Chiara Damiani

Orcid: 0000-0002-5742-8302

According to our database1, Chiara Damiani authored at least 47 papers between 2008 and 2024.

Collaborative distances:
  • Dijkstra number2 of four.
  • Erdős number3 of four.

Timeline

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Bibliography

2024
Adjusting for false discoveries in constraint-based differential metabolic flux analysis.
J. Biomed. Informatics, 2024

2023
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution.
BMC Bioinform., December, 2023

Unity is strength: Improving the detection of adversarial examples with ensemble approaches.
Neurocomputing, October, 2023

scFBApy: A Python Framework for Super-Network Flux Balance Analysis.
Proceedings of the Artificial Life and Evolutionary Computation, 2023

Coupling constrained-based flux sampling and clustering to tackle cancer metabolic heterogeneity.
Proceedings of the 31st Euromicro International Conference on Parallel, 2023

2022
INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation.
PLoS Comput. Biol., 2022

Machine Learning for Efficient Prediction of Protein Redox Potential: The Flavoproteins Case.
J. Chem. Inf. Model., 2022

Combining denoising of RNA-seq data and flux balance analysis for cluster analysis of single cells.
BMC Bioinform., 2022

PMCE: efficient inference of expressive models of cancer evolution with high prognostic power.
Bioinform., 2022

An Efficient Implementation of Flux Variability Analysis for Metabolic Networks.
Proceedings of the Artificial Life and Evolutionary Computation - 16th Italian Workshop, 2022

Best Practices in Flux Sampling of Constrained-Based Models.
Proceedings of the Machine Learning, Optimization, and Data Science, 2022

2021
GPRuler: Metabolic gene-protein-reaction rules automatic reconstruction.
PLoS Comput. Biol., 2021

Combining multi-target regression deep neural networks and kinetic modeling to predict relative fluxes in reaction systems.
Inf. Comput., 2021

EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks.
CoRR, 2021

Accelerated global sensitivity analysis of genome-wide constraint-based metabolic models.
BMC Bioinform., 2021

Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks.
Proceedings of the Annual Modeling and Simulation Conference, 2021

2020
FBCA, A Multiscale Modeling Framework Combining Cellular Automata and Flux Balance Analysis.
J. Cell. Autom., 2020

The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System.
Fundam. Informaticae, 2020

2019
Integration of single-cell RNA-seq data into population models to characterize cancer metabolism.
PLoS Comput. Biol., 2019

Integration of Single-Cell RNA-Sequencing Data into Flux Balance Cellular Automata.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

2018
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power.
J. Biomed. Informatics, 2018

Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes.
BMC Bioinform., 2018

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System.
Proceedings of the Artificial Life and Evolutionary Computation - 13th Italian Workshop, 2018

Global Sensitivity Analysis of Constraint-Based Metabolic Models.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2018

Modeling Spatio-Temporal Dynamics of Metabolic Networks with Cellular Automata and Constraint-Based Methods.
Proceedings of the Cellular Automata, 2018

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.
PLoS Comput. Biol., 2017

Dynamical regimes in non-ergodic random Boolean networks.
Nat. Comput., 2017

popFBA: tackling intratumour heterogeneity with Flux Balance Analysis.
Bioinform., 2017

2016
Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models.
Comput. Biol. Chem., 2016

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
BMC Bioinform., 2016

Constraint-Based Modeling and Simulation of Cell Populations.
Proceedings of the Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry, 2016

Linking Alterations in Metabolic Fluxes with Shifts in Metabolite Levels by Means of Kinetic Modeling.
Proceedings of the Advances in Artificial Life, Evolutionary Computation, and Systems Chemistry, 2016

COSYS: A Computational Infrastructure for Systems Biology.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2016

Constraining Mechanism Based Simulations to Identify Ensembles of Parametrizations to Characterize Metabolic Features.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2016

2014
A stochastic model of catalytic reaction networks in protocells.
Nat. Comput., 2014

An ensemble evolutionary constraint-based approach to understand the emergence of metabolic phenotypes.
Nat. Comput., 2014

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model.
Proceedings of the Advances in Artificial Life and Evolutionary Computation, 2014

On RAF Sets and Autocatalytic Cycles in Random Reaction Networks.
Proceedings of the Advances in Artificial Life and Evolutionary Computation, 2014

2013
A model of protocell based on the introduction of a semi-permeable membrane in a stochastic model of catalytic reaction networks.
Proceedings of the Proceedings Wivace 2013, 2013

Recent developments in research on catalytic reaction networks.
Proceedings of the Proceedings Wivace 2013, 2013

An ensemble approach to the study of the emergence of metabolic and proliferative disorders via Flux Balance Analysis.
Proceedings of the Proceedings Wivace 2013, 2013

Parameter sensitivity analysis of stochastic models: Application to catalytic reaction networks.
Comput. Biol. Chem., 2013

The role of backward reactions in a stochastic model of catalytic reaction networks.
Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life, 2013

2011
Dynamical Properties of a Boolean Model of Gene Regulatory Network with Memory.
J. Comput. Biol., 2011

Model Identification Using Correlation-Based Inference and Transfer Entropy Estimation.
Proceedings of the UKSim 5th European Symposium on Computer Modeling and Simulation, 2011

2010
Information Transfer among Coupled Random Boolean Networks.
Proceedings of the Cellular Automata, 2010

2008
The Diffusion of Perturbations in a Model of Coupled Random Boolean Networks.
Proceedings of the Cellular Automata, 2008


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