Marco Antoniotti

71 papers A* 2B 2C 2Misc 2Journal 39Unranked 21

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Phylogenetic analysis of TET2 gene variants in Pakistani acute myeloid Leukemia patients. Briefings Bioinform. Mawada Elmagboul Abdalla Abakar, Mehad Almagboul Abdalla Abaker, Marco Antoniotti, Alex Graudenzi
2024	J	`jnl`	Scalable integration of multiomic single-cell data using generative adversarial networks. Bioinform. Valentina Giansanti, Francesca Giannese, Oronza A. Botrugno, Giorgia Gandolfi, Chiara Balestrieri, Marco Antoniotti, Giovanni Tonon, Davide Cittaro
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	J	`jnl`	LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti, Marco Antoniotti, Alex Graudenzi
2023	J	`jnl`	Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2022	J	`jnl`	J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinform. Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi
2022	J	`jnl`	LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. J. Comput. Sci. Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi
2021	J	`jnl`	EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi
2021	—	`conf`	Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. ANNSIM Fabrizio Angaroni, Chiara Damiani, Giulia Ramunni, Marco Antoniotti
2021	J	`jnl`	VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza
2020	C	`conf`	A closed-loop optimization framework for personalized cancer therapy design. CIBCB Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi
2020	J	`jnl`	Investigating the Compositional Structure Of Deep Neural Networks. CoRR Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
2020	—	`conf`	Investigating the Compositional Structure of Deep Neural Networks. LOD (1) Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti
2020	B	`conf`	On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile
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	—	`conf`	Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti
2020	—	`conf`	Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point. ELS Marco Antoniotti
2020	J	`jnl`	Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp. CoRR Marco Antoniotti
2019	J	`jnl`	Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. J. Comput. Sci. Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
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	—	`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
2018	J	`jnl`	Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani
2018	—	`conf`	Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
2018	—	`conf`	Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani
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`	Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi
2017	J	`jnl`	Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models. CoRR Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti
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	J	`jnl`	Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti
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	C	`conf`	Parallel implementation of efficient search schemes for the inference of cancer progression models. CIBCB Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti
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`	CLAZY: Lazy Calling for Common Lisp. CoRR Marco Antoniotti
2014	J	`jnl`	Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. J. Clin. Bioinform. Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti
2014	—	`conf`	Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti
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`	A Model of Colonic Crypts using SBML Spatial. WIVACE Daniele Ramazzotti, Carlo Maj, Marco Antoniotti
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	J	`jnl`	Characterizing the computational power of energy-based P systems. Int. J. Comput. Math. Artiom Alhazov, Marco Antoniotti, Alberto Leporati
2013	B	`conf`	Copy-Number Alterations for Tumor Progression Inference. AIME Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti
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	—	`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
2012	—	`conf`	Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. BIOINFORMATICS Italo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Francesco Rocco, Giancarlo Albo, André M. Deelder, Yuri E. M. van der Burgt, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri
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`	Mutual Information Optimization for Mass Spectra Data Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. Italo Zoppis, Erica Gianazza, Massimiliano Borsani, Clizia Chinello, Veronica Mainini, Carmen Galbusera, Carlo Ferrarese, Gloria Galimberti, Alessandro Sorbi, Barbara Borroni, Fulvio Magni, Marco Antoniotti, Giancarlo Mauri
2012	—	`conf`	Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination. ICCABS Italo Zoppis, Massimiliano Borsani, Erica Gianazza, Clizia Chinello, Giancarlo Albo, Francesco Rocco, André M. Deelder, Yuri E. M. van der Burgt, Marco Antoniotti, Fulvio Magni, Giancarlo Mauri
2012	—	`ed.`	Proceedings of ELS 2012 - 5th European Lisp Symposium, Zadar, Croatia, April 30 - May 1, 2012. ELS Marco Antoniotti
2012	J	`jnl`	Self-Stabilization in Membrane Systems. Comput. Sci. J. Moldova Marco Antoniotti, Rudolf Freund, Alberto Leporati, Giancarlo Mauri
2011	J	`jnl`	A comparison of machine learning techniques for survival prediction in breast cancer. BioData Min. Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Marco Antoniotti, Paolo Provero, Mario Giacobini
2010	J	`jnl`	An application of kernel methods to gene cluster temporal meta-analysis. Comput. Oper. Res. Marco Antoniotti, Marco Carreras, Antonella Farinaccio, Giancarlo Mauri, Daniele Merico, Italo Zoppis
2010	J	`jnl`	An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. J. Biomed. Informatics Gianluca Colombo, Daniele Merico, Giorgio Boncoraglio, Flavio De Paoli, John Ellul, Giuseppe Frisoni, Zoltán Nagy, Aad van der Lugt, István Vassányi, Marco Antoniotti
2010	—	`conf`	Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. EvoBIO Leonardo Vanneschi, Antonella Farinaccio, Mario Giacobini, Giancarlo Mauri, Marco Antoniotti, Paolo Provero
2009	J	`jnl`	Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge. Knowl. Eng. Rev. Gianluca Colombo, Daniele Merico, Zoltán Nagy, Flavio De Paoli, Marco Antoniotti, Giancarlo Mauri
2008	—	`conf`	CLAZY: Lazy Calling for Common Lisp. ELS Marco Antoniotti
2007	—	`conf`	Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. ISBRA Italo Zoppis, Daniele Merico, Marco Antoniotti, Bud Mishra, Giancarlo Mauri
2007	—	`conf`	Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. KES (3) Daniele Merico, Italo Zoppis, Marco Antoniotti, Giancarlo Mauri
2007	J	`jnl`	From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra
2007	—	`conf`	Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic. Description Logics Gianluca Colombo, Daniele Merico, Marco Antoniotti, Flavio De Paoli, Giancarlo Mauri
2005	A*	`conf`	Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. CAV Carla Piazza, Marco Antoniotti, Venkatesh Mysore, Alberto Policriti, Franz Winkler, Bud Mishra
2004	J	`jnl`	Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. Theor. Comput. Sci. Marco Antoniotti, Carla Piazza, Alberto Policriti, Marta Simeoni, Bud Mishra
2003	Misc	`conf`	Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. Pacific Symposium on Biocomputing Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra
2003	—	`conf`	Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. CMSB Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, Marta Simeoni
2002	Misc	`conf`	XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. HiPC Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra
2001	—	`conf`	Embedded system design specification: merging reactive control and data computation. CDC Marco Antoniotti, Alberto Ferrari, Luciano Lavagno, Alberto L. Sangiovanni-Vincentelli, Ellen Sentovich
1997	—	`conf`	SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation. DSL Marco Antoniotti, Aleks Göllü
1995	A*	`conf`	Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. ICRA Marco Antoniotti, Bud Mishra
1995	—	`—`	Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the "Control-D" System. Marco Antoniotti