Nicosia. A Network of Cellular Automata for the simulation of the immune system. Int J Mod Phys C, 10(4): 677-686 (1999)

M. Bernaschi, F. Castiglione, P.E. Seiden and S. Succi. Learning cascade in the immune system dynamics: a numerical simulation. Comp Phys Comm, 121(1-3): 122 (1999)

F. Castiglione. Antigen recognition and evolution in a bit-string population model. Int J Mod Phys C, 10(6): 989-1002 (1999)

M. Bernaschi, F. Castiglione and S. Succi. A high performance simulator of the immune response. Future Gen Comp Sys, 15(3): 333-342 (1999), Elsevier Science ed.

M. Bernaschi, F. Castiglione and S. Succi. A parallel simulator of the Immune response. Lect Notes Comp Sci, 1401: 163-172 (1998)

S. Succi, F. Castiglione and M. Bernaschi. Collective Dynamics in the Immune System Response, Phys Rev Lett, 79(22): 4493-4496 (1997)

F. Castiglione, M. Bernaschi and S. Succi. Simulating the Immune Response on a Distributed Parallel Computer. Int J Mod Phys C 8(3): 527-545 (1997)


F. Castiglione, E. Mancini, M. Pedicini, A. S. Jarrah. Quantitative Modelling Approaches.

In: Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.)  Encyclopedia of Bioinformatics and Computational Biology. (2018).  (doi

P. Tieri, L. Farina, M. Petti, L. Astolfi, P. Paci and F. Castiglione. Network inference and reconstruction in bioinformatics.  In: Ranganathan, S., Nakai, K., Schönbach C. and Gribskov, M. (eds.)  Encyclopedia of Bioinformatics and Computational Biology. (2018). (doi: 10.1016/B978-0-12-809633-8.20290-2)

M. Pedicini M., M-C. Palumbo  and F. Castiglione. Computing Hierarchical Transition Graphs of Asynchronous Genetic Regulatory Networks. In: Pelillo M., Poli I., Roli A., Serra R., Slanzi D., Villani M. (eds.) ``Artificial Life and Evolutionary Computation.'' WIVACE 2017. Communications in Computer and Information Science, vol 830. Springer, Cham (2018) (doi

T. Mendes, F. Castiglione, P. Tieri and L. Felicori. Systems and Synthetic Biology Applied to Health, In Current Developments in Biotechnology and Bioengineering, Elsevier, p. 183-213, (2017) (ISBN 9780444636607)

P. Tieri, V. Prana, T. Colombo, D. Santoni, F. Castiglione. Multi-scale simulation of T helper lymphocyte differentiation, in ``Advances in Bioinformatics and Computational Biology'', S rgio Campos (Ed.), Lecture Notes in Computer Science, Vol. 8826, pp. 123-134, Springer Verlag (2014) (ISBN 978-3-319-12417-9)

F. Castiglione, P-L. Lollini, S Motta, A. Palladini, F. Pappalardo, M. Pennisi. Computational models as novel tools for cancer vaccines, in  New Challenges for Cancer Systems Biomedicine (Simai Springer Series) , A. D Onofrio, P. Cerrai, A. Gandolfi (Eds.), Springer Verlag (2012) (ISBN: 978-8847025707)

F. Castiglione, B. Ribba, O. Brass. Comparing in-silico results to in vivo and ex-vivo of influenza-specific immune responses after vaccination or infection in humans. In  Innovation in Vaccinology, from design, through to delivery and testing , Baschieri Selene (Ed.). Springer Verlag (July 31, 2012) (ISBN: 978-94-007-4542-1)

F. Castiglione. A Monte Carlo simulation for the construction of cytotoxic T lymphocytes repertoire. In  Applications of Monte Carlo Methods in Biology, Medicine and Other Fields of Science , Mode Charles J. (Ed.), InTech Publishing. (2011) (ISBN: 978-953-307-427-6)

F. Castiglione, D. Santoni and M. Pedicini. Implementing agent s rules with gene regulatory networks in mesoscopic-lev

el models of cellular interactions. In   A practical guide to bioinformatics analysis . iConcept Press, Annerley, Australia (2010) (ISBN: 978-1-4536086-2-3).

F. Castiglione. Agent Based Modeling and Simulation, Introduction to.  In  Encyclopedia of Complexity and Systems Science , Meyers, Robert (Ed.). Vol 1, pp 197-200. Springer New York. (2009)

M. Bernaschi and F. Castiglione. Understanding the immune system by computer modeling. Proceedings of the 1st Internationall Immunoinformatics Symposium, Yokohama, Feb 26-27, 2004 Volume  Immunoinformatics  in  Immunomics Reviews  Series of Springer Science+Business Media LLC, New York, USA (2007).

F. Castiglione, V. Sleitser and Z. Agur. Analyzing hypersensitivity to chemotherapy in a Cellular Automata model of the immune system, in Cancer Modeling and Simulation, Preziosi L. (ed.), Chapman & Hall/CRC Press (UK), London, June 26,2003, pp 333-365.

F. Castiglione. Forecasting price increments using an artificial Neural Network, in Modeling Complexity in Economic and Social Systems, F. Schweitzer (ed.), World Scientific, Singapore 2002, 395 pp. 45-56 (ISBN 981-238-034-5)

F. Castiglione, M. Bernaschi and S. Succi. Simulating the immune response on a distributed parallel computer and F Castiglione, A Users Guide to CimmSim 1.1, on Dynamical Modeling in Biotechnologies, edited by F. Bagnoli and S. Ruffo, World Scientific textbook eds. (2000)

F. Castiglione. A Users Guide to CimmSim 1.1. In Bagnoli, Franco and Ruffo, Stefano (Eds.), Dynamical Modeling in Biotechnologies. World Scientific textbook eds. (Dec 2000)


L. Martins de Freitas, T. Uceli Maioli, H. de Assis Lopes Ribeiro, P. Tieri and F. Castiglione. A mathematical model of Chagas disease infection predicts inhibition of the immune system. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1374-1379.


H. de Assis Lopes Ribeiro, T. Uceli Maioli, L. Martins de Freitas, P. Tieri and F. Castiglione. A mathematical model of murine macrophage infected with Leishmania sp. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1425-1430.


A. Presbitero, E. Mancini, F. Castiglione, V. V. Krzhizhanovskaya, R. Quax. Evolutionary game theory can explain the choice between apoptotic and  necrotic pathways in neutrophils. 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Madrid, Spain, 2018, pp. 1401-1405.


F. Castiglione, D. Ghersi, F. Celada. In-Silico Analysis of the ``Memory Anti-Na\"ive'' Effect in Anti-Viral Cross-Reactive.

2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Kansas City, MO, USA, 2017, pp. 1433-1437.


Liso, A, Massenzio, F, Pucciarini, A , Bigerna, B, Luca, P, Zoppoli, P , F. Castiglione, Palumbo, MC, Conese, M, Castellani, S , Stracci, F, Landriscina, M, Specchia, G, Bach, L, Falini, B. Human monocyte-derived dendritic cells exposed to hyperthermia show a distinct gene expression profile and selective upregulation of IGFBP-6.

Haematologica, 99(1):440-441.

Proceedings of the 19th Congress of the European-Hematology-Association Milan, Italy, Jun 12-15, 2014

M. Rucco, F. Castiglione, E. Merelli, M. Pettini. Characterisation of the idiotypic immune network through persistent entropy. S. Battiston {\it et al.} (eds.), Proceedings of ECCS 2014, Springer Proceedings in Complexity,

doi 10.1007/978-3-319-29228-1

F. Pappalardo, F. Castiglione Castiglione, C. Bianca, G. Russo, M. Pennisi, S. Motta. Multiscale modelling of living systems: a mathematical and computational perspective SIMAI2014, Taormina, Italy, July 7-10, 2014

F. Castiglione, Merelli E., Pettini M. and Rucco M. Correlation between topological complexity and entropy in Idiotypic Network ECCS'14: Satellite Meeting  - Information Processing in Complex Systems (IPCS'14)

Lucca, Italy,   September 24, 2014.

F. Castiglione and F. Pappalardo. ``Computational biology modeling across different scales'' in Simulation and Modeling Methodologies, Technologies and Applications (SIMULTECH 2013), 3rd International Conference on

(Reykjavik, Iceland, July 29 - 31, 2013)

F. Castiglione and Bernaschi M. ``Epitope screening and cell cooperation in the immune response'' in Intelligent Systems, Modelling and Simulation (ISMS2011), International Conference on, (Kuala Lumpur 24 January, Phnom Penh 27-28 January 2011) ISMS2010 papers in the IEEE computer Society Digital Library (CSDL) {IEEE Computer Society}, {Los Alamitos, CA, USA} 0: 127--132 (2011)

ISBN 978-0-7695-4336-9

F. Castiglione, F. Pappalardo. Toward multi-organs simulations of immune-pathogen interactions, in Ninth International Conference on Intelligent Systems Design and Applications, ISDA 2009, Pisa, Italy, Nov 30 -- Dec 2, 2009, pg. 330--334, 2009.

G. Dell'Acqua, F. Castiglione. ``A mathematical model of Duchenne muscular dystrophy'', in Applied and Industrial Mathematics in Italy III (AIMI III), Proceedings of the SIMAI 9th Congress, Rome, September 15-19, 2008.

P. Paci, F. Castiglione, M. Bernaschi, V. Baldazzi, ``A Discrete/Continuous Model of Anti-HIV Response and Therapy'',

uksim, pp. 481-486,  Tenth International Conference on Computer Modeling and Simulation (uksim 2008),  2008.

F. Castiglione, F. Toschi, M. Bernaschi, S. Succi, R. Benedetti, B. Falini and A. Liso. Computational modeling of the immune response to tumor antigens: implications for vaccination. 43rd IEEE Conference on Decision and Control (CDC), Nassau, Bahamas, Dec 14-17, 2004.

F. Castiglione and B. Piccoli. Optimal control in a model of dendritic cell transfection cancer immunotherapy.

``Decision and Control, 2004. CDC. 43rd IEEE  Conference on''. Vol 1,  pages: 585- 590

F. Castiglione and M.Bernaschi. C-ImmSim: Playing with the immune response. Proceedings of the Sixteenth International Symposium on Mathematical Theory of Networks and Systems (MTNS2004) July 5-9, 2004 - Katholieke Universiteit Leuven, Belgium (ISBN 90-5682-517-8)

F. Castiglione, M. Bernaschi, M. Spizzichino. From un-realistic to quasi-realistic rules for trading in a microscopic model of financial markets with N>>1 assets. International Conference, ``Scientific achievements for wellbeing and development of society'', March 4-5, 2004, Rezeknes Augstskola, 2004 (ISBN 9984-585-34-4).

F. Castiglione. Agent-based micro-simulations in Immunology and Finance. Proceedings of the 4th International Scientific and Practical Conference, June 26-28, 2003, Rezeknes Augstskola, Latvia, 2003 (ISBN 9984-585-68-9)

F. Castiglione, S. Motta, G. Nicosia. Pattern Recognition with a Multi-Agent model of the Immune System. International NAISO Symposium on Information Science Innovations in Engineering of Natural and Artificial Intelligent Systems (ENAIS'2001), ICSC Academic Press, March 17-21, 2001 at the American University in Dubai, U.A.E.

F. Castiglione. Immune system simulation. 4th World Multiconference on Systemics, Cybernetics and Informatics (SCI'2000) and the 6th International Conference on Information Systems Analysis and Synthesis (ISAS'2000), Orlando, USA, July 23 - 26, 2000. SCI proceedings 2000/ISAS 2000 VOLUME X