Chiara Damiani

Publication Activity (10 Years)

Years Active: 2008-2024
Publications (10 Years): 34

Top Topics

Metabolic Networks

Stochastic Model

Sensitivity Analysis

Top Venues

PLoS Comput. Biol.

Publications

Bruno G. Galuzzi, Luca Milazzo, Chiara Damiani
Adjusting for false discoveries in constraint-based differential metabolic flux analysis. J. Biomed. Informatics 150 (2024)
Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing 554 (2023)
Bruno G. Galuzzi, Chiara Damiani
scFBApy: A Python Framework for Super-Network Flux Balance Analysis. WIVACE (2023)
Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. 24 (1) (2023)
Bruno G. Galuzzi, Stefano Izzo, Fabio Giampaolo, Salvatore Cuomo, Marco Vanoni, Lilia Alberghina, Chiara Damiani, Francesco Piccialli
Coupling constrained-based flux sampling and clustering to tackle cancer metabolic heterogeneity. PDP (2023)
Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. 38 (3) (2022)
Bruno G. Galuzzi, Marco Vanoni, Chiara Damiani
Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells. BMC Bioinform. (6) (2022)
Bruno Giovanni Galuzzi, Antonio Mirarchi, Edoardo Luca Viganò, Luca De Gioia, Chiara Damiani, Federica Arrigoni
Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. J. Chem. Inf. Model. 62 (19) (2022)
Bruno G. Galuzzi, Luca Milazzo, Chiara Damiani
Best Practices in Flux Sampling of Constrained-Based Models. LOD (2) (2022)
Marzia Di Filippo, Dario Pescini, Bruno Giovanni Galuzzi, Marcella Bonanomi, Daniela Gaglio, Eleonora Mangano, Clarissa Consolandi, Lilia Alberghina, Marco Vanoni, Chiara Damiani
INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. PLoS Comput. Biol. 18 (2) (2022)
Bruno G. Galuzzi, Chiara Damiani
An Efficient Implementation of Flux Variability Analysis for Metabolic Networks. WIVACE (2022)
Fabrizio Angaroni, Chiara Damiani, Giulia Ramunni, Marco Antoniotti
Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. ANNSIM (2021)
Marzia Di Filippo, Chiara Damiani, Dario Pescini
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PLoS Comput. Biol. 17 (11) (2021)
Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR (2021)
Marco S. Nobile, Vasco Coelho, Dario Pescini, Chiara Damiani
Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models. BMC Bioinform. (2) (2021)
Lucrezia Patruno, Francesco Craighero, Davide Maspero, Alex Graudenzi, Chiara Damiani
Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. Inf. Comput. 281 (2021)
Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae 171 (1-4) (2020)
Alex Graudenzi, Davide Maspero, Chiara Damiani
FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. 15 (1-2) (2020)
Davide Maspero, Marzia Di Filippo, Fabrizio Angaroni, Dario Pescini, Giancarlo Mauri, Marco Vanoni, Alex Graudenzi, Chiara Damiani
Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. CIBB (2019)
Chiara Damiani, Davide Maspero, Marzia Di Filippo, Riccardo Colombo, Dario Pescini, Alex Graudenzi, Hans V. Westerhoff, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. PLoS Comput. Biol. 15 (2) (2019)
Chiara Damiani, Dario Pescini, Marco S. Nobile
Global Sensitivity Analysis of Constraint-Based Metabolic Models. CIBB (2018)
Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani
Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE (2018)
Alex Graudenzi, Davide Maspero, Chiara Damiani
Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI (2018)
Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics 87 (2018)
Riccardo Colombo, Chiara Damiani, David R. Gilbert, Monika Heiner, Giancarlo Mauri, Dario Pescini
Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinform. (7) (2018)
Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. Bioinform. 33 (14) (2017)
Marco Villani, Davide Campioli, Chiara Damiani, Andrea Roli, Alessandro Filisetti, Roberto Serra
Dynamical regimes in non-ergodic random Boolean networks. Nat. Comput. 16 (2) (2017)
Chiara Damiani, Riccardo Colombo, Daniela Gaglio, Fabrizia Mastroianni, Dario Pescini, Hans V. Westerhoff, Giancarlo Mauri, Marco Vanoni, Lilia Alberghina
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. 13 (9) (2017)
Marzia Di Filippo, Chiara Damiani, Riccardo Colombo, Dario Pescini, Giancarlo Mauri
Constraint-Based Modeling and Simulation of Cell Populations. WIVACE (2016)
Fabio Cumbo, Marco S. Nobile, Chiara Damiani, Riccardo Colombo, Giancarlo Mauri, Paolo Cazzaniga
COSYS: A Computational Infrastructure for Systems Biology. CIBB (2016)
Riccardo Colombo, Chiara Damiani, Giancarlo Mauri, Dario Pescini
Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features. CIBB (2016)
Marzia Di Filippo, Riccardo Colombo, Chiara Damiani, Dario Pescini, Daniela Gaglio, Marco Vanoni, Lilia Alberghina, Giancarlo Mauri
Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. Comput. Biol. Chem. 62 (2016)
Chiara Damiani, Riccardo Colombo, Marzia Di Filippo, Dario Pescini, Giancarlo Mauri
Linking Alterations in Metabolic Fluxes with Shifts in Metabolite Levels by Means of Kinetic Modeling. WIVACE (2016)
Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. 17 (2016)
Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
A stochastic model of catalytic reaction networks in protocells. CoRR (2014)
Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti
Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE (2014)
Chiara Damiani, Dario Pescini, Riccardo Colombo, Sara Molinari, Lilia Alberghina, Marco Vanoni, Giancarlo Mauri
An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. Nat. Comput. 13 (3) (2014)
Alessandro Filisetti, Marco Villani, Chiara Damiani, Alex Graudenzi, Andrea Roli, Wim Hordijk, Roberto Serra
On RAF Sets and Autocatalytic Cycles in Random Reaction Networks. WIVACE (2014)
Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini
A stochastic model of catalytic reaction networks in protocells. Nat. Comput. 13 (3) (2014)
Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra
Recent developments in research on catalytic reaction networks. WIVACE (2013)
Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani, Roberto Serra
The role of backward reactions in a stochastic model of catalytic reaction networks. ECAL (2013)
Roberto Serra, Alessandro Filisetti, Alex Graudenzi, Chiara Damiani, Marco Villani
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. WIVACE (2013)
Chiara Damiani, Riccardo Colombo, Sara Molinari, Dario Pescini, Daniela Gaglio, Marco Vanoni, Lilia Alberghina, Giancarlo Mauri
An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis. WIVACE (2013)
Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca
Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. 42 (2013)
Alex Graudenzi, Roberto Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman
Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. J. Comput. Biol. 18 (10) (2011)
Chiara Damiani, Paola Lecca
Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation. EMS (2011)
Chiara Damiani, Stuart A. Kauffman, Roberto Serra, Marco Villani, Annamaria Colacci
Information Transfer among Coupled Random Boolean Networks. ACRI (2010)
Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci
The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI (2008)