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Yayın Discovering cis-regulatory modules by optimizing barbecues(Elsevier Science Bv, 2009-05-28) Mosig, Axel; Bıyıkoğlu, Türker; Prohaska, Sonja J.; Stadler, Peter F.Gene expression in eukaryotic cells is regulated by a complex network of interactions, in which transcription factors and their binding sites on the genomic DNA play a determining role. As transcription factors rarely, if ever, act in isolation, binding sites of interacting factors are typically arranged in close proximity forming so-called cis-regulatory modules. Even when the individual binding sites are known, module discovery remains a hard combinatorial problem, which we formalize here as the Best Barbecue Problem. It asks for simultaneously stabbing a maximum number of differently colored intervals from K arrangements of colored intervals. This geometric problem turns out to be an elementary, yet previously unstudied combinatorial optimization problem of detecting common edges in a family of hypergraphs, a decision version of which we show here to be NP-complete. Due to its relevance in biological applications, we propose algorithmic variations that are suitable for the analysis of real data sets comprising either many sequences or many binding sites. Being based on set systems induced by interval arrangements, our problem setting generalizes to discovering patterns of co-localized itemsets in non-sequential objects that consist of corresponding arrangements or induce set systems of co-localized items. In fact, our optimization problem is a generalization of the popular concept of frequent itemset mining.Yayın Risk scalable and modular security architectures(Işık Üniversitesi, 2005-04) Kunter, Ünal; Koç, Çetin Kaya; Işık Üniversitesi, Fen Bilimleri Enstitüsü, Bilgisayar Mühendisliği Yüksek Lisans ProgramıNetwork security is ensuring the availability, the integrity and the confidentiality in the business activities. Network security is not only limiting acess to the resources; İt is mainly structring the acess to the match the business needs and ensure the availability of the resources. To demonstrate these principals, the deployment of a secure environment for different enterprises level companies will be examined. In this thesis, the acess requirement and restriction for the different group of security infrastructeres will be examined. The business operation will be detailed as well as the priority of the resources in terms of business interest in order to design a network that match the business model. An overview of the security layers will be shown. The intent is to demonstrate that no designs are perfect and may not resist to some type of attacks. In order to optimize the cost on security, the assets under risk should be taken into consideration. The case studies mentioned in the thesis vary from simple ones to more complicated ones. That is strongly related to what you store in databases. In all the cases it is considered that database is the core business and should be protected. Both inward and outward traffic should be under control in order to by-pass the attacks. There is never perfect security, but increasing the security for a small amount will result a bigger prevention against attacks
