Software

 

 

Current Projects

 

[2014:current]

Biowine is a knowledge base of genomic data of Vitis-vinifera, containing NGS data from several samples of grapevine.

 

[2014:current]

DT-Web is 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.

 

[2013:current] 

MiTHrIL is a JAVA command-line application that implements an extension of the  Draghici et al., 2007 and Tarca et al., 2008 methods for the impact analysis on KEGG signaling pathways.

 

[2014:current]

ncPred is an algorithm for the inference of ncRNA-disease association based on recommendation technique. We represent our knowledge through a tripartite network, whose nodes are ncRNAs, targets, or diseases. Interactions in such a network associate each ncRNA with a disease through its targets. Our algorithm, starting from such a network, computes weights between each ncRNA-disease pair using a multi-level resource transfer technique that at each step takes into account the resource transferred in the previous one.

 

[2014:current] 

ncRNA-DB is an integrative data base of human non-coding RNA interactions.

 

[2014:current] 

AIRlINER is an algorithm for prediction of A-to-I editing sites in mRNA double stranded sequences.

 

[2014:current]

PROPOSAL (PROtein comparison through Probabilistic Optimal Structure local ALignment) is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures.

 

[2013:current]

GASOLINE (Greedy and Stochastic Algorithm for Optimal Local alignment of Interaction Networks) is an algorithm for multiple local network alignment based on statistical iterative sampling in connection to a greedy strategy.  Available also as Cytoscape App here

 

[2013:current]

DT-Hybrid is a R package that implements the homonymous algorithm for the prediction of interactions between small-molecules (i.e. Drug-Target Interactions).

 

[2013:current]

RI is a general purpose algorithm for one-to-one exact subgraph isomorphism problem maintaining topological constraints. It is both a C++ library and a standalone tool, providing developing API and a command line interface, with no dependencies out of standard GNU C++ library.

 

[2012: current]

miRandola is a database that provides information about all kind of extracellular miRNAs.

 

[2007:current]

NetMatch is a Cytoscape app for sub-graph mathcing in Biological Networks.

 

[2009:current]

miRò is a web-based knowledge base that provides users with miRNA–phenotype associations in humans.

 

 

 

Past Projects

 

[2013:2013]

GRAPES is a querying system for parallel searching in databases of graphs, and single target graph, using symmetric multiprocessing (SMP) architectures. It implements a parallel version of well established graph searching algorithms providing efficient solutions for graphs indexing and matching.

 

[2012:2013]

MIDClass is a simple and accurate method for gene expression classification. The method relies on associative classification and is based on the idea that the expression range of genes may efficiently identify subtypes in the same class.

 

[2012:2012]

VIRGO is Visualization tool of A-to-I RNA editing sites in genomic sequences

 

[2012:2012]

miR-EdiTar is a database of predicted A-to-I edited miRNA binding sites.

 

[2011:2011]

DBStrata is a software application that allows you to apply different density-based clustering methods on spatial databases with noise.

 

[2009:2010]

SIGMA: A Set-cover-based Inexact Graph Matching Algorithm. SIGMA is an indexing system for inexact graph matching. Best Paper Award at CBS 2009

 

[2010:2010]

GraphGrepSX is a querying system for databases of graphs. It is based on its predecessor GraphGrep. Please see related papers for complete algorithmic details. The system implements efficient graph searching algorithms together with advanced filtering techniques that allow an initial approximate search. It allows users to select candidate subgraphs rather than entire graphs. SING is an indexing system designed to query a graph (e.g. a molecular structure or a network motif) against a large target graph (i.e. a PPI network) or a collection of target graphs.

 

[2009:2010]

miRSscape is a Cytoscape plugin allowing mining on biological networks annotated with microRNAs.

 

[2009:2010]

miRiam is a fast and reliable tool for screening mRNA sequences for miRNA binding sites.

 

[2009:2009]

 

BitCube is a system for the multidimensional cube materialization.

 

[2004:2007] 

Locality Sensitive Backtranslation and  EasyBack  are two systems for Protein backtranslation.

 

[2003:2004]

Anticlustal++  is a system for Multiple Sequence Alignment

 

[2003:2003]

ClosestMatch is a fast approximate algorithm for Matching two set of points in the plane.