We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a networ... more We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.
The identification of drug-target interactions (DTI) is a costly and time-consuming step in drug ... more 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 field. Algorithms may aim to design new therapies based on a single approved drug or a combination of them. Recently, recommendation methods relying on network-based inference in connection with knowledge coming from the specific domain have been proposed. Here we propose a web-based interface to the DT-Hybrid algorithm, which applies a recommendation technique based on bipartite network projection implementing resources transfer within the network. This technique combined with domain-specific knowledge expressing drugs and targets similarity is used to compute recommendations for each drug. Our web interface allows the users: (i) to browse all the predictions inferred by the algorithm; (ii) to upload their custom data on which they wish to obtain a prediction through a DT-Hybrid ...
MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of vari... more 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 found in extracellular human body fluids (e.g. plasma and serum) and some circulating miRNAs in the blood have been successfully revealed as biomarkers for diseases including cardiovascular diseases and cancer. Released miRNAs do not necessarily reflect the abundance of miRNAs in the cell of origin. It is claimed that release of miRNAs from cells into blood and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. Moreover, miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. In particular, the use of drugs should be taken into consideration while analyzing plasma miRNA levels as drug treatment. This may impair their employment as biomarkers. We enriched our manually curat...
Frontiers in bioengineering and biotechnology, 2014
Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs... more Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By acces...
Abstract. Approximate graph searching plays a key role from biology to computer graphics. Here we... more Abstract. Approximate graph searching plays a key role from biology to computer graphics. Here we propose RelaxGrep, a tool that guides the user to find subgraphs in the database that are isomorphic to a re-laxation of an original query Q, (ie, a graph obtained after removing ...
Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model s... more 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 systems that search for all occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed. This paper presents GraphGrepSX. The system implements efficient graph searching algorithms together with an advanced filtering technique. GraphGrepSX is compared with SING, GraphFind, CTree and GCoding. Experiments show that GraphGrepSX outperforms the compared systems on a very large collection of molecular data. In particular, it reduces the size and the time for the construction of large database index and outperforms the most popular systems.
We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a networ... more We present NetMatchStar, a Cytoscape app to find all the occurrences of a query graph in a network and check for its significance as a motif with respect to seven different random models. The query can be uploaded or built from scratch using Cytoscape facilities. The app significantly enhances the previous NetMatch in style, performance and functionality. Notably NetMatchStar allows queries with wildcards.
The identification of drug-target interactions (DTI) is a costly and time-consuming step in drug ... more 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 field. Algorithms may aim to design new therapies based on a single approved drug or a combination of them. Recently, recommendation methods relying on network-based inference in connection with knowledge coming from the specific domain have been proposed. Here we propose a web-based interface to the DT-Hybrid algorithm, which applies a recommendation technique based on bipartite network projection implementing resources transfer within the network. This technique combined with domain-specific knowledge expressing drugs and targets similarity is used to compute recommendations for each drug. Our web interface allows the users: (i) to browse all the predictions inferred by the algorithm; (ii) to upload their custom data on which they wish to obtain a prediction through a DT-Hybrid ...
MicroRNAs (miRNAs) are small noncoding RNAs that play an important role in the regulation of vari... more 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 found in extracellular human body fluids (e.g. plasma and serum) and some circulating miRNAs in the blood have been successfully revealed as biomarkers for diseases including cardiovascular diseases and cancer. Released miRNAs do not necessarily reflect the abundance of miRNAs in the cell of origin. It is claimed that release of miRNAs from cells into blood and ductal fluids is selective and that the selection of released miRNAs may correlate with malignancy. Moreover, miRNAs play a significant role in pharmacogenomics by down-regulating genes that are important for drug function. In particular, the use of drugs should be taken into consideration while analyzing plasma miRNA levels as drug treatment. This may impair their employment as biomarkers. We enriched our manually curat...
Frontiers in bioengineering and biotechnology, 2014
Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs... more Research attention has been powered to understand the functional roles of non-coding RNAs (ncRNAs). Many studies have demonstrated their deregulation in cancer and other human disorders. ncRNAs are also present in extracellular human body fluids such as serum and plasma, giving them a great potential as non-invasive biomarkers. However, non-coding RNAs have been relatively recently discovered and a comprehensive database including all of them is still missing. Reconstructing and visualizing the network of ncRNAs interactions are important steps to understand their regulatory mechanism in complex systems. This work presents ncRNA-DB, a NoSQL database that integrates ncRNAs data interactions from a large number of well established on-line repositories. The interactions involve RNA, DNA, proteins, and diseases. ncRNA-DB is available at http://ncrnadb.scienze.univr.it/ncrnadb/. It is equipped with three interfaces: web based, command-line, and a Cytoscape app called ncINetView. By acces...
Abstract. Approximate graph searching plays a key role from biology to computer graphics. Here we... more Abstract. Approximate graph searching plays a key role from biology to computer graphics. Here we propose RelaxGrep, a tool that guides the user to find subgraphs in the database that are isomorphic to a re-laxation of an original query Q, (ie, a graph obtained after removing ...
Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model s... more 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 systems that search for all occurrences of a query graph. To deal efficiently with graph searching, advanced methods for indexing, representation and matching of graphs have been proposed. This paper presents GraphGrepSX. The system implements efficient graph searching algorithms together with an advanced filtering technique. GraphGrepSX is compared with SING, GraphFind, CTree and GCoding. Experiments show that GraphGrepSX outperforms the compared systems on a very large collection of molecular data. In particular, it reduces the size and the time for the construction of large database index and outperforms the most popular systems.
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