Chiara Damiani

50 papers C 1Journal 27Unranked 22

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Predicting Metalloprotein Redox Potentials with Machine Learning: A Focus on Iron-Sulfur Systems. J. Chem. Inf. Model. Francesca Persico, Bruno G. Galuzzi, Miriana Pellegrino, Anne-Lise Claudel, Luca De Gioia, Flavia Nastri, Gianfranco Gilardi, Chiara Damiani, Francesca Valetti, Marco Chino, Federica Arrigoni
2024	J	`jnl`	Adjusting for false discoveries in constraint-based differential metabolic flux analysis. J. Biomed. Informatics Bruno G. Galuzzi, Luca Milazzo, Chiara Damiani
2023	C	`conf`	Coupling constrained-based flux sampling and clustering to tackle cancer metabolic heterogeneity. PDP Bruno G. Galuzzi, Stefano Izzo, Fabio Giampaolo, Salvatore Cuomo, Marco Vanoni, Lilia Alberghina, Chiara Damiani, Francesco Piccialli
2023	—	`conf`	Identifying Damage-Related Features in scRNA-seq Data. CIBB Giovanni Marteletto, Bruno G. Galuzzi, Chiara Damiani
2023	J	`jnl`	LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
2023	J	`jnl`	Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2023	—	`conf`	scFBApy: A Python Framework for Super-Network Flux Balance Analysis. WIVACE Bruno G. Galuzzi, Chiara Damiani
2022	—	`conf`	An Efficient Implementation of Flux Variability Analysis for Metabolic Networks. WIVACE Bruno G. Galuzzi, Chiara Damiani
2022	—	`conf`	Best Practices in Flux Sampling of Constrained-Based Models. LOD (2) Bruno G. Galuzzi, Luca Milazzo, Chiara Damiani
2022	J	`jnl`	Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells. BMC Bioinform. Bruno G. Galuzzi, Marco Vanoni, Chiara Damiani
2022	J	`jnl`	INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. PLoS Comput. Biol. Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani
2022	J	`jnl`	Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J. Chem. Inf. Model. Bruno Giovanni Galuzzi, Antonio Mirarchi, Edoardo Luca Viganò, Luca De Gioia, Chiara Damiani, Federica Arrigoni
2022	J	`jnl`	PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti
2021	J	`jnl`	Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models. BMC Bioinform. Marco S. Nobile, Vasco Coelho, Dario Pescini, Chiara Damiani
2021	J	`jnl`	Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. Inf. Comput. Lucrezia Patruno, Francesco Craighero, Davide Maspero, Alex Graudenzi, Chiara Damiani
2021	J	`jnl`	EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2021	J	`jnl`	GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PLoS Comput. Biol. Marzia Di Filippo, Chiara Damiani, Dario Pescini
2021	—	`conf`	Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. ANNSIM Fabrizio Angaroni, Chiara Damiani, Giulia Ramunni, Marco Antoniotti
2020	J	`jnl`	FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. Alex Graudenzi, Davide Maspero, Chiara Damiani
2020	J	`jnl`	The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
2019	—	`conf`	Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. CIBB Davide Maspero, Marzia Di Filippo, Fabrizio Angaroni, Dario Pescini, Giancarlo Mauri, Marco Vanoni, Alex Graudenzi, Chiara Damiani
2019	J	`jnl`	Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Comput. Biol. Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri
2018	J	`jnl`	Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinform. Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
2018	—	`conf`	Global Sensitivity Analysis of Constraint-Based Metabolic Models. CIBB Chiara Damiani, Dario Pescini, Marco S. Nobile
2018	J	`jnl`	Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani
2018	—	`conf`	Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI Alex Graudenzi, Davide Maspero, Chiara Damiani
2018	—	`conf`	Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani
2017	J	`jnl`	A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: The WarburQ effect. PLoS Comput. Biol. Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans V. Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina
2017	J	`jnl`	Dynamical regimes in non-ergodic random Boolean networks. Nat. Comput. Marco Villani, Davide Campioli, Chiara Damiani, Andrea Roli, Alessandro Filisetti, Roberto Serra
2017	J	`jnl`	popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. Bioinform. Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri
2016	J	`jnl`	CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
2016	—	`conf`	COSYS: A Computational Infrastructure for Systems Biology. CIBB Fabio Cumbo, Marco S. Nobile, Chiara Damiani, Riccardo Colombo, Giancarlo Mauri, Paolo Cazzaniga
2016	—	`conf`	Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features. CIBB Riccardo Colombo, Chiara Damiani, Giancarlo Mauri, Dario Pescini
2016	—	`conf`	Constraint-Based Modeling and Simulation of Cell Populations. WIVACE Marzia Di Filippo, Chiara Damiani, Riccardo Colombo, Dario Pescini, Giancarlo Mauri
2016	—	`conf`	Linking Alterations in Metabolic Fluxes with Shifts in Metabolite Levels by Means of Kinetic Modeling. WIVACE Chiara Damiani, Riccardo Colombo, Marzia Di Filippo, Dario Pescini, Giancarlo Mauri
2016	J	`jnl`	Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. Comput. Biol. Chem. Marzia Di Filippo, Riccardo Colombo, Chiara Damiani, Dario Pescini, Daniela Gaglio, Marco Vanoni, Lilia Alberghina, Giancarlo Mauri
2014	J	`jnl`	A stochastic model of catalytic reaction networks in protocells. CoRR Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
2014	J	`jnl`	A stochastic model of catalytic reaction networks in protocells. Nat. Comput. Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
2014	J	`jnl`	An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. Nat. Comput. Chiara Damiani, Dario Pescini, Riccardo Colombo, Sara Molinari, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri
2014	—	`conf`	Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti
2014	—	`conf`	On RAF Sets and Autocatalytic Cycles in Random Reaction Networks. WIVACE Alessandro Filisetti, Marco Villani, Chiara Damiani, Alex Graudenzi, Andrea Roli, Wim Hordijk, Roberto Serra
2013	—	`conf`	A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. WIVACE Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani
2013	—	`conf`	An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis. WIVACE Chiara Damiani, Riccardo Colombo, Sara Molinari, Dario Pescini, Daniela Gaglio, Marco Vanoni, Lilia Alberghina, Giancarlo Mauri
2013	J	`jnl`	Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca
2013	—	`conf`	Recent developments in research on catalytic reaction networks. WIVACE Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra
2013	—	`conf`	The role of backward reactions in a stochastic model of catalytic reaction networks. ECAL Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani, Roberto Serra
2011	J	`jnl`	Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. Alex Graudenzi, Roberto Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman
2011	—	`conf`	Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation. EMS Chiara Damiani, Paola Lecca
2010	—	`conf`	Information Transfer among Coupled Random Boolean Networks. ACRI Chiara Damiani, Stuart A. Kauffman, Roberto Serra, Marco Villani, Annamaria Colacci
2008	—	`conf`	The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci