Browsing by Author "Erten, Cesim"
Now showing items 1-18 of 18
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BEAMS: backbone extraction and merge strategy for the global many-to-many alignment of multiple PPI networks
Alkan, Ferhat; Erten, Cesim (Oxford University Press, 2014)Motivation: Global many-to-many alignment of biological networks has been a central problem in comparative biological network studies. Given a set of biological interaction networks the informal goal is to group together ... -
Biclustering Expression Data Based on Expanding Localized Substructures
Erten, Cesim; Sözdinler, Melih (Springer-Verlag Berlin, 2009)Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. We provide ... -
Bionetaling: biyokimyasal ağlarda fonksiyonel ortoloji çıkarımı amaçlı global hizalamalar
[Abstract Not Available] -
CAMPways: constrained alignment framework for the comparative analysis of a pair of metabolic pathways
Abaka, Gamze; Biyikoglu, Turker; Erten, Cesim (Oxford University Press, 2013)Motivation: Given a pair of metabolic pathways an alignment of the pathways corresponds to a mapping between similar substructures of the pair. Successful alignments may provide useful applications in phylogenetic tree ... -
Dağınık Çok Çekirdekli CPU ve Çoklu GPU Sistemleri İçin Heterojen Programlama Kütüphanesi
Bozkuş, Zeki; Erten, Cesim (2015)Son yıllarda, yüksek hesaplama performansına ihtiyaç duyan uygulamaların en çok tercih ettiğibilgisayar mimarisi, çok çekirdekli CPU’lara eklenmiş çoklu GPUlardan oluşan heterojen sistemlerdir.Fakat bu tür sistemlerin ... -
Force-Directed Approaches to Sensor Localization
Efrat, Alon; Forrester, David; Iyer, Anand; Kobourov, Stephen G.; Erten, Cesim; Kılış, Ozan (Association for Computing Machinery, 2010)As the number of applications of sensor networks increases so does the interest in sensor network localization that is in recovering the correct position of each node in a network of sensors from partial connectivity ... -
Fully Decentralized and Collaborative Multilateration Primitives for Uniquely Localizing WSNs
Çakıroğlu, Arda; Erten, Cesim (Springer International Publishing Ag, 2010)We provide primitives for uniquely localizing WSN nodes. The goal is to maximize the number of uniquely localized nodes assuming a fully decentralized model of computation. Each node constructs a cluster of its own and ... -
Fully decentralized, collaborative multilateration primitives for uniquely localizing WSNs
Cakiroglu, Arda; Erten, Cesim (Springer, 2009)We provide primitives for uniquely localizing WSN nodes. The goal is to maximize the number of uniquely localized nodes assuming a fully decentralized model of computation. Each node constructs a cluster of its own and ... -
Global alignment of metabolic pathways and protein-protein interaction networks
Abaka, Gamze (Kadir Has Üniversitesi, 2014)Metabolic pathways and protein interaction networks are essential at almost every function for living organisms. Simply, while reactions produce life energy within cells, protein interaction networks provide biological ... -
Improving performances of suboptimal greedy iterative biclustering heuristics via localization
Erten, Cesim; Sözdinler, Melih (Oxford University Press, 2010)Motivation: Biclustering gene expression data is the problem of extracting submatrices of genes and conditions exhibiting significant correlation across both the rows and the columns of a data matrix of expression values. ... -
An integrated model for visualizing biclusters from gene expression data and PPI networks
We provide a model to integrate the visualization of biclusters extracted from gene expresion data and the underlying PPI networks. Such an integration conveys the biologically relevant interconnection between these two ... -
Message-passing based algorithm for the global alignment of clustered pairwise PPI networks
Yenigün, Doğan Yiğit (Kadir Has Üniversitesi, 2013)Constrained global network alignments on pairwise protein-protein interaction (PPI) networks involve matchings between two organisms where proteins are grouped together in a great number of clusters, produced by algorithms ... -
RedNemo: topology-based PPI network reconstruction via repeated diffusion with neighborhood modifications
Alkan, Ferhat; Erten, Cesim (Oxford University Press, 2017)Motivation: Analysis of protein-protein interaction (PPI) networks provides invaluable insight into several systems biology problems. High-throughput experimental techniques together with computational methods provide ... -
Reliability-Oriented bioinformatic networks visualization
Aladağ, Ahmet Emre; Erten, Cesim; Sözdinler, Melih (Oxford University Press, 2011)We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or ... -
A Robust Localization Framework to Handle Noisy Measurements in Wireless Sensor Networks
Erten, Cesim; Karataş, Ömer (IEEE, 2009)We construct a robust localization framework to handle noisy measurements in wireless sensor networks. Traditionally many approaches employ the distance information gathered from ranging devices of the sensor nodes to ... -
SiPAN: simultaneous prediction and alignment of protein-protein interaction networks
Alkan, Ferhat; Erten, Cesim (Oxford University Press, 2015)Motivation: Network prediction as applied to protein-protein interaction (PPI) networks has received considerable attention within the last decade. Because of the limitations of experimental techniques for interaction ... -
SPINAL: scalable protein interaction network alignment
Aladağ, Ahmet Emre; Erten, Cesim (Oxford University Press, 2013)Motivation: Given protein-protein interaction (PPI) networks of a pair of species a pairwise global alignment corresponds to a one-to-one mapping between their proteins. Based on the presupposition that such a mapping ... -
Visualization of protein-protein interaction networks
Aladağ, Ahmet Emre (Kadir Has Üniversitesi, 2011)We provide a model to visualize and verify PPi Networks using Gene Expression andGene Ontology data. A clustered dual (central/peripheral) visualization model is providedand user can cluster PPi Networks according to ...