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Graphics processing units in bioinformatics, computational biology and systems biology
- Marco S. Nobile, P. Cazzaniga, A. Tangherloni, D. Besozzi
- Computer Science, Medicine
- Briefings Bioinform.
- 7 July 2016
We present a collection of GPU-powered tools recently developed to perform computational analyses in life science disciplines, emphasizing the advantages and the drawbacks in the use of these parallel architectures. Expand
A GPU-Based Multi-swarm PSO Method for Parameter Estimation in Stochastic Biological Systems Exploiting Discrete-Time Target Series
Parameter estimation (PE) of biological systems is one of the most challenging problems in Systems Biology. Expand
USE-Net: incorporating Squeeze-and-Excitation blocks into U-Net for prostate zonal segmentation of multi-institutional MRI datasets
We propose a novel Convolutional Neural Network (CNN), called USE-Net, which incorporates Squeeze-and-Excitation (SE) blocks into U-Net. Expand
An excursion in reaction systems: From computer science to biology
- Luca Corolli, C. Maj, F. Marini, D. Besozzi, G. Mauri
- Computer Science
- Theor. Comput. Sci.
- 1 October 2012
Reaction systems are a formal model based on the regulation mechanisms of facilitation and inhibition between biochemical reactions, which underlie the functioning of living cells. Expand
Modeling and stochastic simulation of the Ras/cAMP/PKA pathway in the yeast Saccharomyces cerevisiae evidences a key regulatory function for intracellular guanine nucleotides pools.
- P. Cazzaniga, D. Pescini, D. Besozzi, G. Mauri, S. Colombo, E. Martegani
- Biology, Medicine
- Journal of biotechnology
- 1 February 2008
In the yeast Saccharomyces cerevisiae, the Ras/cAMP/PKA pathway is involved in the regulation of metabolism and cell cycle progression. The pathway is tightly regulated by several control mechanisms,… Expand
A Comparison of Genetic Algorithms and Particle Swarm Optimization for Parameter Estimation in Stochastic Biochemical Systems
We tackle the problem of estimating the unknown parameters of stochastic biochemical systems by means of two optimization heuristics, genetic algorithms and particle swarm optimization. Expand
Parallel Rewriting P Systems with Deadlock
We analyze P systems with different parallel methods for string rewriting and the computational power of systems with and without deadlock. Expand
Gemmating P systems: collapsing hierarchies
- D. Besozzi, G. Mauri, G. Paun, C. Zandron
- Computer Science, Mathematics
- Theor. Comput. Sci.
- 8 March 2003
We continue the analysis of P systems with gemmation of mobile membranes. Expand
Dynamical Probabilistic P Systems: Definitions and Applications
We introduce dynamical probabilistic P systems, a variant where probabilities associated to the rules change during the evolution of the system, as a new approach to the analysis and simulation of the behavior of complex systems. Expand