Bilkent Journal Publications

Department of Computer Engineering
Select a period:
 In Press
  • S. Battini, C. Bund, F.M. Moussallieh, A.E. Cicek, J.D. Seze, I.J. Namer, "Metabolomics approaches in experimental allergic encephalomyelitis", J of Neuroimmunology..
  • E. Ayday, Q. Tang, A. Yilmaz, "Cryptographic Solutions for Credibility and Liability Issues of Genomic Data", IEEE Trans on Dependable and Secure Computing..  PDF
  • M.M. Ozdal, "Hardware Accelerator Platforms for Data Centers", IEEE Design and Test..  PDF
  • O. Ozturk, U. Orhan, W. Ding, M. Kandemir, P. Yedlapalli, "Cache Hierarchy-Aware Query Mapping On Emerging Multicore Architectures", IEEE Trans on Computers..  PDF
  • A. Ayupov, S. Yesil, M.M. Ozdal, T. Kim, S. Burns, O. Ozturk, "A Template-Based Design Methodology for Graph-Parallel Hardware Accelerators", IEEE Trans on Computer Aided Des. Integr. Circ. Systems..  PDF
  • B. Berg-Johansen, M. Han, A.J. Fields, E.C. Liebenberg, B.J. Lim, P.E.Z. Larson, C. Gunduz-Demir, G.J. Kazakia, R. Krug, J.C. Lotz, "Cartilage endplate thickness variation measured by ultrashort echo-time MRI is associated with adjacent disc degeneration", Spine..  PDF
  • C. Mercan, S. Aksoy, E. Mercan, L.G. Shapiro, D.L. Weaver, J.G. Elmore, "Multi-instance Multi-label Learning for Multi-class Classification of Whole Slide Breast Histopathology Images", IEEE Trans on Medical Imaging..  PDF
  • E. Kayaaslan, C. Aykanat, B. Ucar, "1.5D Parallel Sparse Matrix-Vector Multiply", SIAM J on Scientific Computing..  PDF
  • E. Sarigil, S. Altingovde, R. Blanco, B. Cambazoglu, R. Ozcan, O. Ulusoy, "Characterizing, predicting, and handling web search queries that match very few or no results", J of the Association for Information Science and Technology..  PDF
  • E. Yilmaz, H. Ferhatosmanoglu, E. Ayday, R.C. Aksoy, "Privacy-Preserving Aggregate Queries for Optimal Location Selection", IEEE Trans on Dependable and Secure Computing..  PDF
  • F. Calisir, M. Bastan, O. Ulusoy, U. Gudukbay, "Mobile multi-view object image search", Multimedia Tools and Applications..  PDF
  • G. Sumbul, R.G. Cinbis, S. Aksoy, "Fine-Grained Object Recognition and Zero-Shot Learning in Remote Sensing Imagery", IEEE Trans on Geoscience and Remote Sensing..  PDF
  • H. Aksu, I. Korpeoglu, O. Ulusoy, "An Analysis of Social Networks based on Tera-scale Telecommunication Datasets", IEEE Trans on Emerging Topics in Computing..  PDF
  • H.R. Bonab, F. Can, "GOOWE: Geometrically optimum and online-weighted ensemble classifier for evolving data streams", ACM Trans on Knowledge Discovery..  PDF
  • I. Daznabi, M. Mobayen, N. Jafari, O. Tastan, E. Ayday, "An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information", Bioinformatics..  PDF
  • J. Detour, C. Bund, C. Behr, H. Cebula, A.E. Cicek, …, I.J. Namer, "Metabolomic characterization of human hippocampus from drug resistant epilepsy with mesial temporal seizures", Epilepsia..  PDF
  • K. Akbudak, O. Selvitopu, C. Aykanat, "Partitioning Models for Scaling Parallel Sparse Matrix-Matrix Multiplication", ACM Trans on Parallel Computing..  PDF
  • K. Bingol, B. Eravci, C.O. Ethemoglu, H. Ferhatosmanoglu, B. Gedik, "Topic-Based Influence Computation in Social Networks under Resource Constraints", IEEE Trans on Services Computing..  PDF
  • M. Koc, I. Korpeoglu, "Traffic- and Energy-Load-Based Sink Mobility Algorithms for Wireless Sensor Networks", Int J of Sensor Networks..  PDF
  • O. Sanli, I. Korpeoglu, A. Yazici, "Rule-Based Inference and Decomposition for Distributed In-Network Processing in Wireless Sensor Networks", Knowledge and Information Systems..  PDF
 2018
  • The Computational Pan - Genomics Consortium, … C. Alkan, "Computational pan-genomics: status, promises and challenges", Briefings in Bioinformatics, 19, 118-135 (2018)  PDF
 2017
  • A. Rahimzadeh Ilkhechi, I. Korpeoglu, U. Gudukbay, O. Ulusoy, "PETAL: A Fully Distributed Location Service for Wireless Ad Hoc Networks", J of Network and Computer Applications, 83, 1-11 (2017)
  • A. Soylev, C. Kockan, F. Hormozdiari, C. Alkan, "Toolkit for automated and rapid discovery of structural variants", Methods, 129, 3-7 (2017)
  • D. Katircioglu-Ozturk, H.A. Guvenir, U. Ravens, N. Baykal, "A window-based time series feature extraction method", Computers in Biology and Medicine, 89, 466-486 (2017)
  • G. Tuna, D.G. Kogiasb, V.C. Gungor, C. Sezer, E. Taskin, E. Ayday, "A Survey on Information Security Threats and Solutions for Machine to Machine (M2M) Communications", J of Parallel and Distributed Computing, 109, 142-154 (2017)
  • P. Buchholz, T. Dayar, J. Kriege, M.C. Orhan, "On Compact Solution Vectors in Kronecker-based Markovian Analysis", Performance Evaluation, 115, 132-149 (2017)
  • T. Kucukyilmaz, B.B. Cambazoglu, C. Aykanat, R. Baeza-Yates, "A machine learning approach for result caching in web search engines", Information Processing & Management, 53, 834-850 (2017)
  • A.E. Cicek, "k-shell decomposition reveals structural properties of gene co-expression network for neurodevelopment", Turkish J of Biology, 41, 333-341 (2017)  PDF
  • E. Ayday, M. Humbert, "Inference Attacks Against Kin Genomic Privacy", IEEE Security and Privacy Magazine, 15, 1-9 (2017)  PDF
  • M.M. Ozdal, S. Yesil, T. Kim, A. Ayupov, J. Greth, S. Burns, O. Ozturk, "Graph Analytics Accelerators for Cognitive Systems", IEEE Micro, 37, 42-51 (2017)  PDF
  • R.G. Cinbis, J. Verbeek, C. Schmid, "Weakly Supervised Object Localization with Multi-fold Multiple Instance Learning", IEEE Trans on Pattern Analysis and Machine Intelligence, 39, 189-203 (2017)  PDF
  • V. Akman, "Burn All Your Textbooks", Australasian Journal of Logic, 14, 378-382 (2017)  PDF
  • A. Nguyen, F.M. Moussallieh, A. Mackay, A.E. Cicek, A. Coca, C.M. Pierre, N. Weingerter, B. Lhermitte, E. Letouze, E. Guerin, …, N. Entz-Werle, "Characterization of the transcriptional and metabolic responses of pediatric high grade gliomas to mTOR-HIF-1α axis inhibition", Oncotarget., 1-22 (2017)  PDF
  • A. Yasar, B. Gedik, H. Ferhatosmanoglu, "Distributed block formation and layout for disk-based management of large-scale graphs", Distributed and Parallel Databases..  PDF
  • B. Otlu, C. Firtina, S. Keles, O. Tastan, "GLANET: genomic loci annotation and enrichment tool", Bioinformatics, 18, 2818-2828 (2017)
  • C. Auffray, M. Sagner, S. Abdelhak, …., U. Dogrusoz, …, F. Sanz, F. Nobrega, "Viva Europa, a Land of Excellence in Research and Innovation for Health and Wellbeing", Progress in Medicine, 2.  PDF
  • C. Toraman, F. Can, "Discovering story chains: A framework based on zigzagged search and news actors", J of the Association for Information Science and Technology, 68, 2795-2808 (2017)  PDF
  • E. Oto, S. Okutucu, D. Katircioglu-Öztürk, H.A. Güvenir, E. Karaagaoglu, M. Borggrefe, G. Breithardt, A. Goette, U. Ravens, G. Steinbeck, K. Wegscheider, A. Oto, P. Kirchhof, "Predictors of sinus rhythm after electrical cardioversion of atrial fibrillation: results from a data mining project on the Flec-SL trial data set", EP Europace, 19, 921-928 (2017)  PDF
  • F. Basil, B. Gedik, C. Ozgenc, H. Ferhatosmanoglu, "Spatio-Temporal Linkage over Location-Enhanced Services", IEEE Trans on Mobile Computing..  PDF
  • F.S. Torun, M. Manguoglu, C. Aykanat, "Parallel minimum norm solution of sparse block diagonal column overlapped underdetermined systems", ACM Trans Math Software, 43, 31-1--21 (2017)  PDF
  • G. Kale, E. Ayday, O. Tastan, "A Utility Maximizing and Privacy Preserving Approach for Protecting Kinship in Genomic Databases", Bioinformatics..  PDF
  • H. Balci, U. Gudukbay, "Sun position estimation and tracking for virtual object placement in time-lapse videos", Signal Image and Video Processing, 11, 817-824 (2017)  PDF
  • I. Bahceci, U. Dogrusoz, K.C. La, O. Babur, J. Gao, N. Schultz, "PathwayMapper: a collaborative visual web editor for cancer pathways and genomic data", Bioinformatics, 33, 2238-2240 (2017)  PDF
  • I.M. Ozcelik, I. Korpeoglu, A. Agrawala, "Energy Efficient IP-Connectivity with IEEE 802.11 for Home M2M Networks", Computer Journal, 60, 883-897 (2017)  PDF
  • J. Gao, E. Ciftci, P. Raman, P. Lukasse, …, U. Dogrusoz, T. Pugh, …, N. Schultz, "The cBioPortal for Cancer Genomics: an open source platform for accessing and interpreting complex cancer genomics data in the era of precision medicine", Cancer Research, 77, 2607-2607 (2017)  PDF
  • K. Akbudak, C. Aykanat, "Exploiting Locality in Sparse Matrix-Matrix Multiplication on Many-Core Architectures", IEEE Trans on Parallel and Distributed Systems, 28, 2258-2271 (2017)  PDF
  • K. Kullu, U. Gudukbay, D. Manocha, "ACMICS: An Agent Communication Model for Interacting Crowd Simulation", Autonomous Agents and Multi-Agent Systems, 31, 1403-1423 (2017)  PDF
  • K.M. Steinberg, V.A. Schneider, C. Alkan, M.J. Montague, W.C. Warren, D.M. Church, R.K. Wilson, "Building and Improving Reference Genome Assemblies", Proceedings of the IEEE., 1-14 (2017)  PDF
  • M. Alser, H. Hassan, H. Xin, O. Ergin, O. Mutlu, C. Alkan, "GateKeeper: a new hardware architecture for accelerating pre-alignment in DNA short read mapping", Bioinformatics, 33, 3355-3363 (2017)  PDF
  • M. Alser, O. Mutlu, C. Alkan, "MAGNET: understanding and improving the accuracy of genome pre-alignment filtering", IPSI Trans on Internet Research, 13, 1-10 (2017)  PDF
  • M. Hirzel, S. Schneider, B. Gedik, "SPL: An Extensible Language for Distributed Stream Processing", ACM Trans on Programming Languages and Systems, 39.  PDF
  • M. Humbert, E. Ayday, A. Telenti, J.P. Hubaux, "Quantifying Interdependent Risks in Genomic Privacy", ACM Trans on Privacy and Security, 20, 1-31 (2017)  PDF
  • M.E. Rasekh, G. Chaitante, M. Microballo, J. Tang, M. Ventura, C.T. Amemiya, E.E. Eichler, F. Antonacci, C. Alkan, "Discovery of large genomic inversions using long range information", BMC Genomics, 18, 65 (2017)  PDF
  • O. Selvitopu, S. Acer, C. Aykanat, "A Recursive Hypergraph Bipartitioning Framework for Reducing Bandwidth and Latency Costs Simultaneously", IEEE Trans on Parallel and Distributed Systems, 28, 345-358 (2017)  PDF
  • P. Kavak, Y-Y. Lin, I. Numanagic, H. Asghari, T. Gungor, C. Alkan, F. Hach, "Discovery and genotyping of novel sequence insertions in many sequenced individuals", Bioinformatics, 33, 161-169 (2017)  PDF
  • S. Alipour, M. Ghodsi, U. Gudukbay, M. Golkari, "An appoximation algorithms for visibility computationand testing over a terrain", Applied Geomatics, 9, 53-59 (2017)  PDF
  • S. Battini, F. Faitot, A. Imperiale, A.E. Cicek, C. Heimburger, G. Averous, P. Bachellier, I.J. Namer, "Metabolomics approaches in pancreatic adenocarcinoma tumor metabolism profiling predicts clinical outcome of patients", BMC Medicine, 15, 56-1--16 (2017)  PDF
  • S. Okutucu, D. Katircioglu-Ozturk, E. Oto, H.A. Guvenir, E. Karaagaoglu, A. Oto, T. Meinertz, A. Goette, "Data mining experiments on the Angiotensin II-Antagonist in Paroxysmal Atrial Fibrillation (ANTIPAF-AFNET 2) trial: ‘exposing the invisible", EP Europace, 19, 741-746 (2017)  PDF
  • S.E. Solmaz, B. Gedik, H. Ferhatosmanoglu, S. Sozuer, E. Zeydan, C.O. Etemoglu, "ALACA: A Platform for Dynamic Alarm Collection and Alert Notification in Network Management Systems", Int J of Network Management, 24, 1-17 (2017)  PDF
 2016
  • B. Gedik, H.G. Ozsema, O. Ozturk, "Pipelined Fission for Stream Programs with Dynamic Selectivity and Partitioned State", J of Parallel and Distributed Computing, 96, 106-120 (2016)
  • B. Kahveci, I.S. Altingovde, O. Ulusoy, "Integrating social features into mobile local search", J of Systems and Software, 122, 155-164 (2016)
  • F. Deniz, H. Bagci, I. Korpeoglu, A. Yazici, "An Adaptive, Energy-Aware and Distributed Fault-Tolerant Topology-Control Algorithm for Heterogeneous Wireless Sensor Networks", Ad Hoc Networks, 44, 104-117 (2016)
  • O. Selvitopu, C. Aykanat, "Reducing latency cost in 2D sparse matrix partitioning models", Parallel Computing, 57, 1-24 (2016)
  • S. Acer, O. Selvitopu, C. Aykanat, "Improving performance of sparse matrix dense matrix multiplication on large-scale parallel systems", Parallel Computing, 59, 71-96 (2016)
  • S. Battini, A. Imperiale, D. Taïeb, K. Elbayed, A.E. Cicek, F Sebag, L. Brunaud, I-J. Namer, "High-resolution magic angle spinning 1H nuclear magnetic resonance spectroscopy metabolomics of hyperfunctioning parathyroid glands", Surgery, 160, 384-394 (2016)
  • T. Dayar, M.C. Orhan, "Cartesian Product Partitioning of Multi-dimensional Reachable State Spaces", Probability in the Engineering and Informational Sciences, 30, 413-430 (2016)  PDF
  • T. Dayar, M.C. Orhan, "Steady-state Analysis of a Multi-class MAP/PH/c Queue with Acyclic PH Retrials", J of Applied Probability, 53, 1098-1110 (2016)  PDF
  • V. Akman, M.B. Senol, "The Truth about "It is True that..."", Pragmatics and Cognition, 23, 284-299 (2016)  PDF
  • A.E. Sariyuce, B. Gedik, G. Jacques-Silva, K-L. Wu, U.V. Catalyurek, "SONIC: Streaming Overlapping Community Detection", Data Mining and Knowledge Discovery, 30, 819-847 (2016)  PDF
  • A.E. Sariyuce, B. Gedik, G. Jacques-Silva, K-L. Wu, U.V. Catalyurek, "Incremental k-core decomposition: Algorithms and evaluation", VLDB Journal, 25, 425-447 (2016)  PDF
  • A.H. Freedman, R.M. Schweizer, D. O. Vecchyo, E. Han, B.W. Davis, I. Gronau, P.M. Silva, M. Galaverni, Z. Fan, P. Marx, B. Lorente-Galdos, O. Ramirez, F. Hormozdiari, C. Alkan, … , R.K. Wayne, J. Novembre, "Demographically-Based Evaluation of Genomic Regions under Selection in Domestic Dogs", Plos Genetics, 12, 1005851-1--23 (2016)  PDF
  • A.R. Ulucinar, I. Korpeoglu, "Distributed Joint Flow-Radio and Channel Assignment Using Partially Overlapping Channels in Multi-Radio Wireless Mesh Networks", Wireless Networks, 22, 83-104 (2016)  PDF
  • B. Demir, I. Kahyaoglu, H.A. Guvenir, N. Yerebasmaz, S.K. Altinbas, B. Dilbaz, S. Dilbaz, L. Mollamahmutoglu, "Progesterone change in the late follicular phase affects pregnancy rates both agonist and antagonist protocols in normoresponders: a case-controlled study in ICSI cycles", Gynecological Endocrinology, 32, 361-365 (2016)  PDF
  • B. Genc, U. Dogrusoz, "An Algorithm for Automated Layout of Process Description Maps Drawn in SBGN", Bioinformatics, 32, 77-84 (2016)  PDF
  • C. Firtina, C. Alkan, "On genomic repeats and reproducibility", Bioinformatics, 32, 2243-2247 (2016)  PDF
  • C. Terzi, I. Korpeoglu, "Tree-based Channel Assignment Schemes for Multi-channel Wireless Sensor Networks", Wireless Communications and Mobile Computing, 16, 1694-1712 (2016)  PDF
  • C.F. Koyuncu, E. Akhan, T. Ersahin, R. Cetin-Atalay, C. Gunduz-Demir, "Iterative h-minima-based marker-controlled watershed for cell nucleus segmentation", Cytometry: Part A, 89, 338-349 (2016)  PDF
  • E. Mercan, S. Aksoy, L.G. Shapiro, D.L. Weaver, T.T. Brunye, J.G. Elmore, "Localization of Diagnostically Relevant Regions of Interest in Whole Slide Images: A Comparative Study", Journal of Digital Imaging, 29, 496-506 (2016)  PDF
  • E. Sarigil, O. Yilmaz, I.S. Altingovde, R. Ozcan, O. Ulusoy, "A "Suggested" Picture of Web Search in Turkish", ACM Trans on Asian and Low-Resource Language Inf. Processing, 15, 24-1--11 (2016)  PDF
  • F. Durupinar, U. Gudukbay, A. Aman, N.I. Badler, "Psychological Parameters for Crowd Simulation: from Audiences to Mobs", IEEE Trans on Visualization and Computer Graphics, 22, 2145-2159 (2016)  PDF
  • H. Xin, S. Nahar, R. Zhu, J. Emmons, G. Pekhimenko, C. Kingsford, Can Alkan, O. Mutlu, "Optimal seed solver: optimizing seed selection in read mapping", Bioinformatics, 32, 1632-1642 (2016)  PDF
  • H.G. Akcay, S. Aksoy, "Automatic Detection of Compound Structures by Joint Selection of Region Groups from a Hierarchical Segmentation", IEEE Trans on Geoscience and Remote Sensing, 54, 3485-3501 (2016)  PDF
  • J. Gao, J. Lindsay, S. Watt, I. Bahceci, …, U. Dogrusoz, T. Pugh, C. Sander, E. Cerami, N. Schultz, "The cBioPortal for cancer genomics and its application in precision oncology", Cancer Research, 76, 5277-5277 (2016)  PDF
  • M. Tekkalmaz, I. Korpeoglu, "Distributed Power-Source-Aware Routing in Wireless Sensor Networks", Wireless Networks, 22, 1381-1399 (2016)  PDF
  • M.F. Cardone, P. D'Addabbo, Can Alkan, C. Bergamini, C.R. Catacchio, F. Anaclerio, G. Chiatante, A. Marra, G. Giannuzzi, R. Perniola, M. Ventura, D. Antonacci, "Inter-varietal structural variation in grapevine genomes", The Plant Journal, 88, 648-661 (2016)  PDF
  • M.O. Karsavuran, K. Akbudak, C. Aykanat, "Locality-Aware Parallel Sparse Matrix-Vector and Matrix-Transpose-Vector Multiplication on Many-Core Processors", IEEE Trans on Parallel and Distributed Systems, 27, 1713-1726 (2016)  PDF
  • P.J. McLaren, J.L. Raisaro, A. Manel, M. Rotger, E. Ayday, I. Bartha, M.B. Delgado, Y. Vallet, H.F. Gunthard, M. Cavassini, H. Furrer, T. Doco-Lecompte, C. Mazolini, P. Schmid, C.Di Benedetto, A. Telenti, Swiss HIV Cohort Study, "Privacy-preserving genomic testing in the clinic: a model using HIV treatment", Genetics in Medicine, 18, 814-822 (2016)  PDF
  • S. Schneider, B. Gedik, M. Hirzel, "Language Runtime and Optimizations in IBM Streams", Bulletin of the IEEE Comp. Soc. Tech. Comm. On Data Eng., 38, 61-72 (2016)  PDF
  • Z. Huang, E. Ayday, H. Lin, R.S. Aiyar, A. Molyneaux, Z. Xu, J. Fellay, L.M. Steinmetz, J-P. Hubaux, "A Privacy-Preserving Solution for Compressed Storage and Selective Retrieval of Genomic Data", Genome Research, 26, 1687-1696 (2016)  PDF
 2015
  • A.R. Ilkhechi, I. Korpeoglu, O. Ulusoy, "Network-Aware Virtual Machine Placement in Cloud Data Centers with Multiple Traffic-Intensive Components", Computer Networks Journal, 91, 508-527 (2015)
  • D. Lee, F. Hormozdiari, H. Xin, F. Hach, O. Mutlu, C. Alkan, "Fast and accurate mapping of Complete Genomics reads", Methods, 79, 3-10 (2015)
  • E. Tuzun, B. Tekinerdogan, "Analyzing impact of experience curve on ROI in the software product line adoption process", Information and Software Technology, 59, 136-148 (2015)
  • N.C. Kiliboz, U. Gudukbay, "A Hand Gesture Recognition Technique for Human-Computer Interaction", J of Visual Communication and Image Representation, 28, 97-104 (2015)
  • S.J. Sanders, X. He, J. Willsey, …., A.E. Cicek, …., M.W. State, "Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci", Neuron, 87, 1215-1233 (2015)
  • H.A. Guvenir, G. Misirli, S. Dilbaz, O. Ozdegirmeci, B. Demir, B. Dilbaz, "Estimating the chance of success in IVF treatment using a ranking algorithm", Medical & Biological Engineering & Computing, 53, 911-920 (2015)  PDF
  • O. Ozturk, I. Akturk, I. Kadayif, S. Tosun, "Energy Reduction in 3D NoCs Through Communication Optimization", Computing, 97, 593-609 (2015)  PDF
  • S. Genc, M. Bastan, U. Gudukbay, V. Atalay, O. Ulusoy, "HandVR: a hand-gesture-based interface to a video retrieval system", Signal Image and Video Processing, 9, 1717-1726 (2015)  PDF
  • T. Dayar, M.C. Orhan, "On Vector-Kronecker Product Multiplication with Rectangular Factors", SIAM J on Scientific Computing, 37, 526-543 (2015)  PDF
  • C. Mergenci, I. Korpeoglu, "Routing in Delay-tolerant Networks with Periodic Connections", Eurasip Journal on Wireless Communication and Networking, 2015, 202 (2015)  PDF
  • C. Toraman, F. Can, "A front-page news-selection algorithm based on topic modeling", J of Information Science, 41, 676-685 (2015)  PDF
  • C. Yao, B.H. Chen, R. Joehanes, B. Otlu, X. Zhang, C. Liu, T. Huan, O. Tastan, L.A. Cupples, … , D. Levy, "Integromic Analysis of Genetic Variation and Gene Expression Identifies Networks for Cardiovascular Disease Phenotypes", Circulation, 131, 536-549 (2015)  PDF
  • F. Basik, B.Gedik, H. Ferhatosmanoglu, M. Kalender, "S3-TM Scalable Streaming Short Text Matching", VLDB Journal, 24, 849-866 (2015)  PDF
  • F. Bulut, M. Demirbas, H. Ferhatosmanoglu, "LineKing: Coffee Shop Wait-Time Monitoring Using Smartphones", IEEE Trans on Mobile Computing, 14, 2045-2058 (2015)  PDF
  • H. Aksu, M. Canim, Y-C. Chang, I. Korpeoglu, O. Ulusoy, "Efficient Community Identification and Maintenance at Multiple Resolutions on Distributed Datastores", Data and Knowledge Engineering, 100, 133-147 (2015)  PDF
  • H. Bagci, I. Korpeoglu, A. Yazici, "A Distributed Fault-Tolerant Topology Control algorithm for Heterogeneous Wireless Sensor Networks", IEEE Trans on Parallel and Distributed Systems, 26, 914-923 (2015)  PDF
  • H. Xin, J. Greth, J. Emmons, G. Pekhimenko, C. Kingsford, C. Alkan, O. Mutlu, "Shifted Hamming Distance: a fast and accurate SIMD-friendly filter to accelerate alignment verification in read mapping", Bioinformatics, 15, 1553-1560 (2015)  PDF
  • I. Gur, M. Guvercin, H. Ferhatosmanoglu, "Scaling Forecasting Algorithms using Clustered Modeling", VLDB Journal, 24, 51-65 (2015)  PDF
  • M. Ashouri-Talouki, A. Baraani-Dastjerdi, A.A. Selcuk, "The Cloaked-Centroid Protocol: Location Privacy Protection for a Group of Users of Location-Based Services", Knowledge and Information Systems, 45, 589-615 (2015)  PDF
  • M. Dallachiesa, G. Jaque-Silva, B. Gedik, K-L. Wu, T. Palpanas, "Sliding windows over uncertain data streams", Knowledge and Information Systems, 45, 159-190 (2015)  PDF
  • M. Koc, I. Korpeoglu, "Coordinated Movement of Multiple Mobile Sinks in a Wireless Sensor Network for Improved Lifetime", Eurasip Journal on Wireless Communication and Networking, 2015, 245 (2015)  PDF
  • M. Naveed, E. Ayday, E.W. Clayton, J. Fellay, C.A. Gunter, J.P. Hubaux, B.A. Malin, X. Wang, "Privacy in the Genomic Era", ACM Computing Surveys, 48.  PDF
  • M.A. Abbasoglu, B. Gedik, H. Ferhatosmanoglu, "Aggregate Profile Clustering for Streaming Analytics", Computer Journal, 58, 2092-2108 (2015)  PDF
  • O. Acar, E. Ozkurt, G. Demir, H. Sarac, C. Alkan, T. Esen, M. Somel, N.A. Lack, "Determining the origin of synchronous multifocal bladder cancer by exome sequencing", BMC Genomics, 15, 871 (2015)  PDF
  • P.H. Sudmant, T. Rausch, …, C. Alkan, …, The Genome Consortium, …, J.O. Korbel, "An integrated map of structural variation in 2.504 human genomes", Nature, 526, 75-81 (2015)  PDF
  • R. Soule, B. Gedik, "RailwayDB: Adaptive Storage of Interaction Graphs", VLDB Journal..  PDF
  • R. Soule, M. Hirzel, B. Gedik, R. Grimm, "River: An Intermediate Language for Stream Processing", Software - Practice and Experience..  PDF
  • R.O. Selvitopi, M.M. Ozdal, C. Aykanat, "A Novel Method for Scaling Iterative Solvers: Avoiding Latency Overhead of Parallel Sparse-Matrix Vector Multiplies", IEEE Trans on Parallel and Distributed Systems, 26, 632-645 (2015)  PDF
  • S. Schneider, M. Hirzel, B. Gedik, K-L. Wu, "Safe Data Parallelism for General Streaming", IEEE Trans on Computers, 64, 504-518 (2015)  PDF
  • S. Tosun, O. Ozturk, E. Ozkan, M. Ozen, "Application mapping algorithms for mesh-based network-on-chip architectures", J of Supercomputing, 71, 995-1017 (2015)  PDF
  • S. Tosun, V. Ajabshir, O. Mercanoglu, O. Ozturk, "Fault-Tolerant Topology Generation Method for Application-Specific Network-on-Chips", IEEE Trans on Computer Aided Design, 34, 1495-1508 (2015)
  • T. Gultekin, C.F. Koyuncu, C. Sokmensuer, C. Gunduz-Demir, "Two-tier tissue decomposition for histopathological image representation and classification", IEEE Trans on Medical Imaging, 34, 275-283 (2015)  PDF
  • The 1000 Genomes Project Consortium, "A global reference for human genetic variation", Nature, 526, 98-74 (2015)  PDF
  • U. Ravens, D. Katircioglu-Ozturk, E. Wettwer, T. Christ, D. Dobrev, N. Voight, C. Poulet, S. Loose, ….., H.A. Guvenir, "Application of the RIMARC algorithm to a large data set of action potentials and clinical parameters for risk prediction of atrial fibrillation", Medical & Biological Engineering & Computing, 53, 263-270 (2015)  PDF
  • X. He, A.E. Cicek, Y. Wang, M. Schulz, H.S. Le, Z. Bar-Joseph, "De-Novo Chip-Seq Analysis", Genome Biology, 16, 205:1-10 (2015)  PDF
 2014
  • O. Tastan, A. Dutta, P. Booth, J. Klein-Seetharaman, "Retinal proteins as model systems for membrane protein folding", Biochimica et Biophysica Acta, 1837, 656-663 (2014)
  • A. Demiriz, N. Bagherzadeh, O. Ozturk, "Voltage Island Based Heterogeneous NoC Design Through Constraint Programming", Computers and Electrical Engineering, 40, 307-316 (2014)
  • A.R. Ulucinar, I. Korpeoglu, E. Karasan, "Effects of physical channel separation on application flows in a multi-radio multi-hop wireless mesh network: An experimental study on BilMesh testbed", J of Network and Computer Applications, 39, 253-265 (2014)
  • E. Okuyan, U. Gudukbay, "BilKristal 2.0: A tool for pattern information extraction from crystal structures", Computer Physics Communications, 185, 442-443 (2014)
  • E. Okuyan, U. Gudukbay, C. Bulutay, K.H. Heinig, "MaterialVis: Material visualization tool using direct volume and surface rendering techniques", J of Molecular Graphics and Modelling, 50, 50-60 (2014)
  • U. Gultepe, U. Gudukbay, "Real-time Virtual Fitting with Body Measurement and Motion Smoothing", Computers and Graphics, 43, 31-43 (2014)
  • B. Gedik, R. Bordawekar, "Disk-based Management of Interaction Graphs", IEEE Trans on Knowledge and Data Engineering, 26, 2689-2702 (2014)  PDF
  • B. Gedik, S. Schneider, M. Hirzel, K-L. Wu, "Elastic Scaling for Data Stream Processing", IEEE Trans on Parallel and Distributed Systems, 25, 1447-1463 (2014)  PDF
  • C. Alkan, P. Kavak, M. Somel, O. Gokcumen, S. Ugurlu, C. Saygi, E. Dal, K. Bugra, T. Gungor, S.C. Sahinalp, N. Ozoren, C. Bekpen, "Whole genome sequencing of Turkish genomes reveals functional private alleles and impact of genetic interactions with Europe, Asia and Africa", BMC Genomics, 15, 963-1--12 (2014)  PDF
  • P. Duygulu, D. Arifoglu, M. Kalpakli, "Cross-document word matching for segmentation and retrieval of Ottoman divans", Pattern Analysis and Applications..  PDF
  • U. Gudukbay, S. Bayraktar, C. Koca, B. Ozguc, "Particle-based simulation of the interaction between fluid and knitwear", Signal, Image and Video Processing, 8, 415-422 (2014)  PDF
  • A. Turk, R.O. Selvitopi, H. Ferhatosmanoglu, C. Aykanat, "Temporal Workload-Aware Replicated Partitioning for Social Networks", IEEE Trans on Knowledge and Data Engineering, 26, 1-14 (2014)  PDF
  • A.H. Freedman, I. Gronau, R.M. Schweizer, ..., C. Alkan, ...., T. Marques-Bonet, R.K. Wayne, J. Novembre, "Genome Sequencing Highlights the Dynamic Early History of Dogs", Plos Genetics, 10, 1004016-1--12 (2014)  PDF
  • C. Ari, S. Aksoy, "Detection of Compound Structures Using a Gaussian Mixture Model with Spectral and Spatial Constraints", IEEE Trans on Geoscience and Remote Sensing, 52, 6627-6638 (2014)
  • C. Koca, U. Gudukbay, "A Hybrid Representation for Modeling, Iteractive Editing, and Real-time Visualization of Terrains with Volumetric Features", Int J of Geographical Information Science, 28, 1821-1847 (2014)  PDF
  • D. Demirbas, I. Akturk, O. Ozturk, U. Gudukbay, "Application-Specific Heterogeneous Network-on-Chip Design", Computer Journal, 57, 1117-1131 (2014)  PDF
  • D. Gucer, B. Ozguc, "Simulation of a flowing snow avalanche using molecular dynamics", Turkish J of Electrical Engineering & Computer Sciences, 22, 1596-1610 (2014)  PDF
  • E. Okuyan, U. Gudukbay, "Direct volume rendering of unstructured tetrahedral meshes using CUDA and OpenMP", J of Supercomputing, 67, 324-344 (2014)  PDF
  • E.K. Tabak, B.B. Cambazoglu, C. Aykanat, "Improving the Performance of Independent Task Assignment Heuristics MinMin, MaxMin and Sufferage", IEEE Trans on Parallel and Distributed Systems, 25, 1244-1256 (2014)  PDF
  • F. Hach, I. Sarrafi, F. Hormozdiari, C. Alkan, E.E. Eichler, S.C. Sahinalp, "mrsFAST-Ultra: a compact, SNP-aware mapper for high performance sequencing applications", Nucleic Acids Research, 42, 494-500 (2014)  PDF
  • G. Olgun, C. Sokmensuer, C. Gunduz-Demir, "Local Object Patterns for Representation and Classification of Colon Tissue Images", IEEE J of Biomedical and Health Informatics, 18, 1390-1396 (2014)  PDF
  • G. Tamazian, S. Simonov, P. Dobrynin, A. Makunin, A. Logachev, ..., C. Alkan, ..., S.J. O'Brien, "Annotated features of domestic cat-Felis catus genome", GigaScience, 3, 13 (2014)  PDF
  • G.M. Dal, B. Erguner, M.S. Sagiroglu, B. Yuksel, O.E. Onat, C. Alkan, T. Ozcelik, "Early postzygotic mutations contribute to de novo variation in a healthy monozygotic twin pair", J of Medical Genetics, 51, 455-459 (2014)  PDF
  • H. Aksu, M. Canim, Y.C. Chang, I. Korpeoglu, O. Ulusoy, "Distributed k-Core View Materialization and Maintenance for Large Dynamic Graphs", IEEE Trans on Knowledge and Data Engineering, 26, 439-452 (2014)  PDF
  • J. Huddleston, S. Ranade, M. Malig, F. Antonacci, M. Chaisson, L. Hon, P.H. Sudmant, ... , C. Alkan, ...., E.E. Eichler, "Reconstructing complex regions of genomes using long-read sequencing technology", Genome Research, 24, 688-696 (2014)  PDF
  • K. Akbudak, C. Aykanat, "Simultaneous Input and Output Matrix Partitioning for Outer-product-parallel Sparse Matrix-Matrix Multiplication", SIAM J on Scientific Computing, 36, 568-590 (2014)  PDF
  • M. Hirzel, R. Soute, S. Schneider, B. Gedik, R. Grimm, "A Catalog of Streaming Optimizations", ACM Computing Surveys, 46.  PDF
  • M. Koc, I. Korpeoglu, "Controlled Sink mobility Algorithms for Wireless Sensor Networks", Int J of Distributed Sensor Networks., 167508 (2014)  PDF
  • M.J. Montague, G. Li, B. Gandolfi, R. Khan, B.L. Aken, ..., T. Marques-Bonet, C. Alkan, G.W.C. Thomas, ..., W.C. Warren, "Comparative analysis of the domestic cat genome reveals genetic signatures underlying feline biology and demiestication", Proceedings of National Academy of Sciences USA, 11, 17230-17235 (2014)  PDF
  • O. Babur, U. Dogrusoz, M. Cakir, B.A. Aksoy, N. Shultz, C. Sander, E. Demir, "Integrating biological pathways and genomic profiles with cHiBE 2", BMC Genomics, 15, 642-1--9 (2014)  PDF
  • S. Arslan, E. Ozyurek, C. Gunduz-Demir, "A color and shape based algorithm for segmentation of white blood cells in peripheral blood and bone marrow images", Cytometry: Part A, 85, 480-490 (2014)  PDF
  • T. Jartti, O. palomares, M. Waris, O. Tastan, R. Nieminen, T. Puhakka, … , C.A. Akdis, "Distinct regulation of tonsillar immune response in virus infection", Allergy, 69, 658-667 (2014)  PDF
  • V. Yazici, C. Aykanat, "Constrained Min-Cut Replication for K-Way Hypergraph Partitioning", Informs Journal of Computing, 36, 303-320 (2014)  PDF
 2013
  • U. Gudukbay, I. Demir, Y. Dedeoglu, "Motion capture and human pose reconstruction from a single-view video sequence", Digital Signal Processing, 23, 1441-1450 (2013)
  • E. Karasabun, I. Korpeoglu, C. Aykanat, "Active Node Determination for Correlated Data Gathering in Wireless Sensor Networks", Computer Networks Journal, 57, 1124-1138 (2013)
  • E. Kayaaslan, B.B. Cambazoglu, C. Aykanat, "Document replication strategies for geographically distributed web search engines", Information Processing & Management, 49, 51-66 (2013)
  • H. Baumann, T. Dayar, M.C. Orhan, W. Sandmann, "On the numerical solution of Kronecker-based infinite level-dependent QBD processes", Performance Evaluation, 70, 663-681 (2013)
  • I. Sengor-Altingovde, O.N. Subakan, O. Ulusoy, "Cluster searching strategies for collaborative recommendation systems", Information Processing & Management, 49, 688-697 (2013)
  • O. Oguz, F. Durupinar, U. Gudukbay, "Dynamic Point-Region Quadtrees for Particle Simulations", Information Sciences, 218, 133-145 (2013)
  • O.E. Albayrak, I. Akturk, O. Ozturk, "Improving Application Behavior on Heterogeneous Manycore Systems Through Kernel Mapping", Parallel Computing, 39, 867-878 (2013)
  • S. Baysal, P. Duygulu, "A Line Based Pose Representation for Human Action Recognition", Signal Processing: Image Communication, 28, 458-471 (2013)
  • T. Celik, B. Tekinerdogan, "S-IDE: A tool framework for Optimizing Deployment Architecture of High Level Architecture Based Simulation Systems", J of Systems and Software, 86, 2520-2541 (2013)
  • B. Gedik, "Generic windowing support for extensible stream processing systems", Software - Practice and Experience..  PDF
  • B. Gedik, "Auto-tuning Similarity Search Algorithms on Multi-core Architectures", Int J of Parallel Programming, 41, 595-620 (2013)  PDF
  • B. Gedik, "Discriminative Fine-Grained Mixing for Adaptive Compression of Data Streams", IEEE Trans on Computers..  PDF
  • B. Gedik, "Partitioning functions for steteful data parallelism in stream processing", VLDB Journal..  PDF
  • H.A. Guvenir, M. Kurtcephe, "Ranking Instances by Maximizing the Area under ROC Curve", IEEE Trans on Knowledge and Data Engineering, 25, 2356-2366 (2013)  PDF
  • O. Ozturk, M. Kandemir, G. Chen, "Compiler-Directed Energy Reduction Using Dynamic Voltage Scaling and Voltage Islands for Embedded Systems", IEEE Trans on Computers, 62, 268-278 (2013)  PDF
  • U. Dogrusoz, M.E. Belviranli, A. Dilek, "CISE: A Circular Spring Embedder Layout Algortihm", IEEE Trans on Visualization and Computer Graphics, 19, 953-966 (2013)
  • A. Akaydin, U. Gudukbay, "Adaptive Grids: An image-based Approach to Generate Navigation Meshes", Optical Engineering, 52, 027002-1--12 (2013)  PDF
  • A. Turk, K.Y. Oktay, C. Aykanat, "Query-Log Aware Replicated Declustering", IEEE Trans on Parallel and Distributed Systems, 24, 987-995 (2013)  PDF
  • A.R. Ulucinar, I. Korpeoglu, E. Karasan, "A novel measurement-based approach for modeling and computing interference factors for wireless channels", Eurasip Journal on Wireless Communication and Networking, 68, 1-16 (2013)  PDF
  • B. Diouf, C. Hantas, A. Cohen, O. Ozturk, J. Palsberg, "A Decoupled Local-Memory Allocator", ACM Trans on Architecture and Code Optimization, 9, 34 (2013)
  • B.B. Cambazoglu, E. Kayaaslan, S. Jonassen, C. Aykanat, "A Term-Based Inverted Index Partitioning Model for Efficient Distributed Query Processing", ACM Trans on the Web, 7, 15-1--23 (2013)  PDF
  • B.B. Cambazoglu, I. Sengor-Altingovde, R. Ozcan, O. Ulusoy, "Cache-Based Query Processing for Search Engines", ACM Trans on the Web, 6, 14-1--23 (2013)  PDF
  • C. Telkenaroglu, T. Capin, "Dual-Finger 3D Interaction Techniques for Mobile Devices", J of Personal and Ubiquitous Computing, 17, 1551-1572 (2013)  PDF
  • E. Ozdemir, C. Gunduz-Demir, "A hybrid classification model for digital pathology using structural and statistical pattern recognition", IEEE Trans on Medical Imaging, 32, 474-483 (2013)  PDF
  • E.F. Can, F. Can, P. Duygulu, M. Kalpakli, "Automatic categorization of Ottoman poems", Glottotheory: International J of Theoretical Linguistics, 4, 40-57 (2013)  PDF
  • F. Hormozdiari, ..... , C. Alkan, ....M.A. Batzer, E..E. Eichler, "Rates and patterns of great ape retrotransposition", Proceedings of National Academy of Sciences USA, 110, 13457-13462 (2013)  PDF
  • G. Cimen, H. Ilhan, T. Capin, H. Gurcay, "Classification of human motion based on affective state descriptors", Computer Animation and Virtual Worlds, 24, 355-363 (2013)  PDF
  • H. Sozer, B. Tekinerdogan, M. Aksit, "Optimizing Decomposition of Software Architecture for Local Recovery", Software Quality Journal, 21, 203-240 (2013)  PDF
  • H. Sun, A. Sacan, H. Ferhatosmanoglu, Y. Wang, "Smolign: A Spatial Motifs Based Protein Multiple Structural Alignment Method", IEEE - ACM Trans on Computational Biology and Bioinformatics, 9, 249-261 (2013)
  • H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu, C. Alkan, "Accelerating read mapping with FastHASH", BMC Genomics, 14, 1-13 (2013)
  • I. Akturk, O. Ozturk, "Reliability-Aware Heterogeneous 3D Chip Multiprocessor Design", J of Electronic Testing, 29, 177-184 (2013)
  • I. Kadayif, M. Turkcan, S. Kiziltepe, O. Ozturk, "Hardware/Software Approaches for Reducing the Process Vriation Impact on Instruction Fetches", ACM Trans on Design Automation of Electronic Systems, 18, 54-1--23 (2013)  PDF
  • J. Gao, B.A. Aksoy, U. Dogrusoz, G. Dresdner, B. Gross, S.O. Sumer, Y. Sun, A. Jacobsen, R. Sinha, E. Larsson, E. Cerami, C. Sander, N. Schultz, "Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal", Science Signaling, 6, 629-1--11 (2013)  PDF
  • J. Prado-Martinez, ...., C. Alkan, ....E.E. Eichler, T. Marques-Bonet, "The genome sequencing of an albino Western lowland gorilla reveals inbreeing in the wild", BMC Genomics, 14, 1-7 (2013)
  • J. Prado-Martinez, ...., C. Alkan, ....E.E. Eichler, T. Marques-Bonet, "Great ape Genetic Diversity and Population History", Nature, 499, 471-475 (2013)  PDF
  • K. Akbudak, E. Kayaaslan, C. Aykanat, "Hypergraph Partitioning Based Models and Methods for Exploiting Cache Locality in Sparse Matrix-Vector Multiplication", SIAM J on Scientific Computing, 35, 237-262 (2013)  PDF
  • M. Hirzel, H. Andrade, B. Gedik, G. Jacques-Silva, R. Khandekar, V. Kumar, M. Mendell, H. Nasgaard, S. Schneider, R. Soule, K.J. Wu, "IBM Streams Processing Language: Analyzing Big Data in Motion", IBM J of Research and Development, 57, 7-1--11 (2013)
  • M. Kurtcephe, H.A. Guvenir, "A Discretization Method Based on Maximizing the Area Under Receiver Operating Characteristic Curve", Int J of Pattern Recognition and Artificial Intelligence, 27, 1350002-1--26 (2013)  PDF
  • O. Kucuktunc, H. Ferhatosmanoglu, "Lambda-Diverse Nearest Neighbors Browsing for Multi-dimensional Data", IEEE Trans on Knowledge and Data Engineering, 25, 481-493 (2013)  PDF
  • R. Ali, C. Gunduz-Demir, T. Szilagyi, B. Durkee, E.E. Graves, "Semi-automatic segmentation of subcutaneous tumuours from micro-computed tomography images", Physics in Medicine and Biology, 58, 8007-8019 (2013)  PDF
  • R. Ozcan, I.S. Altingovde, B.B. Cambazoglu, O. Ulusoy, "Second Chance: A Hybrid Approach for Dynamic Result Caching and Prefetching in Search Engines", ACM Trans on the Web, 8, 3-1--22 (2013)  PDF
  • S. Acer, E. Kayaaslan, C. Aykanat, "A Recursive Bipartitioning Algorithm for Permuting Sparse Square Matrices into Block Diagonal Form with Overlap", SIAM J on Scientific Computing, 35, 99-121 (2013)
  • S. Arslan, T. Ersahin, R. Cetin-Atalay, C. Gunduz-Demir, "Attributed Relational Graphs for Cell Nucleus Segmentation in Fluorescence Microscopy Images", IEEE Trans on Medical Imaging, 32, 1121-1131 (2013)  PDF
  • T. Celik, B. Tekinerdogan, K. Imre, "Deriving Feasible Deployment Alternatives for Parallel and Distributed Simulation Systems", ACM Trans on Modeling and Computer Simulation, 23, 18-1--24 (2013)  PDF
  • U. Celikcan, G. Cimen, E.B. Kevinc, T. Capin, "Attention-Aware Disparty Control in interactive environments", Visual Computer, 29, 685-694 (2013)  PDF
  • Y. Tang, B. Gedik, "Auto-pipelining for Date Stream Processing", IEEE Trans on Parallel and Distributed Systems, 24, 1-12 (2013)
  • Z. Cipiloglu-Yildiz, A. Bulbul, T. Capin, "A Framework for Applying the Principles of Depth Perception to Information Visualization", ACM Trans on Applied Perception, 10, 19-1--22 (2013)  PDF
 2012
  • A. Dayanik, "Learning feature-projection based classifiers", Expert Systems with Applications, 39, 4532-4544 (2012)
  • A. Genctav, S. Aksoy, S. Onder, "Unsupervised segmentation and classification of cervical cell images", Pattern Recognition, 45, 4151-4168 (2012)
  • C. Ari, S. Aksoy, O. Arikan, "Maximum likelihood estimation of Gaussian mixture models using stochastic search", Pattern Recognition, 45, 2804-2816 (2012)
  • K.D. Aral, H.A. Guvenir, I. Sabuncuoglu, A.R. Akar, "A Prescription Fraud Detection Model", Computer Methods and Programs in Biomedicine, 106, 37-46 (2012)
  • M. Ashouri-Talouki, A. Baraani-Dastjerdi, A.A. Selcuk, "GLP: A cryptographic approach for group location privacy", Computer Communications, 35, 1527-1533 (2012)
  • R. Ozcan, I. Sengor-Altingovde, B.B. Cambazoglu, F.P. Junqueira, O. Ulusoy, "Five-level Static Cache Architecture for Web Search Engines", Information Processing & Management, 48, 828-840 (2012)
  • R.O. Selvitopu, A. Turk, C. Aykanat, "Replicated partitioning for undirected hypergraphs", J of Parallel and Distributed Computing, 72, 547-563 (2012)
  • S. Arpa, A. Bulbul, T. Capin, B. Ozguc, "Perceptual 3D rendering based on principles of analytical cubism", Computers and Graphics, 36, 991-1004 (2012)
  • Y.E. Aslan, I. Korpeoglu, O. Ulusoy, "A framework for use of wireless sensor networks in forest fire detection and monitoring", Computers, Environment and Urban Systems, 36, 614-625 (2012)
  • B. Tekinerdogan, "First Turkish Software Product Line Engineering Workshop Summary", ACM Sigsoft Software Engineering Notes, 37, 30-34 (2012)  PDF
  • B. Tekinerdogan, "Reflection on Turkish Aspect-Oriented Software Development Workshop Series", ACM Sigsoft Software Engineering Notes, 37, 30-33 (2012)  PDF
  • B. Tekinerdogan, H. Sozer, M. Aksit, "Feature-Based Rationale Management System for Supporting Software Architecture Adaptation", Int J of Software Engineering and Knowledge Engineering, 22, 945-964 (2012)
  • B. Tekinerdogan, S. Cetin, M.A. Babar, P. Lago, J. Makio, "Architecting in Global Software Engineering", ACM Sigsoft Software Engineering Notes, 37, 1-7 (2012)  PDF
  • D. Davenport, "Computationalism: Still the only game in town", Minds and Machines, 22, 183-190 (2012)  PDF
  • S. Aksoy, I.Z. Yalniz, K. Tasdemir, "Automatic Detection and Segmentation of Orchards Using Very High-Resolution Imagery", IEEE Trans on Geoscience and Remote Sensing, 50, 3117-3131 (2012)  PDF
  • T. Dayar, M.C. Orhan, "Kronecker-based Infinite Level-Dependent QBD Processes", J of Applied Probability, 49, 1166-1187 (2012)  PDF
  • 1000 Genomes Project Consortium, ....C. Alkan..., "An integrated map of genetic variation from 1,092 human genomes", Nature, 491, 56-65 (2012)  PDF
  • A.C. Simsek, A.B. Tosun, C. Aykanat, C. Sokmensuer, C. Gunduz-Demir, "Multilevel segmentation of histopathological images using cooccurance of tissue objects", IEEE Trans on Biomedical Engineering, 59, 1681-1690 (2012)  PDF
  • C. Aksoy, F. Can, S. Kocberber, "Novelty detection for topic tracking", J of American Society for Information Science & Technology, 63, 777-795 (2012)  PDF
  • E. Cerami, J. Gao, U. Dogrusoz, B.E. Gross, S.O. Sumer, B.A. Aksoy, A. Jacobsen, C.J. Byrne,M.L. Heuer, E. Larsson, Y. Antipin, B. Reva, A.P. Goldberg, C. Sander, N. Schultz, "The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data", Cancer Discovery, 2, 401-404 (2012)  PDF
  • E. Kayaaslan, A. Pinar, U. Catalyurek, C. Aykanat, "Partitioning Hypergraphs in Scientific Computing Applications Through Vertex Separators on Graphs", SIAM J on Scientific Computing, 34, 970-992 (2012)  PDF
  • E. Okuyan, U. Gudukbay, V. Isler, "View-Dependent Refinement of Unstructured Tetrahedral Volumetric Meshes", J of Visualization, 15, 167-178 (2012)
  • E. Ozdemir, C. Sokmensuer, C. Gunduz-Demir, "A resambling-based Markovian model for automated colon cancer diagnosis", IEEE Trans on Biomedical Engineering, 59, 281 (2012)  PDF
  • F. Hach, I. Numanagic, C. Alkan, S.C. Sahinalp, "SCALCE: boosting Sequence Compression Algorithms using Locally Consistent Encoding", Bioinformatics, 28, 3051-7 (2012)  PDF
  • G. Jacques-Silva, B. Gedik, R. Wagle, K-L. Wu, V. Kumar, "Building User-defined Runtime Adaptation Routines for Stream Processing Applications", Proceedings of the VLDB Endowment, 5, 1826-1837 (2012)
  • I. Sengor-Altingovde, R. Ozcan, O. Ulusoy, "Static Index Pruning in Web Search Engines: Combining Term and Document Popularities with Query Views", ACM Trans on Information Systems, 30, 2:1-27 (2012)  PDF
  • M. Ashouri-Talouki, A. Baraani-Dastjerdi, A.A. Selcuk, "Preserving Location Privacy for a Group of Users", Turkish J of Electrical Engineering & Computer Sciences, 21, 1857-1870 (2012)
  • M. Meyer, M. Kircher, M-T. Gansauge, H. Li, ..., C. Alkan, ..., "A High-Coverage Genome Sequence from an Archaic Denisovan Individual", Science, 338, 222-226 (2012)  PDF
  • M.P. Van Iersel, A.C. Villeger, T. Czauderna, S.E. Boyd, F.T. Bergmann, A.Luna, E. Demir, A. Sorokin, U. Dogrusoz, Y. Matsuoka, A. Funahashi, M.I. Aladjem, H. Mi, S.L. Moodie, H. Kitano, N. Le Novere, F. Schreiber, "Software support for SBGN maps: SBGN-ML and LibSBGN", Bioinformatics, 28, 2016-2021 (2012)  PDF
  • N.H. Younan, S. Aksoy, "Foreword to the Special Issue on Pattern Recognition in Remote Sensing", IEEE J of Selected Topics in Appl. Earth Observ.Rem. Sens., 5, 1331-1333 (2012)  PDF
  • O. Arslan, U. Saranli, "Reactive Planning and Control of Planar Spring-Mass Running on Rough Terrain", IEEE Trans on Robotics, 28.
  • T. Kucukyilmaz, A. Turk, C. Aykanat, "A Parallel Framework for In-Memory Construction of Term-Partitioned Inverted Indexes", Computer Journal, 55, 1317-1330 (2012)  PDF
  • Z. Isik, T. Ersahin, V. Atalay, C. Aykanat, R. Cetin-Atalay, "A Signal Transduction Score Flow Algorithm for Cyclic Cellular Pathway Anlaysis, which Combines Transcriptome and ChIP-seg Data", Molecular BioSystems, 8, 3224-3231 (2012)  PDF
 2011
  • O. Ozturk, "Reducing Memory Space Consumption Through Dataflow Analysis", Computer Languages, Systems and Structures, 37, 168-177 (2011)
  • O. Ozturk, "Data Locality and Parallelism Optimization Using A Constraint-Based Approach", J of Parallel and Distributed Computing, 71, 280-287 (2011)
  • E.F. Can, P. Duygulu, "A line based representation for matching words in historical manuscripts", Pattern Recognition Letters, 32, 1081-1222 (2011)
  • F. Cakir, U. Gudukbay, O. Ulusoy, "Nearest-Neighbor based Metric Functions for Indoor Scene Recognition", Computer Vision and Image Understanding, 115, 1483-1492 (2011)
  • H. Aksu, D. Aksoy, I. Korpeoglu, "A study of localized metrics: Evaluation of position errors in wireless sensor networks", Computer Networks Journal, 55, 3562-3577 (2011)
  • M. Kas, I. Korpeoglu, E. Karasan, "OLSR-Aware Channel Access Scheduling in Wireless Mesh Networks", J of Parallel and Distributed Computing, 71, 1225-1235 (2011)
  • S. Pehlivan, P. Duygulu, "A new pose-based representation for recognizing actions from multiple cameras", Computer Vision and Image Understanding, 115, 140-151 (2011)
  • B. Tekinerdogan, "Experiences in Teaching a Graduate Course on Model-Driven Software Development", Computer Science Education, 21, 363-387 (2011)  PDF
  • O. Ozturk, "Multicore Education Through Simulation", IEEE Trans on Education, 54, 203-209 (2011)  PDF
  • P. Duygulu, M. Bastan, "Multimedia translation for linking visual data to semantics in videos", Machine Vision and Applications, 22, 99-115 (2011)  PDF
  • S. Tasli-Pektas, B. Ozguc, "Virtual Prototyping for Open Building Design", Open House International, 36, 46-56 (2011)
  • T. Dayar, G.N. Noyan, "Steady-State Analysis of Google-like Stochastic Matrices with Block Iterative Methods", Electronic Transactions on Numerical Anlaysis, 38, 69-97 (2011)
  • T. Dayar, H. Hermanns, D. Spieler, V. Wolf, "Bounding the Equilibrium Distribution of Markov Population Models", Numerical Linear Algebra with Applications, 18, 931-946 (2011)  PDF
  • T. Dayar, W. Sandmann, D. Spieler, V. Wolf, "Infinite Level-Dependent QBDs and Matrix Analytic Solutions for Stochastic Chemical Kinetics", Advances in Applied Probability, 43, 1005-1026 (2011)  PDF
  • A. Bulbul, T. Capin, G. Lavoue, M. Preda, "Assessing Visual Quality of 3-D Polygonal Models", IEEE Signal Processing Magazine, 80, 80-90 (2011)  PDF
  • A. Cevahir, C. Aykanat, A. Turk, B.B. Cambazoglu, "Site-Based Partitioning and Repartitioning Techniques for Parallel PageRank Computation", IEEE Trans on Parallel and Distributed Systems, 22, 786-802 (2011)  PDF
  • A. Gotchev, G.B. Akar, T. Capin, D. Strohmeier, A. Boev, "Three-Dimensional Media for Mobile Devices", Proceedings of the IEEE, 99, 708-741 (2011)  PDF
  • A.B. Tosun, C. Gunduz-Demir, "Graph run-length matrices for histopathological image segmentation", IEEE Trans on Medical Imaging, 30, 721-732 (2011)  PDF
  • A.R. Akar, M. Kutcephe, E. Sener, C. Alhan, S. Durdu, A.G. Kunt, H.A. Guvenir, "Validation of the EuroSCORE risk models in Turkish adult cardiac surgical population", European J of Cardio-thoracic Surgery, 40, 730-735 (2011)  PDF
  • E. Bulut, I. Korpeoglu, "Sleep Scheduing with Expected Common Coverage in Wireless Sensor Networks", Wireless Networks, 17, 19-40 (2011)  PDF
  • E. Ozkural, B. Ucar, C. Aykanat, "Parallel Frequent Item Set Mining with Selective Item Replication", IEEE Trans on Parallel and Distributed Systems, 10, 1632-1640 (2011)  PDF
  • F. Durupinar, N. Pelechano, J.M. Allbeck, U. Gudukbay, N. Badler, "How the OCEAN Personality Model Affects the Perception of Crowds", IEEE Computer Graphics and Applications, 31, 22-31 (2011)  PDF
  • H. Cihan, T. Capin, "Multiscale Motion Saliency for Keyframe Extraction from Motion Capture Sequences", Computer Animation and Virtual Worlds, 22, 3-14 (2011)  PDF
  • H.O. Tan, I. Korpeoglu, I. Stojmenovic, "Computing Localized Power Efficient Data Aggregation Trees for Sensor Networks", IEEE Trans on Parallel and Distributed Systems, 22, 489-500 (2011)  PDF
  • K. Kaya, G. Karakulah, C. Yakicier, A.C. Acar, O. Konu, "mESAdb:microRNA Expression and Sequence Analysis Database", Nucleic Acids Research, 39, 170-180 (2011)  PDF
  • R. Ozcan, I. Sengor-Altingovde, O. Ulusoy, "Cost-Aware Strategies for Query Result Caching in Web Search Engines", ACM Trans on the Web, 5, 9-1--25 (2011)  PDF
  • R. Ozcan, I.S. Altingovde, O. Ulusoy, "Exploiting Navigational Queries for Result Presentation and Caching in Web Search Engines", J of American Society for Information Science & Technology, 62, 714-726 (2011)  PDF
  • U.V. Catalyurek, C. Aykanat, E. Kayaaslan, "Hypergraph Partitioning-Based Fill-Reducing Ordering for Symmetric Matrices", SIAM J on Scientific Computing, 33, 1996-2023 (2011)  PDF
 2010
  • A. Dayanik, "Feature interval learning algorithms for classification", Knowledge Based Systems, 23, 402-417 (2010)
  • C. Gunduz-Demir, M. Kandemir, A.B. Tosun, C. Sokmensuer, "Automatic segmentation of colon glands using object-graphs", Medical Image Analysis, 14, 1-12 (2010)
  • H.A. Guvenir, M. Cakir, "Voting features based classifier with feature construction and its application to predicting financial distress", Expert Systems with Applications, 37, 1713-1718 (2010)
  • O. Ozturk, "Improving Chip Multiprocessor Reliability Through Code Replication", Computers and Electrical Engineering, 36, 480-490 (2010)
  • S. Aksoy, N.H. Younan, L. Bruzzone, "Patern Recognition in Remote Sensing", Pattern Recognition Letters, 31, 1069-1070 (2010)
  • A. Bulbul, Z. Cipiloglu, T. Capin, "A Perceptual Approach for Stereoscopic Rendering Optimization", Computers and Graphics, 34, 145-157 (2010)
  • B. Ozdemir, S. Aksoy, S. Eckert, M. Pesaresi, D. Ehrlich, "Performance measures for object detection evaluation", Pattern Recognition Letters, 31, 1128-1137 (2010)
  • B. Ucar, U.V. Catalyurek, C. Aykanat, "A Matrix Partitioning Interface to PaToH in MATLAB", Parallel Computing, 36, 254-272 (2010)
  • D. Ozkan, P. Duygulu, "Interesting Faces in News: A Graph Based Approach for Finding People", Pattern Recognition, 43, 1717-1735 (2010)
  • E. Demir, C. Aykanat, "Efficient Successor Retrieval Operations for Aggregate Query Processing on Clustered Road Networks", Information Sciences, 180, 2743-2762 (2010)
  • E. Demir, C. Aykanat, B.Barla-Cambazoglu, "A link-based storage scheme for efficient aggregate query processing on clustered road networks", Information systems, 35, 75-93 (2010)
  • E. Saykol, U. Gudukbay, O. Ulusoy, "Scenario-Based Query Processing for Video-Surveillance Archives", Engineering Applications of Artificial Intelligence, 23, 331-345 (2010)
  • E. Soysal, I. Cicekli, N. Baykal, "Design and evaluation of an ontology based information extraction system for radiological reports", Computers in Biology and Medicine, 40, 900-911 (2010)
  • I.Z. Yalniz, S. Aksoy, "Unsupervised Detection and Localization of Structural Textures Using Protection Profiles", Pattern Recognition, 43, 3324-3337 (2010)
  • K. Kose, A.E. Cetin, U. Gudukbay, L. Onural, "3D Model Compression Using Connectivity-Guided Adaptive Wavelet Transform built into 2D SPIHT", J Vis. Commun. Image R., 21, 17-28 (2010)
  • M. Ak, K. Kaya, K. Onarlioglu, A.A. Selcuk, "Efficient Broadcast Encryption with User Profiles", Information Sciences, 180, 1060-1072 (2010)
  • M. Cebe, C. Gunduz-Demir, "Qualitative test-cost sensitive classification", Pattern Recognition Letters, 31, 2043-2051 (2010)
  • O. Kucuktunc, U. Gudukbay, O. Ulusoy, "Fuzzy Color Histogram-based Video Segmentation", Computer Vision and Image Understanding, 114, 125-134 (2010)
  • O. Kucuktunc, M. Bastan, U. Gudukbay, O. Ulusoy, "Video Copy Detection Using Multiple Visual Cues and MPEG-7 Descriptors", J of Visual Communication and Image Representation, 21, 838-849 (2010)
  • O. Oguz, A. Akaydin, T. Yilmaz, U. Gudukbay, "Emergency Crowd Simulation for Outdoor Environments", Computers and Graphics, 34, 136-144 (2010)
  • F. Can, S. Kocberber, O. Baglioglu, S. Kardas, H.C. Ocalan, E. Uyar, "New event detection and topic tracking in Turkish", J of American Society for Information Science & Technology, 61, 802-819 (2010)
  • F. Can, J.M. Patton, "Change of word characteristics in 20th Century Turkish Literature", J of Quantitative Linguistics, 17, 167-190 (2010)
  • I. Ipek, "The Effects of CBI Lesson Sequence Type and Field Dependence on Learning From Computer-Based Cooperative Instruction in WEB", Turkish Online Journal of Educational Technology, 9, 221-234 (2010)
  • O. Ozturk, D. Demirbas, "Heterogeneous NoC Design Through Evolutionary Computing", Int J of Electronics, 97, 1139-1161 (2010)
  • O. Ozturk, M. Kandemir, M.J. Irwin, "On-chip memory space partitioning for chip multiprocessors using polyhedral algebra", IET Computers & Digital Techniques, 4, 484-498 (2010)
  • O. Ozturk, M. Kandemir, M.J. Irwin, S.H.K. Narayanan, "Compiler Directed Network on-chip Reliability Enhancement for Chip Multiprocessor", ACM Sigplan Notices, 45, 85-94 (2010)
  • S. Aksoy, H.G. Akcay, T. Wassenaar, "Automatic Mapping of Linear Woody Vegetation Features in Agricultural Landscapes Using very High Resolution Imagery", IEEE Trans on Geoscience and Remote Sensing, 48, 511-522 (2010)  PDF
  • S. Aksoy, R.G. Cinbis, "Image Mining Using Directional Spatial Constraints", IEEE Geoscience and Remote Sensing Letters, 7, 33-37 (2010)  PDF
  • U. Saranli, A. Avci, M.C. Ozturk, "A Modular, Real-Time Fieldbus Architecture for Mobile Robotic Platforms", IEEE Trans on Instrumentation and Measurement..  PDF
  • U. Saranli, O. Arslan, M.M. Ankarali, O. Morgul, "Approximate Analytic Solutions to Non-symmetric Stance Trajectories of the Passive Spring-Loaded Inverted Pendulum with Damping", Nonlinear Dynamics, 62, 729-731 (2010)
  • A. Bulbul, Z. Cipiloglu, T. Capin, "A Color-Based Face Tracking Algorithm for Enhancing Iteraction with Mobile Devices", Visual Computer, 26, 311-323 (2010)
  • A. Dilek, M.E. Belviranli, U. Dogrusoz, "VISIBIOWeb: visualization and layout services fro BioPAX pathway models", Nucleic Acids Research, 38, W150-154 (2010)
  • B. Ciftlikli, V. Isler, U. Gudukbay, "Increasing the Sense of Presence in a Simulation Environment Using Image Generators Based on Visual Attention", Presence: Teleoperators and Virtual Environments, 19, 557-568 (2010)
  • D. Altunbay, C. Cigir, C. Sokmensuer, C. Gunduz-Demir, "Color Graphs for Automated Cancer Diagnosis and Grading", IEEE Trans on Biomedical Engineering, 57, 665-674 (2010)  PDF
  • E. Demir, M. Cary, S. Paley, K. Fukuda, ..., U. Dogrusoz, ..., C. Sander, G. Bader, "The BioPAX community standard for pathway data sharing", Nature Biotechnology, 28, 935-942 (2010)
  • E. Saykol, M. Bastan, U. Gudukbay, O. Ulusoy, "Keyframe Labeling Technique for Surveillance Event Classification", Optical Engineering, 49, 117203-1--12 (2010)
  • F. Durupinar, U. Gudukbay, "Visualization of Crowd Synchronization on Footbridges", J of Visualization, 13, 69-77 (2010)
  • I.Z. Yalniz, I.S. Altingovde, U. Gudukbay, O. Ulusoy, "Integrated Segmentation and Recognition of Connected Ottoman Script", Optical Engineering, 48, 117205-1--12 (2010)
  • K. Demirtas, N.K. Cicekli, I. Cicekli, "Automatic categorization and summarization of documentaries", J of Information Science, 36.
  • M. Bastan, H. Cam, U. Gudukbay, O. Ulusoy, "BilVideo-7: An MPEG-7-Compatible Video Indexing and Retrieval System", IEEE Multimedia, 17, 62-73 (2010)  PDF
  • M. Kas, I. Korpeoglu, E. Karasan, "Utilization-Based Dynamic Scheduling Algorithm for Wireless Mesh Networks", Eurasip Journal on Wireless Communication and Networking, 2010, 312828-1--11 (2010)
  • M. Kas, B. Yargicoglu, I. Korpeoglu, E. Karasan, "A Survey on Scheduling in IEEE 802.16 Mesh Mode", IEEE Communications Surveys and Tutorials, 12, 205-221 (2010)  PDF
  • M. Kutlu, C. Cigir, I. Cicekli, "Generic Text Summarization", Computer Journal, 53, 1315-1323 (2010)
  • M.M. Ankarali, U. Saranli, "Stride-to-stride energy regulation for robust self-stability of a torque-actuated dissipative spring-mass hopper", Chaos, 20, 033121-1--13 (2010)
  • O. Babur, U. Dogrusoz, E. Demir, C. Sander, "chiBE: Iterative visualization and manipulation of BioPAX pathways models", Bioinformatics, 26, 429-431 (2010)
  • O. Babur, E. Demir, M. Gonen, C. Sander, U. Dogrusoz, "Discovering Modulators of Gene Expression", Nucleic Acids Research, 38, 5648-5656 (2010)
  • S. Bayraktar, U. Gudukbay, B. Ozguc, "Particle-based simulation and visualization of fluid flows through porous media", J of Visualization, 13, 327-336 (2010)
  • S.G. Sevinc, O. Kucuktunc, P. Duygulu, F. Can, "Automatic tag expansion using visual similarity for photo sharing websites", Multimedia Tools and Applications, 49, 81-99 (2010)
  • T. Daybelge, I. Cicekli, "A ranking method for example based machine translation results by learning from user feedback", Applied Intelligence..
  • U.V. Catalyurek, C. Aykanat, B. Ucar, "On two-dimensional sparse matrix partitioning: Models, Methods, and a Recipe", SIAM J on Scientific Computing, 32, 656-683 (2010)
 2009
  • U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, E. Demir, "A Layout Algorithm for Undirected Compound Graphs", Information Sciences, 179, 980-994 (2009)
  • U. Gudukbay, A.A. Alatan, "Special Issue on Advances in Three Dimensional Television and Video: Guest Editorial", Signal Processing: Image Communication, 24, 1-2 (2009)
  • A.B. Tosun, M. Kandemir, C. Sokmensuer, C. Gunduz Demir, "Object-oriented texture analysis for the unsupervised segmentation of biopsy images for cancer detection", Pattern Recognition, 42, 1104-1112 (2009)
  • H. Sozer, M. Tekkalmaz, I. Korpeoglu, "A Peer-to-Peer File Search and Download Protocol for Wireless Ad Hoc Networks", Computer Communications, 32, 41-50 (2009)
  • M. Ak, K. Kaya, A.A. Selcuk, "Optimal subset-difference broadcast encryption with free riders", Information Sciences, 179, 3673-3684 (2009)
  • N. Ikizler, P. Duygulu, "Histogram of oriented rectangles: A new pose descriptor for human action recognition", Image and Vision Computing, 27, 1515-1526 (2009)
  • S. Ciraci, I. Korpeoglu, O. Ulusoy, "Reducing Query Overhead Through Route Learning in Unstructured Peer-to-Peer Network", J of Network and Computer Applications, 32, 550-567 (2009)
  • S. Tatar, I. Cicekli, "Two learning approaches for protein name extraction", J of Biomedical Informatics, 42, 1046-1055 (2009)
  • T. Aydin, H.A. Guvenir, "Modeling interestingness of streaming association rules as a benefit-maximizing classification problem", Knowledge-Based Systems, 22, 85-99 (2009)
  • Z. Yucel, Y. Sara, P. Duygulu, R. Onur, E. Esen, A.B. Ozguler, "Automated discrimination of psychotropic drugs in mice via computer vision-based analysis", J of Neuroscience Methods, 180, 234-242 (2009)
  • O. Ozturk, M. Kandemir, M.J. Irwin, "Using Data Compression for Increasing Memory System Utilization", IEEE Trans on Computer Aided Design, 28, 901-914 (2009)  PDF
  • O. Ozturk, M. Kandemir, S.W. Son, I. Kolcu, "Shared scratch pad memory space management across applications", Int J of Embedded Systems, 4, 54-65 (2009)
  • S. Aksoy, K. Koperski, C. Tusk, G. Marchisio, "Land Cover Classification with Multi-Sensor Fusion of Partly Missing Data", Photogrammetric Engineering & Remote Sensing, 75, 577-593 (2009)
  • S.S.H. Tse, "Online Bicriteria Load Balancing using Object Reallocation", IEEE Trans on Parallel and Distributed Systems, 20, 379-388 (2009)  PDF
  • U. Dogrusoz, A. Cetintas, E. Demir, O. Babur, "Algorithms for effective querying of compound graph-based pathway databases", BMC Bioinformatics, 10, 376--1-16 (2009)
  • E. Imre, A.A. Alatan, U. Gudukbay, "Rate-Distortion Efficient Piecewise Planar 3D Scene Representation from 2-D Images", IEEE Trans on Image Processing, 18, 483-494 (2009)  PDF
  • H. Bagci, I. Korpeoglu, "Distributed and Location Based Multicast Routing Algorithms for Wireless Sensor Networks", Eurasip Journal on Wireless Communication and Networking., 697373-1--14 (2009)
  • H. Sozer, B. Tekinerdogan, M. Aksit, "FLORA: a framework for decomposing software architecture to introduce local recovery", Software - Practice and Experience, 39, 869-889 (2009)
  • I.Z. Yalniz, I.S. Altingovde, U. Gudukbay, O. Ulusoy, "Ottoman Archives Explorer: A Retrieval System for Digital Ottoman Archives", ACM J on Computing and Cultural Heritage, 2, 8-1--20 (2009)
  • M. Karakaya, I. Korpeoglu, O. Ulusoy, "Free Riding in Peer-to-Peer Networks", IEEE Internet Computing, 13, 92-98 (2009)
  • N.LeNovere, M. Hucka, H. Mi, S. Moodie, F. Schreiber, A. Sorokin, E. Demir, K. Wegner, M.I. Aladjem, S.M. Wimalaratne, F.T. Bergman, R. Gauges, P. Ghaza, H. Kawaji, L. Li, Y.Matsuoka, ..., U. Dogrusoz, T. Freeman, A. Funahashi, ..., H. Kitano, "The Systems Biology Graphical Notation", Nature Biotechnology, 27, 735-741 (2009)
  • P. Askar, D. Davenport, "An Investigation of Factors Related to Self-Efficacy for Java Parogramming Among Engineering Students", Turkish Online Journal of Educational Technology, 8, 26-32 (2009)
  • S. Bayraktar, U. Gudukbay, B. Ozguc, "GPU-Based Neighbor-Search Algorithm for Particle Simulations", J of Graphics, GPU, and Game Tools, 14, 31-42 (2009)
 2008
  • C. Aykanat, B.B. Cambazoglu, B. Ucar, "Multi-level Direct K-way Hypergraph Partitioning with Multiple Constraints and Fixed Vertices", J of Parallel and Distributed Computing, 68, 609-625 (2008)
  • A. Pinar, E.K. Tabak, C. Aykanat, "One-dimensional Partitioning for Heterogeneous Systems: Theory and Practice", J of Parallel and Distributed Computing, 68, 1473-1486 (2008)
  • E. Demir, C. Aykanat, B.B. Cambazoglu, "Clustering Spatial Networks for Aggregate Query Processing, a Hypergraph Approach", Information Systems, 33, 1-17 (2008)
  • G. Erozel, N.K. Cicekli, I. Cicekli, "Natural Language Querying for Video Databases", Information Sciences, 178, 2534-2552 (2008)
  • M. Karakaya, I. Korpeoglu, O. Ulusoy, "Counteracting Free Riding in Peer-To-Peer Networks", Computer Networks Journal, 52, 675-694 (2008)
  • M. Karakaya, I. Korpeoglu, O. Ulusoy, "A Connection Management Protocol for Promoting Cooperation in Peer-to-Peer Networks", Computer Communications, 31, 240-256 (2008)
  • O. Oksuz, U. Gudukbay, A.E. Cetin, "A Video-Based Text and Equation Editor for LaTeX", Engineering Applications of Artificial Intelligence, 21, 952-960 (2008)
  • O. Vechtmova, M. Karamuftuoglu, "Lexical Cohesion and Term Proximity in Document Ranking", Information Processing & Management, 44, 1485-1502 (2008)
  • T. Kucukyilmaz, B.B. Cambazoglu, C. Aykanat, F. Can, "Chat Mining: Predicting User and Message Attributes in Computer-Mediated Communication", Information Processing & Management, 44, 1448-1466 (2008)
  • T. Sevilmis, M. Bastan, U. Gudukbay, O. Ulusoy, "Automatic detection of salient objects and spatial relations in videos for a video database system", Image and Vision Computing, 26, 1384-1396 (2008)
  • A.A. Selcuk, "On Probability of Success in Linear and Differential Cryptanalysis", J of Cryptology, 21, 131-147 (2008)
  • A.A. Selcuk, E. Uzun, M.R. Pariente, "A Reputation-Based Trust Management System for P2P Networks", Int J of Network Security, 6, 235-245 (2008)
  • F. Can, S. Kocberber, E. Balcik, C. Kaynak, H.C. Ocalan, O.M. Vursavas, "Information retrieval on Turkish texts", J of American Society for Information Science & Technology, 59, 407-421 (2008)
  • O. Ozturk, M. Kandemir, "ILP Based Energy Minimization Techniques for Banked Memories", ACM Trans on Design Automation of Electronic Systems, 13, 50-1--40 (2008)
  • O. Ozturk, M. Kandemir, G. Chen, "Access Pattern-Based Code Compression for Memory-Constrained Systems", ACM Trans on Design Automation of Electronic Systems, 13, 60-1--30 (2008)
  • T. Capin, K. Pulli, T. Aenine-Moller, "The State of the Art in Mobile Graphics Research", IEEE Computer Graphics and Applications, 28, 74-84 (2008)  PDF
  • T. Dayar, A. Meric, "Kronecker Representation and Decompositional Analysis of Closed Queueing Networks with Phase-Type Service Distributions", Annals of Operations Research, 164, 193-210 (2008)
  • A. Altingovde, E. Demir, F. Can, O. Ulusoy, "Incremental Cluster-Based Retrieval Using Compressed Cluster-Skipping Inverted Files", ACM Trans on Information Systems, 26, 15-1--36 (2008)
  • G. Akcay, S. Aksoy, "Automatic Detection of Geospatial Objects Using Multiple Hierarchical Segmentations", IEEE Trans on Geoscience and Remote Sensing, 46, 2097-2111 (2008)  PDF
  • O. Babur, R. Colak, E. Demir, U. Dogrusoz, "PATIKAmad: analysis of pathways using microarray data", Proteomics, 8, 2196-2198 (2008)
  • R. Aras, B. Basarankut, T. Capin, B. Ozguc, "3D Hair Sketching for Real Time Dynamic & Key Frame Animations", Visual Computer, 24, 577-585 (2008)
  • T. Yilmaz, U. Gudukbay, "Stereoscopic Urban Visualization Based on Graphics Processing Unit", Optical Engineering, 47, 097005 (2008)
  • Y. Bao, I.N. Bozkurt, T. Dayar, X. Sun, K.S. Trivedi, "Decompositional Analysis of Kronecker Structured Markov Chains", Electronic Transactions on Numerical Anlaysis, 31, 271-294 (2008)
 2007
  • C. Aykanat, B.B. Cambazoglu, F. Findik, T.M. Kurc, "Adaptive Decomposition and Remapping Algorithms for Object-Space-Parallel Direct Volume Rendering of Unstructured Grids", J of Parallel and Distributed Computing, 67, 77-99 (2007)
  • C. Gunduz-Demir, "Mathematical modeling of the malignancy of cancer using graph evolution", Mathematıcal Biosciences, 209, 514-527 (2007)
  • U. Dogrusoz, K.G. Kakoulis, B. Madden, I.G. Tollis, "On Labeling in Graph Visualization", Information Sciences, 177, 2459-2472 (2007)
  • B. Ucar, C. Aykanat, M. C. Pinar, T. Malas, "Parallel Image Restoration Using Surrogate Constraint Methods", J of Parallel and Distributed Computing, 67, 186-204 (2007)
  • B.B. Cambazoglu, E. Karaca, T. Kucukyilmaz, A. Turk, C. Aykanat, "Architecture of a Grid-Enabled Search Engine", Information Processing & Management, 43, 609-623 (2007)
  • E. Okuyan, U. Gudukbay, O. Gulseren, "Pattern Information Extraction from Crystal Structures", Computer Physics Communications, 176, 486-506 (2007)
  • F. Durupinar, U. Gudukbay, "Procedural Visualization of Knitwear and Woven Cloth", Computers and Graphics, 31, 778-783 (2007)
  • G. Ercan, I. Cicekli, "Using Lexical Chains for Keyword Extraction", Information Processing & Management, 43, 1705-1714 (2007)
  • K. Kaya, A.A. Selcuk, "Threshold cryptography based on Asmuth-Bloom Secret Sharing", Information Sciences, 177, 4148-4160 (2007)
  • K. Kaya, B. Ucar, C. Aykanat, "Heuristics for scheduling file-sharing tasks on heterogeneous systems with distributed repositories", J of Parallel and Distributed Computing, 67, 271-285 (2007)
  • O. Vechtomova, M. Karamuftuoglu, "Query expansion with terms selected using lexical cohesion analysis of documents", Information Processing & Management, 43, 849-965 (2007)
  • T. Yilmaz, U. Gudukbay, "Conservative Occlusion Culling for Urban Visualization Using a Slice-wise Data Structure", Graphical Models, 69, 191-210 (2007)
  • A.A. Alatan, Y. Yemez, U. Gudukbay, X. Zabulis, K. Muller, C. Erdem, C. Weigel, A. Smolic, "Scene Representation Technologies for 3DTV - A survey", IEEE Trans on Circuits Systems for Video Tech, 17, 1587-1605 (2007)  PDF
  • B. Ucar, C. Aykanat, "Revisiting Hypergraph Models for Sparse Matrix Partitioning", SIAM Review, 49, 595-603 (2007)
  • B. Ucar, C. Aykanat, "Partitioning Sparse Matrices for Parallel Preconditioned Iterative Methods", SIAM J on Scientific Computing, 29, 1683-1709 (2007)
  • B.B. Cambazoglu, C. Aykanat, "Hypergraph-Partitioning-Based Remapping Models for Image-Space-Parallel Direct Volume Rendering of Unstructured Grids", IEEE Trans on Parallel and Distributed Systems, 18, 3-16 (2007)
  • D.A. Clausi, S. Aksoy, J.C. Tilton, "Foreword to the Special Issue on Pattern Recognition in Remote Sensing", IEEE Trans on Geoscience and Remote Sensing, 45, 3855-3856 (2007)
  • E.S. Ayaz, A.A. Selcuk, "Improved DST Cryptanalysis of IDEA", Lecture Notes in Computer Science, 4356, 1-14 (2007)
  • O. Kucuktunc, U. Gudukbay, O. Ulusoy, "A Natural Language Based Interface for Query Specification in a Video Database Management System", IEEE Multimedia, 14, 83-89 (2007)  PDF
  • P. Buchholz, T. Dayar, "On the convergence of a class of multilevel methods for large, sparse markov chains", SIAM J on Matrix Analysis and Applications, 29, 1025-1049 (2007)
  • T. Aydin, H.A. Guvenir, "A Novel Hybrid Approach for Interestingness Analysis of Classification Rules", Lecture Notes in Artificial Intelligence, 3609, 485-496 (2007)
 2006
  • U. Dogrusoz, B. Genc, "A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization", Computers and Graphics, 30, 86-97 (2006)
  • A. Unal, Y. Saygin, O. Ulusoy, "Processing count queries over event streams at multiple time granularities", Information Sciences, 176, 2066-2096 (2006)
  • B. Genc, U. Dogrusoz, "A Layout Algorithm for Signaling Pathways", Information Sciences, 176, 135-149 (2006)
  • B. Ucar, C. Aykanat, K. Kaya, M. Ikinci, "Task Assignment in Heterogeneous Computing Systems", J of Parallel and Distributed Computing, 66, 32-46 (2006)
  • B.B. Cambazoglu, C. Aykanat, "Performance of Query Processing Implementations in Ranking-Based Text Retrieval Systems Using Inverted Indices", Information Processing & Management, 42, 875-898 (2006)
  • B.U. Toreyin, Y. Dedeoglu, U. Gudukbay, A.E. Cetin, "Computer Vision Based Method for Real-time Fire and Flame Detection", Pattern Recognition Letters, 27, 49-58 (2006)
  • K.Y. Lam, O. Ulusoy, "Adaptive schemes for location update generation in execution location-dependent continuous queries", J of Systems and Software, 79, 441-453 (2006)
  • M. Akdere, C. Bilgin, O. Gerdaneri, I. Korpeoglu, O. Ulusoy, U. Cetintemel, "A Comparison of Epidemic Algorithms in Wireless Sensor Networks", Computer Communications, 29, 2450-2457 (2006)
  • N.K. Cicekli, I. Cicekli, "Formalizing the Specification and Execution of Workflows using the Event Calculus", Information Sciences, 176, 2227-2267 (2006)
  • O. Vechtomova, M. Karamuftuoglu, "Elicitation and use of relevance feedback information", Information Processing & Management, 42, 191-206 (2006)
  • R. Nuray, F. Can, "Automatic Ranking of Information Retrieval Systems Using Data Fusion", Information Processing & Management, 42, 595-614 (2006)
  • S.C. Sahinalp, U. Dogrusoz, S. Muthukrishnan, "Preface to special issue on Combinatorial Pattern Matching", Theoretical Computer Science, 368, 195 (2006)
  • F. Can, "Turkish Information Retrieval: Past Changes Future", Lecture Notes in Computer Science, 4243, 13-22 (2006)
  • I. Cicekli, N.K. Cicekli, "Generalizing Predicates with String Arguments", Applied Intelligence, 25, 23-36 (2006)
  • P. Duygulu, M. Bastan, D.A. Forsyth, "Translating images to words for recognizing objects in large image and video collections", Lecture Notes in Computer Science, 4170.
  • S. Aksoy, "Modeling of remote sensing image content using attributed relational graphs", Lecture Notes in Computer Science, 4109, 475-483 (2006)
  • U. Dogrusoz, E.Z. Erson, E. Giral, E. Demir, O. Babur, A. Cetintas, R. Colak, "PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization", Bioinformatics, 22, 374-375 (2006)
  • B.B. Cambazoglu, A. Catal, C. Aykanat, "Effect of Inverted Index Partitioning Schemes on Performance of Query Processing in Parallel Text Retrieval Systems", Lecture Notes in Computer Science, 4263, 717-725 (2006)
  • D. Ozkan, P. Duygulu, "Finding People Frequently Appearing in News", Lecture Notes in Computer Science, 4071, 173-182 (2006)
  • H. Acan, K. Kaya, A.A. Selcuk, "Capture Resilient ElGamal Signature Protocols", Lecture Notes in Computer Science, 4263, 943-951 (2006)
  • K. Dogan, G. Gurel, A.K. Kamci, I. Korpeoglu, "Bluetooth Broadcasting Performance: Reliability and Throughput", Lecture Notes in Computer Science, 3992, 996-999 (2006)
  • K. Kaya, A.A. Selcuk, Z. Tezcan, "Threshold Cryptography Based on Asmuth-Bloom Secret Sharing", Lecture Notes in Computer Science, 4263, 935-942 (2006)
  • K. Kaya, C. Aykanat, "Iterative-Improvement-Based Heuristics for Adaptive Scheduling of Tasks Sharing Files on Heterogeneous Master-Slave Environments", IEEE Trans on Parallel and Distributed Systems, 17, 883-895 (2006)
  • M. Tekkalmaz, H. Sozer, I. Korpeoglu, "Distrubuted Construction and Maintenance of Bandwidth and Energy Efficient Bluetooth Scatternets", IEEE Trans on Parallel and Distributed Systems, 17, 963-974 (2006)  PDF
  • S. Altingovde, F. Can, O. Ulusoy, "Algorithms for Within-Cluster Searches Using Inverted Files", Lecture Notes in Computer Science, 4263, 707-716 (2006)
  • T. Aydin, H.A. Guvenir, "Modeling Interestingness of Streaming Classification Rules as Classification Problem", Lecture Notes in Artificial Intelligence, 3949, 168-176 (2006)
  • T. Kucukyilmaz, B.B. Cambazoglu, C. Aykanat, F. Can, "Chat Mining for Gender Prediction", Lecture Notes in Computer Science, 4243, 274-283 (2006)
  • Y. Dedeoglu, B.U. Toreyin, U. Gudukbay, A. E. Cetin, "Sillouette-Based Method for Object Classification and Human Action Recognition in Video", Lecture Notes in Computer Science, 3979, 64-77 (2006)
 2005
  • E. Saykol, U. Gudukbay, O. Ulusoy, "A Histogram-Based Approach for Object-Based Query-by-Shape-and-Color in Image and Video Databases", Image and Vision Computing, 23, 1170-1180 (2005)
  • M. Koyuturk, C. Aykanat, "Iterative-improvement-Based declustering heuristics for multi-disk databases", Information Systems, 30, 47-70 (2005)
  • N. Pekergin, T. Dayar, D.N. Alparslan, "Componentwise Bounds for Nearly Completely Decomposable Markov Chains Using Stochastic Comparison and Reordering", European J of Operational Research, 165, 810-825 (2005)
  • I. Cicekli, "Inducing translation templates with type constraints", J of Machine Translation, 19, 283-299 (2005)
  • O. Ulusoy, "Database Research at Bilkent University (invited paper)", Sigmod Record, 34, 77-80 (2005)
  • S. Aksoy, K. Koperski, C. Tusk, G. Marchisio, J.C. Tilton, "Learning Bayesian Classifiers for Scene Classification with a Visual Grammar", IEEE Trans on Geoscience and Remote Sensing, 43, 581-589 (2005)
  • T. Dayar, "On Moments of Discrete Phase-Type Distributions", Lecture Notes in Computer Science, 3670, 51-63 (2005)
  • T. Dayar, N. Akar, "Computing Moments of First Passage Times to a Subset of States in Markov Chains", SIAM J on Matrix Analysis and Applications, 27, 396-412 (2005)
  • U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, E. Demir, "A Compound Graph Layout Algorithm for Biological Pathways", Lecture Notes in Computer Science, 3383, 442-447 (2005)
  • A. Kucukyilmaz, B. Ozguc, "An Animation System for Fracturing of Rigid Objects", Lecture Notes in Computer Science, 3733, 688-697 (2005)
  • A.K. Sinop, T. Abaci, U. Akkus, A. Gursoy, U. Gudukbay, "PHR: A Parallel Hierarchical Radiosity System with Dynamic Load Balancing", J of Supercomputing, 31, 249-263 (2005)
  • B. Tekinerdogan, S. Bilir, C. Abatlevi, "Integrating platform selection rules in the model driven architecture approach", Lecture Notes in Computer Science, 3599, 159-173 (2005)
  • E. Saykol, U. Gudukbay, O. Ulusoy, "A Database Model for Querying Visual Surveillance by Integrating Semantic and Low-Level Features", Lecture Notes in Computer Science, 3665, 163-176 (2005)
  • G. Yavas, D. Katsaros, O. Ulusoy, Y. Manolopoulos, "A data mining approach for location prediction in mobile environments", Data and Knowledge Engineering, 54, 121-146 (2005)  PDF
  • M.E. Donderler, E. Saykol, U. Arslan, O. Ulusoy, U. Gudukbay, "BilVideo: Design and Implementation of a Video Database Management System", Multimedia Tools and Applications, 27, 79-104 (2005)
  • N. Ikizler, P. Duygulu, "Person Search Made Easy", Lecture Notes in Computer Science, 3568, 578 (2005)
  • P. Buchholz, T. Dayar, "Block SOR Preconditioned Projection Methods for Kronecker Structured Markovian Representations", SIAM J on Scientific Computing, 26, 1289-1313 (2005)
  • P. Virga, P. Duygulu, "Systematic Evaluation of Machine Translation Methods for Image and Video Annotation", Lecture Notes in Computer Science, 3568, 174 (2005)
  • S. Ciraci, I. Korpeoglu, O. Ulusoy, "Characterizing Gnutella Network Properties for Peer-to-Peer Network Simulation", Lecture Notes in Computer Science, 3733, 274-283 (2005)
  • S.A. Ozalp, O. Ulusoy, "Effective Early Termination Techniques for Text Similarity Join Operator", Lecture Notes in Computer Science, 3733, 791-801 (2005)
 2004
  • F. Can, I.S. Altingovde, E. Demir, "Efficiency and effectiveness of query processing in cluster-based retrieval", Information Systems, 29, 697-717 (2004)
  • F. Can, R. Nuray, A.B. Sevdik, "Automatic performance evaluation of Web search engines", Information Processing & Management, 40, 495-514 (2004)
  • H.A. Guvenir, N. Emeksiz, N. Ikizler, N. Ormeci, "Diagnosis of gastric carcinoma by classification on feature projections", Artificial Intelligence in Medicine, 31, 231-240 (2004)
  • V. Akman, S.T. Erdogan, J. Lee, V. Lifschitz, H. Turner, "Representing the Zoo World and the Traffic World in the language of the Casual Calculator", Artificial Intelligence, 153, 105-140 (2004)
  • A. Pinar, C. Aykanat, "Fast Optimal Load Balancing Algorithms for ID Partioning", J of Parallel and Distributed Computing, 64, 974-996 (2004)
  • G. Unel, M.E. Donderler, O. Ulusoy, U. Gudukbay, "An Efficient Query Optimization Strategy for Spatio-Temporal Queries in Video Databases", J of Systems and Software, 73, 113-131 (2004)
  • P. Buchholz, T. Dayar, "Block SOR for Kronecker Structured Representations", Linear Algebra and Its Applications, 386, 83-109 (2004)
  • A.U. Tansel, "Temporality in databases", Lecture Notes in Computer Science, 3261, 1-3 (2004)
  • C. Aykanat, A. Pinar, U.V. Catalyurek, "Permuting Sparse Rectangular Matrices into Block-diagonal Form", SIAM J on Scientific Computing, 25, 1860-1879 (2004)
  • P. Duygulu, A. Hauptmann, "What's New, What's Not? Associating news videos with words", Lecture Notes in Computer Science, 3115, 132-140 (2004)
  • B. Genc, U. Dogrusoz, "A constrained, force-directed layout algorithm for biological pathways", Lecture Notes in Computer Science, 2912, 314-319 (2004)
  • B. Ucar, C. Aykanat, "Encapsulating Multiple Communication - Cost Metrics in Partitioning Sparse Rectangular Matrices for Parallel Matrix-Vector Multiplies", SIAM J on Scientific Computing, 25, 1837-1859 (2004)
  • B. Ucar, C. Aykanat, "A Message Ordering Problem in Parallel Programs", Lecture Notes in Computer Science, 3241, 131-138 (2004)
  • B.B. Cambazoglu, A. Turk, C. Aykanat, "Data-Parallel Web Crawling Models", Lecture Notes in Computer Science, 3280, 801-809 (2004)
  • E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, A. Ayaz, G. Gulesir, G. Nisanci, R. Cetin-Atalay, "An ontology for collaborative construction and analysis of cellular pathways", Bioinformatics, 20, 349-356 (2004)
  • E. Saykol, U. Gudukbay, O. Ulusoy, "Integrated Querying of Images by Color, Shape, and Texture Content of Salient Objects", Lecture Notes in Computer Science, 3261, 363-371 (2004)
  • E. Saykol, A.K. Sinop, U. Gudukbay, O. Ulusoy, E. Cetin, "Content-Based Retrieval of Historical Ottoman Documents Stored as Textual Images", IEEE Trans on Image Processing, 13, 314-325 (2004)  PDF
  • G. Ozsoylu, I.S. Altingovde, A. Al-Hamdani, S.A. Ozel, O. Ulusoy, Z.M. Ozsoyoglu, "Querying Web Metadata: Native Score Management and Text Support in Databases", ACM Trans on Database Systems, 29, 581-634 (2004)
  • H. Demirci, A.A. Selcuk, E. Ture, "A new meet in the middle attack on the IDEA block cipher", Lecture Notes in Computer Science, 3006, 117-129 (2004)
  • I. Uysal, H.A. Guvenir, "Instance-Based Regression by Partitioning Feature Projections", Applied Intelligence, 21, 57-79 (2004)
  • I.Sengor-Altingovde, O. Ulusoy, "Exploiting Interclass Rules for Focused Crawling", IEEE Intelligent Systems, 19, 66-73 (2004)  PDF
  • M.E. Donderler, O. Ulusoy, U. Gudukbay, "Rule-Based Spatio-Temporal Query Processing for Video Databases", Int J on Very Large Databases(VLDB Journal), 13, 86-102 (2004)
  • M.M. Ozdal, C. Aykanat, "Hypergraph Models and Algorithms for Data-Pattern Based Clustering", Data Mining and Knowledge Discovery, 9, 29-57 (2004)
  • O. Sabuncu, F.N. Alpaslan, V. Akman, "Using criticalities as a Heuristic for Answer Set Programming", Lecture Notes in Artificial Intelligence, 2923, 234-246 (2004)
  • P. Buchholz, T. Dayar, "Comparison of Multilevel Methods for Kronecker-based Markovian Representations", Computing, 73, 349-371 (2004)
  • S.A. Ozel, I. S. Altıngovde, O. Ulusoy, G. Ozsoyoglu, Z.M. Ozsoyoglu, "Metadata-Based Modelling of Information Resources on the Web", J of American Society for Information Science & Technology, 55, 97-110 (2004)
  • T. Aydin, H.A. Guvenir, "Learning Interestingness of Streaming Classification Rules", Lecture Notes in Computer Science, 3280, 62-71 (2004)
  • Y. Sahillioglu, B. Ozguc, "Hair Motion Simulation", Lecture Notes in Computer Science, 3280, 126-135 (2004)
 2003
  • H. Berk, C. Aykanat, U. Gudukbay, "Direct volume rendering of unstructured grids", Computers and Graphics, 27, 387-406 (2003)
  • O. Gusak, T. Dayar, J.M. Fourneau, "Iterative Disaggregation for a Class of Lumpable Discrete-Time Stochastic Automata Networks", Performance Evaluation, 53, 43-69 (2003)
  • O. Gusak, T. Dayar, J.M. Fourneau, "Lumpable Continous-Time Stochastic Automata Networks", European J of Operational Research, 148, 436-451 (2003)
  • T. Dayar, J.M. Fourneau, N. Pekergin, "Transforming Stochastic Matrices for Stochastic Comparison with the ST-Order", RAIRO Operations Research, 37, 85-97 (2003)
  • B. Ucar, C. Aykanat, "Minimizing Communication Cost in Fine-Grain Partitioning of Sparse Matrices", Lecture Notes in Computer Science, 2869, 926-933 (2003)
  • B.B. Cambazoglu, C. Aykanat, "Image-Space-Parallel Direct Volume Rendering on a Cluster of PCs", Lecture Notes in Computer Science, 2869, 457-464 (2003)
  • D. Katsaros, A. Nanopoulos, M. Karakaya, G. Yavas, O. Ulusoy, Y. Manolopoulos, "Clustering Mobile Trajectories for Resource Allocation in Mobile Environments", Lecture Notes in Computer Science, 2810, 319-329 (2003)
  • F. Nar, A.E. Cetin, "Generalization and localization based style imitation for grayscale images", Lecture Notes in Computer Science, 2869, 465-473 (2003)
  • H.O. Tan, I. Korpeoglu, "Power efficient data gathering and aggregation in wireless sensor networks", Sigmod Record, 32, 66-71 (2003)
  • K. Altintas, H.A. Guvenir, "Learning translation templates for closely related languages", Lecture Notes in Artificial Intelligence, 2773, 756-762 (2003)
  • M.E. Donderler, E. Saykol, O. Ulusoy, U. Gudukbay, "BilVideo: A video database management system", IEEE Multimedia, 10, 66-70 (2003)  PDF
  • N. Ikizler, H.A. Guvenir, "Maximizing benefit of classifications using feature intervals", Lecture Notes in Artificial Intelligence, 2773, 339-345 (2003)
 2002
  • U. Dogrusoz, "Two-dimensional packing algorithms for layout of disconnected graphs", Information Sciences, 143, 147-158 (2002)
  • U. Gudukbay, O. Arikan, B. Ozguc, "Visualizer: A Mesh Visualisation System Using View-Dependent Refinement", Computers and Graphics, 26, 491-503 (2002)
  • A.P. Saygin, I. Cicekli, "Pragmatics in human-computer conversations", J of Pragmatics, 34, 227-258 (2002)
  • B. Ari, H.A. Guvenir, "Clustered linear regression", Knowledge Based Systems, 15, 169-175 (2002)
  • Fetzer, V. Akman, "Contexts of social action: Guest editors' introduction", Language and Communication, 22, 391-402 (2002)
  • M.E. Donderler, O. Ulusoy, U. Gudukbay, "A Rule-based Video Database System Architecture", Information Sciences, 143, 13-45 (2002)
  • D. Davenport, "Anonymity on the Internet: Why the Price may be too High", Communications of ACM, 45, 33-35 (2002)
  • T. Dayar, F. Quessette, "Quasi-Birth-and Death Processes with Level-Geometric Distribution", SIAM J on Matrix Analysis and Applications, 24, 281-291 (2002)
  • U. Dogrusoz, B. Genc, "A Framework for Complexity Management in Graph Visualization", Lecture Notes in Computer Science, 2528, 368-369 (2002)
  • U. Dogrusoz, Q. Feng, B. Madden, M. Doorley, A. Frick, "Graph Visualization Toolkits", IEEE Computer Graphics and Applications, 22, 30-37 (2002)  PDF
  • U. Gudukbay, T. Yilmaz, "Stereoscopic View-Dependent Visualization of Terrain Height Fields", IEEE Trans on Visualization and Computer Graphics, 8, 330-345 (2002)  PDF
  • A. B. Sevdik, V. Akman, "Internet in the lives of Turkish women", First Monday, 7.
  • B. Edmonds, V. Akman, "Editorial: Context in Context", Foundations of Science, 7, 233-238 (2002)
  • D.Z. Hakkani-Tur, K. Oflazer, G. Tur, "Statistical morphological disambiguation for agglutinative languages", Computers and the Humanities, 36, 381-410 (2002)
  • E. Demir, O. Babur, U. Dogrusoz, A. Gursoy, G. Nisanci, R. Cetin-Atalay, M. Ozturk, "PATIKA: An Integrated Visual Environment for Collaborative Construction and Analysis of Cellular Pathways", Bioinformatics, 18, 996-1003 (2002)
  • K. Altintas, T. Aydin, V. Akman, "Censoring the Internet: The situation in Turkey", First Monday, 7.
  • K. Freivalds, U. Dogrusoz, P. Kikusts, "Disconnected graph layout and the polyomino packing approach", Lecture Notes in Computer Science, 2265, 378-391 (2002)
  • Y. Saygin, O. Ulusoy, "Exploiting Data Mining Techniques for Broadcasting Data in Mobile Computing Environments", IEEE Trans on Knowledge and Data Engineering, 14, 1387-1399 (2002)  PDF
 2001
  • A. Saygin, I. Cicekli, "Learning Translation Templates from Bilingual Translation Examples", J of Pragmatics, 34, 227-258 (2001)
  • B. Abali, C.B. Stunkel, J. Herring, M. Banikazemi, D.K. Panda, C. Aykanat, Y. Aydogan, "Adaptive routing on the new switch chip for IBM SP Systems", J of Parallel and Distributed Computing, 61, 1148-1179 (2001)
  • I. Cicekli, H.A. Guvenir, "Learning translation templates from bilingual translation examples", Applied Intelligence, 15, 57-76 (2001)
  • A.P. Saygin, I. Cicekli, V. Akman, "Turing test: 50 years later", Minds and Machines, 10, 463-518 (2001)
  • O. Gusak, T. Dayar, J.M. Fourneau, "Stochastic Automata Networks and Near Complete Decomposability", SIAM J on Matrix Analysis and Applications, 23, 581-599 (2001)
  • T. Aydin, H.A. Guvenir, "An Eager Regression Method Based on Best Feature Projections", Lecture Notes in Artificial Intelligence, 2070, 217-226 (2001)
  • Y. Saygin, O. Ulusoy, "Automated construction of fuzzy event sets and its application to active databases", IEEE Trans on Fuzzy Systems, 9, 450-460 (2001)  PDF
 2000
  • H.A. Guvenir, I. Uysal, "Regression on feature projections", Knowledge-Based Systems, 13, 207-214 (2000)
  • H.A. Guvenir, N. Emeksiz, "An expert system for the differential diagnosis of erythemato-squamous diseases", Expert Systems with Applications, 18, 43-49 (2000)
  • V. Akman, "Rethinking context as a social construct", J of Pragmatics, 32, 743-759 (2000)
  • V. Akman, "Relating to Ken Kesey's wise man", J of Pragmatics, 32, 485-489 (2000)
  • E. Shriberg, A. Stolcke, D. HakkaniTur, G. Tur, "Prosody-based automatic segmentation of speech into sentences and topics", Speech Communication, 32, 127-154 (2000)
  • H.G. Gok, O. Ulusoy, "Transmission of continuous query results in mobile computing systems", Information Sciences, 125, 37-63 (2000)
  • A. Gursoy, M. Atun, "Neighbourhood preserving load balancing: A Self-Organizing approach", Lecture Notes in Computer Science, 1900, 234-241 (2000)
  • D. Davenport, "Software piracy is not just economics anymore", Comm of the ACM, 43, 11 (2000)
  • D. Davenport, "Computationalism: the very idea", Conceptus, 14, 121-137 (2000)
  • D. Davenport, "Experience using a project-based approach in an introductory programming course", IEEE Trans on Education, 43, 443-454 (2000)  PDF
  • K. Efe, A.L. Broadwater, A. Fernandez, "Embedding complete binary trees in product graphs", Telecommunication Systems, 13, 99-109 (2000)
  • T. Dayar, W.J. Stewart, "Comparison of partitioning techniques for two-level iterative solvers on large, sparse Markov chains", SIAM J on Scientific Computing, 21, 1691-1705 (2000)
  • U. Gudukbay, F. Erol, N. Erdogan, "Beyond tradition and modernity: digital shadow theater", Leonardo, 33, 264-265 (2000)
  • V. Akman, "Introduction to the special issue on philosophical foundations of artificial intelligence", J of Experimental & Theoretical AI, 12, 247-250 (2000)
  • V. Akman, P. Blackburn, "Editorial: Alan Turing and artificial intelligence", J of Logic, Language & Information, 9, 391-395 (2000)
  • H. Kutluca, T.M. Kurc, C. Aykanat, "Image-space decomposition algorithms for sort-first parallel volume rendering of unstructured grids", J of Supercomputing, 15, 51-93 (2000)
 1999
  • U. Cetintemel, J. Zimmermann, O. Ulusoy, A. Buchmann, "OBJECTIVE: A benchmark for object-oriented active database systems", J of Systems and Software, 45, 31-43 (1999)
  • Y. Saygin, O. Ulusoy, A. Yazici, "Dealing with fuzziness in active mobile database systems", Information Sciences, 120, 23-44 (1999)
  • S. Kocberber, F. Can, J.M. Patton, "Optimization of signature file parameters for databases with varying record lengths", Computer Journal, 42, 11-23 (1999)
  • E. Kayan, O. Ulusoy, "An evaluation of real-time transaction management issues in mobile database systems", Computer Journal, 42, 501-510 (1999)
  • I. Uysal, H.A. Guvenir, "An overview of regression techniques for knowledge discovery", Knowledge Engineering Review, 14, 319-340 (1999)
  • U.V. Catalyurek, C. Aykanat, "Hypergraph-partitioning based decomposition for parallel sparse-matrix vector multiplication", IEEE Trans on Parallel and Distributed Systems, 10, 673-693 (1999)  PDF
 1998
  • C. Aykanat, T. Bultan, I. Haritaoglu, "A fast neural-network algorithm for VLSI cell placement", Neural Networks, 11, 1671-1684 (1998)
  • H.A. Guvenir, E. Erel, "Multicriteria inventory classification using a genetic algorithm", European J Operational Research, 105, 29-37 (1998)
  • H.A. Guvenir, I. Cicekli, "Learning translation templates from examples", Information Systems, 23, 353-363 (1998)
  • H.A. Guvenir, G. Demiroz, N. Ilter, "Learning differential diagnosis of erythemato-squamous diseases using voting feature intervals", Artificial Intelligence in Medicine, 13, 147-165 (1998)
  • O. Ulusoy, "Analysis of concurrency control protocol for real-time database systems", Information Sciences, 111, 1-4 (1998)
  • O. Ulusoy, "Transaction processing in distributed active real-time database systems", Journal of Systems and Software, 42, 247-262 (1998)
  • O. Ulusoy, A. Buchmann, "A real-time concurrency control protocol for main-memory database systems", Information Systems, 23, 109-125 (1998)
  • B. Le Charlier, P. Flener, "Specifications are necessarily informal, or: Some more myths of formal methods", J of Systems and Software, 40, 275-296 (1998)
  • E. Uysal, T. Dayar, "Iterative methods based on splittings for stochastic automata networks", European J Operational Research, 110, 166-186 (1998)
  • T.M. Kurc, C. Aykanat, B. Ozguc, "Object-space parallel polygon rendering on hypercubes", Computers and Graphics, 22, 487-503 (1998)
  • Y. Saygin, O. Ulusoy, S. Chakravarthy, "Concurrent rule execution in active database systems", Information Systems, 23, 39-64 (1998)
  • H.A. Guvenir, H.G. Koc, "Concept representation with overlapping feature intervals", Cybernetics and Systems: An International Journal, 29, 263-282 (1998)
  • I. Cicekli, "Abstract MetaProlog Engine", J of Logic Programming, 34, 169-200 (1998)
  • T. Dayar, "State space orderings for Gauss-Siedel in Markov chains revisited", SIAM J on Scientific Computing, 19, 148-154 (1998)
  • U. Dogrusoz, K.G. Kakoulis, B. Madden, I.G. Tollis, "Edge labeling in the graph layout toolkit", Lecture Notes in Computer Science, 1547, 356-363 (1998)
  • V. Akman, "Guest Editor's introduction", Minds and Machines, 8, 475-477 (1998)
  • A. Dogac, O. Ulusoy, "Preface to special issue on recent advances in database research", J of Database Management, 9, 3 (1998)
  • D.Z. Hakkani, K. Oflazer, "Tactical generation in a free constituent order language", J of Natural Language Engineering, 4.
  • J. Tayeb, O. Ulusoy, O. Wolfson, "A quadtree based dynamic attribute indexing method", Computer Journal, 41, 185-200 (1998)
  • M. Bayraktar, B. Say, V. Akman, "An analysis of English punctuation: the special case of comma", Int J of Corpus Linguistics, 3, 33-57 (1998)
  • U. Akdemir, B. Ozguc, U. Gudukbay, A. Selcuk, "Right triangular subdivision for texture mapping ray traced objects", Visual Computer, 14, 445-454 (1998)
 1997
  • A.S. Kocberber, F. Can, "Vertical framing of superposed signature files using partial evaluation of queries", Information Processing & Management, 33, 353-376 (1997)
  • O. Ulusoy, "An Evaluation of Network Access Protocols for Distributed Real-time Database Systems", J of Systems and Software, 37, 49-60 (1997)
  • U. Gudukbay, "A movable jaw model for the human face", Computers and Graphics, 21, 549-554 (1997)
  • U. Gudukbay, B. Ozguc, Y. Tokad, "A spring force formulation for elastically deformable models", Computers and Graphics, 21, 335-346 (1997)
  • T. Devirmis, O. Ulusoy, "Design and evaluation of a new transaction execution model for multidatabase systems", Information Sciences, 102, 203-238 (1997)
  • A.U. Tansel, E.K. Tin, "The expressive power of temporal relational query languages", IEEE Trans on Knowledge and Data Engineering, 9, 120-134 (1997)
  • E. Tin, V. Akman, "Situated nonmonotonic temporal reasoning with BABY-SIT", AI Communications, 10, 93-109 (1997)
  • I. Cicekli, "An intelligent backtracking schema in a logic programming environment", Sigplan Notices, 32, 42-50 (1997)
  • K. Oflazer, "Error tolerant retrieval of trees", IEEE Trans on PAMI, 19, 1376-1380 (1997)  PDF
  • T. Dayar, W.J. Stewart, "Quasi-lumpability, lower bounding coupling matrices and nearly completely decomposable Markov chains", SIAM J on Matrix Analysis and Applications, 18, 482-498 (1997)
  • V. Akman, M. Surav, "The use of situation theory in context modelling", Computational Intelligence, 13, 427-438 (1997)
  • A. Dasdan, C. Aykanat, "Two novel multiway circuit partitioning algorithms using relaxed locking", IEEE Trans on Computer Aided Design, 16, 169-178 (1997)  PDF
  • B. Say, V. Akman, "Current approaches to punctuation in Computational Linguistics", Computers and the Humanities, 30, 457-469 (1997)
  • T.M. Kurc, C. Aykanat, B. Ozguc, "A parallel scaled conjugate-gradient algorithm for the solution phase of gathering radiosity on hypercubes", Visual Computer, 13, 1-19 (1997)
 1996
  • C. Aykanat, T. Capin, B. Ozguc, "A Parallel Progressive Radiosity Algorithm Based on Patch Data Circulation", Computers and Graphics, 20, 307-324 (1996)
  • S. Kocberber, F. Can, "Partial evaluation of queries for bit-sliced signature files", Information Processing Letters, 60, 305-311 (1996)
  • P. O'Neal, O. Ulusoy, "Guest editorial: real-time database systems", Information Systems, 21, 1-2 (1996)
  • H.A. Guvenir, I. Sirin, "Classification by Feature Partitioning", Machine Learning, 23, 47-67 (1996)
  • K. Oflazer, "Error-tolerant Finite State Recognition with Applications to Morphological Analysis and spelling correction", Computational Linguistics, 22, 73-89 (1996)
  • T. Dayar, W.J. Stewart, "On the effects of using the Grassmann-Taksar-Heyman Method in Iterative Aggregation-disaggregation", SIAM J on Scientific Computing, 17, 287-303 (1996)
  • V. Akman, M. Ersan, "Commonsense Aspects of Buying and Selling", Cybernetics and Systems: An International Journal, 27, 327-352 (1996)
  • V. Akman, M. Pakkan, "Nonstandard Set Theories and Information Management", J of Intelligent Information Systems, 6, 5--31 (1996)
  • V. Akman, M. Surav, "Steps toward formalizing context", Artificial Intelligence Magazine, 17, 55-72 (1996)
  • T.M. Kurc, C. Aykanat, B. Ozguc, "Active Pixel Merging on Hypercube Multicomputers", Lecture Notes in Computer Science, 1067, 319-326 (1996)
  • Y. Turkan, O. Ulusoy, "An efficient memory management algorithm for client-server database management systems", Computer Journal, 39, 374-385 (1996)
 1995
  • O. Ulusoy, "A study of two transaction-processing architectures for distributed real-time database systems", J of Systems and Software, 31, 97-108 (1995)
  • O. Ulusoy, "Research issues in real-time database systems", Information Sciences, 87, 123-151 (1995)
  • O. Ulusoy, "A network access protocol for hard real-time communication systems", Computer Communications, 18, 943-948 (1995)
  • P. Tripathy, B. Sarikaya, "Analysis and representation of test cases generated from Lotos", Computer communications, 18, 493-506 (1995)
  • T. Bultan, C. Aykanat, "Circuit partitioning using mean field annealing", Neurocomputing, 8, 171-194 (1995)
  • C. Aykanat, A. Dervis, "Efficient fast hartley transform algorithms for hypercube-connected multicomputers", IEEE Trans on Parallel and Distributed Systems, 6, 561-577 (1995)  PDF
  • C. Aykanat, O. Ozgu, N. Guven, "Algorithms for Efficient Vectorization of Repeated Sparse Power System network Computations", IEEE Trans on Power Systems, 10, 448-456 (1995)  PDF
  • E. Tin, V. Akman, M. Ersan, "Towards situation oriented programming languages", Sigplan Notices, 30, 27-36 (1995)
  • H.A. Guvenir, "An Object-oriented Tutoring System for Teaching Sets", SIGCSE Bulletin (ACM Press), 27, 39-46 (1995)
  • O. Ulusoy, "Incorporating Real-time Scheduling Methods into Database Management Systems", J of Information Science, 21, 324-328 (1995)
  • O. Ulusoy, G.G. Bedford, "A performance evaluation model for distributed real-time database systems", Int J of Modelling and Simulation, 15, 50-59 (1995)
  • B. Erkan, B. Ozguc, "Object oriented motion abstraction", J of Visualization and Computer Animation, 6, 49-65 (1995)
  • M. Ersan, V. Akman, "Situated Modeling of Epistemic Puzzles", Bulletin (Journal) of IGPL, 3, 51-76 (1995)
  • M. Pakkan, V. Akman, "Hypersolver: a graphical tool for commonsense set theory", Information Sciences Intelligent Systems, 85, 43-61 (1995)
  • Z. Gungordu, K. Oflazer, "Parsing Turkish with the Lexical-Functional Grammar Formalism", J of Machine Translation, 10, 293-319 (1995)
 1994
  • V. Akman, "When silence may mean derision", J of Pragmatics, 22, 211-212 (1994)
  • F. Ulupinar, R. Nevatia, "Recovery of 3-D objects with multiple curved surfaces from 2-D contours", Artificial Intelligence, 67, 1-28 (1994)
  • M. Marhl, V. Akman, "On the correct determination of rotational angles for twisted profile sweep objects", Computers and Graphics, 18, 691-694 (1994)
  • C. Aykanat, A. Dervis, "Efficient overlapped FFT algorithms for hypercube-connected multicomputers", Parallel Algorithms and Applications, 4, 91-110 (1994)
  • C. Aykanat, V. Isler, B. Ozguc, "Efficient parallel spatial subdivision algorithm for object based parallel ray tracing", Computer aided design, 26, 883-890 (1994)
  • E. Tin, V. Akman, "Computational Situation Theory", Sigart Bulletin, 5, 4-17 (1994)
  • K. Oflazer, "Two level description of Turkish Morphology", Literary and Linguistic Computing, 9, 137-148 (1994)
  • O. Ulusoy, "Processing Real time transactions in a replicated database system", Int J of Distributed and Parallel Databases, 2, 405-436 (1994)
  • U. Gudukbay, B. Ozguc, "Animation of deformable models", Computer aided design, 26, 868-875 (1994)
  • V. Akman, "Ripping the Text apart at different seams", Stanford Humanities Review, 4, 31-34 (1994)
  • M. Aktihanoglu, B. Ozguc, C. Aykanat, "MARS: A tool based modelling, animation and parallel rendering system", Visual Computer, 11, 1-14 (1994)
  • M. Pakkan, V. Akman, "Issues in common sense set theory", Artificial Intelligence Review, 8, 279-308 (1994)
 1993
  • O. Ulusoy, G.G. Belford, "Real time transaction scheduling in database systems", Information Systems, 18, 559-580 (1993)
  • U. Gudukbay, B. Ozguc, Y. Tokad, "An animation system for rigid and deformable models", Computers and Graphics, 17, 71-77 (1993)
  • C. Yuceer, K. Oflaze, "A rotation, scaling and translation invariant pattern-classification system", Pattern Recognition, 26, 687-710 (1993)
  • M. Bilgic, B. Sarikaya, "Performance comparison of ASN.1 encoder decoders using FTAM", Computer communications, 16, 229-240 (1993)
  • B. Abali, F. Ozguner, A. Bataineh, "Balanced parallel sort on hypercube multiprocessors", IEEE Trans on Parallel and Distributed Systems, 4, 572-581 (1993)  PDF
  • K. Oflazer, "Solving Tangram puzzles: A connectionist approach", Int J of Intelligent Systems, 8, 603-616 (1993)
  • O. Ulusoy, "An approximate analysis of a real-time database concurrency control protocol via Markov modeling", ACM Sigmetrics:Performance Evaluation Review, 20, 36-48 (1993)
  • O. Ulusoy, "Lock-based concurrency control in distributed real-time database systems", J of Database Management, 4, 3-16 (1993)
  • V. Akman, "Advanced CAD environments: A knowledge-based foundation", Microcomputers in Civil Engineering, 8, 129-139 (1993)
  • A. Solak, K. Oflazer, "Design and Implementation of a spelling checker for Turkish", Literary and Linguistic Computing, 8, 113-130 (1993)
  • F. Polat, H.A. Guvenir, "UVT: A Unification based tool for knowledge based verification", IEEE Expert, 8, 69-75 (1993)  PDF
  • F. Polat, S. Shekhar, H.A. Guvenir, "A negotiation platform for cooperating multi agent systems", Concurrent Engineering, 1, 179-187 (1993)
  • F. Polat, S. Shekhar, H.A. Guvenir, "Distributed conflict resolution among cooperating expert systems", Expert Systems, 10, 227-236 (1993)
  • R. Alhajj, E. Arkun, "An object algebra for object oriented database systems", Database, 24, 13-23 (1993)
  • R. Elhajj, E. Arkun, "Object oriented query language facilitating construction of new objects", ACM Sigmetrics:Performance Evaluation Review, 35, 519-529 (1993)
 1992
  • C. Aykanat, F. Ozguner, "A Fault-Tolerant Hexagonal Systolic Array", Information Processing Letters, 42, 187-196 (1992)
  • V. Akman, A. Arslan, "Sweeping with all graphical ingredients in a topological picturebook", Computers and Graphics, 16, 273-281 (1992)
  • T. Bultan, C. Aykanat, "A new Mapping Heuristic Based on Mean Field Annealing", J of Parallel and Distributed Computing, 16, 292-305 (1992)
  • K. Oflazer, "Highly Parallel Execution of Production Systems - A Model, Algorithms and Architecture", New Generation Computing, 10, 287-313 (1992)
  • O. Ulusoy, "Current research on real-time databases", ACM Sigmod Record, 21, 16-21 (1992)