Dr Francesco Montefusco

Research Fellow

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Telephone: 01392 723623

BIOGRAPHICAL SKETCH

Francesco Montefusco was born in Ischia, Naples, Italy, on September 9^th 1980. He attended the Classic High School in Ischia and received the Diploma di Maturita' (School Leaving Certificate) in 1998. He received the Laurea degree in Electronic Engineering in July 2005, from University of Naples 'Federico II', Italy. He attended Ph.D. Course in Biomedical and Computer Engineering as a full-time student from November 2007 to October 2009 at the 'Magna Graecia' University of Catanzaro, Italy, and he received his Ph.D. in January 2010. From March to June 2009 he was a visiting scholar at the Control and Instrumentation Research Group in the Department of Engineering at the University of Leicester, UK. From 1^st March 2010 he is an Associate Research Fellow in the College of Engineering, Mathematics and Physical Sciences of the University of Exeter, UK.

His current research interests are in the field of systems and control theory, with particular emphasis on its application to the modelling, simulation and identification of biological systems.

Further research interests concern the development of a web-based system for the acquisition and automatic analysis of vocal signals, named Re.V.A. (Remote Voice Analysis). This activity is performed in collaboration with the School of Computer and Biomedical Engineering and Clinical Unit of Otorhinolaryngology of the 'Magna Graecia' University of Catanzaro, Italy, and the Department of Electronics and Telecommunications of the University of Firenze, Italy.

Research Interests

Reverse Engineering of Biological Networks

The problem of reverse engineering the topology of biomolecular interaction networks from time-course experimental data has been the subject of extensive research efforts in the Systems Biology community in recent years. Several approaches have been devised in the literature to tackle the challenge, comprising graph theory, Boolean networks, linear, nonlinear and piecewise-linear differential equations, Bayesian networks, Mutual Information theory, Petri nets and others. Experimental evidences show that biological networks exhibit a scale-free topology: most of the nodes have a low number of interactions, whereas there are only few highly connected nodes (hubs).

In this field he contributed to develop inference techniques, based on dynamical linear systems, by taking into account the effects of measurement noise in the data used for network inference and exploiting qualitative prior knowledge about the network interactions with an edge selection heuristic based on mechanisms underpinning scale-free networks generation, i.e. network growth and preferential attachment (PA). The effectiveness of these techniques has been validated by means of numerical tests over a set of numerically simulated random networks and then, in order to investigate the applicability to real-world case-studies, the devised techniques have been used for reverse-engineering a cell cycle regulatory subnetwork of Saccharomyces cerevisiae and a subnetwork of the DNA-damage response pathway (SOS pathway) in the bacteria Escherichia coli.

A web-based system for the acquisition and automatic analysis of vocal signals

He contributed to perform a remote voice analysis (REVA), a web-based system for the acquisition and automatic analysis of vocal signals. Vocal signals are submitted by the users through a simple web-interface and are analyzed in real-time by using state-of-the-art signal processing techniques, providing first-level information on possible voice alterations. In particular his main contribution consists in the development of signal processing techniques, extrapolating from the audio registration a set of significant parameters to classify the vocal samples.

Software

CORE-Net

CORE-Net is an algorithm for reverse engineering biological interaction networks from both steady-state and time-course experimental data, based on dynamical systems and convex optimization. It was developed by Dr. Francesco Montefusco and Dr. Carlo Cosentino at the Biomechatronics Lab, directed by Prof. Francesco Amato, at the 'Magna Graecia' University of Catanzaro, Italy.

Further details, source code and data can be found on the http://wpage.unina.it/carcosen/CORE-Net.htm

PACTLS

PACTLS is an algorithm for reverse engineering biological interaction networks from both steady-state and time-course experimental data, based on dynamical systems and Constrained Total Least Squares (CTLS). It was developed by Dr. Francesco Montefusco at the College of Engineering, Mathematics and Physical Sciences of the University of Exeter, UK, under the supervision of by Prof. Declan G. Bates, and by Dr. Carlo Cosentino at the Biomechatronics Lab, directed by Prof. Francesco Amato, of the 'Magna Graecia' University of Catanzaro, Italy.

Further details, source code and data can be found on the http://wpage.unina.it/carcosen/PACTLS.htm

Publications

International Journals

F. Montefusco, C. Cosentino, J. Kim, F. Amato and D.G. Bates, Reconstruction of Partially-Known Biomolecular Interaction Networks from Noisy Data, submitted, 2010
F. Montefusco, C. Cosentino, F. Amato, CORE--Net: Exploiting Prior Knowledge and Preferential Attachment to Infer Biological Interaction Networks, IET Syst. Biol., Vol. 4, no. 5, pp. 296-310, Sept. 2010
F. Amato, M. Cannataro, C. Cosentino, A. Garozzo, N. Lombardo, C. Manfredi, F. Montefusco, G. Tradigo, P. Veltri, Early Detection of Voice Disease via a Web- Based System, Biomedical Signal Processing and Control, 2009, 4, pp. 206-212
C. Cosentino, W. Curatola, F. Montefusco, M. Bansal, D. di Bernardo, F. Amato, Linear Matrix Inequalities Approach to Reconstruction of Biological Networks, IET Syst. Biol., Vol. 1, no. 3, pp.164-173, May 2007

International Conferences

F. Montefusco, C. Cosentino, F. Amato, D. G. Bates, “Reverse-Engineering Biological Interaction Networks from Noisy Data using Regularized Least Squares and Instrumental Variables”, accepted at the 50th IEEE Conference on Decision and Control and European Control Conference, December 12-15, 2011, Orlando, FL, USA

F. Montefusco, C. Cosentino, J. Kim, F. Amato and D.G. Bates, Reverse Engineering Partially-Known Interaction Networks from Noisy Data, Proc. of the 18th World Congress of the International Federation of Automatic Control (IFAC), 2011
F. Amato, C. Cosentino, F. Montefusco, Inferring Gene Regulatory Networks with a Partially Known Scale-Free Topology, Proc. of the 10th European Control Conference 2009 (ECC'09), Budapest, Hungary, August 23-26, 2009
F. Amato, C. Cosentino, F. Montefusco, Exploiting Prior Knowledge and Preferential Attachment to Infer Biological Interaction Networks, Proc. of the 17th Mediterranean Conference on Control and Automation 2009 (MED'09), Thessaloniki, Greece, June 24-26, 2009
F. Amato, R. Ambrosino, C. Cosentino, G. De Tommasi, F. Montefusco, Input- output finite-time stability of linear systems, Proc. of the 17th Mediterranean Conference on Control and Automation 2009 (MED'09), Thessaloniki, Greece, June 24-26, 2009
F. Amato, C. Cosentino, F. Montefusco, Inferring Scale-Free Networks via Multiple Linear Regression and Preferential Attachment, Proc. of the 16th Mediterranean Conference on Control and Automation 2008 (MED'08), Ajaccio, Corsica, June 25- 27, 2008
F. Amato, M. Cannataro, C. Cosentino, A. Garozzo, N. Lombardo, C. Manfredi, F. Montefusco, G. Tradigo, P. Veltri, A Web-based System for the Collection and Analysis of Spectra Signals for Early Detection of Voice Alterations, Proc. of the ACM SAC'08, Fortaleza, Ceara', Brazil, March 16-20, 2008
F. Amato, M. Cannataro, C. Cosentino, A. Garozzo, N. Lombardo, C. Manfredi, F. Montefusco, G. Tradigo, P. Veltri, Early Detection of Voice Disease via a Web- Based System, Proc. of the Maveba 2007, Firenze, Italy, December 13-15, 2007