Bilkent Journal Publications

Department of Computer Engineering
Select a period:
 In Press
  • E. Ayday, Q. Tang, A. Yilmaz, "Cryptographic Solutions for Credibility and Liability Issues of Genomic Data", IEEE Trans on Dependable and Secure Computing..  PDF
  • E. Kayaaslan, C. Aykanat, B. Ucar, "1.5D Parallel Sparse Matrix-Vector Multiply", SIAM J on Scientific Computing..  PDF
  • K. Akbudak, O. Selvitopu, C. Aykanat, "Partitioning Models for Scaling Parallel Sparse Matrix-Matrix Multiplication", ACM Trans on Parallel Computing..  PDF
  • S. Acer, E. Kayaaslan, C. Aykanat, "A Hypergraph Partitioning Model for Profile Minimization", SIAM J on Scientific Computing..  PDF
  • H. Bonab, F. Can, "Less Is More: A Comprehensive Framework for the Number of Components of Ensemble Classifiers", IEEE Trans on Neural Networks and Learning Systems..  PDF
  • C.T. Sari, C. Gunduz-Demir, "Unsupervised Feature Extraction via Deep Learning for Histopathological Classification of Colon Tissue Images", IEEE Trans on Medical Imaging..  PDF
  • H. Dibeklioglu, T. Gevers, "Automatic Estimation of Taste Liking through Facial Expression Dynamics", IEEE Trans on Affective Computing..  PDF
  • Y. Dogan, S. Demirci, U. Gudukbay, H. Dibeklioglu, "Augmentation of virtual agents in real crowd videos", Signal Image and Video Processing..  PDF
  • F. Basik, B. Gedik, H. Ferhatosmanoglu, K-L. Wu, "Fair Task Allocation in Crowdsourced Delivery", IEEE Trans on Services Computing..
  • 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
  • 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
  • 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
  • O. Uyanik, I. Korpeoglu, "Multi-channel TDMA Scheduling in Wireless Sensor Networks", Ad Hoc & Sensor Wireless Networks..  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
  • C. Usfekes, E. Tuzun, M. Yilmaz, Y. Macit, P. Clarke, "Auction-Based Serious Game for Bug Tracking", IET Software..  PDF
  • V. Garousi, G. Giray, E. Tuzun, C. Catal, M. Felderer, "Closing the gap between software engineering education and industrial needs", IEEE Software..  PDF
 2019
  • S.R. Arashloo, "Sparse binarised statistical dynamic features for spatio-temporal texture analysis", Signal, Image and Video Processing, 13, 575-582 (2019)  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, 16, 329-343 (2019)  PDF
  • O. Selvitopu, G.V. Demirci, A. Turk, C. Aykanat, "Locality-aware and load-balanced static task scheduling for MapReduce", Future Generation Computer Systems, 90, 49-61 (2019)
  • F. Karatas, I. Korpeoglu, "Fog-Based Data Distribution Service (F-DAD) for Internet of Things (IoT) applications", Future Generation Computer Systems, 93, 156-169 (2019)
  • E. Tuzun, B. Tekinerdogan, Y. Macit, K. Ince, "Adopting Integrated Application Lifecycle Management within a Large-Scale Software Company: An Action Research Approach", J of Systems and Software, 149, 63-82 (2019)
  • V. Garousi, G. Giray, E. Tuzun, C. Catal, M. Felderer, "Aligning software engineering education with industrial needs: A meta-analysis", J of Systems and Software, 156, 65-83 (2019)
  • T. Yilmaz, R. Ozcan, I.S. Altingovde, O. Ulusoy, "Improving Educational Web Search for Question-like Queries through Subject Classification", Information Processing & Management, 56, 228-246 (2019)
 2018
  • B. Gecer, S. Aksoy, E. Mercan, L.G. Shapiro, D.L. Weaver, J.G. Elmore, "Detection and classification of cancer in whole slide breast histopathology images using deep convolutional networks", Pattern Recognition, 84, 345-356 (2018)
  • 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, 37, 316-325 (2018)  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, 37, 316-325 (2018)  PDF
  • C. Firtina, Z-B. Joseph, C. Alkan, E. Cicek, "Hercules: a profile HMM-based hybrid error correction algorithm for long reads", Nucleic Acids Research, 46, 125-1--10 (2018)  PDF
  • D.S. Cali, J.S. Kim, S. Ghose, C. Alkan, O. Mutlu, "Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions", Briefings in Bioinformatics..  PDF
  • E. Dal, C. Alkan, "Evaluation of genome scaffolding tools using pooled clone sequencing", Turkish J of Biology, 42, 471-476 (2018)  PDF
  • H.I. Ozcan, A.M. Ileri, E. Ayday, C. Alkan, "Realizing the potential of blockchain technologies in genomics", Genome Research, 28, 1255-1263 (2018)  PDF
  • I. Numanagic, A.S. Gokkaya, L. Zhang, B. Berger, C. Alkan, F. Hach, "Fast characterization of segmental duplications in genome assemblies", Bioinformatics, 34, 706-714 (2018)  PDF
  • O. Saatci, S. Borgoni, O. Akbulut, S. Durmus, U. Raza, E. Eyupoglu, C. Alkan, A. Akyol, O. Kutuk, S. Wiemann, O. Sahin, "Targeting PLK1 overcomes T-DM1 resistance via CDK1-dependent phosphorylation and inactivation of Bcl-2/xL in HER2-positive breast cancer", Oncogene, 37, 2251-2269 (2018)  PDF
  • The Computational Pan - Genomics Consortium, … C. Alkan, "Computational pan-genomics: status, promises and challenges", Briefings in Bioinformatics, 19, 118-135 (2018)  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, 15, 1333-1343 (2018)  PDF
  • S.Acer, O. Selvitopi, C. Aykanat, "Optimizing nonzero-based sparse matrix partitioning models via reducing latency", J of Parallel and Distributed Computing, 122, 145-158 (2018)
  • F.S. Torun, M. Munganoglu, C. Aykanat, "A Novel Partitioning Method for Accelerating the Block-Cimminio Algorithm", SIAM J on Scientific Computing, 40, 827-850 (2018)  PDF
  • G.V. Demirci, H. Ferhatosmanoglu, C. Aykanat, "Cascade-aware partitioning of Large Databases", VLDB Journal., 1-22 (2018)  PDF
  • N.F.T. Abubaker, K. Akbudak, C. Aykanat, "Spatiotemporal Graph and Hypergraph Partitioning Models for Sparse Matrix-Vector Multiplication on Many-Core Architectures", IEEE Trans on Parallel and Distributed Systems..  PDF
  • S. Acer, T. Torun, C. Aykanat, "Improving Medium-Grain Partitioning for Scalable Sparse Tensor Decomposition", IEEE Trans on Parallel and Distributed Systems, 29, 2814-2825 (2018)  PDF
  • H.R. Bonab, F. Can, "GOOWE: Geometrically optimum and online-weighted ensemble classifier for evolving data streams", ACM Trans on Knowledge Discovery, 12, 25-1--33 (2018)  PDF
  • 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, 314, 94-100 (2018)
  • 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, 59, 607-616 (2018)  PDF
  • N.v. Thenen, E. Ayday, A.E. Cicek, "Re-identification of individuals in genomic data-sharing beacons via allele inference", Bioinformatics..  PDF
  • Y.Liu, Y. Liang, A.E. Cicek, Z. Li, J. Li, …., Z.S. Sun, X. He, "A Statistical Framework for Mapping Risk Genes from De Novo Mutations in Whole-Genome-Sequencing Studies", American J of Human Genetics, 102, 1031-1047 (2018)  PDF
  • T. Dayar, M.C. Orhan, "On Compact Vector Formats in the Solution of the Chemical Master Equation with Backward Differentiation", Numerical Linear Algebra with Applications, 25, 2158-1--21 (2018)  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, 43, 592-600 (2018)  PDF
  • C. F. Koyuncu, R. Cetin-Atalay, C. Gunduz-Demir, "Object-Oriented Segmentation of Cell Nuclei in Fluorescence Microscopy Images", Cytometry: Part A, 93, 1019-1028 (2018)  PDF
  • I. Onal Ertugrul, L.A. Jeni, H. Dibeklioglu, "Modeling and synthesis of kinship patterns of facial expressions", Image and Vision Computing, 79, 133-143 (2018)
  • U. Dogrusoz, A. Karacelik, I. Safarli, H. Balci, L. Dervishi, M.C. Siper, "Efficient methods and readily customizable libraries for managing complexity of large networks", Plos One, 13, 0197238-1--18 (2018)  PDF
  • A. Mazein, M. Ostaszewski, I. Kuperstein, S. Watterson, N. Le Novère, D. Lefaudeux, B. De Meulder, …, U. Dogrusoz, E. Barillot, A. Zinovyev, R. Schneider, R. Balling, C. Auffray, "Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms", NPJ Systems Biology and Applications..  PDF
  • F. Sanchez-Vega, M. Mina, J. Armenia, …, U. Dogrusoz, W. Zhou, …., N. Schultz, "Oncogenic Signaling Pathways in The Cancer Genome Atlas", Cell, 173, 321-337 (2018)
  • M. Ostaszewski, S. Gebel, I. Kuperstein, A. Mazein, A. Zinovyev, U. Dogrusoz, J. Hasenauer, R.M.T. Fleming, N. Le Novère, P. Gawron, T. Ligon, A. Niarakis, D. Nickerson, D. Weindl, R. Balling, E. Barillot, C. Auffray, R. Schneider, "Community-driven roadmap for integrated disease maps", Briefings in Bioinformatics..  PDF
  • S. Sahin, B. Gedik, "C-Stream: A Co-routine-Based Elastic Stream Processing Engine", ACM Trans on Parallel Computing, 4, 1-15 (2018)  PDF
  • A.E. Basak, U. Gudukbay, F. Durupinar, "Using Real Life Incidents for Creating Realistic Virtual Crowds with Data-driven Emotion Contagion", Computers and Graphics, 72, 70-81 (2018)
  • U. Agil, U. Gudukbay, "A Group-based Approach for Gaze Behavior of Virtual Crowds Incorporating Personalities", Computer Animation and Virtual Worlds, 29, 1806-1--26 (2018)  PDF
  • M.M. Ozdal, "Emerging Accelerator Platforms for Data Centers", IEEE Design and Test, 35, 47-54 (2018)  PDF
  • M.M. Ozdal, G.J. Nam, D. Marr, "Guest Editors' Introduction: Hardware Accelerators for Data Centers [editorial]", IEEE Design and Test, 35, 5-6 (2018)  PDF
  • C. Chu, M.M. Ozdal, "Introduction to the Special Section on Advances in Physical Design Automation[editorial]", ACM Trans on Design Automation of Electronic Systems, 23.  PDF
  • I. Alouani, H. Ahangari, O. Ozturk, S. Niar, "A Novel Heterogeneous Approximate Multiplier for Low Power and High Performance", IEEE Embedded Systems Letters, 10, 45-48 (2018)  PDF
  • M. Soltaniyeh, I. Kadayif, O. Ozturk, "Classifying Data Blocks at Subpage Granularity With an On-Chip Page Table to Improve Coherence in Tiled CMPs", IEEE Trans on Computer Aided Des. Integr. Circ. Systems, 37, 806-819 (2018)  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, 69, 256-270 (2018)  PDF
 2017
  • V. Akman, "Burn All Your Textbooks", Australasian Journal of Logic, 14, 378-382 (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
  • A. Soylev, C. Kockan, F. Hormozdiari, C. Alkan, "Toolkit for automated and rapid discovery of structural variants", Methods, 129, 3-7 (2017)
  • 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
  • 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
  • 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)
  • E. Ayday, M. Humbert, "Inference Attacks Against Kin Genomic Privacy", IEEE Security and Privacy Magazine, 15, 1-9 (2017)  PDF
  • G. Kale, E. Ayday, O. Tastan, "A Utility Maximizing and Privacy Preserving Approach for Protecting Kinship in Genomic Databases", Bioinformatics..  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
  • 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)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • P. Buchholz, T. Dayar, J. Kriege, M.C. Orhan, "On Compact Solution Vectors in Kronecker-based Markovian Analysis", Performance Evaluation, 115, 132-149 (2017)
  • 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
  • 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
  • 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
  • A. Yasar, B. Gedik, H. Ferhatosmanoglu, "Distributed block formation and layout for disk-based management of large-scale graphs", Distributed and Parallel Databases..  PDF
  • F. Basil, B. Gedik, C. Ozgenc, H. Ferhatosmanoglu, "Spatio-Temporal Linkage over Location-Enhanced Services", IEEE Trans on Mobile Computing..  PDF
  • M. Hirzel, S. Schneider, B. Gedik, "SPL: An Extensible Language for Distributed Stream Processing", ACM Trans on Programming Languages and Systems, 39.  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
  • 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)
  • F. Calisir, M. Bastan, O. Ulusoy, U. Gudukbay, "Mobile multi-view object image search", Multimedia Tools and Applications, 76, 12433-12456 (2017)  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
  • 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
  • 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
  • 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)
  • 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
  • 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
  • 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
  • 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
  • A. Asad, O. Ozturk, M. Fathy, M.R. Jahed-Motlagh, "Optimization-based power and thermal management for dark silicon aware 3D chip multiprocessors using heterogeneous cache hierarchy", Microprocessors and Microsystems, 51, 76-98 (2017)  PDF
  • B. Otlu, C. Firtina, S. Keles, O. Tastan, "GLANET: genomic loci annotation and enrichment tool", Bioinformatics, 18, 2818-2828 (2017)
 2016
  • V. Akman, M.B. Senol, "The Truth about "It is True that..."", Pragmatics and Cognition, 23, 284-299 (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
  • 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
  • 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
  • C. Firtina, C. Alkan, "On genomic repeats and reproducibility", Bioinformatics, 32, 2243-2247 (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
  • 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
  • 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
  • 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
  • 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)
  • 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
  • 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
  • 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
  • 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
  • B. Genc, U. Dogrusoz, "An Algorithm for Automated Layout of Process Description Maps Drawn in SBGN", Bioinformatics, 32, 77-84 (2016)  PDF
  • 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)
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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)
  • 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
  • M. Tekkalmaz, I. Korpeoglu, "Distributed Power-Source-Aware Routing in Wireless Sensor Networks", Wireless Networks, 22, 1381-1399 (2016)  PDF
  • B. Kahveci, I.S. Altingovde, O. Ulusoy, "Integrating social features into mobile local search", J of Systems and Software, 122, 155-164 (2016)
  • 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
 2015
  • C. Kucuk, B. Jiang, X. Hu, W. Zhang, J. Chan, W. Xiao, N. Lack, C. Alkan, J. Williams, K. Avery, P. Kavak, A. Scuto, …., T. McKeithan, "Activating mutations of STAT5B and STAT3 in lymphomas derived from yS-T or NK cells", Nature Communications, 14, 6025:1-12 (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. Kavak, B. Yuksek, S. Aksu, M.O. Kulukci, T. Gungor, F. Hach, S.C. Sahinalp, Turkish Human Genome Project, C. Alkan, M.S. Sagiroglu, "Robustness of massively parallel sequencing platforms", Plos One, 10, 0138259 (2015)  PDF
  • 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)
  • 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
  • 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
  • The 1000 Genomes Project Consortium, "A global reference for human genetic variation", Nature, 526, 98-74 (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
  • 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
  • C. Toraman, F. Can, "A front-page news-selection algorithm based on topic modeling", J of Information Science, 41, 676-685 (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
  • 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)
  • T. Dayar, M.C. Orhan, "On Vector-Kronecker Product Multiplication with Rectangular Factors", SIAM J on Scientific Computing, 37, 526-543 (2015)  PDF
  • 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
  • M. Sari, I. Bahceci, U. Dogrusoz, S.O. Sumer, B.A. Aksoy, O. Babur, E. Demir, "SBGNViz: a tool for visualization and complexity management of SBGN process description maps", Plos One, 10, 0128985 (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
  • I. Gur, M. Guvercin, H. Ferhatosmanoglu, "Scaling Forecasting Algorithms using Clustered Modeling", VLDB Journal, 24, 51-65 (2015)  PDF
  • M.A. Abbasoglu, B. Gedik, H. Ferhatosmanoglu, "Aggregate Profile Clustering for Streaming Analytics", Computer Journal, 58, 2092-2108 (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
  • 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
  • S. Schneider, M. Hirzel, B. Gedik, K-L. Wu, "Safe Data Parallelism for General Streaming", IEEE Trans on Computers, 64, 504-518 (2015)  PDF
  • 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)
  • 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
  • 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
  • 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)
  • C. Mergenci, I. Korpeoglu, "Routing in Delay-tolerant Networks with Periodic Connections", Eurasip Journal on Wireless Communication and Networking, 2015, 202 (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
  • 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
  • O. Ozturk, I. Akturk, I. Kadayif, S. Tosun, "Energy Reduction in 3D NoCs Through Communication Optimization", Computing, 97, 593-609 (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)
  • 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
  • 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
  • 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)
  • 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
 2014
  • 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. 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • V. Yazici, C. Aykanat, "Constrained Min-Cut Replication for K-Way Hypergraph Partitioning", Informs Journal of Computing, 36, 303-320 (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
  • 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
  • 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
  • P. Duygulu, D. Arifoglu, M. Kalpakli, "Cross-document word matching for segmentation and retrieval of Ottoman divans", Pattern Analysis and Applications..  PDF
  • E. Eser, T. Can, H. Ferhatosmanoglu, "Div-BLAST: Diversification of Sequence Search Results", Plos One, 9.  PDF
  • 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
  • M. Hirzel, R. Soute, S. Schneider, B. Gedik, R. Grimm, "A Catalog of Streaming Optimizations", ACM Computing Surveys, 46.  PDF
  • 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)
  • 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
  • E. Okuyan, U. Gudukbay, "Direct volume rendering of unstructured tetrahedral meshes using CUDA and OpenMP", J of Supercomputing, 67, 324-344 (2014)  PDF
  • M. Koc, I. Korpeoglu, "Controlled Sink mobility Algorithms for Wireless Sensor Networks", Int J of Distributed Sensor Networks., 167508 (2014)  PDF
  • 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)
  • 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
  • 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
  • A. Demiriz, N. Bagherzadeh, O. Ozturk, "Voltage Island Based Heterogeneous NoC Design Through Constraint Programming", Computers and Electrical Engineering, 40, 307-316 (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)
  • 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
  • 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
 2013
  • H. Xin, D. Lee, F. Hormozdiari, S. Yedkar, O. Mutlu, C. Alkan, "Accelerating read mapping with FastHASH", BMC Genomics, 14, 1-13 (2013)
  • 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)
  • 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
  • J. Prado-Martinez, ...., C. Alkan, ....E.E. Eichler, T. Marques-Bonet, "Great ape Genetic Diversity and Population History", Nature, 499, 471-475 (2013)  PDF
  • 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)
  • A. Turk, K.Y. Oktay, C. Aykanat, "Query-Log Aware Replicated Declustering", IEEE Trans on Parallel and Distributed Systems, 24, 987-995 (2013)  PDF
  • 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
  • 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
  • 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)
  • C. Telkenaroglu, T. Capin, "Dual-Finger 3D Interaction Techniques for Mobile Devices", J of Personal and Ubiquitous Computing, 17, 1551-1572 (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
  • U. Celikcan, G. Cimen, E.B. Kevinc, T. Capin, "Attention-Aware Disparty Control in interactive environments", Visual Computer, 29, 685-694 (2013)  PDF
  • 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
  • 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)
  • 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
  • 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
  • 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
  • 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)
  • 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
  • S. Baysal, P. Duygulu, "A Line Based Pose Representation for Human Action Recognition", Signal Processing: Image Communication, 28, 458-471 (2013)
  • 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
  • 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)
  • 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
  • B. Gedik, "Auto-tuning Similarity Search Algorithms on Multi-core Architectures", Int J of Parallel Programming, 41, 595-620 (2013)  PDF
  • B. Gedik, "Generic windowing support for extensible stream processing systems", Software - Practice and Experience..  PDF
  • B. Gedik, "Partitioning functions for steteful data parallelism in stream processing", VLDB Journal..  PDF
  • B. Gedik, "Discriminative Fine-Grained Mixing for Adaptive Compression of Data Streams", IEEE Trans on Computers..  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)
  • Y. Tang, B. Gedik, "Auto-pipelining for Date Stream Processing", IEEE Trans on Parallel and Distributed Systems, 24, 1-12 (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)
  • O. Oguz, F. Durupinar, U. Gudukbay, "Dynamic Point-Region Quadtrees for Particle Simulations", Information Sciences, 218, 133-145 (2013)
  • A. Akaydin, U. Gudukbay, "Adaptive Grids: An image-based Approach to Generate Navigation Meshes", Optical Engineering, 52, 027002-1--12 (2013)  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
  • 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
  • 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
  • O.E. Albayrak, I. Akturk, O. Ozturk, "Improving Application Behavior on Heterogeneous Manycore Systems Through Kernel Mapping", Parallel Computing, 39, 867-878 (2013)
  • 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
  • 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)
  • 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
  • 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)
  • H. Sozer, B. Tekinerdogan, M. Aksit, "Optimizing Decomposition of Software Architecture for Local Recovery", Software Quality Journal, 21, 203-240 (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
  • I. Sengor-Altingovde, O.N. Subakan, O. Ulusoy, "Cluster searching strategies for collaborative recommendation systems", Information Processing & Management, 49, 688-697 (2013)
  • 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
  • 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
 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)
  • 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
  • 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
  • 1000 Genomes Project Consortium, ....C. Alkan..., "An integrated map of genetic variation from 1,092 human genomes", Nature, 491, 56-65 (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
  • 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
  • R.O. Selvitopu, A. Turk, C. Aykanat, "Replicated partitioning for undirected hypergraphs", J of Parallel and Distributed Computing, 72, 547-563 (2012)
  • 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
  • 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
  • C. Aksoy, F. Can, S. Kocberber, "Novelty detection for topic tracking", J of American Society for Information Science & Technology, 63, 777-795 (2012)  PDF
  • D. Davenport, "Computationalism: Still the only game in town", Minds and Machines, 22, 183-190 (2012)  PDF
  • A. Dayanik, "Learning feature-projection based classifiers", Expert Systems with Applications, 39, 4532-4544 (2012)
  • T. Dayar, M.C. Orhan, "Kronecker-based Infinite Level-Dependent QBD Processes", J of Applied Probability, 49, 1166-1187 (2012)  PDF
  • C.F. Koyuncu, S. Arslan, I. Durmaz, R. Cetin-Atalay, C. Gunduz-Demir, "Smart Markers for Watershed-Based Cell Segmentation", Plos One, 7, 48664-1--11 (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
  • 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
  • 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
  • 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
  • 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)
  • E. Okuyan, U. Gudukbay, V. Isler, "View-Dependent Refinement of Unstructured Tetrahedral Volumetric Meshes", J of Visualization, 15, 167-178 (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)
  • S. Arpa, A. Bulbul, T. Capin, B. Ozguc, "Perceptual 3D rendering based on principles of analytical cubism", Computers and Graphics, 36, 991-1004 (2012)
  • O. Arslan, U. Saranli, "Reactive Planning and Control of Planar Spring-Mass Running on Rough Terrain", IEEE Trans on Robotics, 28.
  • M. Ashouri-Talouki, A. Baraani-Dastjerdi, A.A. Selcuk, "GLP: A cryptographic approach for group location privacy", Computer Communications, 35, 1527-1533 (2012)
  • 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)
  • 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
  • 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)
  • 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)
  • 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
 2011
  • 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
  • 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
  • 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
  • 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
  • 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. 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
  • H. Cihan, T. Capin, "Multiscale Motion Saliency for Keyframe Extraction from Motion Capture Sequences", Computer Animation and Virtual Worlds, 22, 3-14 (2011)  PDF
  • 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.B. Tosun, C. Gunduz-Demir, "Graph run-length matrices for histopathological image segmentation", IEEE Trans on Medical Imaging, 30, 721-732 (2011)  PDF
  • E.F. Can, P. Duygulu, "A line based representation for matching words in historical manuscripts", Pattern Recognition Letters, 32, 1081-1222 (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)
  • P. Duygulu, M. Bastan, "Multimedia translation for linking visual data to semantics in videos", Machine Vision and Applications, 22, 99-115 (2011)  PDF
  • F. Cakir, U. Gudukbay, O. Ulusoy, "Nearest-Neighbor based Metric Functions for Indoor Scene Recognition", Computer Vision and Image Understanding, 115, 1483-1492 (2011)
  • 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
  • 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
  • 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)
  • E. Bulut, I. Korpeoglu, "Sleep Scheduing with Expected Common Coverage in Wireless Sensor Networks", Wireless Networks, 17, 19-40 (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
  • S. Tasli-Pektas, B. Ozguc, "Virtual Prototyping for Open Building Design", Open House International, 36, 46-56 (2011)
  • O. Ozturk, "Data Locality and Parallelism Optimization Using A Constraint-Based Approach", J of Parallel and Distributed Computing, 71, 280-287 (2011)
  • O. Ozturk, "Reducing Memory Space Consumption Through Dataflow Analysis", Computer Languages, Systems and Structures, 37, 168-177 (2011)
  • O. Ozturk, "Multicore Education Through Simulation", IEEE Trans on Education, 54, 203-209 (2011)  PDF
  • B. Tekinerdogan, "Experiences in Teaching a Graduate Course on Model-Driven Software Development", Computer Science Education, 21, 363-387 (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
 2010
  • S. Aksoy, N.H. Younan, L. Bruzzone, "Patern Recognition in Remote Sensing", Pattern Recognition Letters, 31, 1069-1070 (2010)
  • B. Ozdemir, S. Aksoy, S. Eckert, M. Pesaresi, D. Ehrlich, "Performance measures for object detection evaluation", Pattern Recognition Letters, 31, 1128-1137 (2010)
  • I.Z. Yalniz, S. Aksoy, "Unsupervised Detection and Localization of Structural Textures Using Protection Profiles", Pattern Recognition, 43, 3324-3337 (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
  • B. Ucar, U.V. Catalyurek, C. Aykanat, "A Matrix Partitioning Interface to PaToH in MATLAB", Parallel Computing, 36, 254-272 (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)
  • 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)
  • 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)
  • 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)
  • A. Bulbul, Z. Cipiloglu, T. Capin, "A Perceptual Approach for Stereoscopic Rendering Optimization", Computers and Graphics, 34, 145-157 (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)
  • 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)
  • K. Demirtas, N.K. Cicekli, I. Cicekli, "Automatic categorization and summarization of documentaries", J of Information Science, 36.
  • M. Kutlu, C. Cigir, I. Cicekli, "Generic Text Summarization", Computer Journal, 53, 1315-1323 (2010)
  • T. Daybelge, I. Cicekli, "A ranking method for example based machine translation results by learning from user feedback", Applied Intelligence..
  • 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)
  • M. Cebe, C. Gunduz-Demir, "Qualitative test-cost sensitive classification", Pattern Recognition Letters, 31, 2043-2051 (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
  • A. Dilek, M.E. Belviranli, U. Dogrusoz, "VISIBIOWeb: visualization and layout services fro BioPAX pathway models", Nucleic Acids Research, 38, W150-154 (2010)
  • O. Babur, E. Demir, M. Gonen, C. Sander, U. Dogrusoz, "Discovering Modulators of Gene Expression", Nucleic Acids Research, 38, 5648-5656 (2010)
  • 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)
  • O. Babur, U. Dogrusoz, E. Demir, C. Sander, "chiBE: Iterative visualization and manipulation of BioPAX pathways models", Bioinformatics, 26, 429-431 (2010)
  • D. Ozkan, P. Duygulu, "Interesting Faces in News: A Graph Based Approach for Finding People", Pattern Recognition, 43, 1717-1735 (2010)
  • E. Saykol, U. Gudukbay, O. Ulusoy, "Scenario-Based Query Processing for Video-Surveillance Archives", Engineering Applications of Artificial Intelligence, 23, 331-345 (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)
  • 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)
  • 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)
  • 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)
  • 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
  • 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)
  • 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)
  • 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
  • S. Bayraktar, U. Gudukbay, B. Ozguc, "Particle-based simulation and visualization of fluid flows through porous media", J of Visualization, 13, 327-336 (2010)
  • O. Ozturk, "Improving Chip Multiprocessor Reliability Through Code Replication", Computers and Electrical Engineering, 36, 480-490 (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)
  • 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)
  • 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)
  • M. Ak, K. Kaya, K. Onarlioglu, A.A. Selcuk, "Efficient Broadcast Encryption with User Profiles", Information Sciences, 180, 1060-1072 (2010)
 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. Tatar, I. Cicekli, "Two learning approaches for protein name extraction", J of Biomedical Informatics, 42, 1046-1055 (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)
  • 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)
  • 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)
  • U. Dogrusoz, E. Giral, A. Cetintas, A. Civril, E. Demir, "A Layout Algorithm for Undirected Compound Graphs", Information Sciences, 179, 980-994 (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)
  • N. Ikizler, P. Duygulu, "Histogram of oriented rectangles: A new pose descriptor for human action recognition", Image and Vision Computing, 27, 1515-1526 (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)
  • 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)
  • 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
  • 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)
  • 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)
  • T. Aydin, H.A. Guvenir, "Modeling interestingness of streaming association rules as a benefit-maximizing classification problem", Knowledge-Based Systems, 22, 85-99 (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)
  • 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)
  • 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)
  • M. Karakaya, I. Korpeoglu, O. Ulusoy, "Free Riding in Peer-to-Peer Networks", IEEE Internet Computing, 13, 92-98 (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)
  • M. Ak, K. Kaya, A.A. Selcuk, "Optimal subset-difference broadcast encryption with free riders", Information Sciences, 179, 3673-3684 (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)
  • S.S.H. Tse, "Online Bicriteria Load Balancing using Object Reallocation", IEEE Trans on Parallel and Distributed Systems, 20, 379-388 (2009)  PDF
 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
  • 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)
  • 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)
  • 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)
  • 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
  • G. Erozel, N.K. Cicekli, I. Cicekli, "Natural Language Querying for Video Databases", Information Sciences, 178, 2534-2552 (2008)
  • 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)
  • 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)
  • O. Babur, R. Colak, E. Demir, U. Dogrusoz, "PATIKAmad: analysis of pathways using microarray data", Proteomics, 8, 2196-2198 (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)
  • 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)
  • T. Yilmaz, U. Gudukbay, "Stereoscopic Urban Visualization Based on Graphics Processing Unit", Optical Engineering, 47, 097005 (2008)
  • O. Vechtmova, M. Karamuftuoglu, "Lexical Cohesion and Term Proximity in Document Ranking", Information Processing & Management, 44, 1485-1502 (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)
  • M. Karakaya, I. Korpeoglu, O. Ulusoy, "Counteracting Free Riding in Peer-To-Peer Networks", Computer Networks Journal, 52, 675-694 (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)
  • 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)
  • 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)
  • 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)
 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)
  • 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)
  • 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)
  • 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)
  • 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)
  • G. Ercan, I. Cicekli, "Using Lexical Chains for Keyword Extraction", Information Processing & Management, 43, 1705-1714 (2007)
  • 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)
  • 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)
  • 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)
  • 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
  • T. Aydin, H.A. Guvenir, "A Novel Hybrid Approach for Interestingness Analysis of Classification Rules", Lecture Notes in Artificial Intelligence, 3609, 485-496 (2007)
  • O. Vechtomova, M. Karamuftuoglu, "Query expansion with terms selected using lexical cohesion analysis of documents", Information Processing & Management, 43, 849-965 (2007)
  • K. Kaya, A.A. Selcuk, "Threshold cryptography based on Asmuth-Bloom Secret Sharing", Information Sciences, 177, 4148-4160 (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
 2006
  • S. Aksoy, "Modeling of remote sensing image content using attributed relational graphs", Lecture Notes in Computer Science, 4109, 475-483 (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.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)
  • 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)
  • T. Kucukyilmaz, B.B. Cambazoglu, C. Aykanat, F. Can, "Chat Mining for Gender Prediction", Lecture Notes in Computer Science, 4243, 274-283 (2006)
  • R. Nuray, F. Can, "Automatic Ranking of Information Retrieval Systems Using Data Fusion", Information Processing & Management, 42, 595-614 (2006)
  • F. Can, "Turkish Information Retrieval: Past Changes Future", Lecture Notes in Computer Science, 4243, 13-22 (2006)
  • N.K. Cicekli, I. Cicekli, "Formalizing the Specification and Execution of Workflows using the Event Calculus", Information Sciences, 176, 2227-2267 (2006)
  • I. Cicekli, N.K. Cicekli, "Generalizing Predicates with String Arguments", Applied Intelligence, 25, 23-36 (2006)
  • U. Dogrusoz, B. Genc, "A Multi-Graph Approach to Complexity Management in Interactive Graph Visualization", Computers and Graphics, 30, 86-97 (2006)
  • B. Genc, U. Dogrusoz, "A Layout Algorithm for Signaling Pathways", Information Sciences, 176, 135-149 (2006)
  • S.C. Sahinalp, U. Dogrusoz, S. Muthukrishnan, "Preface to special issue on Combinatorial Pattern Matching", Theoretical Computer Science, 368, 195 (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)
  • 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.
  • D. Ozkan, P. Duygulu, "Finding People Frequently Appearing in News", Lecture Notes in Computer Science, 4071, 173-182 (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)
  • 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)
  • T. Aydin, H.A. Guvenir, "Modeling Interestingness of Streaming Classification Rules as Classification Problem", Lecture Notes in Artificial Intelligence, 3949, 168-176 (2006)
  • O. Vechtomova, M. Karamuftuoglu, "Elicitation and use of relevance feedback information", Information Processing & Management, 42, 191-206 (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)
  • K. Dogan, G. Gurel, A.K. Kamci, I. Korpeoglu, "Bluetooth Broadcasting Performance: Reliability and Throughput", Lecture Notes in Computer Science, 3992, 996-999 (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
  • H. Acan, K. Kaya, A.A. Selcuk, "Capture Resilient ElGamal Signature Protocols", Lecture Notes in Computer Science, 4263, 943-951 (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)
  • A. Unal, Y. Saygin, O. Ulusoy, "Processing count queries over event streams at multiple time granularities", Information Sciences, 176, 2066-2096 (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)
  • S. Altingovde, F. Can, O. Ulusoy, "Algorithms for Within-Cluster Searches Using Inverted Files", Lecture Notes in Computer Science, 4263, 707-716 (2006)
 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)
  • M. Koyuturk, C. Aykanat, "Iterative-improvement-Based declustering heuristics for multi-disk databases", Information Systems, 30, 47-70 (2005)
  • I. Cicekli, "Inducing translation templates with type constraints", J of Machine Translation, 19, 283-299 (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)
  • 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)
  • P. Buchholz, T. Dayar, "Block SOR Preconditioned Projection Methods for Kronecker Structured Markovian Representations", SIAM J on Scientific Computing, 26, 1289-1313 (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)
  • N. Ikizler, P. Duygulu, "Person Search Made Easy", Lecture Notes in Computer Science, 3568, 578 (2005)
  • P. Virga, P. Duygulu, "Systematic Evaluation of Machine Translation Methods for Image and Video Annotation", Lecture Notes in Computer Science, 3568, 174 (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 Histogram-Based Approach for Object-Based Query-by-Shape-and-Color in Image and Video Databases", Image and Vision Computing, 23, 1170-1180 (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)
  • 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)
  • A. Kucukyilmaz, B. Ozguc, "An Animation System for Fracturing of Rigid Objects", Lecture Notes in Computer Science, 3733, 688-697 (2005)
  • O. Ulusoy, "Database Research at Bilkent University (invited paper)", Sigmod Record, 34, 77-80 (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)
  • 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
  • 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)
  • 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)
  • A. Pinar, C. Aykanat, "Fast Optimal Load Balancing Algorithms for ID Partioning", J of Parallel and Distributed Computing, 64, 974-996 (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)
  • B. Ucar, C. Aykanat, "A Message Ordering Problem in Parallel Programs", Lecture Notes in Computer Science, 3241, 131-138 (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.B. Cambazoglu, A. Turk, C. Aykanat, "Data-Parallel Web Crawling Models", Lecture Notes in Computer Science, 3280, 801-809 (2004)
  • M.M. Ozdal, C. Aykanat, "Hypergraph Models and Algorithms for Data-Pattern Based Clustering", Data Mining and Knowledge Discovery, 9, 29-57 (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)
  • P. Buchholz, T. Dayar, "Block SOR for Kronecker Structured Representations", Linear Algebra and Its Applications, 386, 83-109 (2004)
  • P. Buchholz, T. Dayar, "Comparison of Multilevel Methods for Kronecker-based Markovian Representations", Computing, 73, 349-371 (2004)
  • B. Genc, U. Dogrusoz, "A constrained, force-directed layout algorithm for biological pathways", Lecture Notes in Computer Science, 2912, 314-319 (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)
  • P. Duygulu, A. Hauptmann, "What's New, What's Not? Associating news videos with words", Lecture Notes in Computer Science, 3115, 132-140 (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)
  • 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)
  • I. Uysal, H.A. Guvenir, "Instance-Based Regression by Partitioning Feature Projections", Applied Intelligence, 21, 57-79 (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)
  • 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)
  • A.U. Tansel, "Temporality in databases", Lecture Notes in Computer Science, 3261, 1-3 (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)
  • 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)
  • 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)
  • 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)
 2003
  • H. Berk, C. Aykanat, U. Gudukbay, "Direct volume rendering of unstructured grids", Computers and Graphics, 27, 387-406 (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)
  • O. Gusak, T. Dayar, J.M. Fourneau, "Lumpable Continous-Time Stochastic Automata Networks", European J of Operational Research, 148, 436-451 (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)
  • T. Dayar, J.M. Fourneau, N. Pekergin, "Transforming Stochastic Matrices for Stochastic Comparison with the ST-Order", RAIRO Operations Research, 37, 85-97 (2003)
  • F. Nar, A.E. Cetin, "Generalization and localization based style imitation for grayscale images", Lecture Notes in Computer Science, 2869, 465-473 (2003)
  • K. Altintas, H.A. Guvenir, "Learning translation templates for closely related languages", Lecture Notes in Artificial Intelligence, 2773, 756-762 (2003)
  • N. Ikizler, H.A. Guvenir, "Maximizing benefit of classifications using feature intervals", Lecture Notes in Artificial Intelligence, 2773, 339-345 (2003)
  • H.O. Tan, I. Korpeoglu, "Power efficient data gathering and aggregation in wireless sensor networks", Sigmod Record, 32, 66-71 (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)
  • M.E. Donderler, E. Saykol, O. Ulusoy, U. Gudukbay, "BilVideo: A video database management system", IEEE Multimedia, 10, 66-70 (2003)  PDF
 2002
  • Fetzer, V. Akman, "Contexts of social action: Guest editors' introduction", Language and Communication, 22, 391-402 (2002)
  • 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)
  • K. Altintas, T. Aydin, V. Akman, "Censoring the Internet: The situation in Turkey", First Monday, 7.
  • A.P. Saygin, I. Cicekli, "Pragmatics in human-computer conversations", J of Pragmatics, 34, 227-258 (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, "Two-dimensional packing algorithms for layout of disconnected graphs", Information Sciences, 143, 147-158 (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
  • 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)
  • M.E. Donderler, O. Ulusoy, U. Gudukbay, "A Rule-based Video Database System Architecture", Information Sciences, 143, 13-45 (2002)
  • U. Gudukbay, T. Yilmaz, "Stereoscopic View-Dependent Visualization of Terrain Height Fields", IEEE Trans on Visualization and Computer Graphics, 8, 330-345 (2002)  PDF
  • B. Ari, H.A. Guvenir, "Clustered linear regression", Knowledge Based Systems, 15, 169-175 (2002)
  • D.Z. Hakkani-Tur, K. Oflazer, G. Tur, "Statistical morphological disambiguation for agglutinative languages", Computers and the Humanities, 36, 381-410 (2002)
  • U. Gudukbay, O. Arikan, B. Ozguc, "Visualizer: A Mesh Visualisation System Using View-Dependent Refinement", Computers and Graphics, 26, 491-503 (2002)
  • 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.P. Saygin, I. Cicekli, V. Akman, "Turing test: 50 years later", Minds and Machines, 10, 463-518 (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)
  • A. Saygin, I. Cicekli, "Learning Translation Templates from Bilingual Translation Examples", J of Pragmatics, 34, 227-258 (2001)
  • I. Cicekli, H.A. Guvenir, "Learning translation templates from bilingual translation examples", Applied Intelligence, 15, 57-76 (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
  • V. Akman, "Relating to Ken Kesey's wise man", J of Pragmatics, 32, 485-489 (2000)
  • V. Akman, "Rethinking context as a social construct", J of Pragmatics, 32, 743-759 (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)
  • E. Shriberg, A. Stolcke, D. HakkaniTur, G. Tur, "Prosody-based automatic segmentation of speech into sentences and topics", Speech Communication, 32, 127-154 (2000)
  • D. Davenport, "Software piracy is not just economics anymore", Comm of the ACM, 43, 11 (2000)
  • D. Davenport, "Experience using a project-based approach in an introductory programming course", IEEE Trans on Education, 43, 443-454 (2000)  PDF
  • D. Davenport, "Computationalism: the very idea", Conceptus, 14, 121-137 (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)
  • K. Efe, A.L. Broadwater, A. Fernandez, "Embedding complete binary trees in product graphs", Telecommunication Systems, 13, 99-109 (2000)
  • U. Gudukbay, F. Erol, N. Erdogan, "Beyond tradition and modernity: digital shadow theater", Leonardo, 33, 264-265 (2000)
  • A. Gursoy, M. Atun, "Neighbourhood preserving load balancing: A Self-Organizing approach", Lecture Notes in Computer Science, 1900, 234-241 (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)
  • H.G. Gok, O. Ulusoy, "Transmission of continuous query results in mobile computing systems", Information Sciences, 125, 37-63 (2000)
 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
  • I. Uysal, H.A. Guvenir, "An overview of regression techniques for knowledge discovery", Knowledge Engineering Review, 14, 319-340 (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)
  • 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)
  • E. Kayan, O. Ulusoy, "An evaluation of real-time transaction management issues in mobile database systems", Computer Journal, 42, 501-510 (1999)
 1998
  • V. Akman, "Guest Editor's introduction", Minds and Machines, 8, 475-477 (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)
  • C. Aykanat, T. Bultan, I. Haritaoglu, "A fast neural-network algorithm for VLSI cell placement", Neural Networks, 11, 1671-1684 (1998)
  • T.M. Kurc, C. Aykanat, B. Ozguc, "Object-space parallel polygon rendering on hypercubes", Computers and Graphics, 22, 487-503 (1998)
  • I. Cicekli, "Abstract MetaProlog Engine", J of Logic Programming, 34, 169-200 (1998)
  • E. Uysal, T. Dayar, "Iterative methods based on splittings for stochastic automata networks", European J Operational Research, 110, 166-186 (1998)
  • T. Dayar, "State space orderings for Gauss-Siedel in Markov chains revisited", SIAM J on Scientific Computing, 19, 148-154 (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)
  • 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)
  • H.A. Guvenir, H.G. Koc, "Concept representation with overlapping feature intervals", Cybernetics and Systems: An International Journal, 29, 263-282 (1998)
  • D.Z. Hakkani, K. Oflazer, "Tactical generation in a free constituent order language", J of Natural Language Engineering, 4.
  • U. Akdemir, B. Ozguc, U. Gudukbay, A. Selcuk, "Right triangular subdivision for texture mapping ray traced objects", Visual Computer, 14, 445-454 (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)
  • O. Ulusoy, "Transaction processing in distributed active real-time database systems", Journal of Systems and Software, 42, 247-262 (1998)
  • O. Ulusoy, "Analysis of concurrency control protocol for real-time database systems", Information Sciences, 111, 1-4 (1998)
  • O. Ulusoy, A. Buchmann, "A real-time concurrency control protocol for main-memory database systems", Information Systems, 23, 109-125 (1998)
  • Y. Saygin, O. Ulusoy, S. Chakravarthy, "Concurrent rule execution in active database systems", Information Systems, 23, 39-64 (1998)
  • A. Dogac, O. Ulusoy, "Preface to special issue on recent advances in database research", J of Database Management, 9, 3 (1998)
  • J. Tayeb, O. Ulusoy, O. Wolfson, "A quadtree based dynamic attribute indexing method", Computer Journal, 41, 185-200 (1998)
 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)
  • V. Akman, M. Surav, "The use of situation theory in context modelling", Computational Intelligence, 13, 427-438 (1997)
  • B. Say, V. Akman, "Current approaches to punctuation in Computational Linguistics", Computers and the Humanities, 30, 457-469 (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
  • 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)
  • I. Cicekli, "An intelligent backtracking schema in a logic programming environment", Sigplan Notices, 32, 42-50 (1997)
  • 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)
  • U. Gudukbay, "A movable jaw model for the human face", Computers and Graphics, 21, 549-554 (1997)
  • A.S. Kocberber, F. Can, "Vertical framing of superposed signature files using partial evaluation of queries", Information Processing & Management, 33, 353-376 (1997)
  • K. Oflazer, "Error tolerant retrieval of trees", IEEE Trans on PAMI, 19, 1376-1380 (1997)  PDF
  • U. Gudukbay, B. Ozguc, Y. Tokad, "A spring force formulation for elastically deformable models", Computers and Graphics, 21, 335-346 (1997)
  • O. Ulusoy, "An Evaluation of Network Access Protocols for Distributed Real-time Database Systems", J of Systems and Software, 37, 49-60 (1997)
  • T. Devirmis, O. Ulusoy, "Design and evaluation of a new transaction execution model for multidatabase systems", Information Sciences, 102, 203-238 (1997)
 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)
  • C. Aykanat, T. Capin, B. Ozguc, "A Parallel Progressive Radiosity Algorithm Based on Patch Data Circulation", Computers and Graphics, 20, 307-324 (1996)
  • T.M. Kurc, C. Aykanat, B. Ozguc, "Active Pixel Merging on Hypercube Multicomputers", Lecture Notes in Computer Science, 1067, 319-326 (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)
  • H.A. Guvenir, I. Sirin, "Classification by Feature Partitioning", Machine Learning, 23, 47-67 (1996)
  • S. Kocberber, F. Can, "Partial evaluation of queries for bit-sliced signature files", Information Processing Letters, 60, 305-311 (1996)
  • K. Oflazer, "Error-tolerant Finite State Recognition with Applications to Morphological Analysis and spelling correction", Computational Linguistics, 22, 73-89 (1996)
  • P. O'Neal, O. Ulusoy, "Guest editorial: real-time database systems", Information Systems, 21, 1-2 (1996)
  • Y. Turkan, O. Ulusoy, "An efficient memory management algorithm for client-server database management systems", Computer Journal, 39, 374-385 (1996)
 1995
  • P. Tripathy, B. Sarikaya, "Analysis and representation of test cases generated from Lotos", Computer communications, 18, 493-506 (1995)
  • E. Tin, V. Akman, M. Ersan, "Towards situation oriented programming languages", Sigplan Notices, 30, 27-36 (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)
  • 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
  • H.A. Guvenir, "An Object-oriented Tutoring System for Teaching Sets", SIGCSE Bulletin (ACM Press), 27, 39-46 (1995)
  • Z. Gungordu, K. Oflazer, "Parsing Turkish with the Lexical-Functional Grammar Formalism", J of Machine Translation, 10, 293-319 (1995)
  • B. Erkan, B. Ozguc, "Object oriented motion abstraction", J of Visualization and Computer Animation, 6, 49-65 (1995)
  • O. Ulusoy, "A network access protocol for hard real-time communication systems", Computer Communications, 18, 943-948 (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, "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)
 1994
  • V. Akman, "When silence may mean derision", J of Pragmatics, 22, 211-212 (1994)
  • M. Marhl, V. Akman, "On the correct determination of rotational angles for twisted profile sweep objects", Computers and Graphics, 18, 691-694 (1994)
  • E. Tin, V. Akman, "Computational Situation Theory", Sigart Bulletin, 5, 4-17 (1994)
  • V. Akman, "Ripping the Text apart at different seams", Stanford Humanities Review, 4, 31-34 (1994)
  • M. Pakkan, V. Akman, "Issues in common sense set theory", Artificial Intelligence Review, 8, 279-308 (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)
  • F. Ulupinar, R. Nevatia, "Recovery of 3-D objects with multiple curved surfaces from 2-D contours", Artificial Intelligence, 67, 1-28 (1994)
  • K. Oflazer, "Two level description of Turkish Morphology", Literary and Linguistic Computing, 9, 137-148 (1994)
  • U. Gudukbay, B. Ozguc, "Animation of deformable models", Computer aided design, 26, 868-875 (1994)
  • M. Aktihanoglu, B. Ozguc, C. Aykanat, "MARS: A tool based modelling, animation and parallel rendering system", Visual Computer, 11, 1-14 (1994)
  • O. Ulusoy, "Processing Real time transactions in a replicated database system", Int J of Distributed and Parallel Databases, 2, 405-436 (1994)
 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
  • V. Akman, "Advanced CAD environments: A knowledge-based foundation", Microcomputers in Civil Engineering, 8, 129-139 (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)
  • 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)
  • C. Yuceer, K. Oflaze, "A rotation, scaling and translation invariant pattern-classification system", Pattern Recognition, 26, 687-710 (1993)
  • K. Oflazer, "Solving Tangram puzzles: A connectionist approach", Int J of Intelligent Systems, 8, 603-616 (1993)
  • A. Solak, K. Oflazer, "Design and Implementation of a spelling checker for Turkish", Literary and Linguistic Computing, 8, 113-130 (1993)
  • U. Gudukbay, B. Ozguc, Y. Tokad, "An animation system for rigid and deformable models", Computers and Graphics, 17, 71-77 (1993)
  • O. Ulusoy, G.G. Belford, "Real time transaction scheduling in database systems", Information Systems, 18, 559-580 (1993)
  • O. Ulusoy, "Lock-based concurrency control in distributed real-time database systems", J of Database Management, 4, 3-16 (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)
 1992
  • V. Akman, A. Arslan, "Sweeping with all graphical ingredients in a topological picturebook", Computers and Graphics, 16, 273-281 (1992)
  • C. Aykanat, F. Ozguner, "A Fault-Tolerant Hexagonal Systolic Array", Information Processing Letters, 42, 187-196 (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)