Giulio Caravagna

According to our database, Giulio Caravagna authored at least 43 papers between 2007 and 2023.

Collaborative distances:

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

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., November, 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

Data Science and Artificial Intelligence for Life Sciences at the University of Trieste.

Giulia Barbati, Luca Bortolussi, Giulio Caravagna

Proceedings of the Italia Intelligenza Artificiale, 2023

2022

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

2021

Learning the structure of Bayesian Networks via the bootstrap.

Giulio Caravagna, Daniele Ramazzotti

Neurocomputing, 2021

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

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

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

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

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

Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

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

On learning the structure of Bayesian Networks and submodular function maximization.

Giulio Caravagna, Daniele Ramazzotti, Guido Sanguinetti

CoRR, 2017

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

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

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

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

Matching Models Across Abstraction Levels with Gaussian Processes.

Giulio Caravagna, Luca Bortolussi, Guido Sanguinetti

Proceedings of the Computational Methods in Systems Biology, 2016

2015

Automatising the analysis of stochastic biochemical time-series.

Giulio Caravagna, Luca De Sano, Marco Antoniotti

BMC Bioinform., 2015

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

2014

Preface.

Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri

Nat. 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

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays.

Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri

Inf. Comput., 2014

Inference of Cancer Progression Models with Biological Noise.

Ilya Korsunsky, Daniele Ramazzotti, Giulio Caravagna, Bud Mishra

CoRR, 2014

2013

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts.

Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis

Proceedings of the Proceedings Wivace 2013, 2013

GPU-powered Simulation Methodologies for Biological Systems.

Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re

Proceedings of the Proceedings Wivace 2013, 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

NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP).

Giulio Caravagna, Alberto d'Onofrio, Giancarlo Mauri

Proceedings of the 2013 Spring Simulation Multiconference, SpringSim '13, 2013

Survival vs. revenue: modelling and reasoning on population dynamics (WIP).

Andrea Bracciali, Giulio Caravagna, Amjad Ullah

Proceedings of the 2013 Spring Simulation Multiconference, SpringSim '13, 2013

2012

Bio-PEPAd: A non-Markovian extension of Bio-PEPA.

Giulio Caravagna, Jane Hillston

Theor. Comput. Sci., 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

Effects of delayed immune-response in tumor immune-system interplay

Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio

Proceedings of the Proceedings First International Workshop on Hybrid Systems and Biology, 2012

Fine-tuning anti-tumor immunotherapies via stochastic simulations.

Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio

BMC Bioinform., 2012

Lazy Security Controllers.

Giulio Caravagna, Gabriele Costa, Giovanni Pardini

Proceedings of the Security and Trust Management - 8th International Workshop, 2012

Lazy Monitoring for Distributed Computing Environments.

Giulio Caravagna, Gabriele Costa, Luca Wiegand, Giovanni Pardini

Proceedings of the Sixth International Conference on Innovative Mobile and Internet Services in Ubiquitous Computing, 2012

2011

Formal Modeling and Simulation of Biological Systems with Delays.

Giulio Caravagna

PhD thesis, 2011

Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach.

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Trans. Comp. Sys. Biology, 2011

2010

Modeling biological systems with delays in Bio-PEPA

Giulio Caravagna, Jane Hillston

Proceedings of the Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi, 2010

Aspects of multiscale modelling in a process algebra for biological systems

Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini, Simone Tini

Proceedings of the Proceedings Fourth Workshop on Membrane Computing and Biologically Inspired Process Calculi, 2010

2009

An intermediate language for the stochastic simulation of biological systems.

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Theor. Comput. Sci., 2009

P Systems with Endosomes.

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Int. J. Comput. Commun. Control, 2009

On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems

Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini

Proceedings of the Proceedings Second International Workshop on Computational Models for Cell Processes, 2009

2008

The Calculus of Looping Sequences.

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini

Proceedings of the Formal Methods for Computational Systems Biology, 2008

2007

An Intermediate Language for the Simulation of Biological Systems.

Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo

Proceedings of the First Workshop "From Biology To Concurrency and back", 2007