Davide Chiarugi

According to our database, Davide Chiarugi authored at least 23 papers between 2004 and 2023.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of four.

2023

Porting the Variant Calling Pipeline for NGS data in cloud-HPC environment.

Alberto Mulone, Sherine Awad, Davide Chiarugi, Marco Aldinucci

Proceedings of the 47th IEEE Annual Computers, Software, and Applications Conference, 2023

2022

A Neural Network Approach for the Analysis of Reproducible Ribo-Seq Profiles.

Giorgia Giacomini, Caterina Graziani, Veronica Lachi, Pietro Bongini, Niccolò Pancino, Monica Bianchini, Davide Chiarugi, Angelo Valleriani, Paolo Andreini

Algorithms, 2022

2016

A proof theoretic view of spatial and temporal dependencies in biochemical systems.

Carlos Olarte, Davide Chiarugi, Moreno Falaschi, Diana Hermith

Theor. Comput. Sci., 2016

2015

On the impact of discreteness and abstractions on modelling noise in gene regulatory networks.

Chiara Bodei, Luca Bortolussi, Davide Chiarugi, Maria Luisa Guerriero, Alberto Policriti, Alessandro Romanel

Comput. Biol. Chem., 2015

Single-molecule modeling of mRNA degradation by miRNA: Lessons from data.

Celine Sin, Davide Chiarugi, Angelo Valleriani

BMC Syst. Biol., 2015

A renewal model for the emergence of anomalous solute crowding in liposomes.

Paolo Paradisi, Paolo Allegrini, Davide Chiarugi

BMC Syst. Biol., 2015

Modelling non-Markovian dynamics in biochemical reactions.

Davide Chiarugi, Moreno Falaschi, Diana Hermith, Carlos Olarte, Luca Torella

BMC Syst. Biol., 2015

A Declarative View of Signaling Pathways.

Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi

Proceedings of the Programming Languages with Applications to Biology and Security, 2015

2014

Verification of Spatial and Temporal Modalities in Biochemical Systems.

Davide Chiarugi, Moreno Falaschi, Diana Hermith, Carlos Olarte

Proceedings of the 5th International Workshop on Static Analysis and Systems Biology, 2014

A Flat Process Calculus for Nested Membrane Interactions.

Chiara Bodei, Linda Brodo, Roberto Bruni, Davide Chiarugi

Sci. Ann. Comput. Sci., 2014

Biochemical Reactions as Renewal Processes: the case of mRNA Degradation.

Paolo Paradisi, Davide Chiarugi

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

A framework for modelling spatially dependent interactions of biological systems in CCP.

Davide Chiarugi, Moreno Falaschi, Diana Hermith, Carlos Olarte

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2014

2013

Stochastic modelling of non Markovian Dynamics in Biochemical Reactions.

Davide Chiarugi, Moreno Falaschi, Diana Hermith, Roberto Marangoni, Carlos Olarte

Proceedings of the International Work-Conference on Bioinformatics and Biomedical Engineering, 2013

2012

Simulating Signalling Pathways With BioWayS.

Davide Chiarugi, Moreno Falaschi, Diana Hermith, Michell Guzmán, Carlos Olarte

Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology, 2012

2011

Control Flow Analysis of Generalised Boolean Networks.

Chiara Bodei, Linda Brodo, Davide Chiarugi

Proceedings of the 2nd International Workshop on Static Analysis and Systems Biology, 2011

2010

A Taxonomy of Causality-Based Biological Properties

Chiara Bodei, Andrea Bracciali, Davide Chiarugi, Roberta Gori

Proceedings of the Proceedings Third Workshop From Biology To Concurrency and back, 2010

Compositional modelling of signalling pathways in timed concurrent constraint programming.

Davide Chiarugi, Moreno Falaschi, Carlos Olarte, Catuscia Palamidessi

Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology, 2010

2008

Control Flow Analysis for Brane Calculi.

Chiara Bodei, Andrea Bracciali, Davide Chiarugi

Proceedings of the Second International Meeting on Membrane Computing and Biologically Inspired Process Calculi, 2008

On deducing causality in metabolic networks.

Chiara Bodei, Andrea Bracciali, Davide Chiarugi

BMC Bioinform., 2008

Cells in Silico: A Holistic Approach.

Davide Chiarugi, Pierpaolo Degano, Jan Bert Van Klinken, Roberto Marangoni

Proceedings of the Formal Methods for Computational Systems Biology, 2008

2007

A Computational Approach to the Functional Screening of Genomes.

Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni

PLoS Comput. Biol., 2007

2006

Feedbacks and Oscillations in the Virtual Cell VICE.

Davide Chiarugi, M. Chinellato, Pierpaolo Degano, G. Lo Brutto, Roberto Marangoni

Proceedings of the Computational Methods in Systems Biology, International Conference, 2006

2004

VICE: A VIrtual CEll.

Davide Chiarugi, Michele Curti, Pierpaolo Degano, Roberto Marangoni

Proceedings of the Computational Methods in Systems Biology, International Conference, 2004