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- R. Serra, Michael G. Villani, Alex Graudenzi, S. A. Kauffman
- Journal of theoretical biology
- 2007

In a previous study it was shown that a simple random Boolean network model, with two input connections per node, can describe with a good approximation (with the exception of the smallestâ€¦ (More)

We investigate the role of backward reactions in a stochastic model of catalytic reaction network, with specific regard to the influence on the emergence of autocatalytic sets (ACSs), which areâ€¦ (More)

- Alessandro Filisetti, Alex Graudenzi, +5 authors Irene Poli
- 2011

Autocatalytic cycles are rather common in biological systems and they might have played a major role in the transition from non-living to living systems. Several theoretical models have been proposedâ€¦ (More)

In most theories concerning the origin of life autocatalytic sets are supposed to play an important role in the phase transition between non-living and living matter. Although several theoreticalâ€¦ (More)

- Chiara Damiani, Alessandro Filisetti, Alex Graudenzi, Paola Lecca
- Computational Biology and Chemistry
- 2013

A general numerical methodology for parametric sensitivity analysis is proposed, which allows to determine the parameters exerting the greatest influence on the output of a stochastic computationalâ€¦ (More)

- Daniele Ramazzotti, Giulio Caravagna, +5 authors Bud Mishra
- Bioinformatics
- 2015

UNLABELLED
We devise a novel inference algorithm to effectively solve the cancer progression model reconstruction problem. Our empirical analysis of the accuracy and convergence rate of ourâ€¦ (More)

- Alex Graudenzi, Roberto M Serra, Marco Villani, Chiara Damiani, Annamaria Colacci, Stuart A. Kauffman
- Journal of Computational Biology
- 2011

Classical random Boolean networks (RBN) are not well suited to describe experimental data from time-course microarray, mainly because of the strict assumptions about the synchronicity of theâ€¦ (More)

- Alessandro Filisetti, Alex Graudenzi, +5 authors Irene Poli
- Theory in Biosciences
- 2011

Autocatalytic cycles are rather widespread in nature and in several theoretical models of catalytic reaction networks their emergence is hypothesized to be inevitable when the network is or becomesâ€¦ (More)

- Alex Graudenzi, Roberto M Serra, Marco Villani, Annamaria Colacci, Stuart A. Kauffman
- Journal of Computational Biology
- 2011

The response to different kinds of perturbations of a discrete model of gene regulatory network, which is a generalization of the random Boolean network (RBN) model, is discussed. The model includesâ€¦ (More)

- Giulio Caravagna, Alex Graudenzi, +6 authors Bud Mishra
- Proceedings of the National Academy of Sciencesâ€¦
- 2016

The genomic evolution inherent to cancer relates directly to a renewed focus on the voluminous next-generation sequencing data and machine learning for the inference of explanatory models of how theâ€¦ (More)