Marco Antoniotti

Orcid: 0000-0002-2823-6838

According to our database1, Marco Antoniotti authored at least 63 papers between 1995 and 2023.

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Links

On csauthors.net:

Bibliography

2023
LACE 2.0: an interactive R tool for the inference and visualization of longitudinal cancer evolution.
BMC Bioinform., December, 2023

A Bayesian method to infer copy number clones from single-cell RNA and ATAC sequencing.
PLoS Comput. Biol., November, 2023

Unity is strength: Improving the detection of adversarial examples with ensemble approaches.
Neurocomputing, October, 2023

2022
LACE: Inference of cancer evolution models from longitudinal single-cell sequencing data.
J. Comput. Sci., 2022

J-SPACE: a Julia package for the simulation of spatial models of cancer evolution and of sequencing experiments.
BMC Bioinform., 2022

2021
VERSO: A comprehensive framework for the inference of robust phylogenies and the quantification of intra-host genomic diversity of viral samples.
Patterns, 2021

EAD: an ensemble approach to detect adversarial examples from the hidden features of deep neural networks.
CoRR, 2021

Optimal Control of a Discrete Time Stochastic Model of an Epidemic Spreading in Arbitrary Networks.
Proceedings of the Annual Modeling and Simulation Conference, 2021

2020
The Influence of Nutrients Diffusion on a Metabolism-driven Model of a Multi-cellular System.
Fundam. Informaticae, 2020

Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp.
CoRR, 2020

Investigating the Compositional Structure of Deep Neural Networks.
Proceedings of the Machine Learning, Optimization, and Data Science, 2020

On the automatic calibration of fully analogical spiking neuromorphic chips.
Proceedings of the 2020 International Joint Conference on Neural Networks, 2020

Why You Cannot (Yet) Write an "Interval Arithmetic" Library in Common Lisp ... or: Hammering Some Sense into : ieee-floating-point.
Proceedings of the 13th European Lisp Symposium (ELS 2020), 2020

A closed-loop optimization framework for personalized cancer therapy design.
Proceedings of the IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2020

Understanding Deep Learning with Activation Pattern Diagrams.
Proceedings of the Italian Workshop on Explainable Artificial Intelligence co-located with 19th International Conference of the Italian Association for Artificial Intelligence, 2020

2019
Efficient computational strategies to learn the structure of probabilistic graphical models of cumulative phenomena.
J. Comput. Sci., 2019

Learning mutational graphs of individual tumour evolution from single-cell and multi-region sequencing data.
BMC Bioinform., 2019

cyTRON and cyTRON/JS: Two Cytoscape-Based Applications for the Inference of Cancer Evolution Models.
Proceedings of the Computational Intelligence Methods for Bioinformatics and Biostatistics, 2019

2018
Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power.
J. Biomed. Informatics, 2018

Synchronization Effects in a Metabolism-Driven Model of Multi-cellular System.
Proceedings of the Artificial Life and Evolutionary Computation - 13th Italian Workshop, 2018

Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena.
Proceedings of the Computational Science - ICCS 2018, 2018

2017
Learning mutational graphs of individual tumor evolution from multi-sample sequencing data.
CoRR, 2017

Learning the Probabilistic Structure of Cumulative Phenomena with Suppes-Bayes Causal Networks.
CoRR, 2017

2016
Design of the TRONCO BioConductor Package for TRanslational ONCOlogy.
R J., 2016

Ordering cancer mutational profiles of cross-sectional copy number alterations.
Int. J. Data Min. Bioinform., 2016

Modeling cumulative biological phenomena with Suppes-Bayes causal networks.
CoRR, 2016

CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks.
BMC Bioinform., 2016

TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data.
Bioinform., 2016

Parallel implementation of efficient search schemes for the inference of cancer progression models.
Proceedings of the 2016 IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, 2016

2015
Automatising the analysis of stochastic biochemical time-series.
BMC Bioinform., 2015

CAPRI: efficient inference of cancer progression models from cross-sectional data.
Bioinform., 2015

2014
Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference.
J. Clin. Bioinform., 2014

Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays.
Inf. Comput., 2014

Investigating the Role of Network Topology and Dynamical Regimes on the Dynamics of a Cell Differentiation Model.
Proceedings of the Advances in Artificial Life and Evolutionary Computation, 2014

2013
Characterizing the computational power of energy-based P systems.
Int. J. Comput. Math., 2013

A Model of Colonic Crypts using SBML Spatial.
Proceedings of the Proceedings Wivace 2013, 2013

Analysis of the spatial and dynamical properties of a multiscale model of intestinal crypts.
Proceedings of the Proceedings Wivace 2013, 2013

GeStoDifferent: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process.
Bioinform., 2013

Copy-Number Alterations for Tumor Progression Inference.
Proceedings of the Artificial Intelligence in Medicine, 2013

2012
Mutual Information Optimization for Mass Spectra Data Alignment.
IEEE ACM Trans. Comput. Biol. Bioinform., 2012

Self-Stabilization in Membrane Systems.
Comput. Sci. J. Moldova, 2012

Effects of delayed immune-response in tumor immune-system interplay
Proceedings of the Proceedings First International Workshop on Hybrid Systems and Biology, 2012

Poster: Characterization of distinguishing regions for Renal Cell Carcinoma discrimination.
Proceedings of the IEEE 2nd International Conference on Computational Advances in Bio and Medical Sciences, 2012

Analysis of Correlation Structures in Renal Cell Carcinoma Patient Data.
Proceedings of the BIOINFORMATICS 2012 - Proceedings of the International Conference on Bioinformatics Models, Methods and Algorithms, Vilamoura, Algarve, Portugal, 1, 2012

2011
A comparison of machine learning techniques for survival prediction in breast cancer.
BioData Min., 2011

2010
An ontological modeling approach to cerebrovascular disease studies: The NEUROWEB case.
J. Biomed. Informatics, 2010

An application of kernel methods to gene cluster temporal meta-analysis.
Comput. Oper. Res., 2010

Identification of Individualized Feature Combinations for Survival Prediction in Breast Cancer: A Comparison of Machine Learning Techniques.
Proceedings of the Evolutionary Computation, 2010

2009
Ontological modeling at a domain interface: bridging clinical and biomolecular knowledge.
Knowl. Eng. Rev., 2009

2008
CLAZY: Lazy Calling for Common Lisp.
Proceedings of the 1st European Lisp Symposium (ELS'08), 2008

2007
From Bytes to Bedside: Data Integration and Computational Biology for Translational Cancer Research.
PLoS Comput. Biol., 2007

Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters.
Proceedings of the Knowledge-Based Intelligent Information and Engineering Systems, 2007

Discovering Relations Among GO-Annotated Clusters by Graph Kernel Methods.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

Ontological Modelling for Neurovascular Disease Study: Issues in the Adoption of Description Logic.
Proceedings of the 2007 International Workshop on Description Logics (DL2007), 2007

2005
Algorithmic Algebraic Model Checking I: Challenges from Systems Biology.
Proceedings of the Computer Aided Verification, 17th International Conference, 2005

2004
Taming the complexity of biochemical models through bisimulation and collapsing: theory and practice.
Theor. Comput. Sci., 2004

2003
Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Modeling Cellular Behavior with Hybrid Automata: Bisimulation and Collapsing.
Proceedings of the Computational Methods in Systems Biology, First International Workshop, 2003

2002
XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior.
Proceedings of the High Performance Computing, 2002

2001
Embedded system design specification: merging reactive control and data computation.
Proceedings of the 40th IEEE Conference on Decision and Control, 2001

1997
SHIFT and SMART-AHS: A Language for Hybrid System Engineering Modeling and Simulation.
Proceedings of the Conference on Domain-Specific Languages, 1997

1995
Synthesis and Verification of Controllers for Robotics and Manufacturing Devices with Temporal Logic and the "Control-D" System.
PhD thesis, 1995

Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers.
Proceedings of the 1995 International Conference on Robotics and Automation, 1995


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