VICE: A VIrtual CEll. - Davide Chiarugi; Michele Curti; Pierpaolo Degano; Roberto Marangoni (CMSB, 2004)

Feedbacks and Oscillations in the Virtual Cell VICE. - Davide Chiarugi; M. Chinellato; Pierpaolo Degano; G. Lo Brutto; Roberto Marangoni (CMSB, 2006)

A Computational Approach to the Functional Screening of Genomes. - Davide Chiarugi; Pierpaolo Degano; Roberto Marangoni (PLoS Comput. Biol., 2007)

Cells in Silico: A Holistic Approach. - Davide Chiarugi; Pierpaolo Degano; Jan Bert Van Klinken; Roberto Marangoni (SFM, 2008)

On deducing causality in metabolic networks. - Chiara Bodei; Andrea Bracciali; Davide Chiarugi (BMC Bioinform., 2008)

Control Flow Analysis for Brane Calculi. - Chiara Bodei; Andrea Bracciali; Davide Chiarugi (MeCBIC, 2008)

Compositional modelling of signalling pathways in timed concurrent constraint programming. - Davide Chiarugi; Moreno Falaschi; Carlos Olarte; Catuscia Palamidessi (BCB, 2010)

A Taxonomy of Causality-Based Biological Properties - Chiara Bodei; Andrea Bracciali; Davide Chiarugi; Roberta Gori (FBTC, 2010)

Control Flow Analysis of Generalised Boolean Networks. - Chiara Bodei; Linda Brodo; Davide Chiarugi (SASB, 2011)

Simulating Signalling Pathways With BioWayS. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Michell Guzmán; Carlos Olarte (CS2Bio, 2012)

Stochastic modelling of non Markovian Dynamics in Biochemical Reactions. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Roberto Marangoni; Carlos Olarte (IWBBIO, 2013)

A framework for modelling spatially dependent interactions of biological systems in CCP. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Carlos Olarte (IWBBIO, 2014)

Biochemical Reactions as Renewal Processes: the case of mRNA Degradation. - Paolo Paradisi; Davide Chiarugi (IWBBIO, 2014)

A Flat Process Calculus for Nested Membrane Interactions. - Chiara Bodei; Linda Brodo; Roberto Bruni 001; Davide Chiarugi (Sci. Ann. Comput. Sci., 2014)

Verification of Spatial and Temporal Modalities in Biochemical Systems. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Carlos Olarte (SASB, 2014)

A Declarative View of Signaling Pathways. - Davide Chiarugi; Moreno Falaschi; Carlos Olarte; Catuscia Palamidessi (Programming Languages with Applications to Biology and Security, 2015)

Modelling non-Markovian dynamics in biochemical reactions. - Davide Chiarugi; Moreno Falaschi; Diana Hermith; Carlos Olarte; Luca Torella (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)

Single-molecule modeling of mRNA degradation by miRNA: Lessons from data. - Celine Sin; Davide Chiarugi; Angelo Valleriani (BMC Syst. Biol., 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)

A proof theoretic view of spatial and temporal dependencies in biochemical systems. - Carlos Olarte; Davide Chiarugi; Moreno Falaschi; Diana Hermith (Theor. Comput. Sci., 2016)

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)

Porting the Variant Calling Pipeline for NGS data in cloud-HPC environment. - Alberto Mulone; Sherine Awad; Davide Chiarugi; Marco Aldinucci (COMPSAC, 2023)