Davide Cangelosi

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The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochastic Simulation Algorithm (SSA) is a standard algorithm to simulate well-stirred biochemical systems, but the computational burden makes this algorithm slow to compute for many realistic(More)
Neuroblastoma is the most common pediatric solid tumor. About fifty percent of high risk patients die despite treatment making the exploration of new and more effective strategies for improving stratification mandatory. Hypoxia is a condition of low oxygen tension occurring in poorly vascularized areas of the tumor associated with poor prognosis. We had(More)
In this paper, we introduce a new notion of motifs, called masks, that succinctly represent the repeated patterns for an input sequence T of n symbols drawn from an alphabet Σ. We show how to build the set of all maximal masks of length L and quorum q, in O(2 L n) time and space in the worst case. We analytically show that our algorithms perform better than(More)
Cancer patient's outcome is written, in part, in the gene expression profile of the tumor. We previously identified a 62-probe sets signature (NB-hypo) to identify tissue hypoxia in neuroblastoma tumors and showed that NB-hypo stratified neuroblastoma patients in good and poor outcome [1]. It was important to develop a prognostic classifier to cluster(More)
More than fifty percent of neuroblastoma (NB) patients with adverse prognosis do not benefit from treatment making the identification of new potential targets mandatory. Hypoxia is a condition of low oxygen tension, occurring in poorly vascularized tissues, which activates specific genes and contributes to the acquisition of the tumor aggressive phenotype.(More)
Mathematical modeling and computer simulation are powerful approaches for understanding the complexity of biological systems. In particular, computer simulation represents a strong validation and fast hypothesis verification tool. In the course of the years, several successful attempts have been made to simulate complex biological processes like metabolic(More)
Acknowledgments First of all, I want to thank my supervisor Stefano Chessa for the unvaluable collaboration we had during these years, and all his help in writing this dissertation. My gratitude goes to many more people, to Laura Ricci for being an advisor for my other research topic, and a friend, to all my co-authors, to Roberto di Pietro for being a(More)
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