Books and Journals

• Pietro Lio' and Giuseppe Nicosia (Eds.), Selected articles from the 10th International Conference on Artificial Immune Systems - ICARIS 2011, BMC Bioinformatics, Volume 14, Suppl 6, 2013.

• Giuseppe Nicosia and Panos Pardalos (Eds.), Learning and Intelligent Optimization - 7th International Conference - LION 7, Catania, Italy, January 7-11, 2013, Lecture Notes in Computer Science, Springer 2013 (to appear).

• Carlos A. Coello Coello, Vincenzo Cutello, Kalyanmoy Deb, Stephanie Forrest, Giuseppe Nicosia, Mario Pavone (Eds.), Parallel Problem Solving from Nature - PPSN XII - 12th International Conference, Taormina, Italy, September 1-5, 2012, Proceedings, Part I LNCS vol. 7491 and Part II LNCS vol. 7492 Springer 2012.

• C. A. Coello Coello, J. Greensmith, N. Krasnogor, P. Lio', Giuseppe Nicosia, M. Pavone (Eds), Artificial Immune Systems - 11th International Conference - ICARIS 2012, Taormina, Italy, August 28-31, 2012. Proceedings LNCS Springer, vol. 7597, 2012.

• 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.

• N. Krasnogor, Giuseppe Nicosia, M. Pavone, D. Pelta (Eds), special issue on Nature Inspired Cooperative Strategies for Optimization, Natural Computing Journal, Springer, vol. 9, 2010.

• N. Krasnogor, Giuseppe Nicosia, M. Pavone, D. Pelta (Eds), The second International Workshop on Nature Inspired Cooperative Strategies for Optimization - NICSO 2007, Studies in Computational Intelligence, Springer, vol. 129, 2008.

• B. Apolloni, M. Marinaro, Giuseppe Nicosia, R. Tagliaferri (Eds), 16th Italian Workshop on Neural Nets and the satellite 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

• "Semiconductor Device Design using Bimads Algorithm",
  G. Stracquadanio, V. Romano, G. Nicosia, Journal of Computational Physics, DOI: 10.1016/j.jcp.2013.01.025, 242, pp. 304-320, 2013.

• "Efficient Behavior of Photosynthetic Organelles via Pareto Optimality, Identifiability and Sensitivity Analysis",
  G. Carapezza, R. Umeton, J. Costanza, C. Angione, G. Stracquadanio, A. Papini, P. Lio', G. Nicosia, ACS Synthetic Biology Journal, 2012, DOI: 10.1021/sb300102k.

• "Bose-Einstein Condensation in Satisfiability Problems",
  C. Angione, A. Occhipinti, G. Stracquadanio, G. Nicosia, European Journal of Operational Research, doi: 10.1016/j.ejor.2012.11.039, 227, pp. 44-54, 2013.

• "Robust Design of Microbial Strains",
  J. Costanza, G. Carapezza, C. Angione, P. Lio', Giuseppe Nicosia, Bioinformatics - Oxford Journal, doi: 10.1093/bioinformatics/bts590, Vol. 28, issue 23, pp. 3097-3104, 2012.
  Supplementary Information and Material.

• "OREMPdb: a Semantic Dictionary of Runnable Biological Circuits",
  R. Umeton, Giuseppe Nicosia, C. F. Dewey Jr., BMC Bioinformatics, 2012 Vol. 13(Suppl 4):S6 doi:10.1186/1471-2105-13-S4-S6

• "Clonal Selection - An Immunological Algorithm for Global Optimization over Continuous Spaces",
  M. Pavone, G. Narzisi, Giuseppe Nicosia, Journal of Global Optimization, Volume 53, Issue 4, Pages 769-808, 2012.
  DOI 10.1007/s10898-011-9736-8.

• "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.

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

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

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

• "An Evolutionary Algorithm-Based Approach to Robust Analog Circuit Design using Constrained Multi-Objective Optimization",
  Giuseppe Nicosia, S. Rinaudo, E. Sciacca, Knowledge-Based Systems J., 21(3):175-183, 2008.
  Best Paper Award sponsored by Hewlett-Packard Laboratories.
  The 27th SGAI Int. Conf. on Artificial Intelligence AI-2007.

• "An Immune Algorithm with Stochastic Aging and Kullback Entropy for the Chromatic Number Problem",
  V. Cutello, Giuseppe Nicosia, M. Pavone, Journal of Combinatorial Optimization, 14(1):9-33, 2007.

• "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.

• "Multi-Objective Evolutionary Algorithms and Pattern Search Methods for Circuit Design Problems",
  T. Biondi, C. Ciccazzo, V. Cutello, S. D'Antona, Giuseppe Nicosia, S. Spinella, J. of Universal Computer Science, 12(4):432-449, 2006.

• "Optimizing Inductor Circuit and Two-Stage Operational Transconductance Amplifier by means Evolutionary and Classical Algorithms",
  V. Cutello, Giuseppe Nicosia, R. Rascuna', S. Spinella, Int. J. of Computational Science and Engineering, 2(3/4):158-169, 2006. DOI: 10.1504/IJCSE.2006.012768

• "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, 2005.

Refereed Conference Papers with Proceedings

• "Pareto epsilon-Dominance and Identifiable Solutions for BioCAD Modeling",
  C. Angione, J. Costanza, G. Carapezza, P. Lio', and Giuseppe Nicosia, 50th Design Automation Conference - DAC 2013, June 2-6, Austin Texas (to appear).

• "Multi-Objective Design of Bacterial Communication Networks",
  C. Angione, G. Carapezza, J. Costanza, P. Lio', and Giuseppe Nicosia, 3rd IEEE Int. Workshop on Molecular and Nanoscale Communications - IEEE MoNaCom 2013 held in conjunction with IEEE Int. Conference on Communications 2013 - IEEE ICC 2013, June 9-13, 2013, Budapest, Hungary, IEEE Press (to appear).

• "Rational Design of Organelle Compartments in Cells ",
  C. Angione, G. Carapezza, J. Costanza, P. Lio', and Giuseppe Nicosia, Twelth International Workshop on Network Tools and Applications in Biology - NETTAB 2012 - Focus on Integrated Bio-Search, November 14-16, 2012, Como, Italy. EMBnet Journal Volume 18 Supplement B, pp. 20-22, 2012.

• "Multi-Objective Optimization, Sensitivity and Robustness Analysis in FBA Modeling",
  Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Lio' and Giuseppe Nicosia, The 10th Conference on Computational Methods in Systems Biology - CMSB, 3-5 October 2012 The Royal Society, London, UK, Springer LNCS, pp. 127-147, 2012.
  DOI: 10.1007/978-3-642-33636-2_9; ISBN: 978-3-642-33635-5.

• "The Role of the Genome in the Evolution of the Computation Complexity of Metabolic Machines",
  Claudio Angione, Giovanni Carapezza, Jole Costanza, Pietro Lio' and Giuseppe Nicosia, European Conference in Complex Systems - ECCS'12, Brussels, 3-7 September 2012, Springer Complexity (to appear).

• "Computing with Metabolic Machines",
  Claudio Angione, Giovanni Carapezza, Jole Costanza, Pietro Lio' and Giuseppe Nicosia, Turing 100 Conference, The University in Manchester, June 22-25, 2012.
  Best Paper Award.
  

• "Are Bacteria Unconventional Computing Architectures?",
  Jole Costanza, Claudio Angione, Pietro Lio' and Giuseppe Nicosia, Turing Centenary Conference - CiE 2012 - How the World Computes, University of Cambridge, 18 June - 23 June, 2012

• "metaDesign: Bacterial Strain Design Automation Software",
  Jole Costanza, Giovanni Carapezza, Claudio Angione, Renato Umeton, Pietro Lio' and Giuseppe Nicosia, The Fourth International Workshop on Bio-Design Automation (IWBDA) at the 49th ACM/EDAC/IEEE Design Automation Conference (DAC), June 3-7, 2012 at the Moscone Center, San Francisco, CA, USA.

• "Global Optimization for Algebraic Geometry - Computing Runge-Kutta Methods",
  Ivan Martino and Giuseppe Nicosia, Learning and Intelligent OptimizatioN Conference - LION 6, Paris - France, Jan 16-20, 2012, Springer (to appear).

• "Design of Robust Space Trajectories",
  G. Stracquadanio, A. La Ferla, M. De Felice and Giuseppe Nicosia, 31st SGAI International Conference on Artificial Intelligence - SGAI 2011, December 13-15, 2011, Cambridge, UK, Springer, pages 341-354.

• "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",
  R. Umeton, G. Stracquadanio, 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" - Advances in Experimental Medicine and Biology, 2012, Springer, vol. 736, Part 4, pp. 441-459, DOI: 10.1007/978-1-4419-7210-1_26

• "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.

• "An Information Theoretic Approach for Clonal Selection Algorithms",
  V. Cutello, Giuseppe Nicosia, M. Pavone and G. Stracquadanio, 9th Int. Conf. on Artificial Immune Systems - ICARIS 2010, Edinburgh, UK, July 26-29, 2010. Lecture Notes in Computer Science, Springer, pp. 144-157.

• "An Immunological Algorithm for Doping Profile Optimization in Semiconductors Design",
  G. Stracquadanio, C. Drago, V. Romano, Giuseppe Nicosia, 9th Int. Conf. on Artificial Immune Systems ICARIS 2010, Edinburgh, UK, July 26-29, 2010. Lecture Notes in Computer Science, Springer, pp. 213-222.

• "Effective design of semiconductor devices using evolutionary-based derivative free optimization ", G. Stracquadanio, C. Drago, V. Romano, Giuseppe Nicosia, IEEE World Congress on Computational Intelligence - WCCI 2010, Barcelona, Spain, July 18-23, 2010. IEEE Press, pp. 1-7. DOI: 10.1109/CEC.2010.5585990

• "Entropic Divergence for Population Based Optimization Algorithms",
  V. Cutello, Giuseppe Nicosia, M. Pavone, and G. Stracquadanio, IEEE World Congress on Computational Intelligence - WCCI 2010, Barcelona, Spain, July 18-23, 2010. IEEE Press. DOI: 10.1109/CEC.2010.5586044

• "Multi-Objective Optimization of Doping Profile in Semiconductor Design",
  G. Stracquadanio, C. Drago, V. Romano, Giuseppe Nicosia, ACM Genetic and Evolutionary Computation Conference - GECCO 2010, Portland, Oregon, USA, July 7-11, 2010. ACM Press, pp. 1243-1250.

• "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.

• "Doping Profile Optimization in Semiconductor Design",
  G. Stracquadanio, C. Drago, V. Romano, Giuseppe Nicosia, The 16th IEEE Int. Conf. on Electronics, Circuits and Systems (ICECS 2009), 13-16 December 2009, Hammamet, Tunisie. pp. 255-258, IEEE Press.
  

• "Nominal-Yield-Area Tradeoff in Automatic Synthesis of Analog Circuits: A Genetic Programming Approach using Immune-Inspired Operators",
  P. Conca, Giuseppe Nicosia, G. Stracquadanio, J. Timmis, NASA/ESA Conference on Adaptive Hardware and Systems (AHS-2009), co-located with the 46th Design Automation Conference (DAC 2009), July 29 - August 1, 2009, San Francisco, CA, USA; IEEE Computer Society Press, pp. 399-406.
  

• " 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.

• A. Ciccazzo, P. Conca, Giuseppe Nicosia, G. Stracquadanio, " An Advanced Clonal Selection Algorithm with ad-Hoc Network-based Hypermutation Operators for Synthesis of Topology and Sizing of Analog Electrical Circuits", 7th International Conference on Artificial Immune Systems - ICARIS 2008, 10th-13th August, 2008, Phuket, Thailand. Springer, Lecture Notes in Computer Science, 5132:60-70, 2008.

• A. Ciccazzo, T. Halfmann, A. Marotta, Giuseppe Nicosia, S. Rinaudo, G. Stracquadanio, A. Venturi, " New Coupled EM and Circuit Simulation Flow for Integrated Spiral Inductor by Introducing Symbolic Simplified Expressions", IEEE International Symposium on Industrial Electronics - ISIE 2008, June 30 - July 2, 2008, Cambridge, England, UK. pp. 1203-1208, IEEE Industrial Electronics Society Press.

• Giuseppe Nicosia, S. Rinaudo, E. Sciacca, "An Evolutionary Algorithm-Based Approach to Robust Analog Circuit Design using Constrained Multi-Objective Optimization", The 27th SGAI International Conference on Artificial Intelligence AI-2007, 10-12 December 2007, Cambridge, England, UK. Springer, pp. 7-20.
  Best Paper Award sponsored by Hewlett-Packard Laboratories.

• 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.

• M. Castrogiovanni, Giuseppe Nicosia, R. Rascuna', " Experimental Analysis of the Aging Operator for Static and Dynamic Optimisation Problems", 11th Int. Conf. on Knowledge-Based and Intelligent Information and Engineering Systems - KES 2007, 12-14 September 2007, Vietri sul Mare, Italy. Springer, Lecture Notes in Computer Science 4694:804-811, 2007.

• V. Cutello, Giuseppe Nicosia, P. S. Oliveto, M. Romeo, " On the Convergence of Immune Algorithms", The First IEEE Symp. on Foundations of Computational Intelligence, FOCI 2007, 1-5 April 2007, Honolulu, Hawaii, USA. IEEE Press, pp. 409-415, 2007.

• A. Tarakanov, Giuseppe Nicosia, "Foundations of Immunocomputing", The First IEEE Symp. on Foundations of Computational Intelligence, FOCI 2007, 1-5 April 2007, Honolulu, Hawaii, USA. IEEE Press, pp. 503-508, 2007.

• V. Cutello, N. Krasnogor, Giuseppe Nicosia, M. Pavone, "Immune Algorithm versus Differential Evolution: a Comparative Case Study using High Dimensional Function Optimization", Int. Conf. on Adaptive and Natural Computing Algorithms, ICANNGA 2007, April 11-14, 2007, Warsaw, Poland. Springer, Lecture Notes in Computer Science 4431:93-101, 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.

• V. Cutello, D. Lee, S. Leone, Giuseppe Nicosia, M. Pavone, "Clonal Selection Algorithm with Dynamic Population Size for Bimodal Search Spaces", 2nd International Conference on Natural Computation, ICNC 2006, September 24-28, 2006, Xi'an, China. Springer, Lecture Notes in Computer Science 4221:949-958, 2006.

• V. Cutello, G. Narzisi, Giuseppe Nicosia, M. Pavone, " Real Coded Clonal Selection Algorithm for Global Numerical Optimization using a new Inversely Proportional Hypermutation Operator ", The 21st Annual ACM Symposium on Applied Computing, SAC 2006, April 23 -27, 2006, Dijon, France. ACM Press, vol. 2, pp. 950-954, 2006.

• V. Cutello, Giuseppe Nicosia, P. Oliveto, " Analysis of an Evolutionary Algorithm with Local Search for solving Trap Functions ", The 21st Annual ACM Symposium on Applied Computing, SAC 2006, April 23 -27, 2006, Dijon, France. ACM Press, vol. 2, pp. 945-949, 2006.

• V. Cutello, Giuseppe Nicosia, E. Pavia, "A Parallel Immune Algorithm for Global Optimization", The 7th Int. Conf. on Intelligent Information Systems, IIS 2006, June 19-22, 2006, Ustron, Poland. Springer, Series on Advances in Soft Computing, pp. 467-475, 2006.

• V. Cutello, G. Narzisi, Giuseppe Nicosia, M. Pavone, "An Immunological Algorithm for Global Numerical Optimization", Artificial Evolution: 7th Int. Conference, Evolution Artificielle, EA 2005, October 26-28, 2005, Lille, France. Springer, Lecture Notes in Computer Science 3871:284-295, 2005.

• A. M. Anile, V. Cutello, Giuseppe Nicosia, R. Rascuna', S. Spinella, "Comparison among Evolutionary Algorithms and Classical Optimization Methods for Circuit Design Problems", IEEE Congress on Evolutionary Computation, CEC 2005, September 2-5, 2005, Edinburgh, UK. IEEE Press, vol. 1, pp. 765-772, 2005.

• V. Cutello, G. Narzisi, Giuseppe Nicosia, M. Pavone, " Clonal Selection Algorithms: A Comparative Case Study using Effective Mutation Potentials, optIA versus CLONALG", 4th Int. Conference on Artificial Immune Systems, ICARIS 2005, August 14-17, 2005, Banff, Canada. Springer, Lecture Notes in Computer Science 3627:13-28, 2005.

• 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, Giuseppe Nicosia, "A Clonal Selection Algorithm for Coloring, Hitting Set, and Satisfiability Problems", 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 3931:324-337, 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, "Exploring the Capability of Immune Algorithms: A Characterization of Hypemutation Operators", Third Int. Conference on Artificial Immune Systems, ICARIS 2004, September 13-16, 2004, Catania, Italy. Springer, Lecture Notes in Computer Science 3239:263-276, 2004.

• 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.

• V. Cutello, Giuseppe Nicosia, "Noisy Channel and Reaction-Diffusion Systems: Models for Artificial Immune Systems", The 7th Int. Conference on Knowledge-Based Intelligent Information & Engineering Systems, KES 2003, September 3-5, 2003, Oxford, UK. Springer, Lecture Notes in Computer Science 2774:496-502, 2003.

• V. Cutello, Giuseppe Nicosia, M. Pavone, "A Hybrid Immune Algorithm with Information Gain for the Graph Coloring Problem", Genetic and Evolutionary Computation Conference, GECCO 2003, July 12-16, 2003, Chicago, Illinois, USA. Springer, Lecture Notes in Computer Science 2723:171-182, 2003.

• V. Cutello, Giuseppe Nicosia, "An Immunological Approach to Combinatorial Optimization Problems", Advances in Artificial Intelligence, IBERAMIA 2002, November 12-15, 2002, Seville, Spain. Springer, Lecture Notes in Computer Science 2527:361-370, 2002.

• 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.

Refereed Conference Papers

• Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Lio', Giuseppe Nicosia, "Reducing Atmospheric CO2 by Optimizing the Consumption from Synthetic Organisms", SB 6.0, The Sixth International Meeting on Synthetic Biology, July 9-11, 2013, Imperial College, London, UK.

• C. Angione, A. Occhipinti, Giuseppe Nicosia, "Bose-Einstein Condensation in Satisfiability Networks", NetSci 2012: The International Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.

• J. Costanza, G. Carapezza, C. Angione, P. Lio', Giuseppe Nicosia, "Pareto Front Sensitivity in Large Scale Biological Networks", NetSci 2012: The International Conference on Complex Networks. Northwestern University - Evanston, Illinois. June 18-22, 2012.

• Ivan Martino, Giuseppe Nicosia, "Beyond Parametrization of Algebraic Varieties by means of Global Optimization", SIAM Conference on Applied Algebraic Geometry, North Carolina State University, Raleigh, North Carolina, USA, October 6-9, 2011.

• 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.

• 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 and G. Stracquadanio, "Robust Device and Circuit Design using Effective Constrained Multi-Objective Optimization", Cadence CDNLive! EMEA, 2010. May 4-6, 2010, Munich, Germany.

• Giuseppe Nicosia, C. M. Palano, N. E. Porto, F. D' Amico, G. Morelli, "SMPS Interactive Design Simulator - Efficient Power- Supply Designs", Cadence CDNLive! EMEA, 2010. May 4-6, 2010, Munich, Germany.

• V. Cutello, Giuseppe Nicosia and M. Pavone, "Optimization Algorithms for the Protein Structure Prediction Problem", 24th European Conference on Operational Research - EURO XXIV, Lisbon, Portugal, July 11-14, 2010.

• 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, S. Rinaudo, "Optimization Population-Based Algorithms for High-Performance Analog Circuits", 2008 SIAM Conference on Optimization - OP08, Boston, Massachusetts, USA, May 10-13, 2008.

• F. Fiorante, G. Greco, Giuseppe Nicosia, S. Rinaudo, G. Stracquadanio, "Automatic Layout Optimization of Power Mosfets Using An Effective Population-Based Algorithm", 2008 SIAM Optimization Conference - OP08, Boston, Massachusetts, USA, May 10-13, 2008.

• Giuseppe Nicosia, E. Sciacca, "Pattern Search Algorithms for Circuit Design Optimization", 2008 SIAM Optimization Conference - OP08, Boston, Massachusetts, USA, May 10-13, 2008.

• 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.

• V. Cutello, Giuseppe Nicosia, "Multiple Learning using Immune Algorithms", Proceedings of 4th International Conference on Recent Advances in Soft Computing, RASC 2002, 12-13 December 2002, Nottingham, UK, pp. 102-107, 2002.

• 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.

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.

• P. Conca, Giuseppe Nicosia, G. Stracquadanio, "A Clonal Selection Algorithm for the Automatic Synthesis and Sizing of Low-pass Filters". In: Artificial Life and Evolutionary Computation: Proceedings of Wivace 2008 - Venice, Italy, 8-10 September 2008. World Scientific Publishing Company, pp 69-79, 2009. eISBN: 9789814287456

• 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.

Review Paper

• C. Angione, P. Lio', and Giuseppe Nicosia, "How to Compute with Metabolism in Bacteria?", ERCIM News, 2012

Journals in Italian

• Giuseppe Nicosia, M. Giacobini, M. Pavone, L. Vanneschi (a cura di) "Atti del Primo Workshop Italiano di Vita Artificiale e Computazione Evolutiva - WIVACE 2007", Sistemi Intelligenti, Societa' editrice Il Mulino, a. XX, n.2/agosto 2008.

• V. Cutello, Giuseppe Nicosia, "Sistemi Immunitari Artificiali: Un Nuovo Paradigma Computazionale per l'Ottimizzazione e la Bioinformatica", Sistemi Intelligenti, Societa' editrice Il Mulino, a. XVIII, n.1, pp. 47-54, aprile 2006.

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.