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2020 – today
- 2023
[j28]Gianluca Ascolani, Fabrizio Angaroni, Davide Maspero, Francesco Craighero, Narra Lakshmi Sai Bhavesh, Rocco Piazza, Chiara Damiani, Daniele Ramazzotti
, Marco Antoniotti, Alex Graudenzi:
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution. BMC Bioinform. 24(1): 99 (2023)- [j27]Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi:
Unity is strength: Improving the detection of adversarial examples with ensemble approaches. Neurocomputing 554: 126576 (2023) - [j26]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
- [j25]Fabrizio Angaroni, Alessandro Guidi, Gianluca Ascolani, Alberto d'Onofrio, Marco Antoniotti, Alex Graudenzi:
J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments. BMC Bioinform. 23(1): 269 (2022) - [j24]Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Gianluca Ascolani, Isabella Castiglioni, Rocco Piazza, Marco Antoniotti, Alex Graudenzi:
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data. J. Comput. Sci. 58: 101523 (2022) - 2021
- [j23]Daniele Ramazzotti, Fabrizio Angaroni, Davide Maspero, Carlo Gambacorti Passerini, Marco Antoniotti, Alex Graudenzi, Rocco Piazza:
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples. Patterns 2(3): 100212 (2021) - [c29]Fabrizio Angaroni, Chiara Damiani, Giulia Ramunni, Marco Antoniotti:
Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks. ANNSIM 2021: 1-12 - [i9]Francesco Craighero, Fabrizio Angaroni, Fabio Stella, Chiara Damiani, Marco Antoniotti, Alex Graudenzi:
EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks. CoRR abs/2111.12631 (2021) - 2020
- [j22]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) - [c28]Francesco Craighero, Alex Graudenzi, Fabrizio Angaroni, Fabio Stella, Marco Antoniotti:
Understanding Deep Learning with Activation Pattern Diagrams. XAI.it@AI*IA 2020: 119-126 - [c27]Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi:
A closed-loop optimization framework for personalized cancer therapy design. CIBCB 2020: 1-9 - [c26]Marco Antoniotti:
Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point. ELS 2020: 76-83 - [c25]Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile:
On the automatic calibration of fully analogical spiking neuromorphic chips. IJCNN 2020: 1-8 - [c24]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure of Deep Neural Networks. LOD (1) 2020: 322-334 - [i8]Francesco Craighero, Fabrizio Angaroni, Alex Graudenzi, Fabio Stella, Marco Antoniotti:
Investigating the Compositional Structure Of Deep Neural Networks. CoRR abs/2002.06967 (2020) - [i7]Marco Antoniotti:
Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp. CoRR abs/2003.03831 (2020)
2010 – 2019
- 2019
- [j21]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) - [j20]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena. J. Comput. Sci. 30: 1-10 (2019) - [c23]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 - 2018
- [j19]Alex Graudenzi, Davide Maspero, Marzia Di Filippo, Marco Gnugnoli, Claudio Isella, Giancarlo Mauri, Enzo Medico, Marco Antoniotti, Chiara Damiani:
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. Biomed. Informatics 87: 37-49 (2018) - [c22]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. ICCS (1) 2018: 678-693 - [c21]Davide Maspero, Alex Graudenzi, Satwinder Singh, Dario Pescini, Giancarlo Mauri, Marco Antoniotti, Chiara Damiani:
Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System. WIVACE 2018: 115-126 - 2017
- [i6]Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti:
Parallel Implementation of Efficient Search Schemes for the Inference of Cancer Progression Models. CoRR abs/1703.03038 (2017) - [i5]Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi:
Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks. CoRR abs/1703.03074 (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]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) - 2016
- [j18]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) - [j17]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) - [j16]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) - [j15]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) - [c20]Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti:
Parallel implementation of efficient search schemes for the inference of cancer progression models. CIBCB 2016: 1-6 - [i2]Daniele Ramazzotti, Alex Graudenzi, Marco Antoniotti:
Modeling cumulative biological phenomena with Suppes-Bayes causal networks. CoRR abs/1602.07857 (2016) - 2015
- [j14]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) - [j13]Giulio Caravagna, Luca De Sano, Marco Antoniotti:
Automatising the analysis of stochastic biochemical time-series. BMC Bioinform. 16(S-9): S8 (2015) - 2014
- [j12]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) - [j11]Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti:
Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. J. Clin. Bioinform. 4: 2 (2014) - [c19]Alex Graudenzi, Chiara Damiani, Andrea Paroni, Alessandro Filisetti, Marco Villani, Roberto Serra, Marco Antoniotti:
Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model. WIVACE 2014: 151-168 - [i1]Marco Antoniotti:
CLAZY: Lazy Calling for Common Lisp. CoRR abs/1412.1393 (2014) - 2013
- [j10]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) - [j9]Artiom Alhazov, Marco Antoniotti, Alberto Leporati:
Characterizing the computational power of energy-based P systems. Int. J. Comput. Math. 90(4): 789-800 (2013) - [c18]Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti:
Copy-Number Alterations for Tumor Progression Inference. AIME 2013: 104-109 - [c17]Daniele Ramazzotti, Carlo Maj, Marco Antoniotti:
A Model of Colonic Crypts using SBML Spatial. WIVACE 2013: 74-78 - [c16]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 - [e2]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] - 2012
- [j8]Marco Antoniotti, Rudolf Freund, Alberto Leporati, Giancarlo Mauri:
Self-Stabilization in Membrane Systems. Comput. Sci. J. Moldova 20(2): 133-146 (2012) - [j7]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:
Mutual Information Optimization for Mass Spectra Data Alignment. IEEE ACM Trans. Comput. Biol. Bioinform. 9(3): 934-939 (2012) - [c15]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:
Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data. BIOINFORMATICS 2012: 251-256 - [c14]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:
Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination. ICCABS 2012: 1 - [c13]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 - [e1]Marco Antoniotti:
Proceedings of ELS 2012 - 5th European Lisp Symposium, Zadar, Croatia, April 30 - May 1, 2012. ELSAA 2012 [contents] - 2011
- [j6]Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Marco Antoniotti, Paolo Provero, Mario Giacobini:
A comparison of machine learning techniques for survival prediction in breast cancer. BioData Min. 4: 12 (2011) - 2010
- [j5]Marco Antoniotti, Marco Carreras, Antonella Farinaccio, Giancarlo Mauri, Daniele Merico, Italo Zoppis:
An application of kernel methods to gene cluster temporal meta-analysis. Comput. Oper. Res. 37(8): 1361-1368 (2010) - [j4]Gianluca Colombo, Daniele Merico, Giorgio Boncoraglio, Flavio De Paoli, John Ellul, Giuseppe Frisoni, Zoltán Nagy, Aad van der Lugt, István Vassányi, Marco Antoniotti:
An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case. J. Biomed. Informatics 43(4): 469-484 (2010) - [c12]Leonardo Vanneschi, Antonella Farinaccio, Mario Giacobini, Giancarlo Mauri, Marco Antoniotti, Paolo Provero:
Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques. EvoBIO 2010: 110-121
2000 – 2009
- 2009
- [j3]Gianluca Colombo, Daniele Merico, Zoltán Nagy, Flavio De Paoli, Marco Antoniotti, Giancarlo Mauri:
Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge. Knowl. Eng. Rev. 24(3): 205-224 (2009) - 2008
- [c11]Marco Antoniotti:
CLAZY: Lazy Calling for Common Lisp. ELS 2008: 125-132 - 2007
- [j2]Jomol P. Mathew, Barry S. Taylor, Gary D. Bader, Saiju Pyarajan, Marco Antoniotti, Arul M. Chinnaiyan, Chris Sander, Steven J. Burakoff, Bud Mishra:
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research. PLoS Comput. Biol. 3(2) (2007) - [c10]Gianluca Colombo, Daniele Merico, Marco Antoniotti, Flavio De Paoli, Giancarlo Mauri:
Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic. Description Logics 2007 - [c9]Italo Zoppis, Daniele Merico, Marco Antoniotti, Bud Mishra, Giancarlo Mauri:
Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods. ISBRA 2007: 158-169 - [c8]Daniele Merico, Italo Zoppis, Marco Antoniotti, Giancarlo Mauri:
Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. KES (3) 2007: 892-900 - 2005
- [c7]Carla Piazza, Marco Antoniotti, Venkatesh Mysore, Alberto Policriti, Franz Winkler, Bud Mishra:
Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. CAV 2005: 5-19 - 2004
- [j1]Marco Antoniotti, Carla Piazza, Alberto Policriti, Marta Simeoni, Bud Mishra:
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice. Theor. Comput. Sci. 325(1): 45-67 (2004) - 2003
- [c6]Marco Antoniotti, Bhubaneswar Mishra, Carla Piazza, Alberto Policriti, Marta Simeoni:
Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing. CMSB 2003: 57-74 - [c5]Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra:
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. Pacific Symposium on Biocomputing 2003: 116-127 - 2002
- [c4]Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra:
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. HiPC 2002: 431-442 - 2001
- [c3]Marco Antoniotti, Alberto Ferrari, Luciano Lavagno, Alberto L. Sangiovanni-Vincentelli, Ellen Sentovich:
Embedded system design specification: merging reactive control and data computation. CDC 2001: 3302-3307
1990 – 1999
- 1997
- [c2]Marco Antoniotti, Aleks Göllü:
SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation. DSL 1997: 171-182 - 1995
- [b1]Marco Antoniotti:
Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the "Control-D" System. New York University, USA, 1995 - [c1]Marco Antoniotti, Bud Mishra:
Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. ICRA 1995: 1441-1446
Coauthor Index
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