TACITuS is a portal, which deals with data pre-processing, selection and, eventually, integration of transcriptomic data coming from diverse sources, such as ArrayExpress. In order to take advantage of the functionality provided by this application, you will need to register, or sign in with a previously activated account.
MultiMotif is a tool for finding statistically significant labeled motifs in multi-relational networks with analytically derived p-values. MultiMotif uses a custom version of RI algorithm for counting occurrences of labeled motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. MultiMotif works on both directed and undirected networks and handle non-induced labeled motifs.
FlashMotif is a tool for finding statistically significant colored motifs with analytically derived p-values. FlashMotif uses the GLabTrie algorithm for counting occurrences of colored motifs in a graph and implements an analytical model to assess motifs significance without generating random graphs. FlashMotif works on both directed and undirected networks and can handle induced and non-induced injective and multiset topological colored motifs with color-topology dependency or independency.
SPECifIC (Sub-Pathway Extractor and Enricher). SPECifIC is a network-based systems biology tool capable of extracting disease-perturbed subpathways within pathway networks in connection with expression data. Our system extends pathways with missing regulatory elements, such as microRNAs, and their interactions with genes. The framework enables the extraction, visualization, and analysis of statistically significant disease-specific subpathways computed on a meta-pathway.
MITHrIL (Mirna enrIched paTHway Impact anaLysis) is an algorithm developed for the analysis of signaling pathways. It extends pathways by adding missing regulatory elements, such as microRNAs, and their interactions with genes. The method takes as input the expression values of genes and/or microRNAs and returns a list of pathways sorted according to the degree of their deregulation, together with the corresponding statistical significance (p-values).
SPECTRA (SPECific Tissue/Tumor Related PPI networks Analyzer) is a framework to build and analyze protein-protein interaction networks specific for a set of tissues or tumors (TS-PPI networks). SPECTRA integrates tissue and tumor specific gene expression data from variuos online repositories with high-quality protein-protein interaction data and provides a web interface for constructing, visualizing and comparing TS-PPI networks, with the aim of identify differential interaction/expression patterns in TS-PPI networks (i.e. distinct tissues, or normal and pathological states of the same tissue). Comparison is performed through an adaptive version of GASOLINE algorithm.
Biowine is a knowledge base of genomic data of Vitis-vinifera, containing NGS data from several samples of grapevine.
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.
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.
ncRNA-DB is an integrative data base of human non-coding RNA interactions.
AIRlINER is an algorithm for prediction of A-to-I editing sites in mRNA double stranded sequences.
PROPOSAL (PROtein comparison through Probabilistic Optimal Structure local ALignment) is a Gibbs sampling algorithm for multiple local alignment of 3D protein structures. PROPOSAL can produce biologically significant alignments in reasonable running time, even for large input instances.
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
DT-Hybrid is a R package that implements the homonymous algorithm for the prediction of interactions between small-molecules (i.e. Drug-Target Interactions).
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.
miRandola (2017 Version) is a database that provides information about all kind of extracellular miRNAs.
NetMatch is a Cytoscape app for sub-graph mathcing in Biological Networks.
miRò (V2) is a web-based knowledge base that provides users with miRNA–phenotype associations in humans.
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.
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.
VIRGO is Visualization tool of A-to-I RNA editing sites in genomic sequences
miR-EdiTar is a database of predicted A-to-I edited miRNA binding sites.
DBStrata is a software application that allows you to apply different density-based clustering methods on spatial databases with noise.
SIGMA: A Set-cover-based Inexact Graph Matching Algorithm. SIGMA is an indexing system for inexact graph matching. Best Paper Award at CBS 2009
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.
miRSscape is a Cytoscape plugin allowing mining on biological networks annotated with microRNAs.
miRiam is a fast and reliable tool for screening mRNA sequences for miRNA binding sites.
BitCube is a system for the multidimensional cube materialization.
Anticlustal++ is a system for Multiple Sequence Alignment
ClosestMatch is a fast approximate algorithm for Matching two set of points in the plane.