Download Giuseppe Nicosia`s Publications (September 2014)

Giuseppe Nicosia’s Publications (September 2014)
Refereed Journals
• "Designing and Programming Molecular Machines", (submitted),
C. Angione, J. Costanza, G. Carapezza,
P. Lio', G. Nicosia, Giuseppe Nicosia, [Pareto Optimality; E. coli modelling; Turing Machines;
Molecular Machines; Biological Complexity; Gene Set Programming; von Neumann Architectures;
Minsky's Register Machines]
• "Optimizing constraint-based models through gene expression and codon usage information"
(submitted),
C. Angione, J. Costanza, G. Carapezza, P. Lio', Giuseppe Nicosia, [Multi-objective
optimization algorithms; Bacterial strains; Genetic manipulations; Chemical reactions; Flux Balance
Analysis]
• "Satisfiability by Maxwell-Boltzmann and Bose-Einstein Statistical Distributions",
C. Angione, A.
Occhipinti, Giuseppe Nicosia , Journal of Experimental Algorithms, Volume 19, October 2014. [KSAT Problem; Phase Transition; Bose-Einstein Condensation; SAT solvers; Physics-inspired
computation]
• "Pareto Optimality in Organelle Energy Metabolism Analysis",
C. Angione,_ G. Carapezza, J. Costanza,
P. Lio', Giuseppe Nicosia , IEEE/ACM Transactions on Computational Biology and Bioinformatics,
2013.
DOI: 10.1109/TCBB.2013.95, ISSN: 1545-5963 Supplementary Material. [Mitochondrion;
Chloroplast; Hydrogenosome; Sensitivity Analysis; Multi-objective optimization; Robustness
Analysis]
• "Design and strain selection criteria for bacterial communication networks",
C. Angione, G. Carapezza,
J. Costanza, P. Lio', Giuseppe Nicosia, Nano Communication Networks, 4(4): 155-163,
2013.
http://dx.doi.org/10.1016/j.nancom.2013.08.001 DOI:
10.1016/j.nancom.2013.08.001
[Communication design; Network multi-objective optimisation; Lateral
gene transfer; Molecular machine; Geobacter communication]
• "A Design Automation Framework for Computational Bioenergetics in Biological Networks",
C.
Angione,_ J. Costanza, G. Carapezza, P. Lio', Giuseppe Nicosia, Molecular BioSystems, 9(10):25542564, 2013.
[Identifiability Analysis; Biological Networks; Biological Design Automation; Human
Mitochondria; Algal Metabolism; Chlamydomonas reinhardtii; Algebraic Differential Equations; Flux
Balance Analysis]
• "Semiconductor Device Design using Bimads Algorithm",
G. Stracquadanio, V. Romano, Giuseppe
Nicosia, Journal of Computational Physics, 242:304-320, 2013. [Semiconductors; Optimization; Driftdiffusion; Energy-Transport; Diodes; MESFETs; MOSFETs]
• "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',
Giuseppe Nicosia, ACS Synthetic Biology Journal, 2(5):274-288, 2013. DOI: 10.1021/sb300102k
Supplementary Information and Material. [Metabolic CAD; Synthetic Biology; Multi-Objective
Optimization; Sensitivity Analysis; Robustness Analysis; Global Robustness; Local Robustness;
Photosynthetic Yield]
• "Bose-Einstein Condensation in Satisfiability Problems",
C. Angione, A. Occhipinti, G. Stracquadanio,
Giuseppe Nicosia, European Journal of Operational Research, 227:44-54, 2013, featured in Le
Scienze - Scientific American. [k-SAT, Complex Networks; Bose-Einstein Condensation; Phase
Transition; Performance]
• "Robust Design of Microbial Strains",
J. Costanza, G. Carapezza, C. Angione, P. Lio', Giuseppe Nicosia,
Bioinformatics - Oxford Journal, 28(23):3097-3104, 2012. Supplementary Information and
Material.
[Metabolic Engineering; BioCAD; E. coli; Flux Balance Analysis models; Gene Protein
Reaction Map models; GDLS; OptFlux; OptKnock; OptGene; GDMO]
• "OREMPdb: a Semantic Dictionary of Runnable Biological Circuits", R. Umeton, Giuseppe Nicosia, C.
F. Dewey Jr., BMC Bioinformatics, 13(4):S6, 2012. [Biomedical Ontologies; Pathway models;
Ontology Reasoning Engine; Molecular Pathway; OREMP; BioModels; Biological Engineering]
• "Clonal Selection - An Immunological Algorithm for Global Optimization over Continuous Spaces",
M.
Pavone, G. Narzisi, Giuseppe Nicosia, Journal of Global Optimization, 53(4):769-808,
2012.
[Nonlinear optimization; Global optimization; Derivative-free optimization; Black-box
optimization; Immunological algorithms; Clonal Selection Algorithms; Bio-inspired Algorithms;
Evolutionary algorithms]
• "Identification of Sensitive Enzymes in the Photosynthetic Carbon Metabolism",
R. Umeton, G.
Stracquadanio, A. Papini, J. Costanza, P. Lio', and Giuseppe Nicosia, Advances in Experimental
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Medicine and Biology, special issue on "Advances in Systems Biology" , Springer, 736(4):441-459,
2012. [Sensitivity Analysis; Systems Biology; Chloroplast; Carbon Metabolism Pathway]
"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.
[Protein Alignments; Multiple Alignment Algorithms; Local Optimization; Global Optimization]
"Computational Energy-based Redesign of Robust Proteins",
G.Stracquadanio, Giuseppe Nicosia,
Computers and Chemical Engineering, 35(3):464-473, 2011. [Protein robustness; Robust-proteindesign algorithm; Energetic relative entropy; Kullback-Leibler divergence; Rényi divergence; von
Neumann divergence; Peptides; Proteins; Drugs; DrugBank]
"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, 150(1):525-526, 2010. [Photosynthesis; CO2 uptake vs. Nitrogen;
Pareto Optimality]
"On Discrete Models and Immunological Algorithms for Protein Structure Prediction",
V. Cutello, G.
Morelli, Giuseppe Nicosia, M. Pavone and G. Scollo, Natural Computing Journal, 10(1):91-102, 2010.
[Dill model; HP model; Protein Structure Prediction; Clonal Selection Algorithms; Bio-inspired
Algorithms]
"Generalized Pattern Search Algorithm for Peptide Structure Prediction",
Giuseppe Nicosia,
G.Stracquadanio, Biophysical Journal, 95(10):4988-4999, 2008. [Search and Poll Algorithms; PEPstr;
Protein Structure Prediction; Robustness]
"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. [Analog circuit design; Circuit sizing; Design for
yield; Design for manufacturability; Genetic algorithms; Population-based algorithms; Evolutionary
optimization; Multi-objective optimization; Constrained optimization]
"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):933, 2007. [Immune Algorithm; Information Gain; Graph coloring problem; Chromatic number
problem; Combinatorial optimization]
"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. [Functional model proteins; Protein Structure Prediction; 2D HP model; 3D HP model;
Hypermutation operators; Hypermacromutation operators; Aging operator; Clonal selection
algorithms]
"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. [Clonal Selection Algorithms; DIRECT optimization algorithm; Immune
Algorithms; pattern search methods; protein folding; protein structure prediction; structural
bioinformatics]
"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 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 best folding
algorithm. [multi-objective optimization; Pareto front; protein folding; protein structure prediction;
multi-objective evolutionary algorithms]
"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. [Electronic Design Automation; CAD;
Evolutionary electronics; multi-objective optimization; circuit design problems; evolutionary
algorithms; genetic algorithms; classical optimization methods; pattern search methods; operational
transconductance amplifier; leapfrog filter]
"Optimising an Inductor Circuit and a Two-Stage Operational Transconductance Amplifier using
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. [Electronic Design Automation;
CAD; multi-objective optimization; circuit design problems; evolutionary algorithms; genetic
algorithms; classical optimization methods]
"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. [Immune
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system; artificial immune system; pattern recognition; immune response]
• "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. [Immune system, Celada-Seiden model; Stochastic Cellular Automata; Lattice
Gas Automata; Computational Complexity]
Refereed Conference Papers with Proceedings
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• "Programming Living Machines: the case study of Escherichia coli",
Jole Costanza, Luca Zammataro,
Giuseppe Nicosia, Living Machines - LM2014, the 3rd Conference on Biomimetic and Biohybrid
Systems, Museo Nazionale della Scienza e della Tecnologia "Leonardo da Vinci", Milan, Italy, July 30
- August 1, 2014, Springer LNCS (to appear).
• "Sensitivity Techniques for Effective Optimization of Tandem Thin-Film Silicon Solar Cells",
A.
Patan_e_, A. Santoro_ , G. Carapezza_, V. Romano_, A. La Magna and Giuseppe Nicosia_, The 10th
International Conference on Scientific Computing in Electrical Engineering - SCEE 2014, July 22 July 25, 2014, Wuppertal, Germany.
• "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, ACM Press, 43, 2013.
• "Rational Design of Organelle Compartments in Cells ",
C. Angione, G. Carapezza, J. Costanza, P. Lio',
and Giuseppe Nicosia, Twelfth 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: 978-3-64233635-5.
• "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 on Complex Systems - ECCS'12, Brussels, 3-7 September 2012, DOI: 10.1007/978-3-31900395-5_127, Springer Complexity, pp. 1063-1069, 2013.
• "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, ISSN 2040557X, EPiC Series, 10: 1-15, 2012. Best Paper Award presented by Sir Roger Penrose.
• "Global Optimization for Algebraic Geometry - Computing Runge-Kutta Methods",
Ivan Martino and
Giuseppe Nicosia, Learning and Intelligent OptimizatioN Conference - LION 6, Paris - France, Jan 1620, 2012, Springer, Lecture Notes in Computer Science, 7219:449-454, 2012
• "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, DOI: 10.1007/978-1-4471-2318-7_26, Springer, pages 341-354, 2011.
• "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. MIT Press, pp. 39-46, 2011.
• "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, 2011.
• "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, SpringerVerlag, Cambridge, UK, July 18-21, pp. 15-29, 2011.
• "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,
2010.
• "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, 2010.
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• "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, 2010.
• "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. DOI: 10.1109/CEC.2010.5585990,
IEEE Press, pp. 1-7, 2010.
• "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. DOI: 10.1109/CEC.2010.5586044, IEEE Press, pp.1-8, 2010.
• "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, 2010.
• "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,
2010.
• "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, 2010. DOI:
10.1109/BioSciencesWorld.2010.13 Best Paper Award.
• "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, 2009.
• " 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, 2009.
• " 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, IEEE Press, pp. 1-6, 2008.
• 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. IEEE Industrial Electronics Society Press, pp.
1203-1208, 2008.
• 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, 2007.
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, 29th31st August, 2007, Jesus College Oxford, UK, pp. 102-109, 2007.
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• 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 3931:324337, 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.
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• 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
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• C. Angione, J. Costanza, G. Carapezza, P. Lio', G. Nicosia, "Pareto Front and Identifiability Analysis to
Characterize Mitochondrial Diseases", Mitochondrial Disease: Translating biology into new
treatments, Wellcome Trust Conference Centre, Wellcome Trust Genome Campus, Hinxton,
Cambridge, UK, 2-4 October 2013.
• C. Angione, J. Costanza, G. Carapezza, P. Lio', G. Nicosia, "Identifiability Analysis to Characterise
Mitochondrial Diseases", Proceedings of the 5th International Workshop on Bio-Design Automation
(IWBDA) at Imperial College, London, UK, July 12-13, 2013.
• J. Costanza, C. Angione, G. Carapezza, P. Lio', G. Nicosia, "Multi-objective Optimisation of Escherichia
coli for Direct Production of 1,4-butanediol", Proceedings of the 5th International Workshop on
Bio-Design Automation (IWBDA) at Imperial College, London, UK, July 12-13, 2013.
• J. Costanza, C. Angione, G. Carapezza, P. Li—, and G. Nicosia, "Pareto-based Gene and Pathway Sieve
for Biofuel Production", Proceedings of the 5th International Workshop on Bio-Design Automation
(IWBDA) at Imperial College, London, UK, July 12-13, 2013.
• 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.
• "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).
• "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.
• 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
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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 Francisco,
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 PatternBased 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,
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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.
Books
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• Pietro Lio', Orazio Miglino, Giuseppe Nicosia, Stefano Nolfi and Mario Pavone (Eds.), Advances in
Artificial Life, Proceedings of the 12th European Conference on Artificial Life, MIT Press, 2013.
• 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.
Book chapters
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• 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", inComputational
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
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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, Special Theme "What is Computation - Alan Turing's Legacy", 2012.
Technical Reports
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• C. Angione, Giuseppe Nicosia, G. Stracquadanio, "Characteristic Phase Transitions and Bose-Einstein
Condensation in Networks of Random Satisfiability Problems", University of Catania, Italy, 2009. • C. Angione, Giuseppe Nicosia, G. Stracquadanio, "Chaotic Quicksort: One-dimensional Chaotic Maps to
Improve the Performances of Quicksort Algorithms", University of Catania, Italy, 2008.
Journals in Italian
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• 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.
ISBN: 978-88-15-12385-5
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• 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.
ISSN: 1120-9550, DOI: 10.1422/21789
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