Our group designs and develops tools, methodologies and software for the analysis of biological systems. We develop and enhance algorithms and methods in sensitivity analysis, robustness analysis, multi-objective optimization, machine learning, computational modeling, design automation and applied them to problems in computational biology.

Research topics: protein structure prediction, protein folding; protein robustness and biological robustness; sensitivity analysis for biological systems; artificial immune systems; biological design automation, biological circuit design; artificial photosynthesis.

Books and Journals

• Pietro Lio', Giuseppe Nicosia, T. Stibor (Eds), 10th International Conference on Artificial Immune Systems - ICARIS 2011, Computer Laboratory - University of Cambridge, UK, July 18-21, 2011. Proceedings LNCS Springer, vol. 6825, 2011.

• B. Apolloni, M. Marinaro, Giuseppe Nicosia, R. Tagliaferri (Eds), International Workshop on Natural and Artificial Immune Systems - NAIS 2005, Springer, Lecture Notes in Computer Science, vol. 3931, 2006.

• J. Timmis, S. Stepney, P. J. Benley, Giuseppe Nicosia, V. Cutello (Eds), special issue on Artificial Immune Systems, International Journal on Unconventional Computing, Old City Publishing, Philadelphia, USA, 1(3):197-338, 2005.

• Giuseppe Nicosia, V. Cutello, P. J. Bentley, J. Timmis (Eds), Artificial Immune Systems, Third International Conference - ICARIS 2004, Catania, Italy, September 13-16. Springer, Lecture Notes in Computer Science, vol. 3239, 2004.

Refereed Journals

• "OREMPdb: a Semantic Dictionary of Runnable Biological Circuits",
  R. Umeton, Giuseppe Nicosia, C. F. Dewey Jr., BMC Bioinformatics, (to appear).

• "Protein Multiple Sequence Alignment by Hybrid Bio-Inspired Algorithms",
  V. Cutello, Giuseppe Nicosia, M. Pavone, I. Prizzi, Nucleic Acids Research - Oxford Journals, 39(6):1980-1992, 2011.

• "Computational Energy-based Redesign of Robust Proteins",
  G.Stracquadanio, Giuseppe Nicosia, Computers and Chemical Engineering, 35(3), pp. 464-473, 2011.

• "Generalized Pattern Search Algorithm for Peptide Structure Prediction",
  Giuseppe Nicosia, G.Stracquadanio, Biophysical Journal, 95(10):4988-4999, 2008.

• "An Immune Algorithm for Protein Structure Prediction on Lattice Models",
  V. Cutello, Giuseppe Nicosia, M. Pavone, J. Timmis, IEEE Transactions on Evolutionary Computation, 11(1):101-117, 2007.

• "Determination of protein structure and dynamics combining immune algorithms and pattern search methods",
  A. M. Anile, V. Cutello, G. Narzisi, Giuseppe Nicosia, S. Spinella, Natural Computing, 6(1):55-72, 2007.

• "A Multi-Objective Evolutionary Approach to the Protein Structure Prediction Problem",
  V. Cutello, G. Narzisi, Giuseppe Nicosia, Journal of the Royal Society Interface, Royal Society Publications London, 3(6):139-151, 2006. Download i-paes Algorithm code (C language).
  

  A recent review paper published by the Journal of the Royal Society Interface, G. Helles (2008; 5(21): 387--396) ranks our I-PAES algorithm among the best state-of-art folding algorithm; in fact, I-PAES is the 3rd-4th best folding algorithm.

• "Pattern Recognition by primary and secondary response of an Artificial Immune System",
  F. Castiglione, S. Motta, Giuseppe Nicosia, Theory in Biosciences, 120(2):93-106, 2001.

• "A Network of Cellular Automata for the Simulation of the Immune System",
  F. Castiglione, G. Mannella, S. Motta, Giuseppe Nicosia, Int. J. of Modern Physics C (Physics and Computers), 10(4):677-686, 1999.

PhD Thesis

• Giuseppe Nicosia, "Immune Algorithms for Optimization and Protein Structure Prediction", PhD Thesis, Department of Mathematics and Computer Science, University of Catania, Italy, 2004.

Refereed Conference Proceedings

• "Effective Calibration of Artificial Gene Regulatory Networks",
  D. Agostini, J. Costanza, V. Cutello, L. Zammataro, N. Krasnogor, M. Pavone, Giuseppe Nicosia, 20th European Conference on Artificial Life - ECAL 2011, Paris, France, August 8-12, 2011. pp. 39-46 MIT Press.

• "Design of Robust Metabolic Pathways",
  R. Umeton, G. Stracquadanio, A. Papini, A. Sorathiya P. Lio', and Giuseppe Nicosia, 48th Design Automation Conference - DAC 2011, San Diego - CA, USA, June 5-10, 2011 ACM Press, pp. 747-752.

• "Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response",
  G. Stracquadanio, R. Umeton, J. Costanza, V. Annibali, R. Mechelli, M. Pavone, L. Zammataro, and Giuseppe Nicosia, 10th International Conference on Artificial Immune Systems -ICARIS, LNCS vol. 6825, Springer-Verlag, Cambridge, UK, July 18-21, 2011, pp. 15-29.

• "Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism",
  G. Stracquadanio, R. Umeton, A. Papini, J. Costanza, P. Lio', and Giuseppe Nicosia, 11th Int. Conf. on Systems Biology -ICSB 2010, Edinburgh 10-15 October 2010, Proceedings "Advances in Systems Biology", Springer (to appear).

• "A Cross-format Framework for Consistent Information Integration among Molecular Pathways and Ontologies",
  R. Umeton, B. Yankama, Giuseppe Nicosia, and C. F. Dewey Jr., 6th World Congress on Biomechanics, August 1 - 6, 2010, Singapore. Springer - IFMBE Proceedings series, pp. 1595-1598.

• "Analysis and Optimization of C3 Photosynthetic Carbon Metabolism",
  G. Stracquadanio, R. Umeton, A. Papini, Pietro Lio and Giuseppe Nicosia, 10th IEEE Int. Conf. on Bioinformatics and Bioengineering 2010 - BIBE 2010, Philadelphia, USA, May 31-June 3, 2010. IEEE Press, pp. 44-51.

• "Robust Bio-Active Peptide Prediction using Multi-Objective Optimization",
  G.Narzisi, Giuseppe Nicosia and G. Stracquadanio, The I Int. Conf. on Advances in Bioinformatics and Applications - BIOINFO 2010, March 7-13, 2010, Cancun, Mexico. IEEE Press, pp. 44 - 50. DOI: 10.1109/BioSciencesWorld.2010.13 Best Paper Award.

• " A Design-for-Yield Algorithm to Assess and Improve the Structural and Energetic Robustness of Proteins and Drugs",
  Giuseppe Nicosia, G. Stracquadanio, 8th International Symposium on Experimental Algorithms - SEA 2009, 3-6 June 2009, Dortmund, Germany, Lecture Notes in Computer Science, Springer, 5526:245-256.
  

• " Robust Parameter Identification for Biological Circuit Calibration",
  Giuseppe Nicosia, E. Sciacca, 8th IEEE International Conference on BioInformatics and BioEngineering - IEEE BIBE 2008, Athens, Greece, 8-10 October 2008, pp. 1-6, IEEE Press.

• Giuseppe Nicosia, E. Sciacca, L. Zammataro, " Detecting Constituent Sequences by Means of HP Pattern-Based Grammars to Synthesize Proteins: Inferring Sequence-Structure-Function Relationship", IEEE Int. Conf. on Bioinformatics and Biomedicine - BIBMW'07, November 2-4, 2007 Silicon Valley, USA. IEEE Press, pp. 53-59, 2007.

• Giuseppe Nicosia, G. Stracquadanio, " Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction" , 7th Int. Workshop on Algorithms in Bioinformatics - WABI'07, September 8-9, 2007, Philadelphia, PA, USA. Springer, Lecture Notes in Computer Science 4645:183-193, 2007.

• G. Morelli, Giuseppe Nicosia, "An Effective Immunological Algorithm with Self-Avoiding, Penalty and Repair Heuristics for Protein Structure Prediction in the Hydrophobic-Polar Model on the 3D Cubic Lattice", 7th Int. Workshop on Information Processing in Cells and Tissues - IPCAT'07, 29th-31st August, 2007, Jesus College Oxford, UK, pp. 102-109, 2007.

• V. Cutello, D. Lee, Giuseppe Nicosia, M. Pavone, I. Prizzi, "Aligning Multiple Protein Sequences by Hybrid Clonal Selection Algorithm with Insert-Remove-Gaps and BlockShuffling Operators", 5th International Conference on Artificial Immune Systems, ICARIS 2006, September 4-6, 2006, Oeiras, Portugal. Springer, Lecture Notes in Computer Science 4163:321-334, 2006.

• A. M. Anile, V. Cutello, G. Narzisi, Giuseppe Nicosia, S. Spinella, "Lipschitzian pattern search and Immunological Algorithm with quasi-Newton method for the Protein Folding Problem: An innovative multistage approach", Proceedings of the Int. Workshop on Natural and Artificial Immune Systems, NAIS 2005, 9-10 June, 2005, Vietri sul Mare (SA), Italy. Springer, Lecture Notes in Computer Science 3931:307-323, 2006.

• V. Cutello, G. Narzisi, Giuseppe Nicosia, "A Class of Pareto Archived Evolution Strategy Algorithms using Immune inspired Operators for Ab-Initio Protein Structure Prediction", Third European Workshop on Evolutionary Computation and Bioinformatics, EvoWorkshops 2005, EvoBio 2005, 30 March - April 2005, Lausanne, Switzerland. Springer, Lecture Notes in Computer Science 3449:54-63, 2005. Best Paper Award Candidate. Download i-paes Algorithm code (C language).

• V. Cutello, G. Morelli, Giuseppe Nicosia, M. Pavone, "Immune Algorithms with Aging Operators for the String Folding Problem and the Protein Folding Problem", 5th European Conference on Computation in Combinatorial Optimization, EvoCOP 2005, 30 March - April 2005, Lausanne, Switzerland. Springer, Lecture Notes in Computer Science 3448:80-90, 2005.

• V. Cutello, Giuseppe Nicosia, M. Pavone, "An Immune Algorithm with Hyper-Macromutations for the Dill's 2D Hydrophobic-Hydrophilic Model", IEEE Congress on Evolutionary Computation, CEC 2004, June 19-23, 2004, Portland, Oregon, USA. IEEE Press, vol. 1, pp. 1074-1080, 2004.

• F. Castiglione, S. Motta, Giuseppe Nicosia, "Pattern Recognition with a Multi-Agent model of the Immune System", Int. NAISO Symp. on Information Science Innovations in Engineering of Natural and Artificial Intelligent Systems, ENAIS 2001, March 17-21, 2001, American University in Dubai, U.A.E. ICSC Academic Press, pp. 788-794, 2001.

Book chapters

• R. T. Alves, V. Bevilacqua, M. Delgado, A. A. Freitas, G. Mastronardi, F. Menolascina, Giuseppe Nicosia, A. Paradiso, S. Tommasi, "Artificial Immune Systems in Bioinformatics", in Computational Intelligence in Biomedicine and Bioinformatics: Current Trends and Applications, Smolinski T.G., Milanova M.G., Hassanien A. (Eds), Springer, New York, NY, USA, pp. 305-330, 2008.

• V. Cutello, G. Narzisi, Giuseppe Nicosia, "Computational Studies of Peptide and Protein Structure Prediction Problems via Multi-Objective Evolutionary Algorithms", Joshua Knowles, David Corne and Kalyanmoy Deb (Eds), Multi-Objective Problem Solving from Nature, Springer, London, UK, pp. 93-114, 2008.

• V. Cutello, Giuseppe Nicosia, M. Pavone, I. Prizzi, "Proteomic Multiple Sequence Alignment: Refinement using an Immunological Local Search", Applied and Industrial Mathematics in Italy II, eISBN: 9789812709394 Series on Advances in Mathematics for Applied Sciences, World Scientific, 75:291-302, 2007.

• V. Cutello, Giuseppe Nicosia, "Biomolecular Structure Prediction using Immune Inspired Algorithms", book chapter in D. R. Flower and J. Timmis (Eds), In silico Immunology, Springer, London, UK, pp. 235-263, 2006.

• V. Cutello, Giuseppe Nicosia, "The Clonal Selection Principle for in silico and in vitro Computing", book chapter in L. N. de Castro and F. J. Von zuben (Eds), Recent Developments in Biologically Inspired Computing, Idea Group Publishing, Hershey, PA, USA, pp. 104-145, 2004.

Communications, Posters and other publications

• Jole Costanza, Luca Zammataro, Pietro Lio' and Giuseppe Nicosia, "Pareto Optimal Tradeoffs in Genetic Design Strategies using Global Search", SB5.0: the Fifth International Meeting on Synthetic Biology, Stanford University, Stanford, California USA, June 15-17, 2011.

• Renato Umeton, Raffaella Pizzolato and Giuseppe Nicosia, "OREMPDB, A Semantic Dictionary Of Runnable Biological Circuits; System Overview and First Queries in the Neurology Field", Third International Workshop on Bio-Design Automation (IWBDA 2011) at DAC, San Diego Convention Center, San Diego, California USA, June 6 - 7, 2011.

• Jole Costanza, Luca Zammataro, Pietro Lio' and Giuseppe Nicosia, "Pareto Optimal Fronts in Bacterial Knockout Strategies", Third International Workshop on Bio-Design Automation (IWBDA 2011) at DAC, San Diego Convention Center, San Diego, California USA, June 6 - 7, 2011.

• Jole Costanza, Luca Zammataro, Pietro Lio' and Giuseppe Nicosia, "Optimal Design of the Mitochondrial Bioenergetics", Third International Workshop on Bio-Design Automation (IWBDA 2011) at DAC, San Diego Convention Center, San Diego, California USA, June 6 - 7, 2011.

• R. Umeton, Giuseppe Nicosia, C.F. Dewey Jr, "OREMPdb: a Semantic Dictionary of Runnable Biological Circuits", BITS 2011 - Eighth Annual Meeting of the Bioinformatics Italian Society, Pisa, Italy, June 20-22, 2011.

• Jole Costanza, Luca Zammataro, Pietro Lio', Giuseppe Nicosia, "High-dimensional Pareto Surfaces in the Genetic Design of Escherichia Coli", BITS 2011 - Eighth Annual Meeting of the Bioinformatics Italian Society, June 20-22, Pisa, Italy.

• Jole Costanza, Luca Zammataro, Pietro Lio', Giuseppe Nicosia, "Multi-objective Optimization for the Mitochondrial Bioenergetics", BITS 2011 - Eighth Annual Meeting of the Bioinformatics Italian Society, June 20-22, Pisa, Italy.

• G. Stracquadanio, R. Umeton, A. Papini, P. Lio', and Giuseppe Nicosia, "Automating the Biological Design of C3 Carbon Metabolism for Enhanced Photosynthetic Productivity Minimizing the Nitrogen Employed", Int. Workshop Modeling Natural and Artificial Photosynthesis, Lorentz Center - Leiden, The Netherlands, 7-11 March 2011.

• A. Papini, Giuseppe Nicosia, G. Stracquadanio, P. Lio', R. Umeton "Key Enzymes for the Optimization of CO2 Uptake and Nitrogen Consumption in the C3 Photosynthetic Carbon Metabolism", 14th Int. Biotechnology Symposium and Exhibition - Biotechnology for the Sustainability of Human Society. 14-18 September 2010, Rimini, Italy. Journal of Biotechnology, Vol. 150, S. 1, Nov 2010, pp. 525-526. doi:10.1016/j.jbiotec.2010.09.846

• R. Umeton, B. Yankama, Giuseppe Nicosia, and C. F. Dewey Jr., "OREMP: Ontology Reasoning Engine for Molecular Pathways", in Proceedings of ORES 2010, 1st Int. Workshop on Ontology Repositories and Editors for the Semantic Web - Satellite Conference in ESWC 2010, 7th Extended Semantic Web Conference, 2010, pp. 26-30.

• Giuseppe Nicosia, "From Electronic to Biological Design Automation: Building the Bridge", First International Workshop on Bio-Design Automation - IWBDA 2009, Moscone Center, San Fransisco, CA, USA, July 27, 2009

• Giuseppe Nicosia, E. Sciacca, L. Zammataro, "Detecting Constituent Sequences by means of HP Pattern-Based Grammars to Synthesize AmPs", Synthetic Biology 3.0, 24th-26th June 2007, ETH, Swiss Federal Institute of Technology, Zurich, Switzerland.

• Giuseppe Nicosia, G. Stracquadanio, L. Zammataro, "Modelling infections with stochastic pi-calculus", Synthetic Biology 3.0, 24th-26th June 2007, ETH, Swiss Federal Institute of Technology, Zurich, Switzerland.

• V. Cutello, Giuseppe Nicosia, "Protein folding as a multi-objective optimization problem", 14th Annual Meeting on Mathematical and Statistical Aspects of Molecular Biology, MASAMB-XIV, March 22-23, 2004, Isaac Newton Institute For Mathematical Sciences, University of Cambridge, UK.

• F. Castiglione, S. Motta, Giuseppe Nicosia, L. Zammataro, "The effects of an apoptosis mechanism on the immune response", Eurosim 2001 Congress Shaping Future With Simulation, June 26-29, 2001, Delft, The Netherlands.

• S. Motta, Giuseppe Nicosia, "A plain cellular automata for the simulation of the immune system", Eurosim 2001 Congress Shaping Future With Simulation, June 26-29, 2001, Delft, The Netherlands.

Review Paper

• V. Cutello, G. Morelli, Giuseppe Nicosia, M. Pavone and G. Scollo, "On Discrete Models and Immunological Algorithms for Protein Structure Prediction", Natural Computing Journal, special issue on Modelling Bioprocesses, 2010, 10(1), pp. 91-102, DOI: 10.1007/s11047-010-9196-y.

International Summer Schools and Conferences

• Co-Director of the International School of Functional Genomics, (with Pietro Lio' and Sebastiano Cavallaro)
  5-19 July 2008 Baia Samuele Conference Centre, Scicli-Sicily, Italy. Lectio Magistralis Rita Levi-Montalcini, EBRI, Nobel Laureate.
  



• Co-Director of the Bertinoro International Summer School of Natural Computation - BNC 2008, (with Pietro Lio')
  September 20-27, 2008 University Residential Center Bertinoro - BiCi, Italy.



• Co-Chair of the Workshop on "Biological CAD", Chairs: Pietro Lio' and Giuseppe Nicosia,
  12th International Conference on Systems Biology (ICSB 2011), August 27 - September 1, 2011, Heidelberg/Mannheim, Germany.
  



• Co-Chair of the 10th International Conference on Artificial Immune Systems, University of Cambridge - UK, 18-21 July, 2011. (with Pietro Lio' and T. Stibor)
  



• Co-Chair of International Workshop on Natural and Artificial Immune Systems - NAIS 2005, Vietri sul Mare (SA), Italy, 9-10 June 2005.



• Co-Chair of International Conference on Artificial Immune Systems - ICARIS 2004, Catania, Italy, 13-16 September 2004.

Giuseppe Nicosia, Optimization, Combinatorial Optimization, Numerical Optimization, Non Linear Optimization, Large Scale Optimization, Multi-Objective Optimization, Evolutionary Algorithms, Genetic Algorithms, Immune Algorithms, CLONALG, Artificial Immune Systems, Graph Coloring, String Folding, NP-complete problems, Computational Systems Biology, Synthetic Biology, Circuit Optimization, Circuit Design, Design For Yield, Device Optimization, Bioinformatics, Structural Bioinformatics, Protein Folding, Protein Structure Prediction, HP model.