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- Salvatore Alaimo, Alfredo Pulvirenti, Rosalba Giugno, Alfredo Ferro
- Bioinformatics
- 2013

MOTIVATION
The identification of drug-target interaction (DTI) represents a costly and time-consuming step in drug discovery and design. Computational methods capable of predicting reliable DTI play an important role in the field. Recently, recommendation methods relying on network-based inference (NBI) have been proposed. However, such approaches implement… (More)

- Vincenzo Bonnici, Rosalba Giugno, Alfredo Pulvirenti, Dennis Shasha, Alfredo Ferro
- BMC Bioinformatics
- 2013

Graphs can represent biological networks at the molecular, protein, or species level. An important query is to find all matches of a pattern graph to a target graph. Accomplishing this is inherently difficult (NP-complete) and the efficiency of heuristic algorithms for the problem may depend upon the input graphs. The common aim of existing algorithms is to… (More)

Biological applications, from genomics to ecology, deal with graphs that represents the structure of interactions. Analyzing such data requires searching for subgraphs in collections of graphs. This task is computationally expensive. Even though multicore architectures, from commodity computers to more advanced symmetric multiprocessing (SMP), offer… (More)

- Giovanni Nigita, Dario Veneziano, Alfredo Ferro
- Front. Bioeng. Biotechnol.
- 2015

RNA editing is a dynamic mechanism for gene regulation attained through the alteration of the sequence of primary RNA transcripts. A-to-I (adenosine-to-inosine) RNA editing, which is catalyzed by members of the adenosine deaminase acting on RNA (ADAR) family of enzymes, is the most common post-transcriptional modification in humans. The ADARs bind… (More)

- Luciano Cascione, Pierluigi Gasparini, +9 authors Kay Huebner
- PloS one
- 2013

Triple negative breast cancer (TNBC) is a heterogeneous disease at the molecular, pathologic and clinical levels. To stratify TNBCs, we determined microRNA (miRNA) expression profiles, as well as expression profiles of a cancer-focused mRNA panel, in tumor, adjacent non-tumor (normal) and lymph node metastatic lesion (mets) tissues, from 173 women with… (More)

- Alfredo Ferro, Rosalba Giugno, +4 authors Dennis Shasha
- Bioinformatics
- 2007

UNLABELLED
NetMatch is a Cytoscape plugin which allows searching biological networks for subcomponents matching a given query. Queries may be approximate in the sense that certain parts of the subgraph-query may be left unspecified. To make the query creation process easy, a drawing tool is provided. Cytoscape is a bioinformatics software platform for the… (More)

- Domenico Cantone, Alfredo Ferro, Jacob T. Schwartz
- Journal of Automated Reasoning
- 1987

In this paper we prove the decidability of the class of unquantified formulae of set theory involving the operators ϕ, ∪, ∩, \, {·}, pred < and the predicates =, ∈, $$ \subseteq $$ , Finite, where pred <(s) denotes the collection of all sets having rank strictly less than the rank of s. This work generalizes and combines earlier results published in the… (More)

- Raffaele Di Natale, Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dennis Shasha
- BMC Bioinformatics
- 2009

Finding the subgraphs of a graph database that are isomorphic to a given query graph has practical applications in several fields, from cheminformatics to image understanding. Since subgraph isomorphism is a computationally hard problem, indexing techniques have been intensively exploited to speed up the process. Such systems filter out those graphs which… (More)

- Domenico Cantone, Alfredo Ferro, Alfredo Pulvirenti, Diego Reforgiato Recupero, Dennis Shasha
- IEEE Transactions on Knowledge and Data…
- 2005

Range and k-nearest neighbor searching are core problems in pattern recognition. Given a database S of objects in a metric space M and a query object q in M, in a range searching problem the goal is to find the objects of S within some threshold distance to g, whereas in a k-nearest neighbor searching problem, the k elements of S closest to q must be… (More)

- Misael Mongiovì, Raffaele Di Natale, Rosalba Giugno, Alfredo Pulvirenti, Alfredo Ferro, Roded Sharan
- J. Bioinformatics and Computational Biology
- 2010

Network querying is a growing domain with vast applications ranging from screening compounds against a database of known molecules to matching sub-networks across species. Graph indexing is a powerful method for searching a large database of graphs. Most graph indexing methods to date tackle the exact matching (isomorphism) problem, limiting their… (More)