Mechanistic Translation of Melanoma Genetic Landscape in Enriched Pathways and Oncogenic Protein-Protein Interactions.

Background/aim: Malignant melanoma is a skin cancer originating from the oncogenic transformation of melanocytes located in the epidermal layers. Usually, the patient's prognosis depends on timing of disease detection and molecular and genetic profiling, which may all significantly influence mortality rates. Genetic analyses often detect somatic BRAF, NRAS and cKIT mutations, germline substitutions in CDKN2A, and alterations of the PI3K-AKT-PTEN pathway.

MODIT: MOtif DIscovery in Temporal Networks.

Temporal networks are graphs where each edge is linked with a timestamp, denoting when an interaction between two nodes happens. According to the most recently proposed definitions of the problem, motif search in temporal networks consists in finding and counting all connected temporal graphs (called motifs) occurring in a larger temporal network , such that matched target edges follow the same chronological order imposed by edges in . In the last few years, several algorithms have been proposed to solve motif search, but most of them are limited to very small or specific motifs due to the computational complexity of the problem.

Next generation sequencing in a cohort of patients with rare sarcoma histotypes: A single institution experience.

Sarcomas are mesenchymal-derived cancers with overlapping clinical and pathologic features and a remarkable histological heterogeneity. While a precise diagnosis is often challenging to achieve, systemic treatment of sarcomas is still quite uniform. In this scenario, next generation sequencing (NGS) may be exploited to assist diagnosis and to identify specific targetable alterations.

Computational Methods to Investigate the Impact of miRNAs on Pathways.

Pathway analysis is a wide class of methods allowing to determine the alteration of functional processes in complex diseases. However, biological pathways are still partial, and knowledge coming from posttranscriptional regulators has started to be considered in a systematic way only recently. Here we will give a global and updated view of the main pathway and subpathway analysis methodologies, focusing on the improvements obtained through the recent introduction of microRNAs as regulatory elements in these frameworks.

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 to that input.

INBIA: a boosting methodology for proteomic network inference.

Background: 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, in The Cancer Genome Atlas, collects protein expressions in human cancers and it is a reference resource for the functional study of cancers. However, established protocols to infer interaction networks from protein expressions are still missing.

APPAGATO: an APproximate PArallel and stochastic GrAph querying TOol for biological networks.

Motivation: Biological network querying is a problem requiring a considerable computational effort to be solved. Given a target and a query network, it aims to find occurrences of the query in the target by considering topological and node similarities (i.e.

NetMatchStar: an enhanced Cytoscape network querying app.

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.

SPECTRA: An Integrated Knowledge Base for Comparing Tissue and Tumor-Specific PPI Networks in Human.

Protein-protein interaction (PPI) networks available in public repositories usually represent relationships between proteins within the cell. They ignore the specific set of tissues or tumors where the interactions take place. Indeed, proteins can form tissue-selective complexes, while they remain inactive in other tissues.

GASOLINE: a Cytoscape app for multiple local alignment of PPI networks.

Comparing protein interaction networks can reveal interesting patterns of interactions for a specific function or process in distantly related species. In this paper we present GASOLINE, a Cytoscape app for multiple local alignments of PPI (protein-protein interaction) networks. The app is based on the homonymous greedy and stochastic algorithm.

Proteins comparison through probabilistic optimal structure local alignment.

Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.

GASOLINE: a Greedy And Stochastic algorithm for optimal Local multiple alignment of Interaction NEtworks.

The analysis of structure and dynamics of biological networks plays a central role in understanding the intrinsic complexity of biological systems. Biological networks have been considered a suitable formalism to extend evolutionary and comparative biology. In this paper we present GASOLINE, an algorithm for multiple local network alignment based on statistical iterative sampling in connection to a greedy strategy.

Atopy and risk factors for latex sensitization in a selected population.

The value of recommending latex allergy screening in allergy departments of the Army's Hospital was studied. The purpose of the study was to evaluate whether atopy was a risk factor for latex sensitization in a specific population such as the young male soldiers of the Italian Army. The study was also aimed to assess the role of other risk factors.