Giuseppe Nicosia
Research interests
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InterestsArtificial Immune System, Immunoinformatics, Computational Systems Biology, Electronic Design Automation, Optimization, Synthetic Biology, Computational Immunology, Multiobjective Optimization
Publications
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3.43Impact points
OREMPdb: a semantic dictionary of computational pathway models.
BMC bioinformatics. 01/2012; 13 Suppl 4:S6.
The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. In fact, such models are shared to provide the charact... [more] The information coming from biomedical ontologies and computational pathway models is expanding continuously: research communities keep this process up and their advances are generally shared by means of dedicated resources published on the web. In fact, such models are shared to provide the characterization of molecular processes, while biomedical ontologies detail a semantic context to the majority of those pathways. Recent advances in both fields pave the way for a scalable information integration based on aggregate knowledge repositories, but the lack of overall standard formats impedes this progress. Indeed, having different objectives and different abstraction levels, most of these resources "speak" different languages. Semantic web technologies are here explored as a means to address some of these problems. Employing an extensible collection of interpreters, we developed OREMP (Ontology Reasoning Engine for Molecular Pathways), a system that abstracts the information from different resources and combines them together into a coherent ontology. Continuing this effort we present OREMPdb; once different pathways are fed into OREMP, species are linked to the external ontologies referred and to reactions in which they participate. Exploiting these links, the system builds species-sets, which encapsulate species that operate together. Composing all of the reactions together, the system computes all of the reaction paths from-and-to all of the species-sets. OREMP has been applied to the curated branch of BioModels (2011/04/15 release) which overall contains 326 models, 9244 reactions, and 5636 species. OREMPdb is the semantic dictionary created as a result, which is made of 7360 species-sets. For each one of these sets, OREMPdb links the original pathway and the link to the original paper where this information first appeared.
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2.02Impact points
Identification of sensitive enzymes in the photosynthetic carbon metabolism.
Advances in experimental medicine and biology. 01/2012; 736:441-59.
Understanding and optimizing the CO(2) fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C(3) photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteratio... [more] Understanding and optimizing the CO(2) fixation process would allow human beings to address better current energy and biotechnology issues. We focused on modeling the C(3) photosynthetic Carbon metabolism pathway with the aim of identifying the minimal set of enzymes whose biotechnological alteration could allow a functional re-engineering of the pathway. To achieve this result we merged in a single powerful pipe-line Sensitivity Analysis (SA), Single- (SO) and Multi-Objective Optimization (MO), and Robustness Analysis (RA). By using our recently developed multipurpose optimization algorithms (PAO and PMO2) here we extend our work exploring a large combinatorial solution space and most importantly, here we present an important reduction of the problem search space. From the initial number of 23 enzymes we have identified 11 enzymes whose targeting in the C(3) photosynthetic Carbon metabolism would provide about 90% of the overall functional optimization. Both in terms of maximal CO(2) Uptake and minimal Nitrogen consumption, these 11 sensitive enzymes are confirmed to play a key role. Finally we present a RA to confirm our findings.
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Large Scale Agent-Based Modeling of the Humoral and Cellular Immune Response.
Artificial Immune Systems - 10th International Conference, ICARIS 2011, Cambridge, UK, July 18-21, 2011. Proceedings; 01/2011
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On discrete models and immunological algorithms for protein structure prediction.
Natural Computing. 01/2011; 10:91-102.
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Computational energy-based redesign of robust proteins.
Computers & Chemical Engineering. 01/2011; 35:464-473.
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Design of robust metabolic pathways.
Proceedings of the 48th Design Automation Conference, DAC 2011, San Diego, California, USA, June 5-10, 2011; 01/2011
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7.48Impact points
Protein multiple sequence alignment by hybrid bio-inspired algorithms.
Nucleic acids research. 11/2010; 39(6):1980-92.
This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA ali... [more] This article presents an immune inspired algorithm to tackle the Multiple Sequence Alignment (MSA) problem. MSA is one of the most important tasks in biological sequence analysis. Although this paper focuses on protein alignments, most of the discussion and methodology may also be applied to DNA alignments. The problem of finding the multiple alignment was investigated in the study by Bonizzoni and Vedova and Wang and Jiang, and proved to be a NP-hard (non-deterministic polynomial-time hard) problem. The presented algorithm, called Immunological Multiple Sequence Alignment Algorithm (IMSA), incorporates two new strategies to create the initial population and specific ad hoc mutation operators. It is based on the 'weighted sum of pairs' as objective function, to evaluate a given candidate alignment. IMSA was tested using both classical benchmarks of BAliBASE (versions 1.0, 2.0 and 3.0), and experimental results indicate that it is comparable with state-of-the-art multiple alignment algorithms, in terms of quality of alignments, weighted Sums-of-Pairs (SP) and Column Score (CS) values. The main novelty of IMSA is its ability to generate more than a single suboptimal alignment, for every MSA instance; this behaviour is due to the stochastic nature of the algorithm and of the populations evolved during the convergence process. This feature will help the decision maker to assess and select a biologically relevant multiple sequence alignment. Finally, the designed algorithm can be used as a local search procedure to properly explore promising alignments of the search space.
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An Immunological Algorithm for Doping Profile Optimization in Semiconductors Design.
Artificial Immune Systems, 9th International Conference, ICARIS 2010, Edinburgh, UK, July 26-29, 2010. Proceedings; 01/2010
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Multi-objective optimization of doping profile in semiconductor design.
Genetic and Evolutionary Computation Conference, GECCO 2010, Proceedings, Portland, Oregon, USA, July 7-11, 2010; 01/2010
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Entropic divergence for population based optimization algorithms.
Proceedings of the IEEE Congress on Evolutionary Computation, CEC 2010, Barcelona, Spain, 18-23 July 2010; 01/2010
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Analysis and Optimization of C3 Photosynthetic Carbon Metabolism.
10th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2010, Philadelphia, Pennsylvania, USA, May 31-June 3 2010; 01/2010
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Special issue on Nature Inspired Cooperative Strategies for Optimisation (NICSO).
Natural Computing. 01/2010; 9:1-3.
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An Information-Theoretic Approach for Clonal Selection Algorithms.
Artificial Immune Systems, 9th International Conference, ICARIS 2010, Edinburgh, UK, July 26-29, 2010. Proceedings; 01/2010
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Effective design of semiconductor devices using evolutionary-based derivative free optimization.
Proceedings of the IEEE Congress on Evolutionary Computation, CEC 2010, Barcelona, Spain, 18-23 July 2010; 01/2010
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A Design-for-Yield Algorithm to Assess and Improve the Structural and Energetic Robustness of Proteins and Drugs.
Experimental Algorithms, 8th International Symposium, SEA 2009, Dortmund, Germany, June 4-6, 2009. Proceedings; 01/2009
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4.39Impact points
Generalized Pattern Search Algorithm for Peptide Structure Prediction.
Biophysical journal. 06/2008;
Finding the near-native structure of a protein is one of the most important open problems in structural biology and biological physics. The problem becomes dramatically di ffi cult when a given protein has no regular secondary structure or it does not show a fold similar to already known structures:... [more] Finding the near-native structure of a protein is one of the most important open problems in structural biology and biological physics. The problem becomes dramatically di ffi cult when a given protein has no regular secondary structure or it does not show a fold similar to already known structures: this situation occurs frequently when we need to predict the tertiary structure of small molecules, called peptides. In the present research work, we propose a new ab-initio algorithm, the Generalized Pattern Search Algorithm (GPS), based on the well known class of Search-and-Poll algorithms. Inspired by the approach proposed by Floudas et al.(1), we performed an extensive set of simulations over a well known set of 44 peptides to investigate the robustness and reliability of the proposed algorithm, and comparing the peptide conformation with the state of art algorithm for peptide structure prediction, known as PEPstr (2). In particular, we tested the algorithm on the instances proposed by Kaur et al. (2) to validate the proposed algorithm: the experimental results con fi rm that Gps outperforms PEPstr of 21.17% in terms of average RMSD Calpha.
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An Advanced Clonal Selection Algorithm with Ad-Hoc Network-Based Hypermutation Operators for Synthesis of Topology and Sizing of Analog Electrical Circuits.
Artificial Immune Systems, 7th International Conference, ICARIS 2008, Phuket, Thailand, August 10-13, 2008. Proceedings; 01/2008
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Determination of protein structure and dynamics combining immune algorithms and pattern search methods.
Natural Computing. 01/2007; 6:55-72.
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Generalized Pattern Search and Mesh Adaptive Direct Search Algorithms for Protein Structure Prediction.
Algorithms in Bioinformatics, 7th International Workshop, WABI 2007, Philadelphia, PA, USA, September 8-9, 2007, Proceedings; 01/2007
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On the Convergence of Immune Algorithms.
Proceedings of the IEEE Symposium on Foundations of Computational Intelligence, FOCI 2007, part of the IEEE Symposium Series on Computational Intelligence 2007, Honolulu, Hawaii, USA, 1-5 April 2007; 01/2007
Following (2)
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Neil Dalchau
Microsoft -
Mark Howard-Banks
ResearchGate
Topics (1)
