Models of natural computing (MNC) group

Our research group, established in 2002 at the Department of Computer Science of the University of Verona, is led by Prof. Vincenzo Manca, and it is composed by an assistant professor, Giuditta Franco, a post-doc fellow, Luca Bianco, and three PhD students, Alberto Castellini, Luca Marchetti and Roberto Pagliarini. Its research is focused on Models of Natural Computing (MNC). In this field the group makes both theoretical and applied research. Present research issues deal with the modeling of biomolecular processes and include DNA computing, Membrane computing, and Systems Biology. The MNC group includes people having expertise in computer science, mathematics, and engineering, and collaborates with research groups at the Faculty of Medicine and the Faculty of Natural Sciences. The groupis member of the academic consortium "European Molecular Computing Consortium" (EMCC), and actively cooperates with many international groups.



Prof. Vincenzo Manca   vincenzo.manca_at_univr.it   Link

Vincenzo Manca is a Full Professor, since 2002, at the Computer Science Department of the University of Verona. He obtained his degrees from the University of Pisa, under the guide of Alfonso Caracciolo di Forino and Ennio De Giorgi, where he became Assistant Professor in 1980. E' was Associate Professor at the Universities of Udine and Pisa. His research interests cover a wide class of topics from mathematical logic, discrete mathematics, and theoretical computer science to informational analysis and computational models of biological systems. At present, his investigation is focused on "Natural Computing" (in particular DNA Computing and Membrane Computing, and Synthetic Computational Biology). He is author of more than 100 scientific publications, appearing in international journals and scientific series. He is reviewer for Mathematical Reviews and also referee for many scientific journals and conferences, has been member of PC in many international conferences and was visiting professor and "invited speaker" in many universities and international conferences. He is member of E.M.C.C. (European Molecular Computing Consortium) and directed several research projects in the field of natural computing, collaborating actively with several international research groups. He has advised 6 Ph.D students, and tutored more than 40 M.Sc. students. He is President of the Programme in Bioinformatics, at the University of Verona (the Faculty of Sciences).



Dr. Giuditta Franco   giuditta.franco_at_univr.it   Link

Giuditta Franco graduated in Mathematics at the University of Pisa in 2001 and earned her PhD in Computer Science, with a dissertation titled “Biomolecular Computing --- Combinatorial Algorithms and Laboratory Experiments”, at University of Verona, where she is currently an assistant professor. Her research interests focus on Molecular Computing, namely on DNA & Membrane Computing. Her work involved informational analysis of DNA sequences and dynamical modeling, by means of membrane systems, of immunological processes and of cellular tissue healing. She spent several periods abroad, in the United States, at the University of South Florida, and in Holland, at Leiden Institute of Advanced Computer Science. She gave talks in several international workshops and she is co-author of scientific papers published by prestigious sectoral journals. She is an effective member of both the European Molecular Computing Consortium (EMCC) and the International Society for Nanoscale Science, Computing and Engineering (ISNSCE).



Dr. Alberto Castellini   alberto.castellini_at_univr.it   Link

Alberto Castellini (http://www.albertocastellini.tk) graduated in Computer Science in 2006 and earned his PhD in Computer Science, with a dissertation titled "Algorithms and Software for Biological MP Modeling by Statistical and Optimization Techniques", at the University of Verona. He is currently a postdoc research associate at the Center for BioMedical Computing in Verona.

His research interests focus on complex system modeling (simulation, prediction, etc.) by unconventional computation models, mathematical optimization by traditional end evolutionary strategies, and data analysis, with particular applications to systems biology and bioinformatics. Alberto's recent work mainly involved the development of biological models based on membrane computing, by means of statistical (e.g., regression, variable selection), machine learning (e.g., neural networks) and optimization (e.g., genetic algorithms) tools. He has also developed software tools for the majority of the research problems investigated (e.g., MetaPlab) and he is co-author of scientific papers on these subjects which gained the appreciation in international journals and congresses.

During his PhD Alberto visited for five months the Automated Scheduling Optimization and Planning (ASAP) group at the Nottingham University (UK), and for one month the Science of Complex Interaction Lab (SCI-LAB) at the Nagoya University (Japan). He also partecipated to courses and PhD schools on bioinformatics and bio-inspired calculus.

During his master degree he spent a period at the Heriott Watt University of Edinburgh, where he developed evolutionary optimization algorithms for applications in computer vision. After his graduation he did an internship at the Italian Space Agency where he developed software for the strategical analysis of data related to space products.



Dr. Luca Marchetti   luca.marchetti_at_univr.it   

Luca Marchetti graduated in Computer science at the University of Verona in 2006 with a thesis titled "Applications of the metabolic algorithm in models of biological dynamics", he has now a fellowship at the Center for BioMedical Computation (CBMC) of Verona as a Phd student of the University of Verona. Currently he is one of the developers of the simulator of biological dynamics MPsim and his research mainly concerns the development of JAVA interfaces for simulators of biological dynamics and thestudy of applications of P systems in the field of Bioinformatics. He is co-author of different scientific articles and, recently, he has participated at the IEEE CEC07 (Congress on Evolutionary Computation)that had been held in Singapore since 25 to September 28th 2007.



Dr. Roberto Pagliarini   roberto.pagliarini_at_univr.it   Link

Roberto Pagliarini graduated in Computer Science at the University of Verona in 2007, with a dissertation titled "Esperimenti per la determinazione computazionale dei parametri regolativi nei P sistemi metabolici". He's currently a Ph.D student at the Department of Computer Science in Verona. His research interests focus on System Biology and modeling of biological systems by means of Membrane Computing. In particular he investigates the possibility of obtaining efficient and systematic methods for defining membrane models from experimental data of given processes. He is a collaborator of the biochemistry and vegetal physiology group at Scientific and Technological Department of Verona University, in order to investigate computational models for crucial events related to photosynthetic organisms.



Dr. Luca Bianco   l.bianco_at_cranfield.ac.uk   

Luca Bianco graduated in Computer Science at the University of Verona in 2003 and received his Ph.D. in Computer Science from the same University at the beginning of 2007 (doctoral thesis’ title: “Membrane models of biological systems”). The aim of his research has been the design and implementation of algorithms for the calculation of the dynamics of biological regulatory networks. Within his Ph.D., Luca had also a training period at the University of Sheffield (UK) and actively took part in several conferences both in Europe (Italy, Austria, Spain, United Kingdom, Romania, Holland and Greece where he has been “Invited Speaker” at the 8th International Workshop on Membrane Computing) and in USA (Stanford - CA). Since April 2008 he is research officer within the bioinformatics group of the University of Cranfield (UK). His work is sponsored by the Biotechnology and Biological Sciences Research Council (BBSRC) and it first involved the improvement of a proteomics pipeline to analyze tandem mass spectrometry data. He recently started a new project in quantitative proteomics. Luca is module manager of two modules of the MSc course in Bioinformatics held at Cranfield: Applications of Bioinformatics and Systems Biology. He is involved in the teaching of two short courses in Proteomics as well. He is a member of the British Society for Proteome Research (BSPR) and of the International Society for Computational Biology (ISCB).