Specification of Heterogeneous Agent Architectures. - Simone Marini; Maurizio Martelli; Viviana Mascardi; Floriano Zini (ATAL, 2000)

HEMASL: A Flexible Language to Specify Heterogeneous Agents. - Simone Marini; Maurizio Martelli; Viviana Mascardi; Floriano Zini (WOA, 2000)

3D Shape Matching through Topological Structures. - Silvia Biasotti; Simone Marini; Michela Mortara; Giuseppe Patanè 001; Michela Spagnuolo; Bianca Falcidieno (DGCI, 2003)

An overview on properties and efficacy of topological skeletons in Shape Modelling. - Silvia Biasotti; Simone Marini; Michela Mortara; Giuseppe Patanè 001 (Shape Modeling International, 2003)

From Exact to Approximate Maximum Common Subgraph. - Simone Marini; Michela Spagnuolo; Bianca Falcidieno (GbRPR, 2005)

3D object comparison based on shape descriptors. - Silvia Biasotti; Simone Marini (Int. J. Comput. Appl. Technol., 2005)

3D shape similarity through structural descriptors. - Simone Marini (2005)

Partial Matching by Structural Descriptors. - Simone Marini; Silvia Biasotti; Bianca Falcidieno (Content-Based Retrieval, 2006)

Structural Descriptors for 3D Shapes. - Michela Spagnuolo; Silvia Biasotti; Bianca Falcidieno; Simone Marini (Content-Based Retrieval, 2006)

Sub-part correspondence using structure and geometry. - Silvia Biasotti; Simone Marini (Eurographics Italian Chapter Conference, 2006)

A Comparison Framework for 3D Object Classification Methods. - Silvia Biasotti; Daniela Giorgi; Simone Marini; Michela Spagnuolo; Bianca Falcidieno (MRCS, 2006)

Sub-part correspondence by structural descriptors of 3D shapes. - Silvia Biasotti; Simone Marini; Michela Spagnuolo; Bianca Falcidieno (Comput. Aided Des., 2006)

3D Shape Description and Matching Based on Properties of Real Functions. - Silvia Biasotti; Bianca Falcidieno; Patrizio Frosini; Daniela Giorgi; Claudia Landi 001; Simone Marini; Giuseppe Patanè 001; Michela Spagnuolo (Eurographics (Tutorials), 2007)

3D Classification Via Structural Prototypes. - Silvia Biasotti; Daniela Giorgi; Simone Marini; Michela Spagnuolo; Bianca Falcidieno (SAMT, 2007)

Structural Shape Prototypes for the Automatic Classification of 3D Objects. - Simone Marini; Michela Spagnuolo; Bianca Falcidieno (IEEE Computer Graphics and Applications, 2007)

SHape REtrieval contest 2008: Classification of watertight models. - Daniela Giorgi; Simone Marini (Shape Modeling International, 2008)

SHREC'09 Track: Structural Shape Retrieval on Watertight Models. - J. Hartveldt; Michela Spagnuolo; Apostolos Axenopoulos; Silvia Biasotti; Petros Daras; Helin Dutagaci; Takahiko Furuya; Afzal Godil; Xiaolan Li; Athanasios Mademlis; Simone Marini; Thibault Napoléon; et al. (3DOR@Eurographics, 2009)

A Critical Assessment of 2D and 3D Face Recognition Algorithms. - Daniela Giorgi; Marco Attene; Giuseppe Patanè 001; Simone Marini; Corrado Pizzi; Silvia Biasotti; Michela Spagnuolo; Bianca Falcidieno; Marco Corvi; L. Usai; L. Roncarolo; Giovanni Garibotto (AVSS, 2009)

The Fast Reject Schema for Part-in-Whole 3D Shape Matching. - Marco Attene; Simone Marini; Michela Spagnuolo; Bianca Falcidieno (3DOR@Eurographics, 2010)

Feature Selection for Enhanced Spectral Shape Comparison . - Simone Marini; Giuseppe Patanè 001; Michela Spagnuolo; Bianca Falcidieno (3DOR@Eurographics, 2010)

Thesaurus-based 3D Object Retrieval with Part-in-Whole Matching. - Alfredo Ferreira; Simone Marini; Marco Attene; Manuel J. Fonseca; Michela Spagnuolo; Joaquim A. Jorge; Bianca Falcidieno (Int. J. Comput. Vis., 2010)

An Ontology-Driven Search Module for Accessing Chronic Pathology Literature. - Stephan Kiefer; Jochen Rauch; Riccardo Albertoni; Marco Attene; Franca Giannini; Simone Marini; Luc Schneider; Carlos Mesquita; Xin Xing 001 (OTM Workshops, 2011)

The CHRONIOUS Ontology-Driven Search Tool: Enabling Access to Focused and Up-to-Date Healthcare Literature - Stephan Kiefer; Jochen Rauch; Riccardo Albertoni; Marco Attene; Franca Giannini; Simone Marini; Luc Schneider; Carlos Mesquita; Xin Xing 001; Michael Lawo (CoRR, 2011)

Part-in-whole 3D shape matching and docking. - Marco Attene; Simone Marini; Michela Spagnuolo; Bianca Falcidieno (Vis. Comput., 2011)

Spectral feature selection for shape characterization and classification. - Simone Marini; Giuseppe Patanè 001; Michela Spagnuolo; Bianca Falcidieno (Vis. Comput., 2011)

Understanding Zooplankton Long Term Variability through Genetic Programming. - Simone Marini; Alessandra Conversi (EvoBIO, 2012)

Automated Gelatinous Zooplankton Acquisition and Recognition. - Lorenzo Corgnati; Luca Mazzei; Simone Marini; Stefano Aliani; Alessandra Conversi; Annalisa Griffa; Bruno Isoppo; Ennio Ottaviani (CVAUI@ICPR, 2014)

Automated Video Imaging System for Counting Deep-Sea Bioluminescence Organisms Events. - Luca Mazzei; Simone Marini; Jessica Craig; Jacopo Aguzzi; Emanuela Fanelli; Imants G. Priede (CVAUI@ICPR, 2014)

A Genomic Data Fusion Framework to Exploit Rare and Common Variants for Association Discovery. - Simone Marini; Ivan Limongelli; Ettore Rizzo; Tan Da; Riccardo Bellazzi (AIME, 2015)

Preclinical Tests for Cerebral Stroke. - Maria Francesca Zini; Nadia Pisanti; E. Biasci; A. Podda; V. Mey; F. Piras; G. L. L'Abbate; Simone Marini; D. Fratta; S. Bonaretti; S. Trasciatti (ASONAM, 2015)

PaPI: pseudo amino acid composition to score human protein-coding variants. - Ivan Limongelli; Simone Marini; Riccardo Bellazzi (BMC Bioinform., 2015)

A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes. - Simone Marini; Emanuele Trifoglio; Nicola Barbarini; Francesco Sambo; Barbara Di Camillo; Alberto Malovini; Marco Manfrini; Claudio Cobelli; Riccardo Bellazzi (J. Biomed. Informatics, 2015)

Learning T2D Evolving Complexity from EMR and Administrative Data by Means of Continuous Time Bayesian Networks. - Simone Marini; Arianna Dagliati; Lucia Sacchi; Riccardo Bellazzi (HEALTHINF, 2016)

Looking inside the Ocean: Toward an Autonomous Imaging System for Monitoring Gelatinous Zooplankton. - Lorenzo Corgnati; Simone Marini; Luca Mazzei; Ennio Ottaviani; Stefano Aliani; Alessandra Conversi; Annalisa Griffa (Sensors, 2016)

Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity. - Simone Marini; Nelson Nazzicari; Filippo Biscarini; Guang-Zhong Wang (Bioinform., 2017)

MTopGO: a tool for module identification in PPI Networks. - Danila Vella; Simone Marini; Francesca Vitali; Riccardo Bellazzi (PeerJ Prepr., 2017)

Patient similarity for precision medicine: A systematic review. - Enea Parimbelli; Simone Marini; Lucia Sacchi; Riccardo Bellazzi (J. Biomed. Informatics, 2018)

A Semi-supervised Learning Approach for Pan-Cancer Somatic Genomic Variant Classification. - Giovanna Nicora; Simone Marini; Ivan Limongelli; Ettore Rizzo; Stefano Montoli; Francesca Floriana Tricomi; Riccardo Bellazzi (AIME, 2019)

Underwater Fish Detection with Weak Multi-Domain Supervision. - Dmitry A. Konovalov; Alzayat Saleh; Michael Bradley; Mangalam Sankupellay; Simone Marini; Marcus Sheaves (IJCNN, 2019)

Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. - Yu Bao; Simone Marini; Takeyuki Tamura; Mayumi Kamada; Shingo Maegawa; Hiroshi Hosokawa; Jiangning Song; Tatsuya Akutsu (Briefings Bioinform., 2019)

Protease target prediction via matrix factorization. - Simone Marini; Francesca Vitali; Sara Rampazzi; Andrea Demartini; Tatsuya Akutsu (Bioinform., 2019)

A Flexible Autonomous Robotic Observatory Infrastructure for Bentho-Pelagic Monitoring. - Jacopo Aguzzi; Jan Albiez; Sascha Flögel; Olav Rune Godø; Endre Grimsbø; Simone Marini; Olaf Pfannkuche; Erik Rodríguez; Laurenz Thomsen; Terje Torkelsen; Javier Valencia; Vanesa López-Vázquez; et al. (Sensors, 2020)

The Hierarchic Treatment of Marine Ecological Information from Spatial Networks of Benthic Platforms. - Jacopo Aguzzi; Damianos Chatzievangelou; Marco Francescangeli; Simone Marini; Federico Bonofiglio; Joaquín del Río; Roberto Danovaro (Sensors, 2020)

Towards Naples Ecological REsearch for Augmented Observatories (NEREA): The NEREA-Fix Module, a Stand-Alone Platform for Long-Term Deep-Sea Ecosystem Monitoring. - Emanuela Fanelli; Jacopo Aguzzi; Simone Marini; Joaquín del Río; Marc Nogueras; Simonepietro Canese; Sergio Stefanni; Roberto Danovaro; Fabio Conversano (Sensors, 2020)

Video Image Enhancement and Machine Learning Pipeline for Underwater Animal Detection and Classification at Cabled Observatories. - Vanesa López-Vázquez; José Manuel López-Guede; Simone Marini; Emanuela Fanelli; Espen Johnsen; Jacopo Aguzzi (Sensors, 2020)

An Automated Pipeline for Image Processing and Data Treatment to Track Activity Rhythms of Paragorgia arborea in Relation to Hydrographic Conditions. - Ander Zuazo; Jordi Grinyó; Vanesa López-Vázquez; Erik Rodríguez; Corrado Costa; Luciano Ortenzi; Sascha Flögel; Javier Valencia; Simone Marini; Guosong Zhang; Henning Wehde; Jacopo Aguzzi (Sensors, 2020)

KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. - Mattia Prosperi; Simone Marini (BHI, 2021)

Fast and exact quantification of motif occurrences in biological sequences. - Mattia Prosperi; Simone Marini; Christina Boucher 001 (BMC Bioinform., 2021)

Research Trends and Future Perspectives in Marine Biomimicking Robotics. - Jacopo Aguzzi; Corrado Costa; Marcello Calisti; Fabrizio Vecchi; Lewis Dartnell; Valerio Funari; Peter Weiss; Kathrin Nowak; Sergio Stefanni; Damianos Chatzievangelou; Roberto Danovaro; Simone Marini; et al. (Sensors, 2021)

Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. - Mattia Prosperi; Brittany Rife Magalis; Simone Marini; Marco Salemi (BIBM, 2022)

Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. - Mattia Prosperi; Jie Xu 012; Jingchuan Serena Guo; Jiang Bian 001; Wei-Han William Chen; Shantrel Canidate; Simone Marini; Mo Wang (BIBM, 2022)

Dynamic Prediction of Non-Neutral SARS-Cov-2 Variants Using Incremental Machine Learning. - Giovanna Nicora; Simone Marini; Marco Salemi; Riccardo Bellazzi (MIE, 2022)

Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. - Mattia Prosperi; Christina Boucher 001; Jiang Bian 001; Simone Marini (Artif. Intell. Medicine, 2022)

Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. - Simone Marini; Rodrigo A. Mora; Christina Boucher 001; Noelle Robertson Noyes; Mattia Prosperi (Briefings Bioinform., 2022)

Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. - Simone Marini; Carla Mavian; Alberto Riva; Mattia Prosperi; Marco Salemi; Brittany Rife Magalis (Bioinform., 2022)

Joint Application of the Target Trial Causal Framework and Machine Learning Modeling to Optimize Antibiotic Therapy: Use Case on Acute Bacterial Skin and Skin Structure Infections due to Methicillin-resistant Staphylococcus aureus. - Inyoung Jun; Simone Marini; Christina Boucher 001; J. Glenn Morris; Jiang Bian 001; Mattia Prosperi (CoRR, 2022)

Optimizing Dynamic Antibiotic Treatment Strategies against Invasive Methicillin-Resistant Staphylococcus Aureus Infections using Causal Survival Forests and G-Formula on Statewide Electronic Health Record Data. - Inyoung Jun; Scott A. Cohen; Sarah E. Ser; Simone Marini; Robert J. Lucero; Jiang Bian 001; Mattia Prosperi (CDPD, 2023)

Correction: Lopez-Vazquez et al. Video Image Enhancement and Machine Learning Pipeline for Underwater Animal Detection and Classification at Cabled Observatories. Sensors 2020, 20, 726. - Vanesa López-Vázquez; José Manuel López-Guede; Simone Marini; Emanuela Fanelli; Espen Johnsen; Jacopo Aguzzi (Sensors, 2023)

MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. - Nathalie Bonin; Enrique Doster; Hannah Worley; Lee J. Pinnell; Jonathan E. Bravo; Peter Ferm; Simone Marini; Mattia Prosperi; Noelle R. Noyes; Paul S. Morley; Christina Boucher 001 (Nucleic Acids Res., 2023)

Sequencing Efforts and Epidemiological Trends: Analyzing SARS-CoV-2 Dynamics Across European Nations. - Simone Rancati; Daniele Pala; Simone Marini; Marco Salemi; Riccardo Bellazzi; Giovanna Nicora (BIBM, 2024)

Learning on Forecasting HIV Epidemic Based on Individuals' Contact Networks. - Chaoyue Sun; Yiyang Liu; Christina Parisi; Rebecca Fisk-Hoffman; Marco Salemi; Ruogu Fang; Brandi Danforth; Mattia Prosperi; Simone Marini (BIOSTEC (2), 2024)

An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. - Mattia Prosperi; Simone Marini; Christina Boucher 001 (ICHI, 2024)

Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. - Michael Aaron G. Sy; Mattia Prosperi; Mohammadali Serajian; Christina Boucher 001; Panayotis Takis Benos; Simone Marini (MIE, 2024)

Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders. - Simone Rancati; Giovanna Nicora; Mattia Prosperi; Riccardo Bellazzi; Marco Salemi; Simone Marini (Briefings Bioinform., 2024)

Scalable de novo classification of antibiotic resistance of Mycobacterium tuberculosis. - Mohammadali Serajian; Simone Marini; Jarno N. Alanko; Noelle R. Noyes; Mattia Prosperi; Christina Boucher 001 (Bioinform., 2024)

Automated species classification and counting by deep-sea mobile crawler platforms using YOLO. - Luciano Ortenzi; Jacopo Aguzzi; Corrado Costa; Simone Marini; Daniele D'Agostino; Laurenz Thomsen; Fabio C. De Leo; Paulo V. Correa; Damianos Chatzievangelou (Ecol. Informatics, 2024)

SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein. - Simone Rancati; Giovanna Nicora; Laura Bergomi; Tommaso Mario Buonocore; Daniel M. Czyz; Enea Parimbelli; Riccardo Bellazzi; Marco Salemi; Mattia Prosperi; Simone Marini (Briefings Bioinform., 2025)

Underwater Mediterranean image analysis based on the compute continuum paradigm. - Michele Ferrari; Daniele D'Agostino; Jacopo Aguzzi; Simone Marini (Future Gener. Comput. Syst., 2025)