The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. - Roberto Serra; Marco Villani 001; Chiara Damiani; Alex Graudenzi; Annamaria Colacci (ACRI, 2008)

Information Transfer among Coupled Random Boolean Networks. - Chiara Damiani; Stuart A. Kauffman; Roberto Serra; Marco Villani 001; Annamaria Colacci (ACRI, 2010)

Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation. - Chiara Damiani; Paola Lecca (EMS, 2011)

Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory. - Alex Graudenzi; Roberto Serra; Marco Villani 001; Chiara Damiani; Annamaria Colacci; Stuart A. Kauffman (J. Comput. Biol., 2011)

The role of backward reactions in a stochastic model of catalytic reaction networks. - Alessandro Filisetti; Alex Graudenzi; Chiara Damiani; Marco Villani 001; Roberto Serra (ECAL, 2013)

Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. - Chiara Damiani; Alessandro Filisetti; Alex Graudenzi; Paola Lecca (Comput. Biol. Chem., 2013)

An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis. - Chiara Damiani; Riccardo Colombo; Sara Molinari; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (WIVACE, 2013)

Recent developments in research on catalytic reaction networks. - Chiara Damiani; Alessandro Filisetti; Alex Graudenzi; Marco Villani 001; Roberto Serra (WIVACE, 2013)

A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks. - Roberto Serra; Alessandro Filisetti; Alex Graudenzi; Chiara Damiani; Marco Villani 001 (WIVACE, 2013)

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks. - Alessandro Filisetti; Marco Villani 001; Chiara Damiani; Alex Graudenzi; Andrea Roli; Wim Hordijk; Roberto Serra (WIVACE, 2014)

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. - Alex Graudenzi; Chiara Damiani; Andrea Paroni; Alessandro Filisetti; Marco Villani 001; Roberto Serra; Marco Antoniotti (WIVACE, 2014)

An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes. - Chiara Damiani; Dario Pescini; Riccardo Colombo; Sara Molinari; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (Nat. Comput., 2014)

A stochastic model of catalytic reaction networks in protocells. - Roberto Serra; Alessandro Filisetti; Marco Villani 001; Alex Graudenzi; Chiara Damiani; Tommaso Panini (Nat. Comput., 2014)

Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features. - Riccardo Colombo; Chiara Damiani; Giancarlo Mauri; Dario Pescini (CIBB, 2016)

COSYS: A Computational Infrastructure for Systems Biology. - Fabio Cumbo; Marco S. Nobile; Chiara Damiani; Riccardo Colombo; Giancarlo Mauri; Paolo Cazzaniga (CIBB, 2016)

Linking Alterations in Metabolic Fluxes with Shifts in Metabolite Levels by Means of Kinetic Modeling. - Chiara Damiani; Riccardo Colombo; Marzia Di Filippo; Dario Pescini; Giancarlo Mauri (WIVACE, 2016)

Constraint-Based Modeling and Simulation of Cell Populations. - Marzia Di Filippo; Chiara Damiani; Riccardo Colombo; Dario Pescini; Giancarlo Mauri (WIVACE, 2016)

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. - Andrea Paroni; Alex Graudenzi; Giulio Caravagna; Chiara Damiani; Giancarlo Mauri; Marco Antoniotti (BMC Bioinform., 2016)

Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. - Marzia Di Filippo; Riccardo Colombo; Chiara Damiani; Dario Pescini; Daniela Gaglio; Marco Vanoni; Lilia Alberghina; Giancarlo Mauri (Comput. Biol. Chem., 2016)

popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. - Chiara Damiani; Marzia Di Filippo; Dario Pescini; Davide Maspero; Riccardo Colombo; Giancarlo Mauri (Bioinform., 2017)

Dynamical regimes in non-ergodic random Boolean networks. - Marco Villani 001; Davide Campioli; Chiara Damiani; Andrea Roli; Alessandro Filisetti; Roberto Serra (Nat. Comput., 2017)

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. - Chiara Damiani; Riccardo Colombo; Daniela Gaglio; Fabrizia Mastroianni; Dario Pescini; Hans V. Westerhoff; Giancarlo Mauri; Marco Vanoni; Lilia Alberghina (PLoS Comput. Biol., 2017)

Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. - Alex Graudenzi; Davide Maspero; Chiara Damiani (ACRI, 2018)

Global Sensitivity Analysis of Constraint-Based Metabolic Models. - Chiara Damiani; Dario Pescini; Marco S. Nobile (CIBB, 2018)

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. - Davide Maspero; Alex Graudenzi; Satwinder Singh; Dario Pescini; Giancarlo Mauri; Marco Antoniotti; Chiara Damiani (WIVACE, 2018)

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. - Riccardo Colombo; Chiara Damiani; David R. Gilbert; Monika Heiner; Giancarlo Mauri; Dario Pescini (BMC Bioinform., 2018)

Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. - Alex Graudenzi; Davide Maspero; Marzia Di Filippo; Marco Gnugnoli; Claudio Isella; Giancarlo Mauri; Enzo Medico; Marco Antoniotti; Chiara Damiani (J. Biomed. Informatics, 2018)

Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata. - Davide Maspero; Marzia Di Filippo; Fabrizio Angaroni; Dario Pescini; Giancarlo Mauri; Marco Vanoni; Alex Graudenzi; Chiara Damiani (CIBB, 2019)

Integration of single-cell RNA-seq data into population models to characterize cancer metabolism. - Chiara Damiani; Davide Maspero; Marzia Di Filippo; Riccardo Colombo; Dario Pescini; Alex Graudenzi; Hans V. Westerhoff; Lilia Alberghina; Marco Vanoni; Giancarlo Mauri (PLoS Comput. Biol., 2019)

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. - Davide Maspero; Chiara Damiani; Marco Antoniotti; Alex Graudenzi; Marzia Di Filippo; Marco Vanoni; Giulio Caravagna; Riccardo Colombo; Daniele Ramazzotti; Dario Pescini (Fundam. Informaticae, 2020)

FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. - Alex Graudenzi; Davide Maspero; Chiara Damiani (J. Cell. Autom., 2020)

Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. - Fabrizio Angaroni; Chiara Damiani; Giulia Ramunni; Marco Antoniotti (ANNSIM, 2021)

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models. - Marco S. Nobile; Vasco Coelho; Dario Pescini; Chiara Damiani (BMC Bioinform., 2021)

EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. - Francesco Craighero; Fabrizio Angaroni; Fabio Stella; Chiara Damiani; Marco Antoniotti; Alex Graudenzi (CoRR, 2021)

Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems. - Lucrezia Patruno; Francesco Craighero; Davide Maspero; Alex Graudenzi; Chiara Damiani (Inf. Comput., 2021)

GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. - Marzia Di Filippo; Chiara Damiani; Dario Pescini (PLoS Comput. Biol., 2021)

Best Practices in Flux Sampling of Constrained-Based Models. - Bruno G. Galuzzi; Luca Milazzo; Chiara Damiani (LOD (2), 2022)

An Efficient Implementation of Flux Variability Analysis for Metabolic Networks. - Bruno G. Galuzzi; Chiara Damiani (WIVACE, 2022)

PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. - Fabrizio Angaroni; Kevin Chen; Chiara Damiani; Giulio Caravagna; Alex Graudenzi; Daniele Ramazzotti (Bioinform., 2022)

Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells. - Bruno G. Galuzzi; Marco Vanoni; Chiara Damiani (BMC Bioinform., 2022)

Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case. - Bruno Giovanni Galuzzi; Antonio Mirarchi; Edoardo Luca Viganò; Luca De Gioia; Chiara Damiani; Federica Arrigoni (J. Chem. Inf. Model., 2022)

INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. - Marzia Di Filippo; Dario Pescini; Bruno Giovanni Galuzzi; Marcella Bonanomi; Daniela Gaglio; Eleonora Mangano; Clarissa Consolandi; Lilia Alberghina; Marco Vanoni; Chiara Damiani (PLoS Comput. Biol., 2022)

Identifying Damage-Related Features in scRNA-seq Data. - Giovanni Marteletto; Bruno G. Galuzzi; Chiara Damiani (CIBB, 2023)

Coupling constrained-based flux sampling and clustering to tackle cancer metabolic heterogeneity. - Bruno G. Galuzzi; Stefano Izzo; Fabio Giampaolo; Salvatore Cuomo; Marco Vanoni; Lilia Alberghina; Chiara Damiani; Francesco Piccialli (PDP, 2023)

scFBApy: A Python Framework for Super-Network Flux Balance Analysis. - Bruno G. Galuzzi; Chiara Damiani (WIVACE, 2023)

Unity is strength: Improving the detection of adversarial examples with ensemble approaches. - Francesco Craighero; Fabrizio Angaroni; Fabio Stella; Chiara Damiani; Marco Antoniotti; Alex Graudenzi (Neurocomputing, 2023)

LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. - Gianluca Ascolani; Fabrizio Angaroni; Davide Maspero; Francesco Craighero; Narra Lakshmi Sai Bhavesh; Rocco Piazza; Chiara Damiani; Daniele Ramazzotti; Marco Antoniotti; Alex Graudenzi (BMC Bioinform., 2023)

Adjusting for false discoveries in constraint-based differential metabolic flux analysis. - Bruno G. Galuzzi; Luca Milazzo; Chiara Damiani (J. Biomed. Informatics, 2024)