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Publication Metadata only 3D model retrieval using probability density-based shape descriptors(IEEE Computer Society, 2009) Akgul, Ceyhun Burak; Sankur, Buelent; Schmitt, Francis; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We address content-based retrieval of complete 3D object models by a probabilistic generative description of local shape properties. The proposed shape description framework characterizes a 3D object with sampled multivariate probability density functions of its local surface features. This density-based descriptor can be efficiently computed via kernel density estimation (KDE) coupled with fast Gauss transform. The nonparametric KDE technique allows reliable characterization of a diverse set of shapes and yields descriptors which remain relatively insensitive to small shape perturbations and mesh resolution. Density-based characterization also induces a permutation property which can be used to guarantee invariance at the shape matching stage. As proven by extensive retrieval experiments on several 3D databases, our framework provides state-of-the-art discrimination over a broad and heterogeneous set of shape categories.Publication Metadata only 3D reconstruction of real objects with high resolution shape and texture(Elsevier, 2004) Schmitt, F; Department of Computer Engineering; Yemez, Yücel; Faculty Member; Department of Computer Engineering; College of Engineering; 107907We present a robust and accurate system for 3D reconstruction of real objects with high resolution shape and texture. Our reconstruction method is passive, the only information needed being 2D images obtained with a calibrated camera from different view angles as the object rotates on a turntable. The triangle surface model is obtained by a scheme combining octree construction and marching cubes algorithm, which is adapted to the shape from silhouette problem. We develop a texture mapping strategy based on surface particles to adequately address photography related problems such as inhomogeneous lighting, highlights and occlusion. Reconstruction results are included to demonstrate the attained quality.Publication Open Access 3D spatial organization and network-guided comparison of mutation profiles in Glioblastoma reveals similarities across patients(Public Library of Science, 2019) Dinçer, Cansu; Kaya, Tuğba; Tunçbağ, Nurcan; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Faculty Member; Department of Chemical and Biological Engineering; Department of Computer Engineering; Koç University Research Center for Translational Medicine (KUTTAM) / Koç Üniversitesi Translasyonel Tıp Araştırma Merkezi (KUTTAM); College of Engineering; 26605; 8745Glioblastoma multiforme (GBM) is the most aggressive type of brain tumor. Molecular heterogeneity is a hallmark of GBM tumors that is a barrier in developing treatment strategies. In this study, we used the nonsynonymous mutations of GBM tumors deposited in The Cancer Genome Atlas (TCGA) and applied a systems level approach based on biophysical characteristics of mutations and their organization in patient-specific subnetworks to reduce inter-patient heterogeneity and to gain potential clinically relevant insights. Approximately 10% of the mutations are located in "patches" which are defined as the set of residues spatially in close proximity that are mutated across multiple patients. Grouping mutations as 3D patches reduces the heterogeneity across patients. There are multiple patches that are relatively small in oncogenes, whereas there are a small number of very large patches in tumor suppressors. Additionally, different patches in the same protein are often located at different domains that can mediate different functions. We stratified the patients into five groups based on their potentially affected pathways, revealed from the patient-specific subnetworks. These subnetworks were constructed by integrating mutation profiles of the patients with the interactome data. Network-guided clustering showed significant association between each group and patient survival (P-value = 0.0408). Also, each group carries a set of signature 3D mutation patches that affect predominant pathways. We integrated drug sensitivity data of GBM cell lines with the mutation patches and the patient groups to analyze the therapeutic outcome of these patches. We found that Pazopanib might be effective in Group 3 by targeting CSF1R. Additionally, inhibiting ATM that is a mediator of PTEN phosphorylation may be ineffective in Group 2. We believe that from mutations to networks and eventually to clinical and therapeutic data, this study provides a novel perspective in the network-guided precision medicine.Publication Metadata only A genome-wide functional screen identifies enhancer and protective genes for amyloid beta-peptide toxicity(Multidisciplinary Digital Publishing Institute (MDPI), 2023) Picon-Pages, Pol; Bosch-Morato, Monica; Subirana, Laia; Rubio-Moscardo, Francisca; Guivernau, Biuse; Fanlo-Ucar, Hugo; Herrera-Fernandez, Victor; Vicente, Ruben; Fernandez-Fernandez, Jose M.; Garcia-Ojalvo, Jordi; Oliva, Baldomero; Posas, Francesc; de Nadal, Eulalia; Munoz, Francisco J.; N/A; N/A; N/A; Department of Computer Engineering; Department of Computer Engineering; Zeylan, Melisa Ece; Şenyüz, Simge; Gürsoy, Attila; Keskin, Özlem; PhD Student; Master Student; Faculty Member; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; Graduate School of Sciences and Engineering; College of Engineering; College of Engineering; N/A; N/A; 8745; 26605Alzheimer's disease (AD) is known to be caused by amyloid beta-peptide (A beta) misfolded into beta-sheets, but this knowledge has not yet led to treatments to prevent AD. To identify novel molecular players in A beta toxicity, we carried out a genome-wide screen in Saccharomyces cerevisiae, using a library of 5154 gene knock-out strains expressing A beta(1-42). We identified 81 mammalian orthologue genes that enhance A beta(1-42) toxicity, while 157 were protective. Next, we performed interactome and text-mining studies to increase the number of genes and to identify the main cellular functions affected by A beta oligomers (oA beta). We found that the most affected cellular functions were calcium regulation, protein translation and mitochondrial activity. We focused on SURF4, a protein that regulates the store-operated calcium channel (SOCE). An in vitro analysis using human neuroblastoma cells showed that SURF4 silencing induced higher intracellular calcium levels, while its overexpression decreased calcium entry. Furthermore, SURF4 silencing produced a significant reduction in cell death when cells were challenged with oA beta(1-42), whereas SURF4 overexpression induced A beta(1-42) cytotoxicity. In summary, we identified new enhancer and protective activities for A beta toxicity and showed that SURF4 contributes to oA beta(1-42) neurotoxicity by decreasing SOCE activity.Publication Metadata only A simplified grid method of camera-captured images may be a practical alternative if validated ai-assisted counting is inaccessible(Elsevier Science Inc, 2023) Adsay, David; Eren, Ozgur; Basturk, Olca; Department of Computer Engineering; Esmer, Rohat; Armutlu, Ayşe; Taşkın, Orhun Çığ; Koç, Soner; Tezcan, Nuray; Aktaş, Berk Kaan; Kulaç, İbrahim; Kapran, Yersu; Demir, Çiğdem Gündüz; Saka, Burcu; Department of Computer Engineering; School of Medicine; Graduate School of Sciences and Engineering; College of EngineeringN/APublication Metadata only A split execution model for SpTRSV(IEEE Computer Society, 2021) Yilmaz, Buse; N/A; Department of Computer Engineering; Ahmad, Najeeb; Erten, Didem Unat; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; 219274Sparse Triangular Solve (SpTRSV) is an important and extensively used kernel in scientific computing. Parallelism within SpTRSV depends upon matrix sparsity pattern and, in many cases, is non-uniform from one computational step to the next. In cases where the SpTRSV computational steps have contrasting parallelism characteristics- some steps are more parallel, others more sequential in nature, the performance of an SpTRSV algorithm may be limited by the contrasting parallelism characteristics. In this work, we propose a split-execution model for SpTRSV to automatically divide SpTRSV computation into two sub-SpTRSV systems and an SpMV, such that one of the sub-SpTRSVs has more parallelism than the other. Each sub-SpTRSV is then computed using different SpTRSV algorithms, which are possibly executed on different platforms (CPU or GPU). By analyzing the SpTRSV Directed Acyclic Graph (DAG) and matrix sparsity features, we use a heuristics-based approach to (i) automatically determine the suitability of an SpTRSV for split-execution, (ii) find the appropriate split-point, and (iii) execute SpTRSV in a split fashion using two SpTRSV algorithms while managing any required inter-platform communication. Experimental evaluation of the execution model on two CPU-GPU machines with a matrix dataset of 327 matrices from the SuiteSparse Matrix Collection shows that our approach correctly selects the fastest SpTRSV method (split or unsplit) for 88 percent of matrices on the Intel Xeon Gold (6148) + NVIDIA Tesla V100 and 83 percent on the Intel Core I7 + NVIDIA G1080 Ti platform achieving speedups up to 10x and 6.36x respectively.Publication Metadata only A strategy based on protein-protein interface motifs may help in identifying drug off-targets(American Chemical Society (ACS), 2012) Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; Keskin, Özlem; Gürsoy, Attila; Ergin, Billur Çelebi; Faculty Member; Faculty Member; Teaching Faculty; Department of Chemical and Biological Engineering; Department of Computer Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; College of Engineering; 26605; 8745; 261792Networks are increasingly used to study the impact of drugs at the systems level. From the algorithmic standpoint, a drug can "attack" nodes or edges of a protein-protein interaction network In this work, we propose a new network strategy, "The Interface Attack", based on protein-protein interfaces. Similar interface architectures can occur between unrelated proteins. Consequently, in principle, a drug that binds to one has a certain probability of binding to others. The interface attack strategy simultaneously removes from the network all interactions that consist of similar interface motifs. This strategy is inspired by network pharmacology and allows inferring potential off-targets. We introduce a network model that we call "Protein Interface and Interaction Network (P2IN)", which is the integration of protein-protein interface structures and protein interaction networks. This interface based, network organization clarifies which protein pairs have structurally similar interfaces and which proteins may compete to bind the same surface region. We built the P2IN with the p53 signaling network and performed network robustness analysis. We show that (1) "hitting" frequent interfaces (a set of edges distributed around the network) might be as destructive as eleminating high degree proteins (hub nodes), (2) frequent interfaces are not always topologically critical elements in the network, and (3) interface attack may reveal functional changes in the system better than the attack of single proteins. In the off target detection case study, we found that drugs blocking the interface between CDK6 and CDKN2D may also affect the interaction between CDK4 and CDKN2D.Publication Metadata only A survey of available tools and web servers for analysis of protein-protein interactions and interfaces(Oxford University Press (OUP), 2009) Nussinov, Ruth; Department of Chemical and Biological Engineering; Department of Computer Engineering; N/A; Department of Chemical and Biological Engineering; Keskin, Özlem; Gürsoy, Attila; Makinacı, Gözde Kar; Tunçbağ, Nurcan; Faculty Member; Faculty Member; PhD Student; Faculty Member; Department of Computer Engineering; Department of Chemical and Biological Engineering; The Center for Computational Biology and Bioinformatics (CCBB); College of Engineering; College of Engineering; Graduate School of Sciences and Engineering; College of Engineering; 26605; 8745; N/A; 245513The unanimous agreement that cellular processes are (largely) governed by interactions between proteins has led to enormous community efforts culminating in overwhelming information relating to these proteins; to the regulation of their interactions, to the way in which they interact and to the function which is determined by these interactions. These data have been organized in databases and servers. However, to make these really useful, it is essential not only to be aware of these, but in particular to have a working knowledge of which tools to use for a given problem; what are the tool advantages and drawbacks; and no less important how to combine these for a particular goal since usually it is not one tool, but some combination of tool-modules that is needed. This is the goal of this review.Publication Metadata only A survey of energy efficiency in SDN: Software-based methods and optimization models(Elsevier, 2019) N/A; N/A; Department of Computer Engineering; Assefa, Beakal Gizachew; Özkasap, Öznur; PhD Student; Faculty Member; Department of Computer Engineering; Graduate School of Sciences and Engineering; College of Engineering; N/A; N/A; 113507Software Defined Networking (SDN) paradigm has the benefits of programmable network elements by separating the control and the forwarding planes, efficiency through optimized routing and flexibility in network management. As the energy costs contribute largely to the overall costs in networks, energy efficiency has become a significant design requirement for modem networking mechanisms. However, designing energy efficient solutions is non-trivial since they need to tackle the trade-off between energy efficiency and network performance. In this article, we address the energy efficiency capabilities that can be utilized in the emerging SDN. We provide a comprehensive and novel classification of software-based energy efficient solutions into subcategories of traffic aware, end system aware and rule placement. We propose general optimization models for each subcategory, and present the objective function, the parameters and constraints to be considered in each model. Detailed information on the characteristics of state-of-the-art methods, their advantages, drawbacks are provided. Hardware-based solutions used to enhance the efficiency of switches are also described. Furthermore, we discuss the open issues and future research directions in the area of energy efficiency in SDN.Publication Metadata only A survey on energy efficiency in P2P systems: file distribution, content streaming, and epidemics(Association for Computing Machinery (ACM), 2015) Brienza, Simone; Masoumzadeh, Seyed Saeid; Hlavacs, Helmut; Anastasi, Giuseppe; Department of Computer Engineering; Department of Computer Engineering; Cebeci, Sena Efsun; Özkasap, Öznur; Researcher; Faculty Member; Department of Computer Engineering; College of Engineering; College of Engineering; N/A; 113507Several Peer-to-Peer (P2P) protocols and applications have been developed to allow file distribution/sharing, video and music streaming, and data and information dissemination. These P2P systems are regularly used by a large number of users, both in desktop and mobile environments, and they generate a remarkable portion of the overall Internet traffic. However, many common P2P protocols and applications were designed neglecting the energy problem. In fact, they often require always-on devices in order to work properly, thus producing significant energy waste. The problem is even more relevant in the mobile context, since the battery lifetime of mobile devices is limited. Therefore, energy efficiency in P2P systems is a highly debated topic in the literature. New P2P approaches-more energy efficient than traditional client/server solutions-have been proposed. In addition, several improvements to existing P2P protocols have been introduced to reduce their energy consumption. In this article, we present a general taxonomy to classify state-of-the-art approaches to the energy problem in P2P systems and applications. Then, we survey themain solutions available in the literature, focusing on three relevant classes of P2P systems and applications: file sharing/distribution, content streaming, and epidemics. Furthermore, we outline open issues and provide future research guidelines for each class of P2P systems.