Giulio Caravagna

Publication Activity (10 Years)

Years Active: 2008-2023
Publications (10 Years): 18

Top Topics

Gaussian Process

Gene Regulatory

Top Venues

Publications

Lucrezia Patruno, Salvatore Milite, Riccardo Bergamin, Nicola Calonaci, Alberto d'Onofrio, Fabio Anselmi, Marco Antoniotti, Alex Graudenzi, Giulio Caravagna
A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing. PLoS Comput. Biol. 19 (11) (2023)
Fabio Anselmi, Luca Manzoni, Alberto d'Onofrio, Alex Rodriguez, Giulio Caravagna, Luca Bortolussi, Francesca Cairoli
Data Symmetries and Learning in Fully Connected Neural Networks. IEEE Access 11 (2023)
Giulia Barbati, Luca Bortolussi, Giulio Caravagna
Data Science and Artificial Intelligence for Life Sciences at the University of Trieste. Ital-IA (2023)
Fabrizio Angaroni, Kevin Chen, Chiara Damiani, Giulio Caravagna, Alex Graudenzi, Daniele Ramazzotti
PMCE: efficient inference of expressive models of cancer evolution with high prognostic power. Bioinform. 38 (3) (2022)
Giulio Caravagna, Daniele Ramazzotti
Learning the structure of Bayesian Networks via the bootstrap. Neurocomputing 448 (2021)
Davide Maspero, Chiara Damiani, Marco Antoniotti, Alex Graudenzi, Marzia Di Filippo, Marco Vanoni, Giulio Caravagna, Riccardo Colombo, Daniele Ramazzotti, Dario Pescini
The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System. Fundam. Informaticae 171 (1-4) (2020)
Giulio Caravagna, Guido Sanguinetti, Trevor A. Graham, Andrea Sottoriva
The MOBSTER R package for tumour subclonal deconvolution from bulk DNA whole-genome sequencing data. BMC Bioinform. 21 (1) (2020)
Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data. BMC Bioinform. 20 (1) (2019)
Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models. CIBB (2019)
Ketevan Chkhaidze, Timon Heide, Benjamin Werner, Marc J. Williams, Weini Huang, Giulio Caravagna, Trevor A. Graham, Andrea Sottoriva
Spatially constrained tumour growth affects the patterns of clonal selection and neutral drift in cancer genomic data. PLoS Comput. Biol. 15 (7) (2019)
Giulio Caravagna, Daniele Ramazzotti, Guido Sanguinetti
On learning the structure of Bayesian Networks and submodular function maximization. CoRR (2017)
Lucrezia Patruno, Edoardo Galimberti, Daniele Ramazzotti, Giulio Caravagna, Luca De Sano, Marco Antoniotti, Alex Graudenzi
cyTRON and cyTRON/JS: two Cytoscape-based applications for the inference of cancer evolution models. CoRR (2017)
Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR (2017)
Alex Graudenzi, Giulio Caravagna, Iuliana M. Bocicor, Claudia Cava, Marco Antoniotti, Giancarlo Mauri
Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Min. Bioinform. 15 (1) (2016)
Luca De Sano, Giulio Caravagna, Daniele Ramazzotti, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Marco Antoniotti
TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinform. 32 (12) (2016)
Marco Antoniotti, Giulio Caravagna, Luca De Sano, Alex Graudenzi, Giancarlo Mauri, Bud Mishra, Daniele Ramazzotti
Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R J. 8 (2) (2016)
Giulio Caravagna, Luca Bortolussi, Guido Sanguinetti
Matching Models Across Abstraction Levels with Gaussian Processes. CMSB (2016)
Andrea Paroni, Alex Graudenzi, Giulio Caravagna, Chiara Damiani, Giancarlo Mauri, Marco Antoniotti
CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinform. 17 (2016)
Giulio Caravagna, Luca De Sano, Marco Antoniotti
Automatising the analysis of stochastic biochemical time-series. BMC Bioinform. 16 (S-9) (2015)
Daniele Ramazzotti, Giulio Caravagna, Loes Olde Loohuis, Alex Graudenzi, Ilya Korsunsky, Giancarlo Mauri, Marco Antoniotti, Bud Mishra
CAPRI: efficient inference of cancer progression models from cross-sectional data. Bioinform. 31 (18) (2015)
Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri
Preface. Nat. Comput. 13 (3) (2014)
Ilya Korsunsky, Daniele Ramazzotti, Giulio Caravagna, Bud Mishra
Inference of Cancer Progression Models with Biological Noise. CoRR (2014)
Sebastiano de Franciscis, Giulio Caravagna, Alberto d'Onofrio
Bounded noises as a natural tool to model extrinsic fluctuations in biomolecular networks. Nat. Comput. 13 (3) (2014)
Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri
Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Inf. Comput. 236 (2014)
Andrea Bracciali, Giulio Caravagna, Amjad Ullah
Survival vs. revenue: modelling and reasoning on population dynamics (WIP). SpringSim (TMS-DEVS) (2013)
Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giovanni De Matteis
Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts. WIVACE (2013)
Marco Antoniotti, Gary D. Bader, Giulio Caravagna, Silvia Crippa, Alex Graudenzi, Giancarlo Mauri
GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process. Bioinform. 29 (4) (2013)
Giulio Caravagna, Alberto d'Onofrio, Giancarlo Mauri
NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP). SpringSim (TMS-DEVS) (2013)
Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re
GPU-powered Simulation Methodologies for Biological Systems. WIVACE (2013)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Simone Tini
Foundational aspects of multiscale modeling of biological systems with process algebras. Theor. Comput. Sci. 431 (2012)
Giulio Caravagna, Gabriele Costa, Giovanni Pardini
Lazy Security Controllers. STM (2012)
Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio
Fine-tuning anti-tumor immunotherapies via stochastic simulations. BMC Bioinform. 13 (S-4) (2012)
Giulio Caravagna, Gabriele Costa, Luca Wiegand, Giovanni Pardini
Lazy Monitoring for Distributed Computing Environments. IMIS (2012)
Giulio Caravagna, Jane Hillston
Bio-PEPAd: A non-Markovian extension of Bio-PEPA. Theor. Comput. Sci. 419 (2012)
Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio
Effects of delayed immune-response in tumor immune-system interplay HSB (2012)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach. Trans. Comp. Sys. Biology 13 (2011)
Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini, Simone Tini
Aspects of multiscale modelling in a process algebra for biological systems MeCBIC (2010)
Giulio Caravagna, Jane Hillston
Modeling biological systems with delays in Bio-PEPA MeCBIC (2010)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
P Systems with Endosomes. Int. J. Comput. Commun. Control 4 (3) (2009)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
An intermediate language for the stochastic simulation of biological systems. Theor. Comput. Sci. 410 (33-34) (2009)
Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini
On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems COMPMOD (2009)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo
An Intermediate Language for the Simulation of Biological Systems. Electron. Notes Theor. Comput. Sci. 194 (3) (2008)
Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini
The Calculus of Looping Sequences. SFM (2008)