| 2020 | CIBCB | A closed-loop optimization framework for personalized cancer therapy design. | Fabrizio Angaroni, Mattia Pennati, Lucrezia Patruno, Davide Maspero, Marco Antoniotti, Alex Graudenzi |
| 2020 | IJCNN | On the automatic calibration of fully analogical spiking neuromorphic chips. | Daniele M. Papetti, Simone Spolaor, Daniela Besozzi, Paolo Cazzaniga, Marco Antoniotti, Marco S. Nobile |
| 2018 | ICCS | Structural Learning of Probabilistic Graphical Models of Cumulative Phenomena. | Daniele Ramazzotti, Marco S. Nobile, Marco Antoniotti, Alex Graudenzi |
| 2016 | CIBCB | Parallel implementation of efficient search schemes for the inference of cancer progression models. | Daniele Ramazzotti, Marco S. Nobile, Paolo Cazzaniga, Giancarlo Mauri, Marco Antoniotti |
| 2013 | AIME | Copy-Number Alterations for Tumor Progression Inference. | Claudia Cava, Italo Zoppis, Manuela Gariboldi, Isabella Castiglioni, Giancarlo Mauri, Marco Antoniotti |
| 2007 | KES | Evaluating Graph Kernel Methods for Relation Discovery in GO-Annotated Clusters. | Daniele Merico, Italo Zoppis, Marco Antoniotti, Giancarlo Mauri |
| 2005 | CAV | Algorithmic Algebraic Model Checking I: Challenges from Systems Biology. | Carla Piazza, Marco Antoniotti, Venkatesh Mysore, Alberto Policriti, Franz Winkler, Bud Mishra |
| 2003 | PSB | Foundations of a Query and Simulation System for the Modeling of Biochemical and Biological Processes. | Marco Antoniotti, F. Park, Alberto Policriti, Nadia Ugel, Bud Mishra |
| 2002 | HiPC | XS-systems: eXtended S-Systems and Algebraic Differential Automata for Modeling Cellular Behavior. | Marco Antoniotti, Alberto Policriti, Nadia Ugel, Bud Mishra |
| 1995 | ICRA | Descrete Events Models + Temporal Logic = Supervisory Controller: Automatic Synthesis of Locomotion Controllers. | Marco Antoniotti, Bud Mishra |