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2020 – today
- 2024
[j44]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)- [j43]Luca Gallo
, Vito Latora, Alfredo Pulvirenti:
MultiplexSAGE: A Multiplex Embedding Algorithm for Inter-Layer Link Prediction. IEEE Trans. Neural Networks Learn. Syst. 35(10): 14075-14084 (2024) - [c23]Emanuele Martorana, Roberto Grasso, Giovanni Micale, Salvatore Alaimo, Dennis E. Shasha, Rosalba Giugno, Alfredo Pulvirenti:
Motif Finding Algorithms: A Performance Comparison. From Computational Logic to Computational Biology 2024: 250-267 - [e1]Domenico Cantone, Alfredo Pulvirenti:
From Computational Logic to Computational Biology - Essays Dedicated to Alfredo Ferro to Celebrate His Scientific Career. Lecture Notes in Computer Science 14070, Springer 2024, ISBN 978-3-031-55247-2 [contents] - [i7]Marco Bongiovanni, Luca Gallo, Roberto Grasso, Alfredo Pulvirenti:
MPXGAT: An Attention based Deep Learning Model for Multiplex Graphs Embedding. CoRR abs/2403.19246 (2024) - 2023
- [j42]Elisabetta C. Sciacca, Salvatore Alaimo, Gianmarco Silluzio, Alfredo Ferro, Vito Latora, Costantino Pitzalis, Alfredo Pulvirenti, Myles J. Lewis:
DEGGs: an R package with shiny app for the identification of differentially expressed gene-gene interactions in high-throughput sequencing data. Bioinform. 39(4) (2023) - [c22]Giorgio Locicero, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti:
MASFENON: Multi-Agent Adaptive Simulation Framework for Evolution in Networks of Networks. BIBM 2023: 3714-3720 - 2022
- [j41]Alessandro Muscolino, Antonio Di Maria, Rosaria Valentina Rapicavoli, Salvatore Alaimo, Lorenzo Bellomo, Fabrizio Billeci, Stefano Borzì, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti:
NETME: on-the-fly knowledge network construction from biomedical literature. Appl. Netw. Sci. 7(1): 1-24 (2022) - [j40]Grete Francesca Privitera, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti:
Virus finding tools: current solutions and limitations. Briefings Bioinform. 23(4) (2022) - [c21]Ilaria Cosentini, Vincenza Barresi, Daniele Filippo Condorelli, Alfredo Ferro, Alfredo Pulvirenti, Salvatore Alaimo:
COMBO: A Computational Framework to Analyze RNA-seq and Methylation Data Through Heterogeneous Multi-layer Networks. COMPLEX NETWORKS (1) 2022: 251-264 - [i6]Luca Gallo, Vito Latora, Alfredo Pulvirenti:
MultiSAGE: a multiplex embedding algorithm for inter-layer link prediction. CoRR abs/2206.13223 (2022) - 2021
- [j39]Giovanni Micale, Giorgio Locicero, Alfredo Pulvirenti, Alfredo Ferro:
TemporalRI: subgraph isomorphism in temporal networks with multiple contacts. Appl. Netw. Sci. 6(1): 55 (2021) - [j38]Alessandro La Ferlita, Salvatore Alaimo, Sebastiano Di Bella, Emanuele Martorana, Georgios I. Laliotis, Francesco Bertoni, Luciano Cascione, Philip N. Tsichlis, Alfredo Ferro, Roberta Bosotti, Alfredo Pulvirenti:
RNAdetector: a free user-friendly stand-alone and cloud-based system for RNA-Seq data analysis. BMC Bioinform. 22(1): 298 (2021) - [j37]Roberto Grasso, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti:
MODIT: MOtif DIscovery in Temporal Networks. Frontiers Big Data 4 (2021) - [j36]Salvatore Alaimo, Rosaria Valentina Rapicavoli, Gioacchino P. Marceca, Alessandro La Ferlita, Oksana B. Serebrennikova, Philip N. Tsichlis, Bud Mishra, Alfredo Pulvirenti, Alfredo Ferro:
PHENSIM: Phenotype Simulator. PLoS Comput. Biol. 17(6) (2021) - 2020
- [j35]Emanuele Martorana, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti:
Establish the expected number of induced motifs on unlabeled graphs through analytical models. Appl. Netw. Sci. 5(1): 58 (2020) - [j34]Sebastiano Di Bella, Alessandro La Ferlita, Giovanni Carapezza, Salvatore Alaimo, Antonella Isacchi, Alfredo Ferro, Alfredo Pulvirenti, Roberta Bosotti:
A benchmarking of pipelines for detecting ncRNAs from RNA-Seq data. Briefings Bioinform. 21(6): 1987-1998 (2020) - [c20]Alessandro Muscolino, Antonio Di Maria, Salvatore Alaimo, Stefano Borzì, Paolo Ferragina, Alfredo Ferro, Alfredo Pulvirenti:
NETME: On-the-Fly Knowledge Network Construction from Biomedical Literature. COMPLEX NETWORKS (2) 2020: 386-397 - [c19]Giorgio Locicero, Giovanni Micale, Alfredo Pulvirenti, Alfredo Ferro:
TemporalRI: A Subgraph Isomorphism Algorithm for Temporal Networks. COMPLEX NETWORKS (2) 2020: 675-687 - [i5]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)
2010 – 2019
- 2019
- [j33]Alessandro La Ferlita, Salvatore Alaimo, Dario Veneziano, Giovanni Nigita, Veronica Balatti, Carlo Maria Croce, Alfredo Ferro, Alfredo Pulvirenti:
Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. Database J. Biol. Databases Curation 2019: baz115 (2019) - [j32]Salvatore Alaimo, Antonio Di Maria, Dennis E. Shasha, Alfredo Ferro, Alfredo Pulvirenti:
TACITuS: transcriptomic data collector, integrator, and selector on big data platform. BMC Bioinform. 20-S(9): 366:1-366:11 (2019) - [j31]Giovanni Micale, Alfredo Pulvirenti, Alfredo Ferro, Rosalba Giugno, Dennis E. Shasha:
Fast methods for finding significant motifs on labelled multi-relational networks. J. Complex Networks 7(6): 817-837 (2019) - [c18]Emanuele Martorana, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti:
Establish the Expected Number of Injective Motifs on Unlabeled Graphs Through Analytical Models. COMPLEX NETWORKS (2) 2019: 255-267 - [i4]Alessandro Pluchino, Giulio Burgio, Andrea Rapisarda, Alessio Emanuele Biondo, Alfredo Pulvirenti, Alfredo Ferro, Toni Giorgino:
Exploring the Role of Interdisciplinarity in Physics: Success, Talent and Luck. CoRR abs/1901.03607 (2019) - 2018
- [j30]Davide S. Sardina, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
INBIA: a boosting methodology for proteomic network inference. BMC Bioinform. 19-S(7): 77-88 (2018) - [j29]Giovanni Micale, Rosalba Giugno, Alfredo Ferro, Misael Mongiovì, Dennis E. Shasha, Alfredo Pulvirenti:
Fast analytical methods for finding significant labeled graph motifs. Data Min. Knowl. Discov. 32(2): 504-531 (2018) - [j28]Nicola Lettieri, Antonio Altamura, Rosalba Giugno, Alfonso Guarino, Delfina Malandrino, Alfredo Pulvirenti, Francesco Vicidomini, Rocco Zaccagnino:
Ex Machina: Analytical platforms, Law and the Challenges of Computational Legal Science. Future Internet 10(5): 37 (2018) - [j27]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) - [c17]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 - [p3]Misael Mongiovì, Giovanni Micale, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha:
gLabTrie: A Data Structure for Motif Discovery with Constraints. Graph Data Management 2018: 71-95 - 2017
- [j26]Davide S. Sardina, Salvatore Alaimo, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
A novel computational method for inferring competing endogenous interactions. Briefings Bioinform. 18(6): 1071-1081 (2017) - [c16]Andre Petermann, Giovanni Micale, Giacomo Bergami, Alfredo Pulvirenti, Erhard Rahm:
Mining and ranking of generalized multi-dimensional frequent subgraphs. ICDIM 2017: 236-245 - 2016
- [j25]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) - [j24]Angelo Nuzzo, Giovanni Carapezza, Sebastiano Di Bella, Alfredo Pulvirenti, Antonella Isacchi, Roberta Bosotti:
KAOS: a new automated computational method for the identification of overexpressed genes. BMC Bioinform. 17(S-12): 5-14 (2016) - 2015
- [j23]Anna P. Privitera, Rosario Distefano, Hugo A. Wefer, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno:
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder. Database J. Biol. Databases Curation 2015 (2015) - [j22]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) - [j21]Alfredo Pulvirenti, Rosalba Giugno, Rosario Distefano, Giuseppe Pigola, Misael Mongiovì, Girolamo Giudice, Vera Vendramin, Alessandro Lombardo, Federica Cattonaro, Alfredo Ferro:
A knowledge base for Vitis vinifera functional analysis. BMC Syst. Biol. 9(S-3): S5 (2015) - [i3]Salvatore Alaimo, Rosalba Giugno, Mario Acunzo, Dario Veneziano, Alfredo Ferro, Alfredo Pulvirenti:
Post-transcriptional knowledge in pathway analysis increases the accuracy of phenotypes classification. CoRR abs/1510.08237 (2015) - [i2]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) - 2014
- [i1]Giovanni Micale, Andrea Continella, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti:
GASOLINE: a Cytoscape app for multiple local alignment of PPI networks. F1000Research 3: 140 (2014) - 2013
- [j20]Salvatore Alaimo, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro:
Drug-target interaction prediction through domain-tuned network-based inference. Bioinform. 29(16): 2004-2008 (2013) - [j19]Carmela Gissi, Paolo Romano, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Angelo M. Facchiano, Manuela Helmer-Citterich:
Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics. BMC Bioinform. 14(S-7): S1 (2013) - [j18]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) - [j17]Rosario Distefano, Giovanni Nigita, Valentina Macca, Alessandro Laganà, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro:
VIRGO: visualization of A-to-I RNA editing sites in genomic sequences. BMC Bioinform. 14(S-7): S5 (2013) - [j16]Carmelo Cassisi, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti:
Enhancing density-based clustering: Parameter reduction and outlier detection. Inf. Syst. 38(3): 317-330 (2013) - 2012
- [j15]Alessandro Laganà, Alessio Paone, Dario Veneziano, Luciano Cascione, Pierluigi Gasparini, Stefania Carasi, Francesco Russo, Giovanni Nigita, Valentina Macca, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha, Alfredo Ferro, Carlo Maria Croce:
miR-EdiTar: a database of predicted A-to-I edited miRNA target sites. Bioinform. 28(23): 3166-3168 (2012) - 2011
- [j14]S. Cristaldi, Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti:
Obstacles constrained group mobility models in event-driven wireless networks with movable base stations. Ad Hoc Networks 9(3): 400-417 (2011) - [j13]Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti:
Editorial. Briefings Bioinform. 12(6): 547-548 (2011) - [j12]Paolo Romano, Rosalba Giugno, Alfredo Pulvirenti:
Tools and collaborative environments for bioinformatics research. Briefings Bioinform. 12(6): 549-561 (2011) - [c15]Marco Aliotta, Andrea Cannata, Carmelo Cassisi, Rosalba Giugno, Placido Montalto, Alfredo Pulvirenti:
DBStrata: a system for density-based clustering and outlier detection based on stratification. SISAP 2011: 107-108 - [p2]Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha:
Behind Efficient Algorithms to Search in Graphs. Graph Data Management 2011: 89-111 - 2010
- [j11]Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis E. Shasha:
SING: Subgraph search In Non-homogeneous Graphs. BMC Bioinform. 11: 96 (2010) - [j10]Misael Mongiovì, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro, Roded Sharan:
Sigma: a Set-Cover-Based Inexact Graph Matching Algorithm. J. Bioinform. Comput. Biol. 8(2): 199-218 (2010) - [c14]Alfredo Ferro, Rosalba Giugno, Piera Laura Puglisi, Alfredo Pulvirenti:
An Efficient Duplicate Record Detection Using q-Grams Array Inverted Index. DaWak 2010: 309-323 - [c13]Alfredo Ferro, Rosalba Giugno, Piera Laura Puglisi, Alfredo Pulvirenti:
MySQL Data Mining: Extending MySQL to Support Data Mining Primitives (Demo). KES (3) 2010: 438-444 - [c12]Vincenzo Bonnici, Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha:
Enhancing Graph Database Indexing by Suffix Tree Structure. PRIB 2010: 195-203
2000 – 2009
- 2009
- [j9]Alessandro Laganà, Stefano Forte, A. Giudice, M. R. Arena, Piera Laura Puglisi, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha, Alfredo Ferro:
miRò: a miRNA knowledge base. Database J. Biol. Databases Curation 2009 (2009) - [c11]Alfredo Ferro, Rosalba Giugno, Piera Laura Puglisi, Alfredo Pulvirenti:
BitCube: A Bottom-Up Cubing Engineering. DaWaK 2009: 189-203 - [c10]Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti:
Distributed randomized algorithms for low-support data mining. IPDPS 2009: 1-7 - 2008
- [j8]Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dmitry Skripin, Dennis E. Shasha:
GraphFind: enhancing graph searching by low support data mining techniques. BMC Bioinform. 9(S-4) (2008) - 2007
- [j7]Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Dmitry Skripin, Gary D. Bader, Dennis E. Shasha:
NetMatch: a Cytoscape plugin for searching biological networks. Bioinform. 23(7): 910-912 (2007) - [j6]Alfredo Ferro, Rosalba Giugno, Giuseppe Pigola, Alfredo Pulvirenti, Cinzia Di Pietro, Michele Purrello, Marco Ragusa:
Sequence similarity is more relevant than species specificity in probabilistic backtranslation. BMC Bioinform. 8 (2007) - 2006
- [c9]Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Giuseppe Pigola, Alfredo Pulvirenti:
Distributed antipole clustering for efficient data search and management in Euclidean and metric spaces. IPDPS 2006 - 2005
- [j5]Domenico Cantone, Gianluca Cincotti, Alfredo Ferro, Alfredo Pulvirenti:
An Efficient Approximate Algorithm for the 1-Median Problem in Metric Spaces. SIAM J. Optim. 16(2): 434-451 (2005) - [j4]Domenico Cantone, Alfredo Ferro, Alfredo Pulvirenti, Diego Reforgiato Recupero, Dennis E. Shasha:
Antipole Tree Indexing to Support Range Search and K-Nearest Neighbor Search in Metric Spaces. IEEE Trans. Knowl. Data Eng. 17(4): 535-550 (2005) - [c8]Rosalba Giugno, Alfredo Pulvirenti, Diego Reforgiato Recupero:
Clustered Trie Structures for Approximate Search in Hierarchical Objects Collections. ICAPR (1) 2005: 63-70 - [c7]Domenico Cantone, Alfredo Ferro, Rosalba Giugno, Giuseppe Lo Presti, Alfredo Pulvirenti:
Multiple-Winners Randomized Tournaments with Consensus for Optimization Problems in Generic Metric Spaces. WEA 2005: 265-276 - [p1]Cinzia Di Pietro, Alfredo Ferro, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa, Dennis E. Shasha:
AntiClustAl: Multiple Sequence Alignment by Antipole Clustering. Data Mining in Bioinformatics 2005: 43-57 - 2004
- [c6]Rosalba Giugno, Alfredo Pulvirenti, Marco Ragusa, Loredana Facciola, Laura Patelmo, Valentina Di Pietro, Cinzia Di Pietro, Michele Purrello, Alfredo Ferro:
Locally sensitive backtranslation based on multiple sequence alignment. CIBCB 2004: 231-237 - 2003
- [b1]Alfredo Pulvirenti:
Data structures and algorithms for optimization problems and advanced search in high-dimension metric spaces. University of Catania, Italy, 2003 - [j3]A. Andronico, Roberto Barbera, Alberto Falzone, Peter Z. Kunszt, Giuseppe Lo Re, Alfredo Pulvirenti, A. Rodolico:
GENIUS: a simple and easy way to access computational and data grids. Future Gener. Comput. Syst. 19(6): 805-813 (2003) - [j2]Alfredo Ferro, Giuseppe Pigola, Alfredo Pulvirenti, Dennis E. Shasha:
Fast Clustering and Minimum Weight Matching Algorithms for Very Large Mobile Backbone Wireless Networks. Int. J. Found. Comput. Sci. 14(2): 223-236 (2003) - [c5]Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti:
Efficient Boundary Values Generation in General Metric Spaces for Software Component Testing. Verification: Theory and Practice 2003: 318-331 - [c4]Cinzia Di Pietro, Valentina Di Pietro, Giovanni Emmanuele, Alfredo Ferro, T. Maugeri, E. Modica, Giuseppe Pigola, Alfredo Pulvirenti, Michele Purrello, Marco Ragusa, Marina Scalia, Dennis E. Shasha, Salvo Travali, V. Zimmitti:
ANTICLUSTAL: Multiple Sequence Alignment by Antipole Clustering and Linear Approximate 1-Median Computation. CSB 2003: 326-336 - [c3]Giuseppe Andronico, Roberto Barbera, Alberto Falzone, Giuseppe Lo Re, Alfredo Pulvirenti, A. Rodolico:
The GENIUS web portal: grid computing made easy. ITCC 2003: 425-431 - [c2]Sebastiano Battiato, Alfredo Pulvirenti, Diego Reforgiato Recupero:
Antipole Clustering for Fast Texture Synthesis. WSCG 2003 - 2001
- [j1]Alfredo Ferro, Giovanni Gallo, Rosalba Giugno, Alfredo Pulvirenti:
Best-Match Retrieval for Structured Images. IEEE Trans. Pattern Anal. Mach. Intell. 23(7): 707-718 (2001) - [c1]Giovanni Gallo, Giorgio M. Grasso, Salvatore Nicotra, Alfredo Pulvirenti:
Remote Sensed Images Segmentation through Shape Refinement. ICIAP 2001: 137-144
Coauthor Index
[j42] [c22] [j41] [j40] [c21] [j39] [j38] [j37] [j36] [j35] [j34] [c20] [c19] [i5] [j33] [j32] [j31] [c18] [i4] [j30] [j29] [j27] [c17] [p3] [j26] [j23] [j22] [j21] [i3] [i2] [i1] [j20] [j19] [j18] [j17] [j16] [j15] [j14] [p2] [j11] [j10] [c14] [c13] [c12] [j9] [c11] [c10] [j8] [j7] [j6] [c9] [j5] [j4] [c7] [p1] [c6] [j2] [c5] [c4] [j1]
Dennis E. Shasha
aka: Dennis Shasha
aka: Dennis Shasha
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