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Books and Theses

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2023
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Vincenzo Manca, Vincenzo Bonnici:
Infogenomics - The Informational Analysis of Genomes. Springer 2023, ISBN 978-3-031-44500-2, pp. 1-281

Journal Articles

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2024
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Antonino Aparo, Vincenzo Bonnici, Simone Avesani, Luciano Cascione, Rosalba Giugno:
DiGAS: Differential gene allele spectrum as a descriptor in genetic studies. Comput. Biol. Medicine 179: 108924 (2024)
[j17]
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Vincenzo Bonnici, Roberto Grasso, Giovanni Micale, Antonio Di Maria, Dennis Shasha, Alfredo Pulvirenti, Rosalba Giugno:
ArcMatch: high-performance subgraph matching for labeled graphs by exploiting edge domains. Data Min. Knowl. Discov. 38(6): 3868-3921 (2024)
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Vincenzo Bonnici:
A Maximum Value for the Kullback-Leibler Divergence between Quantized Distributions. Inf. 15(9): 547 (2024)
2023
[j15]
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Vincenzo Bonnici, Claudia Mengoni, Manuel Mangoni, Giuditta Franco, Rosalba Giugno:
PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies. J. Biomed. Informatics 148: 104552 (2023)
2021
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Antonino Aparo, Pietro Sala, Vincenzo Bonnici, Rosalba Giugno:
TEDAR: Temporal dynamic signal detection of adverse reactions. Artif. Intell. Medicine 122: 102212 (2021)
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Vincenzo Bonnici, Emiliano Maresi, Rosalba Giugno:
Challenges in gene-oriented approaches for pangenome content discovery. Briefings Bioinform. 22(3) (2021)
[j12]
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Nicola Licheri, Vincenzo Bonnici, Marco Beccuti, Rosalba Giugno:
GRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases. BMC Bioinform. 22(1): 209 (2021)
[j11]
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Manuel Tognon, Vincenzo Bonnici, Erik Garrison, Rosalba Giugno, Luca Pinello:
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs. PLoS Comput. Biol. 17(9) (2021)
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Vincenzo Bonnici, Giuditta Franco, Vincenzo Manca:
Spectral concepts in genome informational analysis. Theor. Comput. Sci. 894: 23-30 (2021)
2018
[j9]
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Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno:
Correction to: cuRnet: an R package for graph traversing on GPU. BMC Bioinform. 19(1): 456:1 (2018)
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Vincenzo Bonnici, Federico Busato, Stefano Aldegheri, Murodzhon Akhmedov, Luciano Cascione, Alberto Arribas Carmena, Francesco Bertoni, Nicola Bombieri, Ivo Kwee, Rosalba Giugno:
cuRnet: an R package for graph traversing on GPU. BMC Bioinform. 19-S(10): 221-230 (2018)
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Vincenzo Bonnici, Giorgio De Caro, Giorgio Constantino, Sabino Liuni, Domenica D'Elia, Nicola Bombieri, Flavio Licciulli, Rosalba Giugno:
Arena-Idb: a platform to build human non-coding RNA interaction networks. BMC Bioinform. 19-S(10): 231-244 (2018)
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Vincenzo Bonnici, Vincenzo Manca:
An Informational Test for Random Finite Strings. Entropy 20(12): 934 (2018)
[j5]
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Francesco Russo, Sebastiano Di Bella, Federica Vannini, Gabriele Berti, Flavia Scoyni, Helen Cook, Alberto Santos, Giovanni Nigita, Vincenzo Bonnici, Alessandro Laganà, Filippo Geraci, Alfredo Pulvirenti, Rosalba Giugno, Federico De Masi, Kirstine Belling, Lars Juhl Jensen, Søren Brunak, Marco Pellegrini, Alfredo Ferro:
miRandola 2017: a curated knowledge base of non-invasive biomarkers. Nucleic Acids Res. 46(Database-Issue): D354-D359 (2018)
2017
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Vincenzo Bonnici, Rosalba Giugno:
On the Variable Ordering in Subgraph Isomorphism Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 14(1): 193-203 (2017)
2016
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Vincenzo Bonnici, Federico Busato, Giovanni Micale, Nicola Bombieri, Alfredo Pulvirenti, Rosalba Giugno:
APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks. Bioinform. 32(14): 2159-2166 (2016)
2015
[j2]
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Salvatore Alaimo, Vincenzo Bonnici, Damiano Cancemi, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti:
DT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference. BMC Syst. Biol. 9(S-3): S4 (2015)
2013
[j1]
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Vincenzo Bonnici, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha, Alfredo Ferro:
A subgraph isomorphism algorithm and its application to biochemical data. BMC Bioinform. 14(S-7): S13 (2013)

Conference and Workshop Papers

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2023
[c13]
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Simone Avesani, Vincenzo Bonnici, Simone Pernice, Marco Beccuti, Rosalba Giugno:
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. CIKM 2023: 5259-5262
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Vincenzo Bonnici, Vincenzo Arceri, Alessio Diana, Flavio Bertini, Eleonora Iotti, Alessia Levante, Valentina Bernini, Erasmo Neviani, Alessandro Dal Palù:
BIOCHAIN: towards a platform for securely sharing microbiological data. IDEAS 2023: 59-63
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Giacomo Boldini, Alessio Diana, Vincenzo Arceri, Vincenzo Bonnici, Roberto Bagnara:
A Machine Learning Approach for Source Code Similarity via Graph-Focused Features. LOD (1) 2023: 53-67
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Silvia Astorino, Vincenzo Bonnici, Giuditta Franco:
An Investigation to Test Spectral Segments as Bacterial Biomarkers. UCNC 2023: 1-16
2021
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Marco Beccuti, Vincenzo Bonnici, Rosalba Giugno:
MODIMO: Workshop on Multi-Omics Data Integration for Modelling Biological Systems. CIKM 2021: 4870-4871
[c8]
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Nicola Licheri, Elvio Amparone, Vincenzo Bonnici, Rosalba Giugno, Marco Beccuti:
An Entropy Heuristic to Optimize Decision Diagrams for Index-driven Search in Biological Graph Databases. CIKM Workshops 2021
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Vincenzo Bonnici, Andrea Cracco, Giuditta Franco:
A k-mer Based Sequence Similarity for Pangenomic Analyses. LOD 2021: 31-44
2019
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Vincenzo Bonnici, Simone Caligola, Giulia Fiorini, Luca Giudice, Rosalba Giugno:
LErNet: characterization of lncRNAs via context-aware network expansion and enrichment analysis. CIBCB 2019: 1-8
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Nicola Bombieri, Vincenzo Bonnici, Rosalba Giugno:
Parallel Searching on Biological Networks. PDP 2019: 307-314
2018
[c4]
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Vincenzo Bonnici, Rosalba Giugno, Nicola Bombieri:
An Efficient Implementation of a Subgraph Isomorphism Algorithm for GPUs. BIBM 2018: 2674-2681
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Vincenzo Bonnici, Simone Caligola, Antonino Aparo, Rosalba Giugno:
Centrality Speeds the Subgraph Isomorphism Search Up in Target Aware Contexts. CIBB 2018: 19-26
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Antonino Aparo, Vincenzo Bonnici, Giovanni Micale, Alfredo Ferro, Dennis E. Shasha, Alfredo Pulvirenti, Rosalba Giugno:
Simple Pattern-only Heuristics Lead to Fast Subgraph Matching Strategies on Very Large Networks. PACBB 2018: 131-138
2010
[c1]
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Vincenzo Bonnici, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha:
Enhancing Graph Database Indexing by Suffix Tree Structure. PRIB 2010: 195-203

Data and Artifacts

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2021
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Vincenzo Bonnici, Giovanni Cicceri, Salvatore Distefano, Letterio Galletta, Marco Polignano, Carlo Scaffidi:
Italian IT Initiatives against COVID-19 (Dataset). Zenodo, 2021

Informal and Other Publications

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2021
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Vincenzo Bonnici, Giuditta Franco, Vincenzo Manca:
Spectral concepts in genome informational analysis. CoRR abs/2106.15351 (2021)
2020
[i4]
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Giovanni Micale, Vincenzo Bonnici, Alfredo Ferro, Dennis E. Shasha, Rosalba Giugno, Alfredo Pulvirenti:
MultiRI: Fast Subgraph Matching in Labeled Multigraphs. CoRR abs/2003.11546 (2020)
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Vincenzo Bonnici:
A maximum value for the Kullback-Leibler divergence between quantum discrete distributions. CoRR abs/2008.05932 (2020)
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Vincenzo Bonnici, Giuditta Franco, Vincenzo Manca:
A word recurrence based algorithm to extract genomic dictionaries. CoRR abs/2009.10449 (2020)
2015
[i1]
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Fabio Rinnone, Giovanni Micale, Vincenzo Bonnici, Gary D. Bader, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
NetMatchStar: an enhanced Cytoscape network querying app. F1000Research 4: 479 (2015)

Coauthor Index

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