September 28, 2020, Monday

From BIMIB

Jump to: navigation, search

Mauri Giancarlo

Personal page of Giancarlo Mauri.


Education and academic positions

• 13.04.1973: Degree (Laurea) in Physics, summa cum laude, Università degli Studi di Milano, Italy

• 01.11.1977 – 16.12.1979: Research grant, Institute of Cybernetics – University of Milano

• 17.12.1979 – 31.07.1980: Assistant professor of Computer Science at the University of Udine

• 01.08.1980 – 22.04.1985: Assistant professor of Computer Science at the University of Milano

• 23.04.1985 – 31.10.1990: Associate professor of Computer Science at the University of Milano

• 01.11.1990 – 31.10.1998: Full professor of Computer Science at the University of Milano

• 01.11.1998 – 31.10.2019: Full professor of Computer Science at the University of Milano-Bicocca

• 01.11.2019 – now : Senior professor of Computer Science at the University of Milano-Bicocca

• 27.02.1992 – 31.10.1997: Director of the Dept. of Information Sciences, University of Milano

• 01.11.2001 – 31.10.2007: Chair of PhD School in Computer Science, University of Milano-Bicocca

• 01.11.2003 – 30.09.2009: Member of the Board of Directors of the University of Milano-Bicocca

• 01.10.2010 – 30.09.2018: Director of the Dept. of Computer Science, Systems and Communication, University of Milano-Bicocca

• 1994 – 1998: Member of the Scientific Council of Laboratory for Parallelism (LIP), Ecole Normale Superieure, Lyon, France

• 01.01.2000 – 31.10.2019: Director of the Laboratory of Bioinformatics and Natural Computing (BIMIB), University of Milano-Bicocca

• 01.01.2004 – 31.10.2013: Member of the Board of Directors of CoRiMAv (Research Consortium on Advanced Materials)

• 13.07.2005 – 12.07.2008: Member of the Scientific Council of the Genopolis Consortium

• 14.01.2010 – 13.01.2013: Member of the Board of Directors of CINI (Interuniversitary National Consortium for Informatics)

• 25.06.2013 – Now: Member of the Council of ELIXIR-ITA, Italian node of the European Bioinformatics Infrastructure ELIXIR

• 20.11.2013 – now: Member of the Council of CINECA (Italian Supercomputing Center)

Research

Topics

My research has touched on various issues in theoretical computer science, including: theory of automata and formal languages, neural networks and machine learning algorithms, unconventional computation models such as DNA computing and membrane computing, evolutionary computing, theory and applications of cellular automata.

In the last 20 years, I became more and more interested in problems of interdisciplinary nature, applying my 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).

During my career, I published about 400 research papers in international journals, books and conference proceedings, on the themes outlined above.


Research projects

I am or have been involved as coordinator of the whole project or of a local unit in the following research projects:

  • Theory of Algorithms (Ministry of the University), 01/11/1981 – 31/10/1984
  • Design and analysis of Algorithms (Ministry of the University), 01/11/1984 – 31/10/1987
  • Algorithms and computation models (Ministry of the University) 01/11/1987 – 31/10/1993
  • ASMICS 1 and 2 - Algebraic and Syntactic Methods In Computer Science (Esprit Basic Research Action) 1990 - 1996
  • Efficiency of algorithms and design of information structures (Ministry of the University) 01/11/1993 – 31/10/1996
  • Approximation algorithms and computational learning (Ministry of the University) 01/11/1995 – 31/10/1997
  • Approximation algorithms and natural computing (Ministry of the University) 01/11/1998 – 31/10/1999
  • Cellular automata (CNR CT94.00452.CT12.115.26124) 1994-1996
  • NEUROCOLT - Neural networks and computational learning theory (Esprit Basic Research Action) 1995 - 1998
  • Automata and formal languages (Ministry of the University) 1998 - 2001
  • NeuroCOLT2 - Neural networks and computational learning theory (Esprit Basic Research Action) 1999-2002
  • 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), 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
  • The Home of Internet of Things (Home IoT) (Regione Lombardia – ID139625), 06/12/2016 – 05/06/2019
  • Information Technology: The Future of Cancer Treatment (FLAG-ERA funds) 2016-2019

Selected papers (last 5 years)

Bioinformatics, radiomics and systems biology

  1. M. S. Nobile, G. Votta, R. Palorini, S. Spolaor, H. De Vitto, P. Cazzaniga, F. Ricciardiello, G. Mauri, L. Alberghina, F. Chiaradonna, D. Besozzi (2020). Fuzzy modeling and global optimization to predict novel therapeutic targets in cancer cells. Bioinformatics 36(7), 2181-2188
  2. M. Di Filippo, C. Damiani, M. Vanoni, D. Maspero, G. Mauri, L. Alberghina, D. Pescini (2020). Single-cell digital twins for cancer preclinical investigation. In: “Metabolic Flux Analysis in Eukaryotic Cells” (Nagrath D. ed) Methods in Molecular Biology, vol 2088, 331-343, Humana, New York, NY
  3. C. Han, L. Rundo, R. Araki, Y. Furukawa, G. Mauri, H. Nakayam a, H. Hayashi (2020). Infinite Brain MR Images: PGGAN-Based Data Augmentation for Tumor Detection. Smart Innovation, Systems and Technologies 151, pp. 291-303
  4. L. Rundo, C. Han, J. Zhang, R. Hataya, Y. Nagano, C. Ferretti, C. Militello, MC. Gilardi, S. Vitabile, H. Nakayama, G. Mauri (2020). CNN-based Prostate Zonal Segmentation on T2-weighted MR Images: A Cross-dataset Study. Smart Innovation, Systems and Technologies 151, pp. 269-280
  5. MS. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri (2019). ginSODA: massive parallel integration of stiff ODE systems on GPUs. Journal of Supercomputing 75(12), 7844–7856
  6. L. Rundo, C. Han, Y. Nagano, J. Zhang, R. Hataya, C. Militello, A.Tangherloni, M.S. Nobile, C. Ferretti, D. Besozzi, M.C. Gilardi, S. Vitabile, G. Mauri, H. Nakayama, P. Cazzaniga (2019). USE-Net: Incorporating Squeeze-and-Excitation Blocks into U-Net for Prostate Zonal Segmentation of Multi-institutional MRI Datasets. Neurocomputing 365, 31-43
  7. M S. Nobile, T. Vlachou, S. Spolaor, D. Bossi, P. Cazzaniga, L. Lanfrancone, G. Mauri, PG. Pelicci, D. Besozzi (2019). Modeling cell proliferation in human acute myeloid leukemia xenografts. Bioinformatics 35(18): 3378–3386
  8. M. S. Nobile, T. Vlachou, S. Spolaor, P. Cazzaniga, G. Mauri, P G Pelicci, D. Besozzi (2019). ProCell: Investigating cell proliferation with Swarm Intelligence. Proc CIBCB 2019 – IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology, pp. 1-8
  9. L. Rundo; A. Tangherloni; P. Cazzaniga; M S Nobile; G. Russo; MC Gilardi; S. Vitabile; G. Mauri; D. Besozzi; C. Militello (2019). A novel framework for MR image segmentation and quantification by using MedGA. Computer Methods and Programs in Biomedicine 176, pp. 159-172
  10. I. Zoppis, S. Manzoni, G. Mauri (2019). A Computational Model for Promoting Targeted Communication and Supplying Social Explainable Recommendations. Proc. CBMS 2019 – 32 th IEEE CBMS International Symposium on Computer-Based Medical Systems, Cordoba, Spain, 5-7 June 2019, 429-434
  11. A. Tangherloni, S. Spolaor, L. Rundo, M S. Nobile, I. Merelli, P. Cazzaniga, D. Besozzi, G. Mauri, P. Liò (2019). GenHap: A Novel Computational Method Based on Genetic Algorithms for Haplotype Assembly. BMC Bioinformatics 2019 20(Suppl 4):172
  12. L. Rundo, A. Tangherloni, M. S. Nobile, C. Militello, G. Russo, S. Vitabile, MC Gilardi, G. Mauri, P. Cazzaniga, D. Besozzi (2019). MedGA: A Novel Evolutionary Method for Medical Image Enhancement. Expert Systems With Applications 119, pp 387-399
  13. C. Damiani, D. Maspero, M. Di Filippo, R. Colombo, D. Pescini, A. Graudenzi, HV. Westerhoff, L. Alberghina, M. Vanoni, G. Mauri (2019). Integration of single-cell RNA-seq data into metabolic models to characterize cancer metabolism. Plos CompBiol 15 (2), e1006733
  14. Spolaor, S., Nobile, M.S., Mauri, G., Cazzaniga, P., Besozzi, D. (2019). Coupling Mechanistic Approaches and Fuzzy Logic to Model and Simulate Complex Systems. IEEE Transactions on Fuzzy Systems
  15. D. Maspero, A. Graudenzi, S. Singh, D. Pescini, G. Mauri, M. Antoniotti, C. Damiani (2019). Synchronization effects in a metabolism-driven model of multi-cellular system. Proc. WIVACE 2018, Comm. in Computer and Information Science (CCIS) 900, 115–126
  16. C. Han, L. Rundo, R. Araki , Y. Nagano, Y. Furukawa, G. Mauri , H. Nakayama, H. Hayashi (2019). Combining Noise-to-Image and Image-to-Image GANs: Brain MR Image Augmentation for Tumor Detection. IEEE Access 7, 8869751, pp. 156966-156977
  17. L. Rundo, A. Tangherloni, S. Galimberti, P. Cazzaniga, R. Woitek, E. Sala, M. S. Nobile, G. Mauri (2019). HaraliCU: GPU-Powered Haralick Feature Extraction on Medical Images Exploiting the Full Dynamics of Gray-scale Levels. Proc PaCT 2019 – Parallel Computing Technologies, Lect. Not. in Computer Science 11657, 304-318
  18. L. Rundo, C. Militello, A. Tangherloni, G. Russo, R. Lagalla, G. Mauri, MC. Gilardi, S. Vitabile (2019). Computer-assisted Approaches for Uterine Fibroid Segmentation in MRgFUS Treatments: Quantitative Evaluation and Clinical Feasibility Analysis. Smart Innovation, Systems and Technologies 103, pp. 229-241
  19. Corchs S, Chioma G, Dondi R, Gasparini F, Manzoni S, Markowska-Kacznar U, Mauri G, Zoppis I, Morreale A (2019). Computational Methods for Resting-State EEG of Patients With Disorders of Consciousness. Frontiers Neurosciences 13:807
  20. G. Pietrabissa, I. Zoppis, G. Mauri, R. Ghiretti, EM. Giusti, R. Cattivelli, C. Spatola, GM. Manzoni, G. Castelnuovo (2019). System of Nudge Theory-Based ICT Applications for Older Citizens: The SENIOR Project. Proc. MindCare 2019 – Int. Symp. on Pervasive Computing Paradigms for Mental Health, LNICST 288, pp 29-42
  21. A. Tangherloni, L. Rundo, S. Spolaor, MS. Nobile, I. Merelli, D. Besozzi, G. Mauri, P. Cazzaniga, P. Liò (2019). High Performance Computing for Haplotyping: Models and Platforms. Proc. Euro-Par 2018 - Parallel Processing Workshops, Lect. Not. in Computer Science 11339, 650-661
  22. S. Spolaor, M. Gribaudo, M. Iacono, T. Kadavy, Z. Komínková Oplatková, G. Mauri, S. Pllana, R. Senkerik, N. Stojanovic, E. Turunen, A. Viktorin, S. Vitabile, A. Zamuda M. S. Nobile (2019). Towards human cell simulation. In “cHiPSet” (J. Kolodziej and H. Gonzalez-Vélez Eds.), Lect. Not. in Computer Science 11400, pp. 221-249
  23. I. Zoppis, R. Dondi, S. Manzoni, G. Mauri (2019). Patient Engagement: Theoretical and Heuristic Approaches for Supporting the Clinical Practice. Proc. AI*AAL 2018 - Fourth Italian Workshop on Artificial Intelligence for Ambient Assisted Living, CEUR-WS 2333, paper 4
  24. D. Vella, F. Vitali, D. Di Silvestre, G. Mauri, R. Bellazzi (2018). MTGO: PPI network analysis via topological and functional module identification. Scientific Reports, 8(1), 5499
  25. A. Graudenzi; D. Maspero; M. Di Filippo; M. Gnugnolo; C. Isella; G. Mauri; E. Medico; M. Antoniotti; C. Damiani (2018). Integration of transcriptomic data and metabolic networks in cancer samples reveals highly significant prognostic power. J. of Biomedical Informatics 87, pp.37-49
  26. MS Nobile, A Tangherloni, L Rundo, S Spolaor, D Besozzi, G Mauri, P. Cazzaniga (2018). Computational Intelligence for Parameter Estimation of Biochemical Systems. Proc.CEC 2018 – IEEE Congress on Evolutionary Computation (CEC), 1-8, Article 8477873
  27. L. Rundo, C. Militello, G. Russo, S. Vitabile, MC. Gilardi, G. Mauri (2018). GTVcut for Neuro-Radiosurgery Treatment Planning: An MRI Brain Cancer Seeded Image Segmentation Method Based on a Cellular Automata Model. Natural Computing 17(3): 521-536
  28. R. Colombo, C. Damiani, D. GIlbert, M. Heiner, G. Mauri, D. Pescini (2018). Emerging ensembles of kinetic parameters to characterize observed metabolic phenotypes. BMC Bioinformatics 2018, 19(Suppl 7):251
  29. I. Zoppis, R. Dondi, D. Coppetti, A. Beltramo, G. Mauri (2018). Distributed Heuristics for Optimizing Cohesive Groups: A Support for Clinical Patient Engagement in Social Network Analysis. Proc. PDP 2018 – 26th Euromicro Int. Conf. on Parallel, Distributed, and Network-Based Processing, 259-266
  30. C. Han, H. Hayashi, L. Rundo, R. Araki, W. Shimoda, S. Muramatsu, F. Yujiro, G. Mauri, H. Nakayama (2018). GAN-Based Synthetic Brain MR Image Generation. Proc. ISBI 2018 – 15th IEEE International Symposium on Biomedical Imaging, pp. 734-738
  31. C.Cava, G. Bertoli, G. Mauri, I. Castiglioni (2018). In-Silico Integration Approach to Identify a Key miRNA Regulating a Gene Network in Aggressive Prostate Cancer. Int. J. Mol. Sci. 2018, 19(3), 910
  32. L. Rundo, C. Militello, A. Tangherloni, G. Russo, S. Vitabile, MC. Gilardi, G. Mauri (2018). NeXt for Neuro-radiosurgery: A Fully Automatic Approach for Necrosis Extraction in Brain Tumor MRI Using an Unsupervised Machine Learning Technique. International Journal of Imaging Systems and Technology 28, 21-37
  33. V. Conti, L. Rundo, C. Militello, G. Mauri, S. Vitabile (2017). Resource-Efficient Hardware Implementation of a Neural-based Node for Automatic Fingerprint Classification. J of Wireless Mobile Networks, Ubiquitous Computing, and Dependable Applications (JoWUA) 8(4),19-36
  34. D. Vella, I. Zoppis, G. Mauri, P. Mauri, D. Di Silvestre (2017). From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data. EURASIP J on Bioinformatics and Systems Biology 2017:6
  35. C. Militello, L. Rundo, V. Conti, L. Minafra, FP Cammarata, G. Mauri, MC. Gilardi, N. Porcino (2017). Area-Based Cell Colony Surviving Fraction Evaluation: A Novel Fully Automatic Approach Using General-Purpose Acquisition Hardware. Computers in Biology and Medicine 89(1), 454-465
  36. C. Damiani, R. Colombo, D. Gaglio, F. Mastroianni, D. Pescini, H.V. Westerhoff, G. Mauri, M. Vanoni, L. Alberghina (2017). A metabolic core model elucidates how enhanced utilization of glucose and glutamine, with enhanced glutamine-dependent lactate production, promotes cancer cell growth: the WarburQ effect'. Plos Computational Biology 13(9), e1005758
  37. L. Rundo, A. Stefano, C. Militello, G. Russo, MG. Sabini, C. D'Arrigo, F. Marletta, M. Ippolito, G. Mauri, S. Vitabile, MC. Gilardi (2017). A Fully Automatic Approach for Multimodal PET and MR Image Segmentation in Gamma Knife Treatment Planning. Computer Methods and Programs in Biomedicine 144, 77-96
  38. L. Rundo, C. Militello, G. Russo, A. Garufi, S. Vitabile, G. Mauri, MC. Gilardi (2017). Automated Prostate Gland Segmentation Based on an Unsupervised Fuzzy C-Means Clustering Technique Using Multispectral T1w and T2w MR Imaging. Information 2017, 8, 49
  39. L. Rundo, A. Tangherloni, C. Militello, MC. Gilardi, G. Mauri (2017). Multimodal Medical Image Registration using Particle Swarm Optimization: A Review. Proc. IEEE SSCI 2016 - IEEE Symposium Series on Computational Intelligence, art. 7850261 pp. 1-8
  40. MS. Nobile, G. Mauri (2017). Accelerated analysis of biological parameters space using GPUs. Proc. PaCT 2017 – 14th Int. Conf. on Parallel Computing Technologies, Lect. Not. in Computer Science 10421, 70-81
  41. R. Colombo, C. Damiani, G. Mauri, D. Pescini (2017). Constraining mechanism based simulations to identify ensembles of parametrizations to characterize metabolic features. CIBB 2016 Lect. Not. in Bioinformatics 10477, 107-117
  42. M. Di Filippo, C. Damiani, R. Colombo, D. Pescini, G. Mauri (2017). Constraint-based Modeling and Simulation of Cell Populations. In “WIVACE 2016”, CCIS 708, pp. 126–137, Springer
  43. Damiani, R. Colombo, M. Di Filippo, D. Pescini, G. Mauri (2017). Linking alterations in metabolic fluxes with shifts in metabolite levels by means of kinetic modeling. In “WIVACE 2016”, CCIS 708, pp. 138–148, Springer
  44. Zoppis, G. Mauri, F. Sicurello, E. Santoro and G. Castelnuovo (2017). Mining complex networks: A new challenge for supporting diagnostic decisions. Communication, Management and Information Technology. Proc. ICCMIT'16 - Int. Conference on Communication, Management and Information Technology, CRC Press, pp. 215–220
  45. F. Cumbo, MS. Nobile, C. Damiani, R. Colombo, G. Mauri, P. Cazzaniga (2017). COSYS: A Computational Infrastructure for Systems Biology. CIBB 2016 – 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, Stirling, UK, Sept 1-3, 2016, Revised Selected Papers, Lect. Not. in Bioinformatics 10477, 82-92
  46. L. Rundo, C. Militello, G. Russo, D. D’Urso, LM. Valastro, A. Garufi, G. Mauri, S. Vitabile, MC. Gilardi (2017). Fully Automatic Multispectral MR Image Segmentation of Prostate Gland Based on the Fuzzy C-Means Clustering Algorithm. in "Multidisciplinary Approaches to Neural Computing", series "Smart Innovation, Systems and Technologies", Vol 69, Pages 23-37, Springer
  47. 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
  48. A. Tangherloni, MS. Nobile, P. Cazzaniga, D. Besozzi, G. Mauri (2017). Gillespie's Stochastic Simulation Algorithm on MIC Coprocessors. J. of Supercomputing 73(2): 676-686
  49. 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 33(21), 3492-3494
  50. 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
  51. 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
  52. C. Damiani, M. Di Filippo, D. Pescini, D. Maspero, R. Colombo, G. Mauri (2017). popFBA: tackling intratumour heterogeneity with Flux Balance Analysis. Bioinformatics, 33, i311–i318
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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):685-696
  63. 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
  64. Ramazzotti, MS. Nobile, P. Cazzaniga, G. Mauri, M. Antoniotti (2016). Parallel implementation of efficient search schemes for the inference of cancer progression models. Proc. IEEE Conference on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB), Article #7758109
  65. L. Rundo, C. Militello, G. Russo, P. Pisciotta, LM. Valastro, MG. Sabini, S. Vitabile, MC. Gilardi, G. Mauri (2016). Neuro-Radiosurgery Treatments: MRI Brain Tumor Seeded Image Segmentation Based on a Cellular Automata Model. Proc ACRI 2016 – 12th Conf. on Cellular Automata for Research and Industry, Lect. Not. in Computer Science 9863, 323–333
  66. P. Cazzaniga, F. Ferrara, M. S. Nobile, D. Besozzi, G. Mauri (2015). Parallelizing biochemical stochastic simulations: A comparison of GPUs and Intel Xeon Phi coprocessors. Proc. PaCT 2015 – 13th Int. Conf. on Parallel Computing Technologies, Lect. Not. in Computer Science 9251, 363–374
  67. Zoppis, R. Dondi, M. Borsani, E. Gianazza, C. Chinello, F. Magni, G. Mauri (2015). Robust Conclusions in Mass Spectrometry Analysis. Proc. ICCS 2015 – International Conference on Computational Science, Procedia Computer Science 51, 2015, 683–692
  68. 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), 3016-3026
  69. 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
  70. 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

Natural and unconventional computing

  1. L. Manzoni, D. M. Papetti, P. Cazzaniga, S. Spolaor, G. Mauri, D. Besozzi, M. S. Nobile (2020). Surfing on Fitness Landscapes: A Boost on Optimization by Fourier Surrogate Modeling. Entropy 22(3), 285, pp. 1-17
  2. A. Leporati, L. Manzoni, G. Mauri, A E. Porreca, C. Zandron (2020). Subroutines in P systems and closure properties of their complexity classes. Theoretical Computer Science 805, 193-205
  3. R. Dondi, G. Mauri, I. Zoppis (2020). Complexity Issues of String to Graph Approximate Matching. Proc. LATA 2020, Lect. Not. in Computer Science 12038, 248–259
  4. M. Castelli, R. Dondi, G. Mauri, I. Zoppis (2019). Comparing Incomplete Sequences via Longest Common Subsequence. Theoretical Computer Science 796, 272–285
  5. A. Tangherloni, S. Spolaor, P. Cazzaniga, D. Besozzi, L. Rundo, G. Mauri, M. S. Nobile (2019). Biochemical parameter estimation vs. benchmark functions: A comparative study of optimization performance and representation design. Applied Soft Computing 81, 105494
  6. R. Dondi, G. Mauri, I. Zoppis (2019). On the Tractability of Finding Disjoint Clubs in a Network. Theoretical Computer Science 777, 243-251
  7. R. Dondi, M. Mehdi Hosseinzadeh, G. Mauri, I. Zoppis (2019). Top-k Overlapping Densest Subgraphs: Approximation and Complexity. Proc ICTCS - 20th Italian Conference on Theoretical Computer Science, CEUR Proc 2504, 110-121
  8. R. Dondi, G. Mauri, F. Sikora, I. Zoppis (2019). Covering a Graphs with Clubs. J of Graph Algorithms and Applications 23(2), 271-292
  9. M. Castelli, R. Dondi, S. Manzoni, G. Mauri, I. Zoppis (2019). Top k 2-Clubs in a Network: A Genetic Algorithm. Proc. ICCS 2019 – 19th Int Conf on Computational Science, Lect. Not. in Computer Science 11540, 656–663
  10. A. Leporati, L. Manzoni, G. Mauri, A E. Porreca, C. Zandron (2019). Open problems in membrane computing and how not to solve them. In “Enjoying Natural Computing”, Lect. Not. in Computer Science 11270, pp.182-191
  11. M.S. Nobile, G. Pasi, P. Cazzaniga, D. Besozzi, R. Colombo, G. Mauri (2018). Fuzzy Self-Tuning PSO: A Settings-free Algorithm for Global Optimization. Swarm and Evolutionary Computation 39, 70-85
  12. R. Dondi, G. Mauri, F.Sikora, I. Zoppis (2018). Covering with Clubs: Complexity and Approximability. Proc. IWOCA 2018 – 29th International Workshop on Combinatorial Algorithms, Lect. Not. in Computer Science 10979, 153-164
  13. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2018). Solving a Special Case of the P Conjecture Using Dependency Graphs with Dissolution. CMC 18 – 18th Int. Conference on Membrane Computing, Selected revised papers, Lect. Not. in Computer Science 10725, 2017, 196–213
  14. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). Characterising the complexity of tissue P systems with fission rules. Journal of Computer and System Sciences 90, 115-128
  15. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). The counting power of P systems with antimatter. Theoretical Computer Science 701, 161-173
  16. M. Castelli, R. Dondi, G. Mauri, I. Zoppis (2017). The Longest Filled Common Subsequence Problem. Proc. CPM 2017 – 28th Annual Symposium on Combinatorial Pattern Matching, Leibniz International Proceedings in Informatics, Dagstuhl Publishing, Article No. 14; pp. 1–13
  17. L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). Shallow Non-Confluent P Systems. Proc. CMC 17 – 17th Int. Conf. on Membrane Computing, Selected revised papers, Lect. Not. Computer Science 10105, 307–316
  18. R. Dondi, G. Mauri, I. Zoppis (2017). Orthology Correction for Gene Tree Reconstruction: Theoretical and Experimental Results. Proc. ICCS 2017 – Int. Conf. on Computational Science, Procedia Computer Science 108, 1115–1124
  19. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2017). Tissue P Systems with Small Cell Volume. Fundamenta Informaticae 154(1-4), 261–275
  20. 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
  21. 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
  22. Leporati, 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(1-4), 307–321
  23. R. Dondi, G. Mauri, I. Zoppis (2016). Clique Editing to Support Case vs Control Discrimination. In “Intelligent Decision Technologies, Part I”, Smart Innovation, Systems and Technologies vol.56, Springer, 27-36
  24. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2016). Trading Geometric Realism for Efficiency in Tissue P Systems. Romanian J. Information, Sci. and Tech. 19(1-2), 17-30
  25. A. Leporati, L. Manzoni, G. Mauri, A. E. Porreca, C. Zandron (2016). Monodirectional P systems. Natural Computing 15, 551-564
  26. P. Bonizzoni, R. Dondi, G. Mauri, I. Zoppis (2015). Restricted and Swap Common Superstring: a Multivariate Algorithmic Perspective. Algorithmica 72(4), 914–939
  27. M. S. Nobile, G. Pasi, P. Cazzaniga, D. Besozzi, R Colombo, G. Mauri (2015). Proactive Particles in Swarm Optimization: A Self-tuning Algorithm Based on Fuzzy Logic. Proc FUZZ-IEEE 2015 - IEEE Int. Conference on Fuzzy Systems, #7337957
  28. Leporati, L. Manzoni, G. Mauri, A.E. Porreca, C. Zandron (2015). Tissue P systems can be simulated efficiently with counting oracles. Proc. CMC 16 – 16th Int. Conf. on Membrane Computing, Selected revised papers, Lect. Not. in Computer Science 9504, 251–261
  29. Mauri, A. Leporati, L. Manzoni, A.E. Porreca, C. Zandron (2015). Complexity Classes for Membrane Systems: A Survey. Proc. LATA 2015, A.H. Dediu et al. (Ed’s), Lect. Not. in Computer Science 8977, 56–69
  30. 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

Links