Doruk Bozdag

Publications

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Journal/Book Conference Report Abstract/Poster

2009

• A Repartitioning Hypergraph Model for Dynamic Load Balancing
  U. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R. Heaphy, L.A. Fisk
  Journal of Parallel and Distributed Computing, vol. 69, no. 8, pg. 711-724, 2009
  
• Compaction of Schedules and a Two-Stage Approach for Duplication-Based DAG Scheduling
  D. Bozdag, F. Ozguner, U. Catalyurek
  IEEE Transactions on Parallel and Distributed Systems, vol. 20, no. 6, pg. 857-871, 2009
  
• Hypergraph-based Dynamic Partitioning and Load Balancing
  U. Catalyurek, D. Bozdag, E.G. Boman, K.D. Devine, R. Heaphy, L.A. Fisk
  Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, Wiley Publishing, 2009, accepted for publication
  
• Parallel Short Sequence Mapping for High Throughput Genome Sequencing
  D. Bozdag, C.C. Barbacioru, U. Catalyurek
  Proc. of 23rd Int'l. Parallel and Distributed Processing Symposium, 2009
  
• A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets
  D. Bozdag, J. D. Parvin, U. Catalyurek
  Proc. of 1st Int'l. Conf. on Bioinformatics and Computational Biology, Springer, vol. 5462, pg. 151-163, 2009
  
• A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments
  H. G. Ozer, D. Bozdag, T. Camerlengo, J. Wu, Y.-W. Huang, T. Hartley, J. D. Parvin, T. Huang, U. V. Catalyurek, K. Huang
  Proc. of 1st Int'l. Conf. on Bioinformatics and Computational Biology, Springer, vol. 5462, pg. 320-330, 2009
  
• Identification of a Breast Cancer Associated Regulatory Network
  J. D. Parvin, Z. Kais, M. Arora, S. Kotian, A. Zha, D. Ransburgh, D. Bozdag, U. Catalyurek, K. Huang
  Bioinformatics, 2009 Ohio Collaborative Conference, IEEE Computer Society, pg. 71-75, 2009
  
• Parallel Computing Strategies for Sequence Mapping of NGS Data
  D. Bozdag, T. Camerlengo, H. G. Ozer, J. Trgovcich, T. Meulia, K. Huang, U. Catalyurek
  Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis, 2009
  
• Combinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and Matching
  D. Bozdag, U. Catalyurek, F. Dobrian, A. Gebremedhin, M. Halappanavar, A. Pothen
  Poster, 21st Supercomputing Conference, 2009
  
• Parallelization of Mapping Algorithms for Next Generation Sequencing Applications
  D. Bozdag, C. C. Barbacioru, U. V. Catalyurek
  Abstract, Combinatorial Scientific Computing, Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, no. 09061, 2009
  

2008

• A framework for scalable greedy coloring on distributed-memory parallel computers
  D. Bozdag, A. H. Gebremedhin, F. Manne, E. G. Boman, U. V. Catalyurek
  Journal of Parallel and Distributed Computing, vol. 68, no. 4, pg. 515-535, 2008
  
• Combinatorial algorithms for computational science and engineering
  E. G. Boman, D. Bozdag, U. V. Catalyurek, K. D. Devine, A. H. Gebremedhin, P. D. Hovland, A. Pothen
  Journal of Physics: Conference Series, vol. 125, pg. , 2008
  

2007

• Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations
  U. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R. Heaphy, L.A. Fisk
  Proc. of 21st Int'l. Parallel and Distributed Processing Symposium, pg. 1-11, 2007, Best Algorithms Paper Award
  
• Enabling high performance computational science through combinatorial algorithms
  E. G. Boman, D. Bozdag, U. V. Catalyurek, K. D. Devine, A. H. Gebremedhin, P. D. Hovland, A. Pothen, M. M. Strout
  Journal of Physics: Conference Series, vol. 78, pg. 012058 (10pp), 2007
  

2006

• Mobility-based communication in wireless sensor networks
  E. Ekici, Y. Gu, D. Bozdag
  IEEE Communications Magazine, vol. 44, no. 7, pg. 56-62, 2006
  
• Data harvesting with mobile elements in wireless sensor networks
  Y. Gu, D. Bozdag, R.W. Brewer, E. Ekici
  Computer Networks (Elsevier), vol. 50, no. 17, pg. 3449-3465, 2006
  
• A task duplication based bottom-up scheduling algorithm for heterogeneous environments
  D. Bozdag, U.V. Catalyurek, F. Ozguner
  Proc. of 20th Int'l. Parallel and Distributed Processing Symposium, 2006
  
• Mobile Element Based Differentiated Message Delivery in Wireless Sensor Networks
  Y. Gu, D. Bozdag, E. Ekici
  Proc. of 7th International Symposium on World of Wireless, Mobile and Multimedia Networks, pg. 83-92, 2006
  

2005

• Partitioning-Based Mobile Element Scheduling in Wireless Sensor Networks
  Y. Gu, D. Bozdag, E. Ekici, F. Ozguner, C.-G. Lee
  Proc. of IEEE Communications Society Conference on Sensor and Ad Hoc Communications and Networks, pg. 386-395, 2005
  
• A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers
  D. Bozdag, U.V. Catalyurek, A.H. Gebremedhin, F. Manne, E.G. Boman, F. Ozguner
  Proc. of 1st Int'l. Conf. on High Performance Computing and Communications, Springer, vol. 3726, pg. 796-806, 2005
  
• A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers
  E.G. Boman, D. Bozdag, U.V. Catalyurek, A.H. Gebremedhin, F. Manne
  Proc. of 11th Int'l. Euro-Par Conf. on Parallel Processing, Springer, vol. 3648, pg. 241-251, 2005
  
• A Task Duplication Based Scheduling Algorithm Using Partial Schedules
  D. Bozdag, F. Ozguner, E. Ekici, U. V. Catalyurek
  Proc. of 34th Int'l. Conf. on Parallel Processing, pg. 630-637, 2005