20 Result(s)
within
Rosalba Giugno
Life Sciences
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Article
Open AccessGRAPES-DD: exploiting decision diagrams for index-driven search in biological graph databases
Graphs are mathematical structures widely used for expressing relationships among elements when representing biomedical and biological information. On top of these representations, several analyses are perform...
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Article
Open AccessThe 2017 Network Tools and Applications in Biology (NETTAB) workshop: aims, topics and outcomes
The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was “Methods, tools and platforms for Personalised Medicine in the Big Data Era”, bu...
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Article
Fast Subgraph Matching Strategies Based on Pattern-Only Heuristics
Many scientific applications entail solving the subgraph isomorphism problem, i.e., given an input pattern graph, find all the subgraphs of a (usually much larger) target graph that are structurally equivalent...
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Article
Open AccessPanDelos: a dictionary-based method for pan-genome content discovery
Pan-genome approaches afford the discovery of homology relations in a set of genomes, by determining how some gene families are distributed among a given set of genomes. The retrieval of a complete gene distri...
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Article
Open AccessCorrection to: cuRnet: an R package for graph traversing on GPU
After publication of this supplement article [1], it was brought to our attention that reference 10 and reference 12 in the article are incorrect.
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Article
Open AccesscuRnet: an R package for graph traversing on GPU
R has become the de-facto reference analysis environment in Bioinformatics. Plenty of tools are available as packages that extend the R functionality, and many of them target the analysis of biological network...
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Article
Open AccessArena-Idb: a platform to build human non-coding RNA interaction networks
High throughput technologies have provided the scientific community an unprecedented opportunity for large-scale analysis of genomes. Non-coding RNAs (ncRNAs), for a long time believed to be non-functional, ar...
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Article
Open AccessINBIA: a boosting methodology for proteomic network inference
The analysis of tissue-specific protein interaction networks and their functional enrichment in pathological and normal tissues provides insights on the etiology of diseases. The Pan-cancer proteomic project, ...
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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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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 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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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 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 ...
