References of "Ostaszewski, Marek 50002792"
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See detailCuration of complex molecular pathways of Parkinson's disease as a collaborative scientific community effort
Antony, Paul UL; Ostaszewski, Marek UL; Gawron, P et al

Scientific Conference (2014, June 12)

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See detailIntegrating Pathways of Parkinson's Disease in a Molecular Interaction Map
Fujita, Kazuhiro A.; Ostaszewski, Marek UL; Matsuoka, Yukiko et al

in Molecular Neurobiology (2014)

Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is ... [more ▼]

Parkinson's disease (PD) is a major neurodegenerative chronic disease, most likely caused by a complex interplay of genetic and environmental factors. Information on various aspects of PD pathogenesis is rapidly increasing and needs to be efficiently organized, so that the resulting data is available for exploration and analysis. Here we introduce a computationally tractable, comprehensive molecular interaction map of PD. This map integrates pathways implicated in PD pathogenesis such as synaptic and mitochondrial dysfunction, impaired protein degradation, alpha-synuclein pathobiology and neuroinflammation. We also present bioinformatics tools for the analysis, enrichment and annotation of the map, allowing the research community to open new avenues in PD research. The PD map is accessible at http://minerva.uni.lu/pd_map . [less ▲]

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See detailThe Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways
Ostaszewski, Marek UL; Fujita, Kazuhiro; Matsuoka, Yukiko et al

Poster (2013, March 09)

Objectives: The pathogenesis of Parkinson's Disease (PD) is multi-factorial and age-related, implicating various genetic and environmental factors. It becomes increasingly important to develop new ... [more ▼]

Objectives: The pathogenesis of Parkinson's Disease (PD) is multi-factorial and age-related, implicating various genetic and environmental factors. It becomes increasingly important to develop new approaches to organize and explore the exploding knowledge of this field. Methods: The published knowledge on pathways implicated in PD, such as synaptic and mitochondrial dysfunction, alpha-synuclein pathobiology, failure of protein degradation systems and neuroinflammation has been organized and represented using CellDesigner. This repository has been linked to a framework of bioinformatics tools including text mining, database annotation, large-scale data integration and network analysis. The interface for online curation of the repository has been established using Payao tool. Results: We present the PD map, a computer-based knowledge repository, which includes molecular mechanisms of PD in a visually structured and standardized way. A bioinformatics framework that facilitates in-depth knowledge exploration, extraction and curation supports the map. We discuss the insights gained from PD map-driven text mining of a corpus of over 50 thousands full text PD-related papers, integration and visualization of gene expression in post mortem brain tissue of PD patients with the map, as well as results of network analysis. Conclusions: The knowledge repository of disease-related mechanisms provides a global insight into relationships between different pathways and allows considering a given pathology in a broad context. Enrichment with available text and bioinformatics databases as well as integration of experimental data supports better understanding of complex mechanisms of PD and formulation of novel research hypotheses. [less ▲]

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See detailEvolutionary conservation and network structure characterize genes of phenotypic relevance for mitosis in human
Ostaszewski, Marek UL; Eifes, Serge UL; del Sol Mesa, Antonio UL

in PLoS ONE (2012), 7(5), 36488

The impact of gene silencing on cellular phenotypes is difficult to establish due to the complexity of interactions in the associated biological processes and pathways. A recent genome-wide RNA knock-down ... [more ▼]

The impact of gene silencing on cellular phenotypes is difficult to establish due to the complexity of interactions in the associated biological processes and pathways. A recent genome-wide RNA knock-down study both identified and phenotypically characterized a set of important genes for the cell cycle in HeLa cells. Here, we combine a molecular interaction network analysis, based on physical and functional protein interactions, in conjunction with evolutionary information, to elucidate the common biological and topological properties of these key genes. Our results show that these genes tend to be conserved with their corresponding protein interactions across several species and are key constituents of the evolutionary conserved molecular interaction network. Moreover, a group of bistable network motifs is found to be conserved within this network, which are likely to influence the network stability and therefore the robustness of cellular functioning. They form a cluster, which displays functional homogeneity and this cluster is significantly enriched in genes phenotypically relevant for mitosis. Additional results reveal a relationship between specific cellular processes and the phenotypic outcomes induced by gene silencing. This study introduces new ideas regarding the relationship between genotype and phenotype in the context of the cell cycle. We show that the analysis of molecular interaction networks can result in the identification of genes relevant to cellular processes, which is a promising avenue for future research. [less ▲]

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See detailMultiobjective Classification with moGEP: An Application in the Network Traffic Domain
Ostaszewski, Marek UL; Bouvry, Pascal UL; Seredynski, Franciszek

in GECCO '09: Proceedings of the 11th Annual conference on Genetic and evolutionary computation (2009)

The paper proposes a multiobjective approach to the problem of malicious network traffic classification, with specificity and sensitivity criteria as objective functions for the problem. The ... [more ▼]

The paper proposes a multiobjective approach to the problem of malicious network traffic classification, with specificity and sensitivity criteria as objective functions for the problem. The multiobjective version of Gene Expression Programming (GEP) called moGEP is proposed and applied to find proper classifiers in the multiobjective search space. The purpose of the classifiers is to discriminate information about the network traffic obtained from Idiotypic Network-based Intrusion Detection System (INIDS), transformed into time series. The proposed approach is validated using the network traffic simulator ns2. Classifiers of high accuracy are obtained and their diversity offers interesting possibilities to the domain of network security. [less ▲]

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See detailNature inspired Algorithm-Based Fault Tolerance on Global Computing Platforms. Application to Symbolic Regression
Varrette, Sébastien UL; Ostaszewski, Marek UL; Bouvry, Pascal UL

in International Conference on Metaheuristics and Nature Inspired Computing (META'08) (2008)

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See detailAn Approach to Intrusion Detection by Means of Idiotypic Networks Paradigm
Ostaszewski, Marek UL; Bouvry, Pascal UL; Seredynski, Franciszek

in IEEE World Congress on Computational Intelligence, WCCI 2008, Congress on Evolutionary Computation CEC 2008, Honk-Kong, June (2008)

In this paper we present a novel intrusion detection architecture based on Idiotypic Network Theory (INIDS), that aims at dealing with large scale network attacks featuring variable properties, like ... [more ▼]

In this paper we present a novel intrusion detection architecture based on Idiotypic Network Theory (INIDS), that aims at dealing with large scale network attacks featuring variable properties, like Denial of Service (DoS). The proposed architecture performs dynamic and adaptive clustering of the network traffic for taking fast and effective countermeasures against such high-volume attacks. INIDS is evaluated on the MITpsila99 dataset and outperforms previous approaches for DoS detection applied to this set. [less ▲]

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See detailAdaptive and Dynamic Intrusion Detection by Means of Idiotypic Networks Paradigm
Ostaszewski, Marek UL; Bouvry, Pascal UL; Seredynski, Franciszek

in The 21th IEEE International Parallel and Distributed Processing Symposium (IPDPS), NIDISC Workshop. (2008)

In this paper we present a novel intrusion detection architecture based on Idiotypic Network Theory (INIDS), that aims at dealing with large scale network attacks featuring variable properties, like ... [more ▼]

In this paper we present a novel intrusion detection architecture based on Idiotypic Network Theory (INIDS), that aims at dealing with large scale network attacks featuring variable properties, like Denial of Service (DoS). The proposed architecture performs dynamic and adaptive clustering of the network traffic for taking fast and effective countermeasures against such high-volume attacks. INIDS is evaluated on the MIT'99 dataset and outperforms previous approaches for DoS detection applied to this set. [less ▲]

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See detailCoevolutionary-based Mechanisms for Network Anomaly Detection
Ostaszewski, Marek UL; Seredynski, Franciszek; Bouvry, Pascal UL

in Journal of Mathematical Modelling and Algorithms (2007), 6(3), 411-431

The paper presents an approach based on the principles of immune systems applied to the anomaly detection problem. Flexibility and efficiency of the anomaly detection system are achieved by building a ... [more ▼]

The paper presents an approach based on the principles of immune systems applied to the anomaly detection problem. Flexibility and efficiency of the anomaly detection system are achieved by building a model of the network behavior based on the self-nonself space paradigm. Covering both self and nonself spaces by hyperrectangular structures is proposed. The structures corresponding to self-space are built using a training set from this space. The hyperrectangular detectors covering nonself space are created using a niching genetic algorithm. A coevolutionary algorithm is proposed to enhance this process. The results of experiments show a high quality of intrusion detection, which outperform the quality of the recently proposed approach based on a hypersphere representation of the self-space. [less ▲]

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