An Intermediate Language for the Simulation of Biological Systems. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo (FBTC@CONCUR, 2007)

The Calculus of Looping Sequences. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo; Giovanni Pardini (SFM, 2008)

On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems - Roberto Barbuti; Giulio Caravagna; Paolo Milazzo; Andrea Maggiolo-Schettini (COMPMOD, 2009)

P Systems with Endosomes. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo (Int. J. Comput. Commun. Control, 2009)

An intermediate language for the stochastic simulation of biological systems. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo (Theor. Comput. Sci., 2009)

Aspects of multiscale modelling in a process algebra for biological systems - Roberto Barbuti; Giulio Caravagna; Paolo Milazzo; Andrea Maggiolo-Schettini; Simone Tini (MeCBIC, 2010)

Modeling biological systems with delays in Bio-PEPA - Giulio Caravagna; Jane Hillston (MeCBIC, 2010)

Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo (Trans. Comp. Sys. Biology, 2011)

Formal Modeling and Simulation of Biological Systems with Delays. - Giulio Caravagna (2011)

Lazy Monitoring for Distributed Computing Environments. - Giulio Caravagna; Gabriele Costa 001; Luca Wiegand; Giovanni Pardini (IMIS, 2012)

Lazy Security Controllers. - Giulio Caravagna; Gabriele Costa 001; Giovanni Pardini (STM, 2012)

Fine-tuning anti-tumor immunotherapies via stochastic simulations. - Giulio Caravagna; Roberto Barbuti; Alberto d'Onofrio (BMC Bioinform., 2012)

Effects of delayed immune-response in tumor immune-system interplay - Giulio Caravagna; Alex Graudenzi; Marco Antoniotti; Giancarlo Mauri; Alberto d'Onofrio (HSB, 2012)

Foundational aspects of multiscale modeling of biological systems with process algebras. - Roberto Barbuti; Giulio Caravagna; Andrea Maggiolo-Schettini; Paolo Milazzo; Simone Tini (Theor. Comput. Sci., 2012)

Bio-PEPAd: A non-Markovian extension of Bio-PEPA. - Giulio Caravagna; Jane Hillston (Theor. Comput. Sci., 2012)

Survival vs. revenue: modelling and reasoning on population dynamics (WIP). - Andrea Bracciali; Giulio Caravagna; Amjad Ullah (SpringSim (TMS-DEVS), 2013)

NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP). - Giulio Caravagna; Alberto d'Onofrio; Giancarlo Mauri (SpringSim (TMS-DEVS), 2013)

GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. - Marco Antoniotti; Gary D. Bader; Giulio Caravagna; Silvia Crippa; Alex Graudenzi; Giancarlo Mauri (Bioinform., 2013)

GPU-powered Simulation Methodologies for Biological Systems. - Daniela Besozzi; Giulio Caravagna; Paolo Cazzaniga; Marco S. Nobile; Dario Pescini; Alessandro Re (WIVACE, 2013)

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. - Giulio Caravagna; Alex Graudenzi; Marco Antoniotti; Giovanni De Matteis (WIVACE, 2013)

Inference of Cancer Progression Models with Biological Noise. - Ilya Korsunsky; Daniele Ramazzotti; Giulio Caravagna; Bud Mishra (CoRR, 2014)

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. - Giulio Caravagna; Alberto d'Onofrio; Marco Antoniotti; Giancarlo Mauri (Inf. Comput., 2014)

Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. - Sebastiano de Franciscis; Giulio Caravagna; Alberto d'Onofrio (Nat. Comput., 2014)

Preface. - Alex Graudenzi; Giulio Caravagna; Giancarlo Mauri (Nat. Comput., 2014)

CAPRI: efficient inference of cancer progression models from cross-sectional data. - Daniele Ramazzotti; Giulio Caravagna; Loes Olde Loohuis; Alex Graudenzi; Ilya Korsunsky; Giancarlo Mauri; Marco Antoniotti; Bud Mishra (Bioinform., 2015)

Automatising the analysis of stochastic biochemical time-series. - Giulio Caravagna; Luca De Sano; Marco Antoniotti (BMC Bioinform., 2015)

Matching Models Across Abstraction Levels with Gaussian Processes. - Giulio Caravagna; Luca Bortolussi; Guido Sanguinetti (CMSB, 2016)

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. - Luca De Sano; Giulio Caravagna; Daniele Ramazzotti; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Marco Antoniotti (Bioinform., 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)

Ordering cancer mutational profiles of cross-sectional copy number alterations. - Alex Graudenzi; Giulio Caravagna; Iuliana M. Bocicor; Claudia Cava; Marco Antoniotti; Giancarlo Mauri (Int. J. Data Min. Bioinform., 2016)

Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. - Marco Antoniotti; Giulio Caravagna; Luca De Sano; Alex Graudenzi; Giancarlo Mauri; Bud Mishra; Daniele Ramazzotti (R J., 2016)

On learning the structure of Bayesian Networks and submodular function maximization. - Giulio Caravagna; Daniele Ramazzotti; Guido Sanguinetti (CoRR, 2017)

Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (CoRR, 2017)

cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. - Lucrezia Patruno; Edoardo Galimberti; Daniele Ramazzotti; Giulio Caravagna; Luca De Sano; Marco Antoniotti; Alex Graudenzi (CIBB, 2019)

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. - Daniele Ramazzotti; Alex Graudenzi; Luca De Sano; Marco Antoniotti; Giulio Caravagna (BMC Bioinform., 2019)

Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. - Ketevan Chkhaidze; Timon Heide; Benjamin Werner; Marc J. Williams; Weini Huang; Giulio Caravagna; Trevor A. Graham; Andrea Sottoriva (PLoS Comput. Biol., 2019)

The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. - Giulio Caravagna; Guido Sanguinetti; Trevor A. Graham; Andrea Sottoriva (BMC Bioinform., 2020)

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)

Learning the structure of Bayesian Networks via the bootstrap. - Giulio Caravagna; Daniele Ramazzotti (Neurocomputing, 2021)

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)

A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations. - Salvatore Milite; Riccardo Bergamin; Lucrezia Patruno; Nicola Calonaci; Giulio Caravagna (Bioinform., 2022)

Data Science and Artificial Intelligence for Life Sciences at the University of Trieste. - Giulia Barbati; Luca Bortolussi; Giulio Caravagna (Ital-IA, 2023)

Data Symmetries and Learning in Fully Connected Neural Networks. - Fabio Anselmi; Luca Manzoni; Alberto d'Onofrio; Alex Rodriguez; Giulio Caravagna; Luca Bortolussi; Francesca Cairoli (IEEE Access, 2023)

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. - Lucrezia Patruno; Salvatore Milite; Riccardo Bergamin; Nicola Calonaci; Alberto d'Onofrio; Fabio Anselmi; Marco Antoniotti; Alex Graudenzi; Giulio Caravagna (PLoS Comput. Biol., 2023)

Deep Learning-Informed Bayesian Model-Based Analysis to Estimate Superspreading Events in Epidemic Outbreaks. - Arianna Tasciotti; Federico Urban; Federica de Dea; Luca Bortolussi; Giulio Caravagna; Alberto d'Onofrio (IEEE Access, 2024)

Mixtures of Neural Cellular Automata: A Stochastic Framework for Growth Modelling and Self-Organization. - Salvatore Milite; Giulio Caravagna; Andrea Sottoriva (CoRR, 2025)