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ORCIDAlfredo Ferro
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- affiliation: University of Catania, Italy
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2020 – today
- 2025
[i6]Giovanni Micale, Antonio Di Maria, Roberto Grasso, Vincenzo Bonnici, Alfredo Ferro, Dennis Shasha, Rosalba Giugno, Alfredo Pulvirenti:
MultiGraphMatch: a subgraph matching algorithm for multigraphs. CoRR abs/2501.09736 (2025)- 2024
- [c23]Alfredo Ferro, Eugenio G. Omodeo:
A Sound and Complete Validity Test for Formulas in Extensional Multi-level Syllogistic. From Computational Logic to Computational Biology 2024: 82-95 - 2023
- [j38]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
- [j37]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) - [j36]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 - 2021
- [j35]Giovanni Micale, Giorgio Locicero, Alfredo Pulvirenti, Alfredo Ferro:
TemporalRI: subgraph isomorphism in temporal networks with multiple contacts. Appl. Netw. Sci. 6(1): 55 (2021) - [j34]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) - [j33]Roberto Grasso, Giovanni Micale, Alfredo Ferro, Alfredo Pulvirenti:
MODIT: MOtif DIscovery in Temporal Networks. Frontiers Big Data 4 (2021) - [j32]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
- [j31]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) - [j30]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
- [j29]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) - [j28]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) - [j27]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
- [j26]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) - [j25]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) - [j24]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
- [j23]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) - 2015
- [j22]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) - [j21]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) - [j20]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
- [e2]Alfredo Ferro, Fabrizio Luccio, Peter Widmayer:
Fun with Algorithms - 7th International Conference, FUN 2014, Lipari Island, Sicily, Italy, July 1-3, 2014. Proceedings. Lecture Notes in Computer Science 8496, Springer 2014, ISBN 978-3-319-07889-2 [contents] - [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
- [j19]Salvatore Alaimo, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro:
Drug-target interaction prediction through domain-tuned network-based inference. Bioinform. 29(16): 2004-2008 (2013) - [j18]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) - [j17]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) - [j16]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) - [j15]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
- [j14]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
- [j13]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) - [p2]Alfredo Ferro, Rosalba Giugno, Alfredo Pulvirenti, Dennis E. Shasha:
Behind Efficient Algorithms to Search in Graphs. Graph Data Management 2011: 89-111 - [e1]Alfredo Ferro:
Fourth International Conference on Similarity Search and Applications, SISAP 2011, Lipari Island, Italy, June 30 - July 01, 2011. ACM 2011, ISBN 978-1-4503-0795-6 [contents] - 2010
- [j12]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) - [j11]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) - [c16]Alfredo Ferro, Rosalba Giugno, Piera Laura Puglisi, Alfredo Pulvirenti:
An Efficient Duplicate Record Detection Using q-Grams Array Inverted Index. DaWak 2010: 309-323 - [c15]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 - [c14]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
- [j10]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) - [c13]Alfredo Ferro, Rosalba Giugno, Piera Laura Puglisi, Alfredo Pulvirenti:
BitCube: A Bottom-Up Cubing Engineering. DaWaK 2009: 189-203 - [c12]Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti:
Distributed randomized algorithms for low-support data mining. IPDPS 2009: 1-7 - 2008
- [j9]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
- [j8]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) - [j7]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
- [c11]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
- [j6]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) - [j5]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) - [c10]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
- [c9]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
- [j4]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) - [c8]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 - [c7]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 - 2001
- [j3]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) - 2000
- [c6]Alfredo Ferro, Giovanni Gallo, Rosalba Giugno:
Approximate search in image database. Storage and Retrieval for Media Databases 2000: 210-214
1990 – 1999
- 1999
- [c5]Alfredo Ferro, Giovanni Gallo, Rosalba Giugno:
Error-Tolerant Database for Structured Images. VISUAL 1999: 51-59 - 1997
- [c4]Enrico Pontelli, Gopal Gupta, Francesco Pulvirenti, Alfredo Ferro:
Automatic Compile-time Parallelization of Prolog Programs for Dependent And-Parallelism. ICLP 1997: 108-122 - 1991
- [j2]Alfredo Ferro:
Decision Procedures for Elementary Sublanguages of Set Theory: XII. Multilevel Syllogistic Extended with Singleton and Choice Operators. J. Autom. Reason. 7(2): 257-270 (1991)
1980 – 1989
- 1989
- [b2]Domenico Cantone, Alfredo Ferro, Eugenio G. Omodeo:
Computable set theory. Volume 1. The international series of monographs on computer science 6, Clarendon Press / Oxford University Press 1989, ISBN 0-19-853807-3 - 1988
- [c3]Domenico Cantone, Vincenzo Cutello, Alfredo Ferro:
Decision Procedures for Elementary Sublanguages of Set Theory. XIV. Three Languages Involving Rank Related Constructs. ISSAC 1988: 407-422 - 1987
- [j1]Domenico Cantone, Alfredo Ferro, Jacob T. Schwartz:
Decision Procedures for Elementary Sublanguages of Set Theory. V. Multilevel Syllogistic Extended by the General Union Operator. J. Comput. Syst. Sci. 34(1): 1-18 (1987) - [c2]Alfredo Ferro, Giovanni Gallo:
Groebner Bases, Ritt's Algorithm and Decision Procedures for Algebraic Theories. AAECC 1987: 230-237 - 1981
- [b1]Alfredo Ferro:
Decision Procedures for some Classes of Unquantified Set Theoretic Formulae. New York University, USA, 1981 - 1980
- [c1]Alfredo Ferro, Eugenio G. Omodeo, Jacob T. Schwartz:
Decision Procedures for Some Fragments of Set Theory. CADE 1980: 88-96
Coauthor Index
[i6] [j38] [c22] [j37] [j36] [c21] [j35] [j34] [j33] [j32] [j31] [j30] [c20] [c19] [i5] [j29] [j28] [j27] [c18] [i4] [j26] [j25] [j24] [c17] [p3] [j23] [j22] [j21] [j20] [i3] [i2] [i1] [j19] [j18] [j17] [j16] [j15] [j14] [j13] [p2] [j12] [j11] [c16] [c15] [c14] [j10] [c13] [c12] [j9] [j8] [j7] [c11] [j6] [j5] [c10] [p1] [c9] [j4] [c8] [c7] [j3]
Dennis E. Shasha
aka: Dennis Shasha
aka: Dennis Shasha
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