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Article
Fast analytical methods for finding significant labeled graph motifs
Network motif discovery is the problem of finding subgraphs of a network that occur more frequently than expected, according to some reasonable null hypothesis. Such subgraphs may indicate small scale interact...
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Chapter
gLabTrie: A Data Structure for Motif Discovery with Constraints
Motif discovery is the problem of finding subgraphs of a network that appear surprisingly often. Each such subgraph may indicate a small-scale interaction feature in applications ranging from a genomic interac...
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Protocol
Recommendation Techniques for Drug–Target Interaction Prediction and Drug Repositioning
The usage of computational methods in drug discovery is a common practice. More recently, by exploiting the wealth of biological knowledge bases, a novel approach called drug repositioning has raised. Several ...
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Article
Open AccessA knowledge base for Vitis vinifera functional analysis
Vitis vinifera (Grapevine) is the most important fruit species in the modern world. Wine and table grapes sales contribute significantly to the economy of major wine producing countries. The most relevant goals i...
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Article
Open AccessDT-Web: a web-based application for drug-target interaction and drug combination prediction through domain-tuned network-based inference
The identification of drug-target interactions (DTI) is a costly and time-consuming step in drug discovery and design. Computational methods capable of predicting reliable DTI play an important role in the fie...
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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 ...
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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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Chapter and Conference Paper
Dynamic Modeling and Simulation of Leukocyte Integrin Activation through an Electronic Design Automation Framework
Model development and analysis of biological systems is recognized as a key requirement for integrating in-vitro and in-vivo experimental data. In-silico simulations of a biochemical model allows one to test d...
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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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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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Chapter and Conference Paper
Business Process Model Retrieval Based on Graph Indexing Method
Nowadays, business process reuse is very important and necessary inside large organizations that continually increase their process collections. Therefore, an efficient system to manage and search for concrete...
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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 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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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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Article
Open AccessErratum to: Involvement of GTA protein NC2beta in Neuroblastoma pathogenesis suggests that it physiologically participates in the regulation of cell proliferation
