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ORCIDFilippo Castiglione
Person information
- affiliation: National Research Council of Italy, Rome, Italy
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Books and Theses
- 2001
[b1]Filippo Castiglione:
Microsimulation of complex system dynamics: automata models in biology and finance. University of Cologne, Germany, 2001
Journal Articles
- 2024
- [j39]Raghvendra Mall
, Ankita Singh, Chirag N. Patel, Gregory Guirimand, Filippo Castiglione:
VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction. Briefings Bioinform. 25(4) (2024) - [j38]Filippo Castiglione, Peteris Daugulis, Emiliano Mancini, Rik Oldenkamp, Constance Schultsz, Vija Vagale:
Predicting Antimicrobial Resistance Trends Combining Standard Linear Algebra with Machine Learning Algorithms. Balt. J. Mod. Comput. 12(1) (2024) - [j37]Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen:
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024) - 2023
- [j36]Maria Concetta Palumbo, Albert A. de Graaf, Micaela Morettini, Paolo Tieri, Shaji Krishnan, Filippo Castiglione:
A computational model of the effects of macronutrients absorption and physical exercise on hormonal regulation and metabolic homeostasis. Comput. Biol. Medicine 163: 107158 (2023) - [j35]Paola Stolfi, Davide Vergni, Filippo Castiglione:
An agent-based multi-level model to study the spread of gonorrhea in different and interacting risk groups. Frontiers Appl. Math. Stat. 9 (2023) - [j34]Filippo Castiglione, Christine Nardini, Elia Onofri, Marco Pedicini, Paolo Tieri:
Explainable Drug Repurposing Approach From Biased Random Walks. IEEE ACM Trans. Comput. Biol. Bioinform. 20(2): 1009-1019 (2023) - 2022
- [j33]Peteris Daugulis, Vija Vagale, Emiliano Mancini, Filippo Castiglione:
A PCA-based Data Prediction Method. Balt. J. Mod. Comput. 10(1) (2022) - 2021
- [j32]Haiying Wang, Estelle Pujos-Guillot, Blandine Comte, Joao Luis de Miranda, Vojtech Spiwok, Ivan Chorbev, Filippo Castiglione, Paolo Tieri, Steven Watterson, Roisin McAllister, Tiago De Melo Malaquias, Massimiliano Zanin, Taranjit Singh Rai, Huiru Zheng:
Deep learning in systems medicine. Briefings Bioinform. 22(2): 1543-1559 (2021) - [j31]Paola Stolfi, Filippo Castiglione:
Emulating complex simulations by machine learning methods. BMC Bioinform. 22-S(14): 483 (2021) - 2020
- [j30]Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio, Filippo Castiglione:
Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. BMC Bioinform. 21-S(17): 508 (2020) - 2019
- [j29]Massimiliano Zanin, Ivan Chorbev, Blaz Stres, Egils Stalidzans, Julio Vera, Paolo Tieri, Filippo Castiglione, Derek Groen, Huiru Zheng, Jan Baumbach, Johannes A. Schmid, José Basilio, Peter Klimek, Natasa Debeljak, Damjana Rozman, Harald H. H. W. Schmidt:
Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Briefings Bioinform. 20(3): 1057-1062 (2019) - [j28]Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax:
Game of neutrophils: modeling the balance between apoptosis and necrosis. BMC Bioinform. 20-S(6): 475 (2019) - [j27]Vinca Prana, Paolo Tieri, Maria Concetta Palumbo, Emiliano Mancini, Filippo Castiglione:
Modeling the Effect of High Calorie Diet on the Interplay between Adipose Tissue, Inflammation, and Diabetes. Comput. Math. Methods Medicine 2019: 7525834:1-7525834:8 (2019) - 2018
- [j26]Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione:
Personalizing physical exercise in a computational model of fuel homeostasis. PLoS Comput. Biol. 14(4) (2018) - 2017
- [j25]Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano:
Computational modeling of immune system of the fish for a more effective vaccination in aquaculture. Bioinform. 33(19): 3065-3071 (2017) - 2016
- [j24]Antonio Cappuccio, Paolo Tieri, Filippo Castiglione:
Multiscale modelling in immunology: a review. Briefings Bioinform. 17(3): 408-418 (2016) - [j23]Filippo Castiglione, Paolo Tieri, Alessandro Palma, Abdul Salam Jarrah:
Statistical ensemble of gene regulatory networks of macrophage differentiation. BMC Bioinform. 17(S-19): 119-128 (2016) - 2015
- [j22]Eugenia Galeota, Caius Gavrila, Filippo Castiglione, Massimo Bernaschi, Gianni Cesareni:
The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. BMC Syst. Biol. 9(S-3): S3 (2015) - 2013
- [j21]Joachim von Eichborn, Anna Lena Woelke, Filippo Castiglione, Robert Preissner:
VaccImm: simulating peptide vaccination in cancer therapy. BMC Bioinform. 14: 127 (2013) - 2012
- [j20]Benjamin Ribba, Hanane El Garch, Sylvie Brunet, Emmanuel Grenier, Filippo Castiglione, H. Poulet, Philippe Vanhems:
Time-Course Analysis of Main Markers of Primary Infection in Cats with the Feline Immunodeficiency Virus. Comput. Math. Methods Medicine 2012: 342602:1-342602:9 (2012) - [j19]Filippo Castiglione, Francesca Mantile, Piergiuseppe De Berardinis, Antonella Prisco:
How the Interval between Prime and Boost Injection Affects the Immune Response in a Computational Model of the Immune System. Comput. Math. Methods Medicine 2012: 842329:1-842329:9 (2012) - 2011
- [j18]Nicolas Rapin, Ole Lund, Filippo Castiglione:
Immune system simulation online. Bioinform. 27(14): 2013-2014 (2011) - 2010
- [j17]Marco Pedicini, Fredrik Barrenäs, Trevor Clancy, Filippo Castiglione, Eivind Hovig, Kartiek Kanduri, Daniele Santoni, Mikael Benson:
Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation. PLoS Comput. Biol. 6(12) (2010) - 2009
- [j16]Francesco Pappalardo, Mark D. Halling-Brown, Nicolas Rapin, Ping Zhang, Davide Alemani, Andrew P. J. Emerson, Paola Paci, Patrice Duroux, Marzio Pennisi, Arianna Palladini, Olivo Miotto, Daniel Churchill, Elda Rossi, Adrian J. Shepherd, David S. Moss, Filippo Castiglione, Massimo Bernaschi, Marie-Paule Lefranc, Søren Brunak, Santo Motta, Pierluigi Lollini, Kaye E. Basford, Vladimir Brusic:
ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings Bioinform. 10(3): 330-340 (2009) - [j15]Valentina Baldazzi, Paola Paci, Massimo Bernaschi, Filippo Castiglione:
Modeling lymphocyte homing and encounters in lymph nodes. BMC Bioinform. 10: 387 (2009) - 2008
- [j14]Daniele Santoni, Marco Pedicini, Filippo Castiglione:
Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinform. 24(11): 1374-1380 (2008) - [j13]Massimo Bernaschi, Filippo Castiglione:
Comments on "Optimization and parallelization strategies for Monte Carlo simulation of HIV infection" by D. Hecquet, H.J. Ruskin and M. Crane Computers in Biology and Medicine, volume 37, 691, 2007. Comput. Biol. Medicine 38(2): 281 (2008) - 2007
- [j12]Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson:
Simulating Epstein-Barr virus infection with C-ImmSim. Bioinform. 23(11): 1371-1377 (2007) - [j11]Filippo Castiglione, Francesco Pappalardo, Massimo Bernaschi, Santo Motta:
Optimization of HAART with genetic algorithms and agent-based models of HIV infection. Bioinform. 23(24): 3350-3355 (2007) - [j10]Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni:
ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. BMC Bioinform. 8(S-1) (2007) - 2006
- [j9]Filippo Castiglione:
Agent based modeling. Scholarpedia 1(10): 1562 (2006) - 2005
- [j8]Francesco Pappalardo, Pierluigi Lollini, Filippo Castiglione, Santo Motta:
Modeling and simulation of cancer immunoprevention vaccine. Bioinform. 21(12): 2891-2897 (2005) - [j7]Federico Massaioli, Filippo Castiglione, Massimo Bernaschi:
OpenMP parallelization of agent-based models. Parallel Comput. 31(10-12): 1066-1081 (2005) - [j6]Filippo Castiglione, Sauro Succi:
Simulating the G-protein cAMP pathway with a two-compartment reactive lattice gas. Theory Biosci. 123(4): 413-429 (2005) - 2001
- [j5]Filippo Castiglione:
Forecasting Price increments using an Artificial Neural Network. Adv. Complex Syst. 4(1): 45-56 (2001) - [j4]Massimo Bernaschi, Filippo Castiglione:
Design and implementation of an immune system simulator. Comput. Biol. Medicine 31(5): 303-331 (2001) - [j3]Filippo Castiglione, Santo Motta, Giuseppe Nicosia:
Pattern recognition by primary and secondary response of an Artificial Immune System. Theory Biosci. 120(2): 93-106 (2001) - 2000
- [j2]Filippo Castiglione, Francesco Castiglione:
Estimating the Keratoconus Index from Ultrasound Images of the Human Cornea. IEEE Trans. Medical Imaging 19(12): 1268-1272 (2000) - 1999
- [j1]Massimo Bernaschi, Filippo Castiglione, Sauro Succi:
A high performance simulator of the immune response. Future Gener. Comput. Syst. 15(3): 333-342 (1999)
Conference and Workshop Papers
- 2023
- [c21]Enrico Mastrostefano, Alessandro Ravoni, Elia Onofri, Paolo Tieri, Filippo Castiglione:
Harnessing computational models to uncover the role of the immune system in tuberculosis treatment. BIBM 2023: 3725-3732 - 2022
- [c20]Paola Stolfi, Davide Vergni, Rik Oldenkamp, Constance Schultsz, Emiliano Mancini, Filippo Castiglione:
An agent-based multi-level model to study the spread of antimicrobial-resistant gonorrhoea. BIBM 2022: 803-808 - 2021
- [c19]Enrico Mastrostefano, Paola Stolfi, Filippo Castiglione:
A data-driven model for the generation of Virtual Cohorts. BIBM 2021: 3291-3298 - [c18]Paola Stolfi, Filippo Castiglione:
A functional data analysis approach to assess the prognostic value of SARS-CoV-2 infections surrogate data. BIBM 2021: 3308-3314 - 2020
- [c17]Paola Stolfi, Filippo Castiglione:
Emulation of dynamic multi-output simulator of risk of type-2 diabetes. BIBM 2020: 1289-1294 - 2019
- [c16]Alessandro Celestini, Marco Cianfriglia, Enrico Mastrostefano, Alessandro Palma, Filippo Castiglione, Paolo Tieri:
Critical nodes reveal peculiar features of human essential genes and protein interactome. BIBM 2019: 2121-2128 - [c15]Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio, Filippo Castiglione:
Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. BIBM 2019: 2214-2221 - 2018
- [c14]Leandro Martins de Freitas, Tatiani Uceli Maioli, Henrique Assis Lopes de Ribeiro, Paolo Tieri, Filippo Castiglione:
A mathematical model of Chagas disease infection predicts inhibition of the immune system. BIBM 2018: 1374-1379 - [c13]Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax:
Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. BIBM 2018: 1401-1405 - [c12]Henrique Assis Lopes de Ribeiro, Tatiani Uceli Maioli, Leandro Martins de Freitas, Paolo Tieri, Filippo Castiglione:
A mathematical model of murine macrophage infected with Leishmania sp. BIBM 2018: 1425-1430 - 2017
- [c11]Filippo Castiglione, Dario Ghersi, Franco Celada:
In-silico analysis of the "memory anti-Naïve" effect in anti-viral cross-reactive responses. BIBM 2017: 1433-1437 - [c10]Marco Pedicini, Maria Concetta Palumbo, Filippo Castiglione:
Computing Hierarchical Transition Graphs of Asynchronous Genetic Regulatory Networks. WIVACE 2017: 88-103 - 2014
- [c9]Matteo Rucco, Filippo Castiglione, Emanuela Merelli, Marco Pettini:
Characterisation of the Idiotypic Immune Network Through Persistent Entropy. ECCS 2014: 117-128 - [c8]Paolo Tieri, Vinca Prana, Teresa Colombo, Daniele Santoni, Filippo Castiglione:
Multi-scale Simulation of T Helper Lymphocyte Differentiation. BSB 2014: 123-134 - 2013
- [c7]Filippo Castiglione, Francesco Pappalardo:
Computational Biology Modeling across Different Scales. SIMULTECH 2013: 617-625 - 2009
- [c6]Filippo Castiglione, Francesco Pappalardo:
Toward Multi-organs Simulations of Immune-Pathogen Interactions. ISDA 2009: 330-334 - 2008
- [c5]Paola Paci, Filippo Castiglione, Massimo Bernaschi, Valentina Baldazzi:
A Discrete/Continuous Model of Anti-HIV Response and Therapy. UKSim 2008: 481-486 - 2004
- [c4]Filippo Castiglione, Federico Toschi, Massimo Bernaschi, Sauro Succi, Roberta Benedetti, Brunangelo Falini, Arcangelo Liso:
Computational modeling of the immune response to tumor antigens: implications for vaccination. CDC 2004: 569-574 - [c3]Filippo Castiglione, Benedetto Piccoli:
Optimal control in a model of dendritic cell transfection cancer immunotherapy. CDC 2004: 585-590 - 1998
- [c2]Massimo Bernaschi, Filippo Castiglione, Sauro Succi:
A Parallel Simulator of the Immune Response. HPCN Europe 1998: 163-172 - 1997
- [c1]Massimo Bernaschi, Filippo Castiglione, Sauro Succi:
A parallel algorithm for the simulation of the Immune Response. WAE 1997: 198-208
Reference Works
- 2019
- [r3]Paolo Tieri, Lorenzo Farina, Manuela Petti, Laura Astolfi, Paola Paci, Filippo Castiglione:
Network Inference and Reconstruction in Bioinformatics. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 805-813 - [r2]Filippo Castiglione, Emiliano Mancini, Marco Pedicini, Abdul Salam Jarrah:
Quantitative Modelling Approaches. Encyclopedia of Bioinformatics and Computational Biology (2) 2019: 874-883 - 2009
- [r1]Filippo Castiglione:
Agent Based Modeling and Simulation, Introduction to. Encyclopedia of Complexity and Systems Science 2009: 197-200
Informal and Other Publications
- 2024
- [i1]Étienne Goffinet, Raghvendra Mall, Ankita Singh, Rahul Kaushik, Filippo Castiglione:
MATE-Pred: Multimodal Attention-based TCR-Epitope interaction Predictor. CoRR abs/2401.08619 (2024)
Coauthor Index
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