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ORCIDGiulio Caravagna
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Books and Theses
- 2011
[b1]Giulio Caravagna:
Formal Modeling and Simulation of Biological Systems with Delays. University of Pisa, Italy, 2011
Journal Articles
- 2023
- [j24]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: 47282-47290 (2023) - [j23]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) - 2022
- [j22]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): 754-762 (2022) - 2021
- [j21]Giulio Caravagna, Daniele Ramazzotti:
Learning the structure of Bayesian Networks via the bootstrap. Neurocomputing 448: 48-59 (2021) - 2020
- [j20]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): 531 (2020) - [j19]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): 279-295 (2020) - 2019
- [j18]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): 210:1-210:13 (2019) - [j17]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) - 2016
- [j16]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): 1911-1913 (2016) - [j15]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: 64 (2016) - [j14]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): 59-83 (2016) - [j13]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): 39 (2016) - 2015
- [j12]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): 3016-3026 (2015) - [j11]Giulio Caravagna, Luca De Sano, Marco Antoniotti:
Automatising the analysis of stochastic biochemical time-series. BMC Bioinform. 16(S-9): S8 (2015) - 2014
- [j10]Giulio Caravagna, Alberto d'Onofrio, Marco Antoniotti, Giancarlo Mauri:
Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Inf. Comput. 236: 19-34 (2014) - [j9]Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri:
Preface. Nat. Comput. 13(3): 285-286 (2014) - [j8]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): 297-307 (2014) - 2013
- [j7]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): 513-514 (2013) - 2012
- [j6]Giulio Caravagna, Roberto Barbuti, Alberto d'Onofrio:
Fine-tuning anti-tumor immunotherapies via stochastic simulations. BMC Bioinform. 13(S-4): S8 (2012) - [j5]Giulio Caravagna, Jane Hillston:
Bio-PEPAd: A non-Markovian extension of Bio-PEPA. Theor. Comput. Sci. 419: 26-49 (2012) - [j4]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: 96-116 (2012) - 2011
- [j3]Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo:
Delay Stochastic Simulation of Biological Systems: A Purely Delayed Approach. Trans. Comp. Sys. Biology 13: 61-84 (2011) - 2009
- [j2]Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo:
P Systems with Endosomes. Int. J. Comput. Commun. Control 4(3): 214-223 (2009) - [j1]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): 3085-3109 (2009)
Conference and Workshop Papers
- 2023
- [c15]Giulia Barbati, Luca Bortolussi, Giulio Caravagna:
Data Science and Artificial Intelligence for Life Sciences at the University of Trieste. Ital-IA 2023: 124-127 - 2019
- [c14]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: 13-18 - 2016
- [c13]Giulio Caravagna, Luca Bortolussi, Guido Sanguinetti:
Matching Models Across Abstraction Levels with Gaussian Processes. CMSB 2016: 49-66 - 2013
- [c12]Giulio Caravagna, Alberto d'Onofrio, Giancarlo Mauri:
NoisySim: exact simulation of stochastic chemically reacting systems with extrinsic bounded noises (WIP). SpringSim (TMS-DEVS) 2013: 12 - [c11]Andrea Bracciali, Giulio Caravagna, Amjad Ullah:
Survival vs. revenue: modelling and reasoning on population dynamics (WIP). SpringSim (TMS-DEVS) 2013: 29 - [c10]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: 79-82 - [c9]Daniela Besozzi, Giulio Caravagna, Paolo Cazzaniga, Marco S. Nobile, Dario Pescini, Alessandro Re:
GPU-powered Simulation Methodologies for Biological Systems. WIVACE 2013: 87-91 - 2012
- [c8]Giulio Caravagna, Gabriele Costa, Luca Wiegand, Giovanni Pardini:
Lazy Monitoring for Distributed Computing Environments. IMIS 2012: 259-265 - [c7]Giulio Caravagna, Gabriele Costa, Giovanni Pardini:
Lazy Security Controllers. STM 2012: 33-48 - [c6]Giulio Caravagna, Alex Graudenzi, Marco Antoniotti, Giancarlo Mauri, Alberto d'Onofrio:
Effects of delayed immune-response in tumor immune-system interplay. HSB 2012: 106-121 - 2010
- [c5]Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini, Simone Tini:
Aspects of multiscale modelling in a process algebra for biological systems. MeCBIC 2010: 54-69 - [c4]Giulio Caravagna, Jane Hillston:
Modeling biological systems with delays in Bio-PEPA. MeCBIC 2010: 85-101 - 2009
- [c3]Roberto Barbuti, Giulio Caravagna, Paolo Milazzo, Andrea Maggiolo-Schettini:
On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems. COMPMOD 2009: 17-29 - 2008
- [c2]Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini:
The Calculus of Looping Sequences. SFM 2008: 387-423 - 2007
- [c1]Roberto Barbuti, Giulio Caravagna, Andrea Maggiolo-Schettini, Paolo Milazzo:
An Intermediate Language for the Simulation of Biological Systems. FBTC@CONCUR 2007: 19-34
Editorship
- 2017
- [e2]Andrea Bracciali, Giulio Caravagna, David Gilbert, Roberto Tagliaferri:
Computational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Stirling, UK, September 1-3, 2016, Revised Selected Papers. Lecture Notes in Computer Science 10477, Springer 2017, ISBN 978-3-319-67833-7 [contents] - 2013
- [e1]Alex Graudenzi, Giulio Caravagna, Giancarlo Mauri, Marco Antoniotti:
Proceedings Wivace 2013 - Italian Workshop on Artificial Life and Evolutionary Computation, Milan, Italy, July 1-2, 2013. EPTCS 130, 2013 [contents]
Informal and Other Publications
- 2017
- [i4]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 abs/1705.03067 (2017) - [i3]Giulio Caravagna, Daniele Ramazzotti, Guido Sanguinetti:
On learning the structure of Bayesian Networks and submodular function maximization. CoRR abs/1706.02386 (2017) - [i2]Daniele Ramazzotti, Alex Graudenzi, Luca De Sano, Marco Antoniotti, Giulio Caravagna:
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data. CoRR abs/1709.01076 (2017) - 2014
- [i1]Ilya Korsunsky, Daniele Ramazzotti, Giulio Caravagna, Bud Mishra:
Inference of Cancer Progression Models with Biological Noise. CoRR abs/1408.6032 (2014)
Coauthor Index
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