Simone Marini - RankMe

72 papers B 5Journal 36Unranked 30

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Leveraging large language models to predict antibiotic resistance in Bioinform. Conrad Testagrose, Sakshi Pandey, Mohammadali Serajian, Simone Marini, Mattia Prosperi, Christina Boucher
2025	—	`conf`	Predicting Pneumococcal Meningitis from Demographics and Early AMR Signals. BCB Michael Aaron G. Sy, Garrett Ellward, Daniel M. Czyz, Vidhu Kariyawasam, Panayiotis V. Benos, Simone Marini
2025	J	`jnl`	SARITA: a large language model for generating the S1 subunit of the SARS-CoV-2 spike protein. Briefings Bioinform. Simone Rancati, Giovanna Nicora, Laura Bergomi, Tommaso Mario Buonocore, Daniel M. Czyz, Enea Parimbelli, Riccardo Bellazzi, Marco Salemi, Mattia Prosperi, Simone Marini
2025	J	`jnl`	Underwater Mediterranean image analysis based on the compute continuum paradigm. Future Gener. Comput. Syst. Michele Ferrari, Daniele D'Agostino, Jacopo Aguzzi, Simone Marini
2024	—	`conf`	An Average-Case Efficient Two-Stage Algorithm for Enumerating All Longest Common Substrings of Minimum Length $k$ Between Genome Pairs. ICHI Mattia Prosperi, Simone Marini, Christina Boucher
2024	J	`jnl`	Automated species classification and counting by deep-sea mobile crawler platforms using YOLO. Ecol. Informatics Luciano Ortenzi, Jacopo Aguzzi, Corrado Costa, Simone Marini, Daniele D'Agostino, Laurenz Thomsen, Fabio C. De Leo, Paulo V. Correa, Damianos Chatzievangelou
2024	J	`jnl`	Forecasting dominance of SARS-CoV-2 lineages by anomaly detection using deep AutoEncoders. Briefings Bioinform. Simone Rancati, Giovanna Nicora, Mattia Prosperi, Riccardo Bellazzi, Marco Salemi, Simone Marini
2024	—	`conf`	Learning on Forecasting HIV Epidemic Based on Individuals' Contact Networks. BIOSTEC (2) Chaoyue Sun, Yiyang Liu, Christina Parisi, Rebecca Fisk-Hoffman, Marco Salemi, Ruogu Fang, Brandi Danforth, Mattia Prosperi, Simone Marini
2024	—	`conf`	Prediction of A. Baumannii Amikacin Resistance in Clinical Metagenomics. MIE Michael Aaron G. Sy, Mattia Prosperi, Mohammadali Serajian, Christina Boucher, Panayotis Takis Benos, Simone Marini
2024	J	`jnl`	Scalable Bioinform. Mohammadali Serajian, Simone Marini, Jarno N. Alanko, Noelle R. Noyes, Mattia Prosperi, Christina Boucher
2024	—	`conf`	Sequencing Efforts and Epidemiological Trends: Analyzing SARS-CoV-2 Dynamics Across European Nations. BIBM Simone Rancati, Daniele Pala, Simone Marini, Marco Salemi, Riccardo Bellazzi, Giovanna Nicora
2023	J	`jnl`	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. Sensors Vanesa López-Vázquez, José Manuel López-Guede, Simone Marini, Emanuela Fanelli, Espen Johnsen, Jacopo Aguzzi
2023	J	`jnl`	MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Nucleic Acids Res. 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
2023	—	`conf`	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. CDPD Inyoung Jun, Scott A. Cohen, Sarah E. Ser, Simone Marini, Robert J. Lucero, Jiang Bian, Mattia Prosperi
2022	J	`jnl`	Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. Artif. Intell. Medicine Mattia Prosperi, Christina Boucher, Jiang Bian, Simone Marini
2022	—	`conf`	Dynamic Prediction of Non-Neutral SARS-Cov-2 Variants Using Incremental Machine Learning. MIE Giovanna Nicora, Simone Marini, Marco Salemi, Riccardo Bellazzi
2022	—	`conf`	Identification of Social and Racial Disparities in Risk of HIV Infection in Florida using Causal AI Methods. BIBM Mattia Prosperi, Jie Xu, Jingchuan Serena Guo, Jiang Bian, Wei-Han William Chen, Shantrel Canidate, Simone Marini, Mo Wang
2022	J	`jnl`	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. CoRR Inyoung Jun, Simone Marini, Christina Boucher, J. Glenn Morris, Jiang Bian, Mattia Prosperi
2022	J	`jnl`	Optimizing viral genome subsampling by genetic diversity and temporal distribution (TARDiS) for phylogenetics. Bioinform. Simone Marini, Carla Mavian, Alberto Riva, Mattia Prosperi, Marco Salemi, Brittany Rife Magalis
2022	J	`jnl`	Towards routine employment of computational tools for antimicrobial resistance determination via high-throughput sequencing. Briefings Bioinform. Simone Marini, Rodrigo A. Mora, Christina Boucher, Noelle Robertson Noyes, Mattia Prosperi
2022	—	`conf`	Transmission cluster characteristics of global, regional, and lineage-specific SARS-CoV-2 phylogenies. BIBM Mattia Prosperi, Brittany Rife Magalis, Simone Marini, Marco Salemi
2021	J	`jnl`	Assessing putative bias in prediction of anti-microbial resistance from real-world genotyping data under explicit causal assumptions. CoRR Mattia Prosperi, Simone Marini, Christina Boucher, Jiang Bian
2021	J	`jnl`	Fast and exact quantification of motif occurrences in biological sequences. BMC Bioinform. Mattia Prosperi, Simone Marini, Christina Boucher
2021	—	`conf`	KARGA: Multi-platform Toolkit for k-mer-based Antibiotic Resistance Gene Analysis of High-throughput Sequencing Data. BHI Mattia Prosperi, Simone Marini
2021	J	`jnl`	Research Trends and Future Perspectives in Marine Biomimicking Robotics. Sensors Jacopo Aguzzi, Corrado Costa, Marcello Calisti, Fabrizio Vecchi, Lewis Dartnell, Valerio Funari, Peter Weiss, Kathrin Nowak, Sergio Stefanni, Damianos Chatzievangelou, Roberto Danovaro, Simone Marini, Helena Gomes
2020	J	`jnl`	A Flexible Autonomous Robotic Observatory Infrastructure for Bentho-Pelagic Monitoring. Sensors 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, Henning Wehde, Guosong Zhang
2020	J	`jnl`	An Automated Pipeline for Image Processing and Data Treatment to Track Activity Rhythms of Paragorgia arborea in Relation to Hydrographic Conditions. Sensors 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
2020	J	`jnl`	The Hierarchic Treatment of Marine Ecological Information from Spatial Networks of Benthic Platforms. Sensors Jacopo Aguzzi, Damianos Chatzievangelou, Marco Francescangeli, Simone Marini, Federico Bonofiglio, Joaquín del Río, Roberto Danovaro
2020	J	`jnl`	Towards Naples Ecological REsearch for Augmented Observatories (NEREA): The NEREA-Fix Module, a Stand-Alone Platform for Long-Term Deep-Sea Ecosystem Monitoring. Sensors Emanuela Fanelli, Jacopo Aguzzi, Simone Marini, Joaquín del Río, Marc Nogueras, Simonepietro Canese, Sergio Stefanni, Roberto Danovaro, Fabio Conversano
2020	J	`jnl`	Video Image Enhancement and Machine Learning Pipeline for Underwater Animal Detection and Classification at Cabled Observatories. Sensors Vanesa López-Vázquez, José Manuel López-Guede, Simone Marini, Emanuela Fanelli, Espen Johnsen, Jacopo Aguzzi
2019	B	`conf`	A Semi-supervised Learning Approach for Pan-Cancer Somatic Genomic Variant Classification. AIME Giovanna Nicora, Simone Marini, Ivan Limongelli, Ettore Rizzo, Stefano Montoli, Francesca Floriana Tricomi, Riccardo Bellazzi
2019	J	`jnl`	Protease target prediction via matrix factorization. Bioinform. Simone Marini, Francesca Vitali, Sara Rampazzi, Andrea Demartini, Tatsuya Akutsu
2019	J	`jnl`	Toward more accurate prediction of caspase cleavage sites: a comprehensive review of current methods, tools and features. Briefings Bioinform. Yu Bao, Simone Marini, Takeyuki Tamura, Mayumi Kamada, Shingo Maegawa, Hiroshi Hosokawa, Jiangning Song, Tatsuya Akutsu
2019	B	`conf`	Underwater Fish Detection with Weak Multi-Domain Supervision. IJCNN Dmitry A. Konovalov, Alzayat Saleh, Michael Bradley, Mangalam Sankupellay, Simone Marini, Marcus Sheaves
2019	J	`jnl`	Underwater Fish Detection with Weak Multi-Domain Supervision. CoRR Dmitry A. Konovalov, Alzayat Saleh, Michael Bradley, Mangalam Sankupellay, Simone Marini, Marcus Sheaves
2018	J	`jnl`	Patient similarity for precision medicine: A systematic review. J. Biomed. Informatics Enea Parimbelli, Simone Marini, Lucia Sacchi, Riccardo Bellazzi
2017	J	`jnl`	Dscam1 web server: online prediction of Dscam1 self- and hetero-affinity. Bioinform. Simone Marini, Nelson Nazzicari, Filippo Biscarini, Guang-Zhong Wang
2017	J	`jnl`	MTopGO: a tool for module identification in PPI Networks. PeerJ Prepr. Danila Vella, Simone Marini, Francesca Vitali, Riccardo Bellazzi
2016	—	`conf`	Learning T2D Evolving Complexity from EMR and Administrative Data by Means of Continuous Time Bayesian Networks. HEALTHINF Simone Marini, Arianna Dagliati, Lucia Sacchi, Riccardo Bellazzi
2016	J	`jnl`	Looking inside the Ocean: Toward an Autonomous Imaging System for Monitoring Gelatinous Zooplankton. Sensors Lorenzo Corgnati, Simone Marini, Luca Mazzei, Ennio Ottaviani, Stefano Aliani, Alessandra Conversi, Annalisa Griffa
2015	J	`jnl`	A Dynamic Bayesian Network model for long-term simulation of clinical complications in type 1 diabetes. J. Biomed. Informatics Simone Marini, Emanuele Trifoglio, Nicola Barbarini, Francesco Sambo, Barbara Di Camillo, Alberto Malovini, Marco Manfrini, Claudio Cobelli, Riccardo Bellazzi
2015	B	`conf`	A Genomic Data Fusion Framework to Exploit Rare and Common Variants for Association Discovery. AIME Simone Marini, Ivan Limongelli, Ettore Rizzo, Tan Da, Riccardo Bellazzi
2015	J	`jnl`	PaPI: pseudo amino acid composition to score human protein-coding variants. BMC Bioinform. Ivan Limongelli, Simone Marini, Riccardo Bellazzi
2015	B	`conf`	Preclinical Tests for Cerebral Stroke. ASONAM 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
2014	—	`conf`	Automated Gelatinous Zooplankton Acquisition and Recognition. CVAUI@ICPR Lorenzo Corgnati, Luca Mazzei, Simone Marini, Stefano Aliani, Alessandra Conversi, Annalisa Griffa, Bruno Isoppo, Ennio Ottaviani
2014	—	`conf`	Automated Video Imaging System for Counting Deep-Sea Bioluminescence Organisms Events. CVAUI@ICPR Luca Mazzei, Simone Marini, Jessica Craig, Jacopo Aguzzi, Emanuela Fanelli, Imants G. Priede
2012	—	`conf`	Understanding Zooplankton Long Term Variability through Genetic Programming. EvoBIO Simone Marini, Alessandra Conversi
2011	—	`conf`	An Ontology-Driven Search Module for Accessing Chronic Pathology Literature. OTM Workshops Stephan Kiefer, Jochen Rauch, Riccardo Albertoni, Marco Attene, Franca Giannini, Simone Marini, Luc Schneider, Carlos Mesquita, Xin Xing
2011	J	`jnl`	Part-in-whole 3D shape matching and docking. Vis. Comput. Marco Attene, Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2011	J	`jnl`	Spectral feature selection for shape characterization and classification. Vis. Comput. Simone Marini, Giuseppe Patanè, Michela Spagnuolo, Bianca Falcidieno
2011	J	`jnl`	The CHRONIOUS Ontology-Driven Search Tool: Enabling Access to Focused and Up-to-Date Healthcare Literature CoRR Stephan Kiefer, Jochen Rauch, Riccardo Albertoni, Marco Attene, Franca Giannini, Simone Marini, Luc Schneider, Carlos Mesquita, Xin Xing, Michael Lawo
2010	—	`conf`	Feature Selection for Enhanced Spectral Shape Comparison . 3DOR@Eurographics Simone Marini, Giuseppe Patanè, Michela Spagnuolo, Bianca Falcidieno
2010	—	`conf`	The Fast Reject Schema for Part-in-Whole 3D Shape Matching. 3DOR@Eurographics Marco Attene, Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2010	J	`jnl`	Thesaurus-based 3D Object Retrieval with Part-in-Whole Matching. Int. J. Comput. Vis. Alfredo Ferreira, Simone Marini, Marco Attene, Manuel J. Fonseca, Michela Spagnuolo, Joaquim A. Jorge, Bianca Falcidieno
2009	B	`conf`	A Critical Assessment of 2D and 3D Face Recognition Algorithms. AVSS Daniela Giorgi, Marco Attene, Giuseppe Patanè, Simone Marini, Corrado Pizzi, Silvia Biasotti, Michela Spagnuolo, Bianca Falcidieno, Marco Corvi, L. Usai, L. Roncarolo, Giovanni Garibotto
2009	—	`conf`	SHREC'09 Track: Structural Shape Retrieval on Watertight Models. 3DOR@Eurographics J. Hartveldt, Michela Spagnuolo, Apostolos Axenopoulos, Silvia Biasotti, Petros Daras, Helin Dutagaci, Takahiko Furuya, Afzal Godil, Xiaolan Li, Athanasios Mademlis, Simone Marini, Thibault Napoléon, Ryutarou Ohbuchi, Masaki Tezuka
2008	—	`conf`	SHape REtrieval contest 2008: Classification of watertight models. Shape Modeling International Daniela Giorgi, Simone Marini
2007	—	`conf`	3D Classification Via Structural Prototypes. SAMT Silvia Biasotti, Daniela Giorgi, Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2007	—	`conf`	3D Shape Description and Matching Based on Properties of Real Functions. Eurographics (Tutorials) Silvia Biasotti, Bianca Falcidieno, Patrizio Frosini, Daniela Giorgi, Claudia Landi, Simone Marini, Giuseppe Patanè, Michela Spagnuolo
2007	J	`jnl`	Structural Shape Prototypes for the Automatic Classification of 3D Objects. IEEE Computer Graphics and Applications Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2006	—	`conf`	A Comparison Framework for 3D Object Classification Methods. MRCS Silvia Biasotti, Daniela Giorgi, Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2006	—	`conf`	Partial Matching by Structural Descriptors. Content-Based Retrieval Simone Marini, Silvia Biasotti, Bianca Falcidieno
2006	—	`conf`	Structural Descriptors for 3D Shapes. Content-Based Retrieval Michela Spagnuolo, Silvia Biasotti, Bianca Falcidieno, Simone Marini
2006	J	`jnl`	Sub-part correspondence by structural descriptors of 3D shapes. Comput. Aided Des. Silvia Biasotti, Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2006	—	`conf`	Sub-part correspondence using structure and geometry. Eurographics Italian Chapter Conference Silvia Biasotti, Simone Marini
2005	J	`jnl`	3D object comparison based on shape descriptors. Int. J. Comput. Appl. Technol. Silvia Biasotti, Simone Marini
2005	—	`—`	3D shape similarity through structural descriptors. Simone Marini
2005	—	`conf`	From Exact to Approximate Maximum Common Subgraph. GbRPR Simone Marini, Michela Spagnuolo, Bianca Falcidieno
2003	—	`conf`	3D Shape Matching through Topological Structures. DGCI Silvia Biasotti, Simone Marini, Michela Mortara, Giuseppe Patanè, Michela Spagnuolo, Bianca Falcidieno
2003	—	`conf`	An overview on properties and efficacy of topological skeletons in Shape Modelling. Shape Modeling International Silvia Biasotti, Simone Marini, Michela Mortara, Giuseppe Patanè
2000	—	`conf`	HEMASL: A Flexible Language to Specify Heterogeneous Agents. WOA Simone Marini, Maurizio Martelli, Viviana Mascardi, Floriano Zini
2000	—	`conf`	Specification of Heterogeneous Agent Architectures. ATAL Simone Marini, Maurizio Martelli, Viviana Mascardi, Floriano Zini