Filippo Castiglione

73 papers C 2Journal 46Unranked 21

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	A PCA-based Data Prediction Method. CoRR Peteris Daugulis, Vija Vagale, Emiliano Mancini, Filippo Castiglione
2025	J	`jnl`	DiffNMR2: NMR Guided Sampling Acquisition Through Diffusion Model Uncertainty. CoRR Étienne Goffinet, Sen Yan, Fabrizio Gabellieri, Laurence Jennings, Lydia Gkoura, Filippo Castiglione, Ryan Young, Idir Malki, Ankita Singh, Thomas Launey
2025	J	`jnl`	DiffNMR3: Advancing NMR Resolution Beyond Instrumental Limits. CoRR Sen Yan, Étienne Goffinet, Fabrizio Gabellieri, Ryan Young, Lydia Gkoura, Laurence Jennings, Filippo Castiglione, Thomas Launey
2025	J	`jnl`	DiffNMR: Advancing Inpainting of Randomly Sampled Nuclear Magnetic Resonance Signals. CoRR Sen Yan, Fabrizio Gabellieri, Étienne Goffinet, Filippo Castiglione, Thomas Launey
2025	J	`jnl`	Mimicking cancer therapy in an agent-based model: The case of hepatoblastoma. Comput. Methods Programs Biomed. Alessandro Ravoni, Enrico Mastrostefano, Roland Kappler, Carolina Armengol, Filippo Castiglione, Christine Nardini
2025	J	`jnl`	Stability of threshold Boolean networks. J. Complex Networks Hadeel Kittaneh, Filippo Castiglione, Abdul Salam Jarrah
2024	—	`conf`	A discrete mathematical model of gene regulation in pediatric Acute Lymphoblastic Leukemia. BIBM Valery Lacoste, Arcangelo Liso, Filippo Castiglione, Abdul Salam Jarrah
2024	—	`conf`	FEATURE-pHLA: Physico-chemical features efficiently predict peptide-HLA binding affinity. BIBM Hamda Alhosani, Raghvendra Mall, Ankita Singh, Filippo Castiglione
2024	J	`jnl`	MATE-Pred: Multimodal Attention-based TCR-Epitope interaction Predictor. CoRR Étienne Goffinet, Raghvendra Mall, Ankita Singh, Rahul Kaushik, Filippo Castiglione
2024	J	`jnl`	Predicting Antimicrobial Resistance Trends Combining Standard Linear Algebra with Machine Learning Algorithms. Balt. J. Mod. Comput. Filippo Castiglione, Peteris Daugulis, Emiliano Mancini, Rik Oldenkamp, Constance Schultsz, Vija Vagale
2024	J	`jnl`	Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 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
2024	J	`jnl`	VISH-Pred: an ensemble of fine-tuned ESM models for protein toxicity prediction. Briefings Bioinform. Raghvendra Mall, Ankita Singh, Chirag N. Patel, Gregory Guirimand, Filippo Castiglione
2023	J	`jnl`	A computational model of the effects of macronutrients absorption and physical exercise on hormonal regulation and metabolic homeostasis. Comput. Biol. Medicine Maria Concetta Palumbo, Albert A. de Graaf, Micaela Morettini, Paolo Tieri, Shaji Krishnan, Filippo Castiglione
2023	J	`jnl`	An agent-based multi-level model to study the spread of gonorrhea in different and interacting risk groups. Frontiers Appl. Math. Stat. Paola Stolfi, Davide Vergni, Filippo Castiglione
2023	J	`jnl`	Explainable Drug Repurposing Approach From Biased Random Walks. IEEE ACM Trans. Comput. Biol. Bioinform. Filippo Castiglione, Christine Nardini, Elia Onofri, Marco Pedicini, Paolo Tieri
2023	—	`conf`	Harnessing computational models to uncover the role of the immune system in tuberculosis treatment. BIBM Enrico Mastrostefano, Alessandro Ravoni, Elia Onofri, Paolo Tieri, Filippo Castiglione
2022	J	`jnl`	A PCA-based Data Prediction Method. Balt. J. Mod. Comput. Peteris Daugulis, Vija Vagale, Emiliano Mancini, Filippo Castiglione
2022	—	`conf`	An agent-based multi-level model to study the spread of antimicrobial-resistant gonorrhoea. BIBM Paola Stolfi, Davide Vergni, Rik Oldenkamp, Constance Schultsz, Emiliano Mancini, Filippo Castiglione
2021	—	`conf`	A data-driven model for the generation of Virtual Cohorts. BIBM Enrico Mastrostefano, Paola Stolfi, Filippo Castiglione
2021	—	`conf`	A functional data analysis approach to assess the prognostic value of SARS-CoV-2 infections surrogate data. BIBM Paola Stolfi, Filippo Castiglione
2021	J	`jnl`	Deep learning in systems medicine. Briefings Bioinform. Haiying Wang, Estelle Pujos-Guillot, Blandine Comte, João Luís 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
2021	J	`jnl`	Emulating complex simulations by machine learning methods. BMC Bioinform. Paola Stolfi, Filippo Castiglione
2020	—	`conf`	Emulation of dynamic multi-output simulator of risk of type-2 diabetes. BIBM Paola Stolfi, Filippo Castiglione
2020	J	`jnl`	Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. BMC Bioinform. Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio, Filippo Castiglione
2019	J	`jnl`	Community effort endorsing multiscale modelling, multiscale data science and multiscale computing for systems medicine. Briefings Bioinform. 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
2019	—	`conf`	Critical nodes reveal peculiar features of human essential genes and protein interactome. BIBM Alessandro Celestini, Marco Cianfriglia, Enrico Mastrostefano, Alessandro Palma, Filippo Castiglione, Paolo Tieri
2019	J	`jnl`	Game of neutrophils: modeling the balance between apoptosis and necrosis. BMC Bioinform. Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax
2019	J	`jnl`	Modeling the Effect of High Calorie Diet on the Interplay between Adipose Tissue, Inflammation, and Diabetes. Comput. Math. Methods Medicine Vinca Prana, Paolo Tieri, Maria Concetta Palumbo, Emiliano Mancini, Filippo Castiglione
2019	—	`ch.`	Network Inference and Reconstruction in Bioinformatics. Encyclopedia of Bioinformatics and Computational Biology (2) Paolo Tieri, Lorenzo Farina, Manuela Petti, Laura Astolfi, Paola Paci, Filippo Castiglione
2019	—	`conf`	Potential predictors of type-2 diabetes risk: machine learning, synthetic data and wearable health devices. BIBM Paola Stolfi, Ilaria Valentini, Maria Concetta Palumbo, Paolo Tieri, Andrea Grignolio, Filippo Castiglione
2019	—	`ch.`	Quantitative Modelling Approaches. Encyclopedia of Bioinformatics and Computational Biology (2) Filippo Castiglione, Emiliano Mancini, Marco Pedicini, Abdul Salam Jarrah
2018	—	`conf`	A mathematical model of Chagas disease infection predicts inhibition of the immune system. BIBM Leandro Martins de Freitas, Tatiani Uceli Maioli, Henrique Assis Lopes de Ribeiro, Paolo Tieri, Filippo Castiglione
2018	—	`conf`	A mathematical model of murine macrophage infected with Leishmania sp. BIBM Henrique Assis Lopes de Ribeiro, Tatiani Uceli Maioli, Leandro Martins de Freitas, Paolo Tieri, Filippo Castiglione
2018	—	`conf`	Evolutionary Game Theory Can Explain the Choice Between Apoptotic and Necrotic Pathways in Neutrophils. BIBM Alva Presbitero, Emiliano Mancini, Filippo Castiglione, Valeria V. Krzhizhanovskaya, Rick Quax
2018	J	`jnl`	Personalizing physical exercise in a computational model of fuel homeostasis. PLoS Comput. Biol. Maria Concetta Palumbo, Micaela Morettini, Paolo Tieri, Fasma Diele, Massimo Sacchetti, Filippo Castiglione
2017	J	`jnl`	Computational modeling of immune system of the fish for a more effective vaccination in aquaculture. Bioinform. Alice Madonia, Cristiano Melchiorri, Simone Bonamano, Marco Marcelli, Chiara Bulfon, Filippo Castiglione, Marco Galeotti, Donatella Volpatti, Francesco Mosca, Pietro-Giorgio Tiscar, Nicla Romano
2017	—	`conf`	Computing Hierarchical Transition Graphs of Asynchronous Genetic Regulatory Networks. WIVACE Marco Pedicini, Maria Concetta Palumbo, Filippo Castiglione
2017	—	`conf`	In-silico analysis of the "memory anti-Naïve" effect in anti-viral cross-reactive responses. BIBM Filippo Castiglione, Dario Ghersi, Franco Celada
2016	J	`jnl`	Multiscale modelling in immunology: a review. Briefings Bioinform. Antonio Cappuccio, Paolo Tieri, Filippo Castiglione
2016	J	`jnl`	Statistical ensemble of gene regulatory networks of macrophage differentiation. BMC Bioinform. Filippo Castiglione, Paolo Tieri, Alessandro Palma, Abdul Salam Jarrah
2015	J	`jnl`	The hierarchical organization of natural protein interaction networks confers self-organization properties on pseudocells. BMC Syst. Biol. Eugenia Galeota, Caius Gavrila, Filippo Castiglione, Massimo Bernaschi, Gianni Cesareni
2014	—	`conf`	Characterisation of the Idiotypic Immune Network Through Persistent Entropy. ECCS Matteo Rucco, Filippo Castiglione, Emanuela Merelli, Marco Pettini
2014	—	`conf`	Multi-scale Simulation of T Helper Lymphocyte Differentiation. BSB Paolo Tieri, Vinca Prana, Teresa Colombo, Daniele Santoni, Filippo Castiglione
2013	C	`conf`	Computational Biology Modeling across Different Scales. SIMULTECH Filippo Castiglione, Francesco Pappalardo
2013	J	`jnl`	VaccImm: simulating peptide vaccination in cancer therapy. BMC Bioinform. Joachim von Eichborn, Anna Lena Woelke, Filippo Castiglione, Robert Preissner
2012	J	`jnl`	How the Interval between Prime and Boost Injection Affects the Immune Response in a Computational Model of the Immune System. Comput. Math. Methods Medicine Filippo Castiglione, Francesca Mantile, Piergiuseppe De Berardinis, Antonella Prisco
2012	J	`jnl`	Time-Course Analysis of Main Markers of Primary Infection in Cats with the Feline Immunodeficiency Virus. Comput. Math. Methods Medicine Benjamin Ribba, Hanane El Garch, Sylvie Brunet, Emmanuel Grenier, Filippo Castiglione, H. Poulet, Philippe Vanhems
2011	J	`jnl`	Immune system simulation online. Bioinform. Nicolas Rapin, Ole Lund, Filippo Castiglione
2010	J	`jnl`	Combining Network Modeling and Gene Expression Microarray Analysis to Explore the Dynamics of Th1 and Th2 Cell Regulation. PLoS Comput. Biol. Marco Pedicini, Fredrik Barrenäs, Trevor Clancy, Filippo Castiglione, Eivind Hovig, Kartiek Kanduri, Daniele Santoni, Mikael Benson
2009	—	`ch.`	Agent Based Modeling and Simulation, Introduction to. Encyclopedia of Complexity and Systems Science Filippo Castiglione
2009	J	`jnl`	ImmunoGrid, an integrative environment for large-scale simulation of the immune system for vaccine discovery, design and optimization. Briefings Bioinform. 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
2009	J	`jnl`	Modeling lymphocyte homing and encounters in lymph nodes. BMC Bioinform. Valentina Baldazzi, Paola Paci, Massimo Bernaschi, Filippo Castiglione
2009	C	`conf`	Toward Multi-organs Simulations of Immune-Pathogen Interactions. ISDA Filippo Castiglione, Francesco Pappalardo
2008	—	`conf`	A Discrete/Continuous Model of Anti-HIV Response and Therapy. UKSim Paola Paci, Filippo Castiglione, Massimo Bernaschi, Valentina Baldazzi
2008	J	`jnl`	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 Massimo Bernaschi, Filippo Castiglione
2008	J	`jnl`	Implementation of a regulatory gene network to simulate the TH1/2 differentiation in an agent-based model of hypersensitivity reactions. Bioinform. Daniele Santoni, Marco Pedicini, Filippo Castiglione
2007	J	`jnl`	Optimization of HAART with genetic algorithms and agent-based models of HIV infection. Bioinform. Filippo Castiglione, Francesco Pappalardo, Massimo Bernaschi, Santo Motta
2007	J	`jnl`	ProtNet: a tool for stochastic simulations of protein interaction networks dynamics. BMC Bioinform. Massimo Bernaschi, Filippo Castiglione, Alessandra Ferranti, Caius Gavrila, Michele Tinti, Gianni Cesareni
2007	J	`jnl`	Simulating Epstein-Barr virus infection with C-ImmSim. Bioinform. Filippo Castiglione, Karen Duca, Abdul Salam Jarrah, Reinhard C. Laubenbacher, Donna Hochberg, David Thorley-Lawson
2006	J	`jnl`	Agent based modeling. Scholarpedia Filippo Castiglione
2005	J	`jnl`	Modeling and simulation of cancer immunoprevention vaccine. Bioinform. Francesco Pappalardo, Pierluigi Lollini, Filippo Castiglione, Santo Motta
2005	J	`jnl`	OpenMP parallelization of agent-based models. Parallel Comput. Federico Massaioli, Filippo Castiglione, Massimo Bernaschi
2005	J	`jnl`	Simulating the G-protein cAMP pathway with a two-compartment reactive lattice gas. Theory Biosci. Filippo Castiglione, Sauro Succi
2004	—	`conf`	Computational modeling of the immune response to tumor antigens: implications for vaccination. CDC Filippo Castiglione, Federico Toschi, Massimo Bernaschi, Sauro Succi, Roberta Benedetti, Brunangelo Falini, Arcangelo Liso
2004	—	`conf`	Optimal control in a model of dendritic cell transfection cancer immunotherapy. CDC Filippo Castiglione, Benedetto Piccoli
2001	J	`jnl`	Design and implementation of an immune system simulator. Comput. Biol. Medicine Massimo Bernaschi, Filippo Castiglione
2001	J	`jnl`	Forecasting Price increments using an Artificial Neural Network. Adv. Complex Syst. Filippo Castiglione
2001	—	`—`	Microsimulation of complex system dynamics: automata models in biology and finance. Filippo Castiglione
2001	J	`jnl`	Pattern recognition by primary and secondary response of an Artificial Immune System. Theory Biosci. Filippo Castiglione, Santo Motta, Giuseppe Nicosia
2000	J	`jnl`	Estimating the Keratoconus Index from Ultrasound Images of the Human Cornea. IEEE Trans. Medical Imaging Filippo Castiglione, Francesco Castiglione
1999	J	`jnl`	A high performance simulator of the immune response. Future Gener. Comput. Syst. Massimo Bernaschi, Filippo Castiglione, Sauro Succi
1998	—	`conf`	A Parallel Simulator of the Immune Response. HPCN Europe Massimo Bernaschi, Filippo Castiglione, Sauro Succi
1997	—	`conf`	A parallel algorithm for the simulation of the Immune Response. WAE Massimo Bernaschi, Filippo Castiglione, Sauro Succi