
From BIMIB
Mauri Giancarlo
Personal page of Giancarlo Mauri.
Education and positions
Giancarlo Mauri graduated in Physics in 1973.
Since 1990 he is full professor of Computer Science, currently at the University of MilanoBicocca.
He was Director of the Department of Information Sciences at the University of Milan from 27.2.1992 to 31.10.1997; at the University of MilanoBicocca he has been Dean of the PhD School in Computer Science from 1.10.2001 to 30.09.2007, member of the Board of Directors from 1.11.2003 to 30.9.2009, and is Director of the Department of Computer Science since 1.10.2010.
Research
Topics
His research has touched on various issues, including: theory of automata and formal languages, neural networks and machine learning algorithms, unconventional computation models such as DNA computing and membrane computing, theory and applications of cellular automata.
In the last 15 years, he became more and more interested in problems of interdisciplinary nature, applying his expertise in designing efficient algorithms and in machine learning to the development of tools for the analysis of biosequences (bioinformatics) and of biomedical data and for the modeling and analysis of complex biological systems (systems biology).
His recent research in the area of Bioinformatics and Systems Biology concerns in particular:
 Development of efficient algorithms for the analysis of biosequences, in particular for discovery of signals or common motifs in DNA or RNA sequences, reconstruction and comparison of phylogenies, prediction of alternative splicing sites, inference of regulatory networks also through the analysis of transcriptomic data and the clustering of coregulated genes.
 Development of biomedical data integration tools through web portals and services. In particular, under the European Neuroweb project, which involved four international clinical neurological centers, it has developed an ontology for integration of data related to cerebrovascular disease (stroke).
 Development of tools for modeling and simulation "in silico", both deterministic and stochastic, of complex biological systems and processes. In particular, some signaling pathways in yeast and bacterial chemotaxis have been modeled and simulated. To speed up the simulations, computationally very demanding, implementations on parallel architectures based on GPU have been realized. Furthermore, some theoretical aspects related to the role of noise and to sensitivity analysis in biochemical reaction networks have been studied.
 Development of tools based on machine learning techniques and probabilistic inference to study the progression of tumors. One line of research within a project of Systems Biology concerns the modeling and simulation of mitochondrial metabolism in normal and mutated cells to compare different metabolic phenotypes. In a different context we have analyzed expression levels of microRNAs and chromosomal instability for the inference of progression models for breast and colorectal cancers. Finally, we are defining a general conceptual scenario based on "probability raising" techniques and efficient and integrated software tools for the inference of tumor progression models.
During his career, Professor Mauri has published about 350 research papers in international journals, books and conference proceedings, on the themes outlined above.
Research projects
He is or has been responsible of the following research projects:
 Theory of Algorithms (Ministry of the University), 1982  1984
 Design and analysis of Algorithms (Ministry of the University), 1984  1986
 ASMICS 1 and 2  Algebraic and Syntactic Methods In Computer Science (Esprit Basic Research Action) 1990  1996
 NEUROCOLT  Neural networks and computational learning theory (Esprit Basic Research Action) 1995  1998
 Algorithms and computation models (Ministry of the University) 1985  1996
 Automata and formal languages (Ministry of the University) 1998  2001
 P–vision (Pirelli Coordinamento Pneumatici SpA), 1996  1998
 OMI/MODES  MOdular MicroElectronicSystem DESign (ESPRIT Contract n. 20.592) 19951998
 CAPP  Cellular Automata for Percolation Processes (Technology Transfer Node NOTSOMAD contract n. 25.999) 19961998
 GRAAL: a language based on graphs (ENEL SpA), 19971998
 Analysis and modelling of semistructured knowledge (ENEL SpA), 19992001
 Deformalization of formal specifications of complex industrial systems (CESI SpA), 19992001
 Bioinformatics and genomics (Ministry of the University) 19992001
 MolCoNet  Molecular Computing Network (5th European framework, Contract Number IST200132008), 2001  2004
 Secure communication protocols (ST Microelettronics S.r.l.), 2001
 Oncology over the Internet, (Ministry of the University), 20012002
 Acquisition and processing of threedimensional data for classification and recognition of people and objects (Comerson S.p.A.), 2000  2002
 Study of cryptographic algorithms and their implementation in embedded systems, (Microsystems Ltd.), 2002
 NEUROWEB: Integration and sharing of information and knowledge in neurology and neurosciences (6th European research framework, Contract no.: 518513), 20062008, responsible of the MilanoBicocca unit
 Bronte: Biological processes Redescriptions by ONtology Expressions, (The IST Programme Support Measures, Action Line: IST20018.1.2), 20062008
 Network Enabled Drug Design (NEDD)  (Lombardy Region, 2010/2013) Responsible of WPA3: Bioinformatics and computational biology
 Systems biology of the mitochondrial energetic (Ministry of the University), 20122015, responsible of the computational unit
Selected papers (last 5 years)
Bioinformatics and systems biology
 D. Pescini, P. Cazzaniga, D. Besozzi, G. Mauri, L. Amigoni, S. Colombo, E. Martegani (2012). Simulation of the Ras/cAMP/PKA pathway in budding yeast highlights the establishment of stable oscillatory states. Biotechnology Advances 30(1), 99–107
 L. Alberghina, D. Gaglio, C. Gelfi, R.M. Moresco, G. Mauri, P. Bertolazzi, C. Messa, M.C. Gilardi, F. Chiaradonna, M. Vanoni (2012). Cancer cell growth and survival as a system–level property sustained by enhanced glycolysis and mitochondrial metabolic remodeling. Frontiers in Physiology 3:362
 F. Archetti, I. Giordani, G. Mauri, E. Messina (2012). A new clustering approach for learning transcriptional modules. Int. J. Data Mining and Bioinformatics 6(3), 304–323
 I. Zoppis, E. Gianazza, M. Borsani, C. Chinello, V. Mainini, C. Galbusera, C. Ferrarese, G. Galimberti, A. Sorbi, B. Borroni, F. Magni, M. Antoniotti, G. Mauri (2012). Mutual Information Optimization for Mass Spectra Data Alignment. IEEEACM Trans Comp Biol and Bioinformatics 9(3), 934–939
 G. Caravagna, G. Mauri, A. d'Onofrio (2013). The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks. PLoS ONE 8(2): e51174
 C. Maj, E. Mosca, I. Merelli, G. Mauri, L. Milanesi (2013). Sensitivity analysis for studying the relation between biochemical reactions and metabolic phenotypes. J of Bioinformatics and Comput Biol 11(1) 1340002
 M. Antoniotti, G. D. Bader, G. Caravagna, S. Crippa, A. Graudenzi, G. Mauri (2013). GeStoDifferent: A Cytoscape plugin for the generation and the identification of Gene Regulatory Networks describing a stochastic cell differentiation process. Bioinformatics 29(4), 513–514
 M. S. Nobile, P. Cazzaniga, D. Besozzi, D. Pescini, G. Mauri (2014). cuTauLeaping: A GPU–Powered Tau–Leaping Stochastic Simulator for Massive Parallel Analyses of Biological Systems. PLoS ONE 9(3): e91963
 C. Chinello, M. Cazzaniga, G. De Sio, A. Smith, E. Gianazza, A. Grasso, F. Rocco, S. Signorini, M. Grasso, S. Bosari, I. Zoppis, M. Dakna, Y. van der Burgt, G. Mauri, F. Magni (2014). Urinary signatures of Renal Cell Carcinoma investigated by peptidomic approaches. PLoS ONE 9(9): e106684
 G. Caravagna, A. D'Onofrio, M. Antoniotti, G.Mauri (2014). Stochastic Hybrid Automata with delayed transitions to model biochemical systems with delays. Information and computation 236, 19–34
 C. Cava, G. Bertoli, I. Zoppis, M. Ripamonti, G. Mauri, I. Castiglioni (2014). Integration of mRNA expression profile, copy number and microRNA expression levels in Breast Cancer to improve grade definition. PLoS ONE 9(5): e97681
 M. S. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri (2014). GPU–accelerated simulations of mass–action kinetics models with cupSODA. J. of Supercomputing 69(1), 17–24
 L. Olde Loohuis, G. Caravagna, A, Graudenzi, D. Ramazzotti, G. Mauri, A. Antoniotti, B. Mishra (2014). Inferring tree causal models of cancer progression with probability raising. PLoS ONE 9(10): e108358
 C. Damiani, D. Pescini, R. Colombo, S. Molinari, L. Alberghina, M. Vanoni, G. Mauri (2014). An ensemble evolutionary constraint–based approach to understand the emergence of metabolic phenotypes. Natural Computing 13(3), 321–331
 P. Cazzaniga, C. Damiani, D. Besozzi, R. Colombo, M. S. Nobile, D. Gaglio, D. Pescini, S. Molinari, G. Mauri, L. Alberghina, M. Vanoni (2014). Computational Strategies for a System–Level Understanding of Metabolism. Metabolites 2014, 4, 1034–1087
 C. Cava, I. Zoppis, M. Gariboldi, I. Castiglioni, G. Mauri, M. Antoniotti (2014). Combined analysis of chromosomal instabilities and gene expression for colon cancer progression inference. J. Clinical Bioinformatics 4(1):2
 D. Ramazzotti, G. Caravagna, L. Olde Loohuis, A. Graudenzi, I. Korsunsky, G. Mauri, M. Antoniotti, B. Mishra (2015). CAPRI: Efficient Inference of Cancer Progression Models from Cross–sectional Data. Bioinformatics 31(18), 2015, 30163026
 C. Chinello, M. Cazzaniga, G. De Sio, A.J. Smith, A. Grasso, B. Rocco, S. Signorini, M. Grasso, S. Bosari, I. Zoppis, G. Mauri, F. Magni (2015). Tumor size, stage and grade alterations of urinary peptidome in RCC. J. of Translational Medicine 13(1):332
 S. Rubinacci, A. Graudenzi, G. Caravagna. G. Mauri, J. Osborne, J. PittFrancis, M. Antoniotti (2015). CoGNaC: a Chaste plugin for the multiscale simulation of Gene regulatory Networks driving the spatial dynamics of tissues and Cancer. Cancer Informatics 2015:14(S4) 53–65
 M. Di Filippo, R. Colombo, C. Damiani, D. Pescini, D. Gaglio, M. Vanoni, L. Alberghina, G. Mauri (2016). Zoomingin on cancer metabolic rewiring with tissue specific constraintbased models. Computational Biology and Chemistry 62, 6069
 L. De Sano, G. Caravagna, D. Ramazzotti, A. Graudenzi, G. Mauri, B. Mishra, M. Antoniotti (2016). TRONCO: an R package for the inference of cancer progression models from heterogeneous genomic data. Bioinformatics 32(12):19111913
 M. Galli, F. Pagni, G.De Sio, A.Smith, C. Chinello, M. Stella, V. L'Imperio, M. Manzoni, M. Garancini, D. Massimini, N. Mosele G. Mauri, I. Zoppis, F. Magni (2017). Proteomic profiles of thyroid tumors by Mass SpectrometryImaging on Tissue Microarrays. BBA  Proteins & Proteomics 1865(7), 817827
 G. Caravagna, A. Graudenzi, D. Ramazzotti, R. SanzPamplona, L. De Sano, G. Mauri, V. Moreno, M. Antoniotti, B. Mishra (2016). Algorithmic methods to infer the evolutionary trajectories in cancer progression. PNAS 113(28): E4025E4034
 A. Graudenzi, G. Caravagna, I.M. Bocicor, C. Cava, M. Antoniotti, G. Mauri (2016). Ordering cancer mutational profiles of crosssectional copy number alterations. Int. J. Data Mining and Bioinformatics 15(1), 5983
 C. Cava, A. Colaprico, G. Bertoli, G. Bontempi, G. Mauri, I. Castiglioni (2016). How interacting pathways are regulated by miRNAs in breast cancer subtypes. BMC Bioinformatics 2016, 17 (Suppl 12):348
 M. Galli, I. Zoppis, G. De Sio, C. Chinello, F. Pagni, F. Magni, G. Mauri (2016). A Support Vector Machine classification of thyroid bioptic specimens using MALDIMSI data. Advances in Bioinformatics 2016, Article ID 3791214
 M. Galli, I. Zoppis, A. Smith, F. Magni, G. Mauri (2016). Machine learning approaches in MALDIMSI: clinical applications.Expert Review of Proteomics, 13(7):68596
 S. de Franciscis, G. Caravagna, G. Mauri, A. d’Onofrio (2016). Gene switching rate determines response to extrinsic perturbations in the selfactivation transcriptional network motif. Scientific Reports 6, Article number: 26980
 A. Tangherloni, M S Nobile, D. Besozzi, G. Mauri, P. Cazzaniga (2017). LASSIE: simulating largescale models of biochemical systems on GPUs. BMC Bioinformatics (2017) 18:246
 A. Tangherloni, MS. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri (2017). Gillespie's Stochastic Simulation Algorithm on MIC Coprocessors. J. of Supercomputing 73(2): 67668
 M.S. Nobile, L.A. Harris, J.C. Pino, D. Besozzi, P. Cazzaniga, G. Mauri, C.F. Lopez (2017). GPUpowered model analysis with PySB and cupSODA. Bioinformatics btx42
 M. Antoniotti, G. Caravagna, L. De Sano, A. Graudenzi, G. Mauri, B. Mishra, D. Ramazzotti (2016). Design of the TRONCO BioConductor Package for TRanslational ONCOlogy. R Journal 8(2), 3959
 A. Paroni, A. Graudenzi, G. Caravagna, C. Damiani, G. Mauri, M. Antoniotti (2016). CABeRNET: a Cytoscape app for augmented Boolean models of gene regulatory NETworks. BMC Bioinformatics (2016) 17:64
 C. Cava, A. Colaprico, G. Bertoli, A. Graudenzi, T.C. Silva, C. Olsen, H. Noushmehr, G. Bontempi, G. Mauri, I. Castiglioni (2017). SpidermiR: An R/Bioconductor package for integrative network analysis with miRNA data. Int. J. of Molecular Science 18(2), 274
 A. Graudenzi, C. Cava, G. Bertoli, B. Fromm, K. Flatmark, G. Mauri, I. Castiglioni (2017). Pathwaybased classification of breast cancer subtypes. Frontiers In Bioscience, Landmark, 22 (10), 16971712
 MS. Nobile, AE. Porreca, S. Spolaor, L. Manzoni, P. Cazzaniga, G. Mauri, D. Besozzi (2017). Efficient simulation of reaction systems on Graphics Processing Units. Fundamenta Informaticae 154 (2017) 1–15
 C. Damiani, M. Di Filippo, D. Pescini, D. Maspero, R. Colombo, G. Mauri (2017). popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. Bioinformatics, 33, 2017, i311–i318
Natural Computing
 L. Corolli, C. Maj, F. Marini, D. Besozzi, G. Mauri (2012). An excursion in reaction systems: from computer science to biology. Theor Comp Sci 454, 95–108
 L. Vanneschi, Y. Pirola, G. Mauri, M. Tomassini, P. Collard, S. Verel (2012). A study of the neutrality in boolean functions landscapes in genetic programming. Theor Comp Sci 425, 34–57
 L. Manzoni, L. Vanneschi, G. Mauri (2012). A Distance Between Populations for One–Point Crossover in Genetic Algorithms. Theoretical Computer Science 429, 213–221
 L. Vanneschi, G. Mauri (2012). A Study on Learning Robustness using Asynchronous 1D Cellular Automata Rules. Natural Computing 11(2), 289–302
 A. Dennunzio, E. Formenti, L. Manzoni, G. Mauri (2013). m–Asynchronous Cellular Automata: from fairness to quasi–fairness. Natural Computing 12(4): 561572
 R. Dondi, G. Mauri, I. Zoppis (2013). The l–diversity Problem: Tractability and Approximability. Theor Comp Sci 511, 159171.
 G. Mauri, A. Leporati, A. E. Porreca, C. Zandron (2013). Recent complexity–theoretic results on P systems with active membranes. J. Logic and Computation 25(4), 2015, 1047–1071
 A. Leporati, A. E. Porreca, C. Zandron, G. Mauri (2013). Improved Universality Results for Parallel Enzymatic Numerical P Systems. Int. J. of Unconventional Computing 9(56): 385404
 A. Alhazov, A. Leporati, G. Mauri, A. E. Porreca, C. Zandron (2014). Space complexity equivalence of P systems with active membranes and Turing machines. Theor Comp Sci 529, 69–81
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2014). Constant–Space P Systems with Active Membranes. Fundamenta Informaticae 134(1–2), 111–128
 A. Valsecchi, L. Vanneschi, G. Mauri (2014). A Study of Search Algorithms’ Optimization Speed. J. of Combinatorial Optimization 27(2): 256–270
 A. Leporati, G. Mauri, A. E. Porreca, C. Zandron (2014). A Gap in the Space Hierarchy of P Systems with Active Membranes. J. Automata, Languages and Combinatorics 19(1–4), 173–184
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2015). Membrane Division, Oracles, and the Counting Hierarchy. Fundamenta Informaticae 138(1–2) 97–111
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2016). Monodirectional P systems. Natural Computing 15, 551564
 A. Dennunzio, E. Formenti, L. Manzoni, G. Mauri, A. E. Porreca (2017). Computational Complexity of Finite Asynchronous Cellular Automata.Theor Comp Sci 664, 131–143
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). A toolbox for simpler active membrane algorithms. Theor Comp Sci 673, 42–57
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). Tissue P Systems with Small Cell Volume. Fundamenta Informaticae 154 (2017), 1–15
 A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). Characterising the complexity of tissue P systems with fission rules. J. Computer and System Sciences, in press
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