Publications

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).

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).

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).

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).

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).

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).

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).

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).