Browsing by Author "Çetin Atalay, Rengül"

Now showing 1 - 6 of 6

Open Access
Biology of hepatocellular cancer
(Lippincott-Raven, 2003) Öztürk, Mehmet; Çetin Atalay, Rengül; Rustg, A.
Open Access
Carcinoma cell line discrimination in microscopic images using unbalanced wavelets
(IEEE, 2012-03) Keskin, Furkan; Suhre, Alexander; Erşahin, Tüli,; Çetin Atalay, Rengül; Çetin, A. Enis
Cancer cell lines are widely used for research purposes in laboratories all over the world. In this paper, we present a novel method for cancer cell line image classification, which is very costly by conventional methods. The aim is to automatically classify 14 different classes of cell lines including 7 classes of breast and 7 classes of liver cancer cells. Microscopic images containing irregular carcinoma cell patterns are represented by randomly selected subwindows which possibly correspond to foreground pixels. For each subwindow, a correlation descriptor utilizing the fractional unbalanced wavelet transform coefficients and several morphological attributes as pixel features is computed. Directionally selective textural features are preferred primarily because of their ability to characterize singularities at multiple orientations, which often arise in carcinoma cell lines. A Support Vector Machine (SVM) classifier with Radial Basis Function (RBF) kernel is employed for final classification. Over a dataset of 280 images, we achieved an accuracy of 88.2%, which outperforms the classical correlation based methods. © 2012 IEEE.
Open Access
Identification of relative protein bands in Polyacrylamide Gel Electrophoresis (PAGE) using multiresolution snake algorithm
(IEEE, 1998-10) Gürcan, Metin Nafi; Koyutürk, Mehmet; Yıldız, H. Serkan; Çetin Atalay, Rengül; Çetin, A. Enis
Polyacrylamide Gel Electrophoresis (PAGE) is one of the most widely used techniques in protein research. In the protein purification process, it is important to determine the efficiency of each purification step in terms of percentage of protein of interest found in the protein mixture. This study provides a rapid and reliable way to determine this percentage. The region of interest containing the protein is detected using the snake algorithm. The iterative snake algorithm is implemented in a multiresolutional framework. The snake is initialized on a low resolution image. Then, the final position of the snake at low resolution is used as the initial position in the higher resolution image. Finally, tile area of the protein is estimated as the area enclosed by the final position of the snake.
Open Access
An ontology for collaborative construction and analysis of cellular pathways
(Oxford University Press, 2004-02-12) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Ayaz, Aslı; Güleşır, Gürcan; Nişancı, Gürkan; Çetin Atalay, Rengül
Motivation: As the scientific curiosity in genome studies shifts toward identification of functions of the genomes in large scale, data produced about cellular processes at molecular level has been accumulating with an accelerating rate. In this regard, it is essential to be able to store, integrate, access and analyze this data effectively with the help of software tools. Clearly this requires a strong ontology that is intuitive, comprehensive and uncomplicated. Results: We define an ontology for an intuitive, comprehensive and uncomplicated representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information via collaboration, and supports manipulation of the stored data. In addition, it facilitates concurrent modifications to the data while maintaining its validity and consistency. Furthermore, novel structures for representation of multiple levels of abstraction for pathways and homologies is provided. Lastly, our ontology supports efficient querying of large amounts of data. We have also developed a software tool named pathway analysis tool for integration and knowledge acquisition (PATIKA) providing an integrated, multi-user environment for visualizing and manipulating network of cellular events. PATIKA implements the basics of our ontology. © Oxford University Press 2004; All rights reserved.
Open Access
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
(Oxford University Press, 2002-06) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet
Motivation: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. Results: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named PATIKA (Pathway Analysis Tool for Integration and Knowledge Acquisition). PATIKA is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that PATIKA will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development.
Open Access
PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways
(American Society for Biochemistry and Molecular Biology(ASBMB), 2002-09) Demir, Emek; Babur, Özgün; Doğrusöz, Uğur; Gürsoy, Atilla; Nişancı, Gürkan; Çetin Atalay, Rengül; Öztürk, Mehmet