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2020 – today
- 2024
[j24]Bruno G. Galuzzi
, Luca Milazzo, Chiara Damiani:
Adjusting for false discoveries in constraint-based differential metabolic flux analysis. J. Biomed. Informatics 150: 104597 (2024)- 2023
- [j23]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): 99 (2023) - [j22]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: 126576 (2023) - [c22]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: 185-192 - [c21]Bruno G. Galuzzi, Chiara Damiani:
scFBApy: A Python Framework for Super-Network Flux Balance Analysis. WIVACE 2023: 88-97 - 2022
- [j21]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): 754-762 (2022) - [j20]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. 23-S(6): 445 (2022) - [j19]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): 4748-4759 (2022) - [j18]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) - [c20]Bruno G. Galuzzi, Luca Milazzo, Chiara Damiani:
Best Practices in Flux Sampling of Constrained-Based Models. LOD (2) 2022: 234-248 - [c19]Bruno G. Galuzzi, Chiara Damiani:
An Efficient Implementation of Flux Variability Analysis for Metabolic Networks. WIVACE 2022: 58-69 - 2021
- [j17]Marco S. Nobile, Vasco Coelho, Dario Pescini, Chiara Damiani:
Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models. BMC Bioinform. 22-S(2): 78 (2021) - [j16]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: 104798 (2021) - [j15]Marzia Di Filippo, Chiara Damiani, Dario Pescini:
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction. PLoS Comput. Biol. 17(11) (2021) - [c18]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: 1-12 - [i2]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 abs/2111.12631 (2021) - 2020
- [j14]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): 279-295 (2020) - [j13]Alex Graudenzi, Davide Maspero, Chiara Damiani:
FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis. J. Cell. Autom. 15(1-2): 75-95 (2020)
2010 – 2019
- 2019
- [j12]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) - [c17]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: 207-215 - 2018
- [j11]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. 19-S(7): 45-59 (2018) - [j10]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: 37-49 (2018) - [c16]Alex Graudenzi, Davide Maspero, Chiara Damiani:
Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods. ACRI 2018: 16-29 - [c15]Chiara Damiani, Dario Pescini, Marco S. Nobile:
Global Sensitivity Analysis of Constraint-Based Metabolic Models. CIBB 2018: 179-186 - [c14]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: 115-126 - 2017
- [j9]Chiara Damiani, Marzia Di Filippo, Dario Pescini, Davide Maspero, Riccardo Colombo, Giancarlo Mauri:
popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. Bioinform. 33(14): i311-i318 (2017) - [j8]Marco Villani, Davide Campioli, Chiara Damiani, Andrea Roli, Alessandro Filisetti, Roberto Serra:
Dynamical regimes in non-ergodic random Boolean networks. Nat. Comput. 16(2): 353-363 (2017) - [j7]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) - 2016
- [j6]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: 64 (2016) - [j5]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: 60-69 (2016) - [c13]Fabio Cumbo, Marco S. Nobile, Chiara Damiani, Riccardo Colombo, Giancarlo Mauri, Paolo Cazzaniga:
COSYS: A Computational Infrastructure for Systems Biology. CIBB 2016: 82-92 - [c12]Riccardo Colombo, Chiara Damiani, Giancarlo Mauri, Dario Pescini:
Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features. CIBB 2016: 107-117 - [c11]Marzia Di Filippo, Chiara Damiani, Riccardo Colombo, Dario Pescini, Giancarlo Mauri:
Constraint-Based Modeling and Simulation of Cell Populations. WIVACE 2016: 126-137 - [c10]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: 138-148 - 2014
- [j4]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): 321-331 (2014) - [j3]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): 367-377 (2014) - [c9]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: 113-126 - [c8]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: 151-168 - [i1]Roberto Serra, Alessandro Filisetti, Marco Villani, Alex Graudenzi, Chiara Damiani, Tommaso Panini:
A stochastic model of catalytic reaction networks in protocells. CoRR abs/1407.8508 (2014) - 2013
- [j2]Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca:
Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks. Comput. Biol. Chem. 42: 5-17 (2013) - [c7]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: 793-801 - [c6]Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Marco Villani, Roberto Serra:
Recent developments in research on catalytic reaction networks. WIVACE 2013: 3-13 - [c5]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: 70-73 - [c4]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: 92-97 - 2011
- [j1]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): 1291-1303 (2011) - [c3]Chiara Damiani, Paola Lecca:
Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation. EMS 2011: 129-134 - 2010
- [c2]Chiara Damiani, Stuart A. Kauffman, Roberto Serra, Marco Villani, Annamaria Colacci:
Information Transfer among Coupled Random Boolean Networks. ACRI 2010: 1-11
2000 – 2009
- 2008
- [c1]Roberto Serra, Marco Villani, Chiara Damiani, Alex Graudenzi, Annamaria Colacci:
The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks. ACRI 2008: 315-322
Coauthor Index
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