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Chapter
Efficient Boundary Values Generation in General Metric Spaces for Software Component Testing
One of the most classical and successful software testing strategies is that of testing boundary values in the input domain (Reid 1997). In this paper we introduce a notion of boundary values for a finite subs...
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Chapter and Conference Paper
Multiple-Winners Randomized Tournaments with Consensus for Optimization Problems in Generic Metric Spaces
Extensions of the randomized tournaments techniques introduced in [6,7] to approximate solutions of 1-median and diameter computation of finite subsets of general metric spaces are proposed. In the linear algo...
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Chapter
AntiClustAl: Multiple Sequence Alignment by Antipole Clustering
In this chapter, we present a new multiple sequence alignment algorithm called AntiClustAl. The method makes use of the commonly used idea of aligning homologous sequences belonging to classes generated by som...
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Article
Open AccessSequence similarity is more relevant than species specificity in probabilistic backtranslation
Backtranslation is the process of decoding a sequence of amino acids into the corresponding codons. All synthetic gene design systems include a backtranslation module. The degeneracy of the genetic code makes ...
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Article
Open AccessGraphFind: enhancing graph searching by low support data mining techniques
Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by ...
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Article
Open AccessInvolvement of GTA protein NC2β in Neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation
The General Transcription Apparatus (GTA) comprises more than one hundred proteins, including RNA Polymerases, GTFs, TAFs, Mediator, and cofactors such as heterodimeric NC2. This complexity contrasts with the ...
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Article
Open AccessErratum to: Involvement of GTA protein NC2beta in Neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation
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Chapter and Conference Paper
BitCube: A Bottom-Up Cubing Engineering
Enhancing on line analytical processing through efficient cube computation plays a key role in Data Warehouse management. Hashing, grou** and mining techniques are commonly used to improve cube pre-computati...
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Chapter and Conference Paper
Enhancing Graph Database Indexing by Suffix Tree Structure
Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, scientists require syste...
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Chapter and Conference Paper
MySQL Data Mining: Extending MySQL to Support Data Mining Primitives (Demo)
The development of predictive applications built on top of knowledge bases is rapidly growing, therefore database systems, especially the commercial ones, are boosting with native data mining analytical tools....
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Chapter and Conference Paper
An Efficient Duplicate Record Detection Using q-Grams Array Inverted Index
Duplicate record detection is a crucial task for data cleaning process in data warehouse systems. Many approaches have been presented to address this problem: some of these rely on the accuracy of the resulted...
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Article
Open AccessSING: Subgraph search In Non-homogeneous Graphs
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 c...
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Chapter
Computational Approaches to RNAi and Gene Silencing
The discovery of small regulatory RNAs in the past few years has deeply changed the RNA molecular biology, revealing more complex pathways involved in the regulation of gene expression and in the defense of th...
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Chapter
Elucidating the Role of microRNAs in Cancer Through Data Mining Techniques
microRNAs (miRNAs) have been shown to play a crucial role in the most important biological processes and their dysregulation has been connected to a variety of diseases, including cancer. The number of computa...
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Article
Motif Discovery on Seismic Amplitude Time Series: The Case Study of Mt Etna 2011 Eruptive Activity
Algorithms searching for similar patterns are widely used in seismology both when the waveforms of the events of interest are known and when there is no a priori-knowledge. Such methods usually make use of the...
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Article
Open AccessBioinformatics in Italy: BITS2012, the ninth annual meeting of the Italian Society of Bioinformatics
The BITS2012 meeting, held in Catania on May 2-4, 2012, brought together almost 100 Italian researchers working in the field of Bioinformatics, as well as students in the same or related disciplines. About 90 ...
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Article
Open AccessVIRGO: visualization of A-to-I RNA editing sites in genomic sequences
RNA Editing is a type of post-transcriptional modification that takes place in the eukaryotes. It alters the sequence of primary RNA transcripts by deleting, inserting or modifying residues. Several forms of R...
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Article
Open AccessA subgraph isomorphism algorithm and its application to biochemical data
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 ...
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Article
Open AccessA knowledge base for the discovery of function, diagnostic potential and drug effects on cellular and extracellular miRNAs
MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of various biological processes through their interaction with cellular mRNAs. A significant amount of miRNAs has been ...
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Protocol
Computational Design of Artificial RNA Molecules for Gene Regulation
RNA interference (RNAi) is a powerful tool for the regulation of gene expression. Small exogenous noncoding RNAs (ncRNAs) such as siRNA and shRNA are the active silencing agents, intended to target and cleave ...
