Publications

(by topics | by date | by type)

2011

  • Menges F., Narzisi G. and Mishra B.:
    TotalReCaller: Improved Accuracy and Performance via Integrated Alignment & Base-Calling.
    Bioinformatics, Oxford Journals, (2011) 27(17): 2330-2337 (DOI: 10.1093/bioinformatics/btr393).

  • Narzisi G. and Mishra B.:
    Comparing De Novo Genome Assembly: The Long and Short of It.
    PLoS ONE 6(4):e19175. April 2011 (DOI: 10.1371/journal.pone.0019175).

  • Narzisi G. and Mishra B.:
    Scoring-and-Unfolding Trimmed Tree Assembler: Concepts, Constructs and Comparisons.
    Bioinformatics, Oxford Journals, (2011) 27 (2): 153-160 (DOI: 10.1093/bioinformatics/btq646).
    [Revision, Feb 10 2011]

  • Narzisi G.:
    Scoring-and-Unfolding Trimmed Tree Assembler: Algorithms for Assembling Genome Sequences Accurately and Efficiently.
    Ph.D. Thesis, Department of Computer Science, Courant Institute of Mathematical Sciences, New York University, New York, USA, May 2011.

  • Narzisi G., Menges F., Mishra B.:
    Improved Assembly Accuracy by integrating Base-Calling, Error Correction and Assembly.
    Eighth Annual Meeting of the Bioinformatics Italian Society (BITS 2011), June 20-22, 2011 Pisa, Italy (poster).

  • Pavone M., Narzisi G., Nicosia G.:
    Clonal Selection - An Immunological Algorithm for Global Optimization over Continuous Spaces.
    Journal of Global Optimization, Springer 2011 (DOI: 10.1007/s10898-011-9736-8).

2010

  • Narzisi G.:
    SUTTA: Scoring-and-Unfolding Trimmed Tree Assembler.
    9th IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS), Cold Spring Harbor Laboratory (CSHL), November 10 - 12, 2010 (poster).

  • Narzisi G. and Mishra B.:
    A novel Technologically Agnostic De Novo Sequence Assembler.
    Systems Biology and New Sequencing Technologies (SBNST), Centre for Genomic Regulation (CRG), Barcelona, 16-17-18 June, 2010 (poster).

  • Narzisi G., Nicosia G. and Stracquadanio G. (Best Paper Award):
    Robust Bio-Active Peptide Prediction using Multi-Objective Optimization.
    The First International Conference on Advances in Bioinformatics and Applications (BIOINFO 2010), March 7-13 2010, Cancun, Mexico, IEEE Press (DOI: 10.1109/BioSciencesWorld.2010.13).

2009

  • Smith S.W., Portelli I., Narzisi G., Nelson L.S., Menges F., Rekow E.D., Mincer J.S., Mishra B., Goldfrank L.R.:
    A Novel Approach to Multi-Hazard Modeling and Simulation.
    Disaster Medicine and Public Health Preparedness (DMPHP), The American Medical Association (AMA), 2009 (DOI: 10.1097/DMP.0b013e3181a88899).

2008

  • Narzisi G.:
    Optimization and Tradeoffs in Protein Structure Prediction.
    Ph.D. Thesis, Department of Mathematics and Computer Science, University of Catania, Italy, October, 2008.

  • Menges F., Mishra B. and Narzisi G.:
    Modeling and Simulation of E-Mail Social Networks: A New Stochastic Agent-Based Approach.
    Winter Simulation Conference (WSC 2008), December 7-10, Miami, Florida, USA (DOI: 10.1109/WSC.2008.4736399).

  • Narzisi G., Mysore V., Byeon J. and Mishra B.:
    Complexities, Catastrophes and Cities: Emergency Dynamics in Varying Scenarios and Urban Topologies.
    Accepted for the print Proceedings of the International Conference on Complex Systems (ICCS), 2008 (pdf, supplementary material).

2007

  • Cutello V., Narzisi G., Nicosia G.:
    Computational Studies of Peptide and Protein Structure Prediction Problems via Multi-Objective Evolutionary Algorithms.
    Book chapter in Joshua Knowles, David Corne and Kalyanmoy Deb (Eds), Multi-Objective Problem Solving from Nature: From Concepts to Applications, Springer 2007, pp 93-114 (DOI: 10.1007/978-3-540-72964-8_5).

  • Narzisi G., Mincer J.S., Smith S., Mishra B.:
    Resilience in the Face of Disaster: Accounting for Varying Disaster Magnitudes, Resource Topologies, and (Sub)Population Distributions in the PLAN C Emergency Planning Tool.
    3rd International Conference on Industrial Applications of Holonic and Multi-Agent Systems (HoloMAS 2007), September 3 - 5, 2007, Regensburg, Germany, Proceedings by Springer, LNAI 4659, pp. 433-446 (DOI: 10.1007/978-3-540-74481-8_41).

  • Smith S.W., Nelson L.S., Rekow E.D., Narzisi G., Mincer J.S., Portelli I., Mishra B. and Goldfrank L.G.:
    A New Approach to Multi-Hazard Modeling and Simulation.
    North American Congress of Clinical Toxicology (NACCT) 2007, 45(6):608-608, October 19-24, 2007, New Orleans, Louisiana, USA (DOI: 10.1080/15563650701610056).

2006

  • Narzisi G., Mysore V. and Mishra B.:
    Multi-Objective Evolutionary Optimization of Agent Based Models: an application to emergency response planning.
    The IASTED International Conference on Computational Intelligence (CI 2006), Proceedings by ACTA Press, pp. 224-230, November 20-22, 2006 San Francisco, California, USA (abstract, pdf).

  • Narzisi G., Mysore V., Nelson L., Rekow D., Triola M., Halcomb L., Portelli I., and Mishra B.:
    Complexities, Catastrophes and Cities: Unraveling Emergency Dynamics.
    InterJournal of Complex Systems (ISSN: 1081-0625), Manuscript Number:[1745], 2006.

  • Mysore V., Narzisi G., Nelson L., Rekow D., Triola M., Shapiro A., Coleman C., Gill O., Daruwala R. S. and Mishra B.:
    Agent Modeling of a Sarin Attack in Manhattan.
    The First International Workshop on Agent Technology for Disaster Management (ATDM), held in conjunction with the Fifth International Joint Conference on Autonomous Agents and Multi-Agent Systems (AAMAS), Future University, Hakodate, JAPAN, 8th May 2006 (proceedings).

  • Cutello V., Narzisi G., Nicosia G.:
    A Multi-Objective Evolutionary Approach to the Protein Structure Prediction Problem.
    Journal of the Royal Society Interface, Royal Society Publications London, vol. 3, issue 6, pp. 139-151, 22 February 2006 (DOI: 10.1098/rsif.2005.0083).

  • Anile A.M., Cutello V., Narzisi G. , Nicosia G., Spinella S.:
    Determination of protein structure and dynamics combining immune algorithms and pattern search methods.
    Natural Computing Int. Journal, Springer 2006 (DOI: 10.1007/s11047-006-9027-3).

  • Cutello V., Narzisi G., Nicosia G., Pavone M.:
    Real coded clonal selection algorithm for unconstrained global optimization using a hybrid inversely proportional hypermutation operator.
    The 21st Annual ACM Symposium on Applied Computing, SAC 2006, Dijon, France, April 23 -27, 2006, ACM Press, vol. 2 pp. 950-954 (DOI: 10.1145/1141277.1141501).

2005

  • Cutello V., Narzisi G., Nicosia G., Pavone M.:
    An Immunological Algorithm for Global Numerical Optimization.
    7th International Conference on Artificial Evolution, EA'05, October 26-28 2005, University of Lille, France, Springer-Verlag, Lecture Notes in Computer Science, vol. 3871, pp. 284-295 (DOI: 10.1007/11740698_25).

  • Cutello V., Narzisi G., Nicosia G., Pavone M.:
    Clonal Selection Algorithms: A Comparative Case Study using Effective Mutation Potentials.
    4th International Conference on Artificial Immune Systems, ICARIS 2005, 14th-17th August, 2005 in Banff, Alberta, Canada, Proceedings by LNCS, vol. 3627, pp. 13-28 Springer (DOI: 10.1007/11536444_2).

  • Anile A.M., Cutello V., Narzisi G., Nicosia G., Spinella S.:
    Lipschitzian pattern search, immunological algorithm and quasi-Newton method for the Protein Folding Problem: An innovative multistage approach.
    Proceedings of the Internation Workshop on Natural and Artificial Immune Systems, NAIS 2005, 9-10 June, 2005, Vietri sul Mare (SA), Italy. Springer-Verlag, Lecture Notes in Computer Science, vol. 3931, pp.307-323, 2006 (DOI: 10.1007/11731177_38).

  • Cutello V., Narzisi G., Nicosia G. (Best Paper Award Candidate):
    A Class of Pareto Archived Evolution Strategy Algorithms Using Immune Inspired Operators for Ab-Initio Protein Structure Prediction.
    EvoWorkshops 2005 - EvoBio 2005, Lausanne, Switzerland, 30 March - 1 April, 2005, Proceedings by LNCS, vol. 3449, pp. 54-63 Springer, (DOI: 10.1007/b106856).

2004

  • Cutello V., Narzisi G., Nicosia G., Pavone M., Sorace G.:
    How to Escape Traps using Clonal Selection Algorithms.
    The First International Conference on Informatics in Control, Automation and Robotics (ICINCO 2004), Setubal, Portugal, August 25-28 INSTICC Press, Vol. 1, pp. 322-326.

  • Cutello V., Nicosia G. and Narzisi G.:
    Protein Structure Prediction with Multi-objective Evolutionary Algorithms and Supersecondary Structure Prediction Constraints.
    First International School on Advanced BioMedicine and BioInformatics, Lipari School for Scientific Research, Lipari Island, May 29 - June 5, 2004 (poster).

Copyright © 2010 Giuseppe Narzisi