September 21, 2017, Thursday

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Mauri Giancarlo

Personal page of Giancarlo Mauri.


Contents

Education and positions

Giancarlo Mauri graduated in Physics in 1973.

Since 1990 he is full professor of Computer Science, currently at the University of Milano-Bicocca.

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 Milano-Bicocca 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 co-regulated 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 MicroElectronic-System DESign (ESPRIT Contract n. 20.592) 1995-1998
  • CAPP - Cellular Automata for Percolation Processes (Technology Transfer Node NOTSOMAD contract n. 25.999) 1996-1998
  • GRAAL: a language based on graphs (ENEL SpA), 1997-1998
  • Analysis and modelling of semi-structured knowledge (ENEL SpA), 1999-2001
  • Deformalization of formal specifications of complex industrial systems (CESI SpA), 1999-2001
  • Bioinformatics and genomics (Ministry of the University) 1999-2001
  • MolCoNet - Molecular Computing Network (5th European framework, Contract Number IST-2001-32008), 2001 - 2004
  • Secure communication protocols (ST Microelettronics S.r.l.), 2001
  • Oncology over the Internet, (Ministry of the University), 2001-2002
  • Acquisition and processing of three-dimensional 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), 2006-2008, responsible of the Milano-Bicocca unit
  • Bronte: Biological processes Redescriptions by ONtology Expressions, (The IST Programme Support Measures, Action Line: IST-2001-8.1.2), 2006-2008
  • 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), 2012-2015, responsible of the computational unit


Selected papers (last 5 years)

Bioinformatics and systems biology

  1. 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
  2. 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
  3. 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
  4. 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. IEEE-ACM Trans Comp Biol and Bioinformatics 9(3), 934–939
  5. G. Caravagna, G. Mauri, A. d'Onofrio (2013). The Interplay of Intrinsic and Extrinsic Bounded Noises in Biomolecular Networks. PLoS ONE 8(2): e51174
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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, 3016-3026
  18. 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
  19. S. Rubinacci, A. Graudenzi, G. Caravagna. G. Mauri, J. Osborne, J. Pitt-Francis, 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
  20. M. Di Filippo, R. Colombo, C. Damiani, D. Pescini, D. Gaglio, M. Vanoni, L. Alberghina, G. Mauri (2016). Zooming-in on cancer metabolic rewiring with tissue specific constraint-based models. Computational Biology and Chemistry 62, 60-69
  21. 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):1911-1913
  22. 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 Spectrometry-Imaging on Tissue Microarrays. BBA - Proteins & Proteomics 1865(7), 817-827
  23. G. Caravagna, A. Graudenzi, D. Ramazzotti, R. Sanz-Pamplona, 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): E4025-E4034
  24. A. Graudenzi, G. Caravagna, I.M. Bocicor, C. Cava, M. Antoniotti, G. Mauri (2016). Ordering cancer mutational profiles of cross-sectional copy number alterations. Int. J. Data Mining and Bioinformatics 15(1), 59-83
  25. 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
  26. 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 MALDI-MSI data. Advances in Bioinformatics 2016, Article ID 3791214
  27. M. Galli, I. Zoppis, A. Smith, F. Magni, G. Mauri (2016). Machine learning approaches in MALDI-MSI: clinical applications.Expert Review of Proteomics, 13(7):685-96
  28. S. de Franciscis, G. Caravagna, G. Mauri, A. d’Onofrio (2016). Gene switching rate determines response to extrinsic perturbations in the self-activation transcriptional network motif. Scientific Reports 6, Article number: 26980
  29. A. Tangherloni, M S Nobile, D. Besozzi, G. Mauri, P. Cazzaniga (2017). LASSIE: simulating large-scale models of biochemical systems on GPUs. BMC Bioinformatics (2017) 18:246
  30. A. Tangherloni, MS. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri (2017). Gillespie's Stochastic Simulation Algorithm on MIC Coprocessors. J. of Supercomputing 73(2): 676-68
  31. M.S. Nobile, L.A. Harris, J.C. Pino, D. Besozzi, P. Cazzaniga, G. Mauri, C.F. Lopez (2017). GPU-powered model analysis with PySB and cupSODA. Bioinformatics btx42
  32. 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), 39-59
  33. 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
  34. 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
  35. A. Graudenzi, C. Cava, G. Bertoli, B. Fromm, K. Flatmark, G. Mauri, I. Castiglioni (2017). Pathway-based classification of breast cancer subtypes. Frontiers In Bioscience, Landmark, 22 (10), 1697-1712
  36. 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
  37. 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

  1. 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
  2. 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
  3. L. Manzoni, L. Vanneschi, G. Mauri (2012). A Distance Between Populations for One–Point Crossover in Genetic Algorithms. Theoretical Computer Science 429, 213–221
  4. L. Vanneschi, G. Mauri (2012). A Study on Learning Robustness using Asynchronous 1D Cellular Automata Rules. Natural Computing 11(2), 289–302
  5. A. Dennunzio, E. Formenti, L. Manzoni, G. Mauri (2013). m–Asynchronous Cellular Automata: from fairness to quasi–fairness. Natural Computing 12(4): 561-572
  6. R. Dondi, G. Mauri, I. Zoppis (2013). The l–diversity Problem: Tractability and Approximability. Theor Comp Sci 511, 159-171.
  7. 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
  8. 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(5-6): 385-404
  9. 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
  10. 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
  11. A. Valsecchi, L. Vanneschi, G. Mauri (2014). A Study of Search Algorithms’ Optimization Speed. J. of Combinatorial Optimization 27(2): 256–270
  12. 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
  13. 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
  14. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2016). Monodirectional P systems. Natural Computing 15, 551-564
  15. 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
  16. 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
  17. 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
  18. 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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