Giulio Caravagna

51 papers Journal 33Unranked 15

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Extending differential gene expression testing to handle genome aneuploidy in cancer. PLoS Comput. Biol. Katsiaryna Davydzenka, Giulio Caravagna, Guido Sanguinetti
2026	J	`jnl`	The Interplay Between Non-Instantaneous Dynamics of mRNA and Bounded Extrinsic Stochastic Perturbations for a Self-Enhancing Transcription Factor. Entropy Lorenzo Cabriel, Giulio Caravagna, Sebastiano de Franciscis, Fabio Anselmi, Alberto d'Onofrio
2025	J	`jnl`	Mixtures of Neural Cellular Automata: A Stochastic Framework for Growth Modelling and Self-Organization. CoRR Salvatore Milite, Giulio Caravagna, Andrea Sottoriva
2024	J	`jnl`	Deep Learning-Informed Bayesian Model-Based Analysis to Estimate Superspreading Events in Epidemic Outbreaks. IEEE Access Arianna Tasciotti, Federico Urban, Federica De Dea, Luca Bortolussi, Giulio Caravagna, Alberto d'Onofrio
2023	J	`jnl`	A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput. Biol. Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna
2023	—	`conf`	Data Science and Artificial Intelligence for Life Sciences at the University of Trieste. Ital-IA Giulia Barbati, Luca Bortolussi, Giulio Caravagna
2023	J	`jnl`	Data Symmetries and Learning in Fully Connected Neural Networks. IEEE Access Fabio Anselmi, Luca Manzoni, Alberto d'Onofrio, Alex Rodriguez, Giulio Caravagna, Luca Bortolussi, Francesca Cairoli
2022	J	`jnl`	A Bayesian method to cluster single-cell RNA sequencing data using copy number alterations. Bioinform. Salvatore Milite, Riccardo Bergamin, Lucrezia Patruno, Nicola Calonaci, Giulio Caravagna
2022	J	`jnl`	PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti
2021	J	`jnl`	Learning the structure of Bayesian Networks via the bootstrap. Neurocomputing Giulio Caravagna, Daniele Ramazzotti
2020	J	`jnl`	The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
2020	J	`jnl`	The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. BMC Bioinform. Giulio Caravagna, Guido Sanguinetti, Trevor A. Graham, Andrea Sottoriva
2019	J	`jnl`	Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
2019	J	`jnl`	Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. PLoS Comput. Biol. Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Trevor A. Graham, Andrea Sottoriva
2019	—	`conf`	cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. CIBB Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
2017	—	`ed.`	Computational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Stirling, UK, September 1-3, 2016, Revised Selected Papers CIBB Andrea Bracciali, Giulio Caravagna, David Gilbert, Roberto Tagliaferri
2017	J	`jnl`	Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
2017	J	`jnl`	On learning the structure of Bayesian Networks and submodular function maximization. CoRR Giulio Caravagna, Daniele Ramazzotti, Guido Sanguinetti
2017	J	`jnl`	cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. CoRR Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
2016	J	`jnl`	CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
2016	J	`jnl`	Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R J. Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti
2016	—	`conf`	Matching Models Across Abstraction Levels with Gaussian Processes. CMSB Giulio Caravagna, Luca Bortolussi, Guido Sanguinetti
2016	J	`jnl`	Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Min. Bioinform. Alex Graudenzi, Giulio Caravagna, Iuliana M. Bocicor, Claudia Cava, Marco Antoniotti, Giancarlo Mauri
2016	J	`jnl`	TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinform. Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti
2015	J	`jnl`	Automatising the analysis of stochastic biochemical time-series. BMC Bioinform. Giulio Caravagna, Luca De Sano, Marco Antoniotti
2015	J	`jnl`	CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinform. Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra
2014	J	`jnl`	Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. Nat. Comput. Sebastiano de Franciscis, Giulio Caravagna, Alberto d'Onofrio
2014	J	`jnl`	Inference of Cancer Progression Models with Biological Noise. CoRR Ilya Korsunsky, Daniele Ramazzotti, Giulio Caravagna, Bud Mishra
2014	J	`jnl`	Preface. Nat. Comput. Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri
2014	J	`jnl`	Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Inf. Comput. Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri
2013	—	`conf`	Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis
2013	—	`conf`	GPU-powered Simulation Methodologies for Biological Systems. WIVACE Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re
2013	J	`jnl`	GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
2013	—	`conf`	NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP). SpringSim (TMS-DEVS) Giulio Caravagna, Alberto d'Onofrio, Giancarlo Mauri
2013	—	`ed.`	Proceedings Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation, Milan, Italy, July 1-2, 2013. WIVACE Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, Marco Antoniotti
2013	—	`conf`	Survival vs. revenue: modelling and reasoning on population dynamics (WIP). SpringSim (TMS-DEVS) Andrea Bracciali, Giulio Caravagna, Amjad Ullah
2012	J	`jnl`	Bio-PEPAd: A non-Markovian extension of Bio-PEPA. Theor. Comput. Sci. Giulio Caravagna, Jane Hillston
2012	—	`conf`	Effects of delayed immune-response in tumor immune-system interplay HSB Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio
2012	J	`jnl`	Fine-tuning anti-tumor immunotherapies via stochastic simulations. BMC Bioinform. Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio
2012	J	`jnl`	Foundational aspects of multiscale modeling of biological systems with process algebras. Theor. Comput. Sci. Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Simone Tini
2012	—	`conf`	Lazy Monitoring for Distributed Computing Environments. IMIS Giulio Caravagna, Gabriele Costa, Luca Wiegand, Giovanni Pardini
2012	—	`conf`	Lazy Security Controllers. STM Giulio Caravagna, Gabriele Costa, Giovanni Pardini
2011	J	`jnl`	Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach. Trans. Comp. Sys. Biology Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
2011	—	`—`	Formal Modeling and Simulation of Biological Systems with Delays. Giulio Caravagna
2010	—	`conf`	Aspects of multiscale modelling in a process algebra for biological systems MeCBIC Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini, Simone Tini
2010	—	`conf`	Modeling biological systems with delays in Bio-PEPA MeCBIC Giulio Caravagna, Jane Hillston
2009	J	`jnl`	An intermediate language for the stochastic simulation of biological systems. Theor. Comput. Sci. Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
2009	—	`conf`	On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems COMPMOD Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini
2009	J	`jnl`	P Systems with Endosomes. Int. J. Comput. Commun. Control Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
2008	—	`conf`	The Calculus of Looping Sequences. SFM Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini
2007	—	`conf`	An Intermediate Language for the Simulation of Biological Systems. FBTC@CONCUR Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo