Ümit V. Çatalyürek

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Publications by Year

Below is a list of my publications by year. Alternative listing can be found at HPC Lab's Publication page. Here is another list at DBLP, or Google Scholar, or Microsoft Academic Search.

2016:

  1. Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei. T. Dytrych, P. Maris, K. D. Launey, J. P. Draayer, J. P. Vary, D. Langr, E. Saule, M. A. Caprio, U. Catalyurek, M. Sosonkina. Computer Physics Communications, to appear.
  2. A Resource Provisioning Framework for Bioinformatics Applications in Multi-Cloud Environments. I. F. Senturk, P. Balakrishnan, A. Abu-Doleh, K. Kaya, Q. Malluhi, and U.V. Catalyurek Future Generation Computer Systems, to appear.
  3. Incremental k-core Decomposition: Algorithms and Evaluation. A.E. Sariyuce, G. Gedik, G. Jacques-Silva,The VLDB Journal, to appear.
  4. SONIC: Streaming Overlapping Community Detection. A.E. Sariyuce, G. Gedik, G. Jacques-Silva, K.-L. Wu, and U.V. Catalyurek. Data Mining and Knowledge Discovery, to appear.
  5. Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States. M. Hoffmann, Y. Luo, S. R. Monday, N. Gonzales-Escalona, A. R. Ottesen, T. Muruvanda, C. Wang, G. Kastanis, C. Keys, D. Janies, I. F. Senturk, U. V. Catalyurek, H. Wang, T. S. Hammack, W. J. Wolfgang, D. Schoonmaker-Bopp, A. Chu, R. Myers, J. Haendiges, P. S. Evans, J. Meng, E. A. Strain, M. W. Allard, E. W. Brown. Journal of Infectious Diseases, Vol. 213, No. 4, pp. 502-508, Apr 2016.
  6. Multi-jagged: A Scalable Parallel Spatial Partitioning Algorithm. M. Deveci, S. Rajamanickam, K.D. Devine, and U.V. Catalyurek. IEEE Transaction on Parallel and Distributed Systems, Vol. 27, No. 3, pp. 803-817, Mar 2016.

2015:

  1. Allele-specific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci. M. M. Gerber, H. Hampel, X. Zhou, N. P. Schulz, A. Suhy, M. Deveci, U.V. Catalyurek, A. E. Toland. International Journal of Cancer, Vol. 137, No. 10, pp. 2323-2331, 2015.
  2. Phylogenetic visualization of the spread of H7 influenza A viruses. D.A. Janies, L.W. Pomeroy, C. Krueger, Y. Zhang, I. Senturk, K. Kaya, U.V. Catalyurek. Cladistics, Vol. 31, No. 6, pp. 679-691, Dec 2015.
  3. Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering. M. Deveci, O. Kucuktunc, K. Eren, D. Bozdag, K. Kaya, U.V. Catalyurek. Methods in Molecular Biology, Springer, Editor P.H. Guzzi, 2015.
  4. Incremental Closeness Centrality in Distributed Memory. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. Parallel Computing, Vol. 47, pp. 3-18, Aug 2015.
  5. Hypergraph partitioning for multiple communication cost metrics: Model and methods. M. Deveci, K. Kaya, B. Ucar, and U.V. Catalyurek. Journal of Parallel and Distributed Computing, Vol. 77, pp. 69-83, Mar 2015.
  6. Spaler: Spark and GraphX based de novo genome assembler. A. Abu-Doleh and U.V. Catalyurek. IEEE International Conference on BigData, Oct 2015.
  7. MICA: MicroRNA Integration for Active Module Discovery. A. Hatem, K. Kaya, J. Parvin, K. Huang, and U.V. Catalyurek. 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), Sep 2015.
  8. Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application. D. Janies, Z. Witter, C. Gibson, T. Kraft, I. Senturk, and U.V. Catalyurek, MEDINFO'15, Aug 2015.
  9. Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions. A.E. Sariyuce, C. Seshadhri, A. Pinar, and U.V. Catalyurek. 24th International World Wide Web Conference (WWW), May 2015. Acceptance rate 14%. Best Paper Award Nominee.
  10. Fast and High Quality Topology-Aware Task Mapping. M. Deveci, K. Kaya, B. Ucar, and U.V. Catalyurek. Proceedings of 29th IEEE International Parallel and Distributed Processing Symposium (IPDPS), May 2014. Acceptance rate 22%.
  11. Regularizing Graph Centrality Computations. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. Journal of Parallel and Distributed Computing, Vol. 76, pp. 106-119, Feb 2015.
  12. Mitigating Bias in Planning Two-Color Microarray Experiments. Ferhatosmanoglu, T.T. Allen, and U.V. Catalyurek. International Journal of Data Mining and Bioinformatics, Vol. 13, No. 1, pp. 31-49, 2015.

2014:

  1. Diversifying Citation Recommendations. O. Kucuktunc, E. Saule, K. Kaya, and U.V. Catalyurek. ACM Transactions on Intelligent Systems and Technology, Vol. 5, No. 5, pp. 55:1-55:21, Dec 2014.
  2. Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory. M. Jung, E.H. Wilson III, W. Choi. J. Shalf. H.M. Aktulga, C. Yang, E. Saule, U.V. Catalyurek, and M. Kandemir. Scientific Programming, Vol. 22, No.2, pp. 125-139, 2014.
  3. mrSNP: Software to detect SNP effects on microRNA binding. M. Deveci, U.V. Catalyurek, and A.E. Toland, BMC Bioinformatics, Vol. 15, pp. 73, 2014.
  4. NUSAP1 influences the DNA damage response by controlling BRCA1 protein levels. S. Kotian, T. Banerjee, A. Lockhart, K. Huang, U.V. Catalyurek, and J.D. Parvin. Cancer Biology & Therapy, Vol. 15, No. 5, pp. 533-543, Feb 2014.
  5. Exploiting Geometric Partitioning in Task Mapping for Parallel Computers M. Deveci, S. Rajamanickam, V. Leung, K. T. Pedretti, S. L. Olivier, D. P. Bunde, U. V. Catalyurek, K.D. Devine. Proceedings of 28th IEEE International Parallel and Distributed Processing Symposium (IPDPS), May 2014. Acceptance rate 21%.
  6. Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. Proceedings of 28th IEEE International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP), May 2014.
  7. Extracting Maximal Exact Matches on GPU. A. Abu-Doleh, K. Kaya, M. Abouelhoda, and U.V. Catalyurek. Proceedings of 28th IEEE International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP), May 2014.
  8. High-Performance Computing in High-Throughput Sequencing.K. Kaya, A. Hatem, H. G. Ozer, K. Huang, U.V. Catalyurek. Biological Knowledge Discovery Handbook, John Wiley & Sons, Editors M. Elloumi, A. Y. Zomaya, 2014.
  9. Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT-2. S.H. Bokhari, U.V. Catalyurek, and M.N. Gurcan. Concurrency and Computation: Practice and Experience, Vol. 26, No. 18, pp. 2836-2855, 2014. Also available as a technical report from Algopath LLC.

2013:

  1. Collective Modes in Light Nuclei from First Principles. T. Dytrych, K.D. Launey, J.P. Draayer, P. Maris, J.P. Vary, E. Saule, U.V. Catalyurek, M. Sosonkina, D. Langr, M. A. Caprio. Physical Review Letters, Vol. 111, No. 25, pp. 252501, Dec 2013.
  2. Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows. L. Wang, A. Hatem, U.V. Catalyurek, M. Morrison, Z. Yu. PLoS ONE, Public Library of Science, Vol. 8, No. 11, pp. e78507, Nov 2013.
  3. A Survey of Pipelined Workflow Scheduling: Models and Algorithms. A. Benoit, U.V. Catalyurek, Y. Robert, and E. Saule. ACM Computing Surveys, Vol. 45, No. 4, pp. 50:1-50:36, Aug 2013. Also available as technical report ENS Lyon, France, LIP, no RR-LIP-2010-28, Sep 2010.
  4. Benchmarking Short Sequence Mapping Tools. A. Hatem, D. Bozdag, A.E. Toland and U.V. Catalyurek. BMC Bioinformatics, Vol 14, No. 1, pp. 184, 2013.
  5. Fast Recommendation on Bibliographic Networks with Sparse-Matrix Ordering and Partitioning. O. Kucuktunc, K. Kaya, E. Saule, and U.V. Catalyurek. Social Network Analysis and Mining, Springer, Vol. 3, No. 4, pp. 1097-1111, Dec 2013.
  6. A Comparative Analysis of Biclustering Algorithms for Gene Expression Data. K. Eren, M. Deveci, O. Kucuktunc, U.V. Catalyurek. Briefings in Bioinformatics, Vol. 14, No. 3, pp. 279-292, May 2013.
  7. Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory. M. Jung, E.H. Wilson III, W. Choi. J. Shalf. H.M. Aktulga, C. Yang, E. Saule, U.V. Catalyurek, and M. Kandemir. Proc. of Conference on High Performance Computing Networking, Storage and Analysis (SC '13), Nov 2013. Acceptance rate 20%, Best Paper and Best Student Paper Finalist.
  8. Incremental Algorithms for Closeness Centrality. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. IEEE International Conference on BigData, Oct 2013.
  9. A Push-Relabel-based Maximum Cardinality Bipartite Matching Algorithm on GPUs. M. Deveci, K. Kaya, B. Ucar, and U.V. Catalyurek. 42nd International Conference on Parallel Processing (ICPP), Oct 2013.
  10. Hypergraph Sparsification and Its Application to Partitioning. M. Deveci, K. Kaya, and U.V. Catalyurek. 42nd International Conference. on Parallel Processing (ICPP), Oct 2013.
  11. STREAMER: a Distributed Framework for Incremental Closeness Centrality Computation. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. IEEE International Conference on Cluster Computing, Sep 2013. Acceptance rate 31%, to appear.
  12. Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs.A. Abu-Doleh, E. Saule, K. Kaya, and U.V. Catalyurek. ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB), Sep 2013.
  13. PRASE: PageRank-based Active Subnetwork Extraction. A. Hatem, K. Kaya, and U.V. Catalyurek. ACM International Conference on Bioinformatics, Computational Biology, and Biomedical Informatics (ACM-BCB), Sep 2013.
  14. Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication. K. Kaya, B. Ucar, and U.V. Catalyurek. Proc of the 10th Int'l Conf. on Parallel Processing and Applied Mathematics (PPAM), Sep 2013.
  15. Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi. E. Saule, K. Kaya, and U.V. Catalyurek. Proc of the 10th Int'l Conf. on Parallel Processing and Applied Mathematics (PPAM), Sep 2013.
  16. GPU accelerated maximum cardinality matching algorithms for bipartite graphs. M. Deveci, K. Kaya, B. Ucar, and U.V. Catalyurek. Proceedings of Euro-Par, Aug 2013. Acceptance rate 27%.
  17. Streaming Algorithms for k-core Decomposition. A.E. Sariyuce, B. Gedik, G. Jacques-Silva, K. Wu, and U.V. Catalyurek. 39th International Conference on Very Large Data Bases (VLDB), Aug 2013.
  18. Towards a Personalized, Scalable, and Exploratory Academic Recommendation ServiceO. Kucuktunc, E. Saule, K. Kaya, and U.V. Catalyurek. Proceedings of IEEE/ACM International Conference on Social Networks Analysis and Mining (ASONAM), Aug 2013. Acceptance rate 28%.
  19. Diversified Recommendation on Graphs: Pitfalls, Measures, and Algorithms. O. Kucuktunc, E. Saule, K. Kaya, and U.V. Catalyurek. 22nd International World Wide Web Conference (WWW), May 2013.
  20. Shattering and Compressing Networks for Betweenness Centrality. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. 13th SIAM International Conference on Data Mining (SDM), May 2013. An extended version is available as a Tech Rep on ArXiv
  21. Betweenness Centrality on GPUs and Heterogeneous Architectures. A.E. Sariyuce, K. Kaya, E. Saule, and U.V. Catalyurek. Workshop on General Purpose Processing Using GPUs (GPGPU), in conjunction with ASPLOS, Mar 2013.
  22. Result Diversification in Automatic Citation Recommendation. O. Kucuktunc, E. Saule, K. Kaya, and U.V. Catalyurek. iConference Workshop on Computational Scientometrics: Theory and Applications, Feb 2013.

2012:

  1. Merging network patterns: a general framework to summarize biomedical network data.Y. Xiang, D. Fuhry, K. Kaya, R. Jin, U.V. Catalyurek, K. Huang. Network Modeling and Analysis in Health Informatics and Bioinformatics, Springer, Vol. 1, No. 3, pp. 103-116, 2012.
  2. Load-Balancing Spatially Located Computations using Rectangular Partitions. E. Saule, E.O. Bas and U.V. Catalyurek. Journal of Parallel and Distributed Computing, Vol. 72, No. 10, pp. 1201-1214, 2012. Also available as technical report, ArXiv, Tech. Rep. no. arXiv:1104.2566v1.
  3. Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs. E. Kayaaslan, A. Pinar, U.V. Catalyurek, and C. Aykanat. SIAM Journal of Scientific Computing, Vol. 34, No. 2, pp. A970-A992, 2012. Also available as technical report.
  4. Improving Performance of Adaptive Component-Based Dataflow Middleware. T.D.R. Hartley, E. Saule and U.V. Catalyurek. Parallel Computing, Vol. 38, No. 6-7, pp. 289-309, 2012.
  5. Optimizing dataflow applications on heterogeneous environments. G. Teodoro, T. Hartley, U.V. Catalyurek, and R. Ferreira. Cluster Computing, Vol. 15, No. 2, pp. 125-144, 2012.
  6. Optimizing the maximum stretch of independent tasks on a cluster: From sequential tasks to moldable tasks. E. Saule, D. Bozdag, and U.V. Catalyurek. Journal of Parallel and Distributed Computing, Vol. 72, No. 4, pp. 489-503, 2012.
  7. Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures. U.V. Catalyurek, J. Feo, A.H. Gebremedhin, M. Halappanavar, and A. Pothen. Parallel Computing, Vol. 38, No. 10-11, pp. 576-594, Oct-Dec, 2012. Also available as arXiv Tech. Rep. no. arXiv:1205.3809.
  8. Microarray vs. RNA-Seq: A comparison for active subnetwork discovery. A. Hatem, K. Kaya and U.V. Catalyurek. ACM International Conference On Bioinformatics, Computational Biology and Biomedicine(ACM-BCB), Oct 2012.
  9. An Out-of-core Eigensolver on SSD-equipped Clusters. Z. Zhou, E. Saule, H.M. Aktulga, C. Yang, E.G. Ng, P. Maris, J.P. Vary, U.V. Catalyurek. Proceedings of the 2012 IEEE International Conference on Cluster Computing (Cluster 2012). Sep 2012.
  10. On shared-memory parallelization of a sparse matrix scaling algorithm. U.V. Catalyurek, K. Kaya, B. Ucar. 2012 International Conference on Parallel Processing (ICPP), Sep 2012.
  11. An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers. Z. Zhou, E. Saule, H.M. Aktulga, C. Yang, E.G. Ng, P. Maris, J.P. Vary, U.V. Catalyurek. 2012 International Conference on Parallel Processing (ICPP) Workshops, Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), Sep 2012.
  12. Direction Awareness in Citation Recommendation. O. Kucuktunc, E. Saule, K. Kaya, U.V. Catalyurek. Proceedings of the 6th International Workshop on Ranking in Databases (DBRank), Aug 2012.
  13. Fast Recommendation on Bibliographic Networks. O. Kucuktunc, K. Kaya, E. Saule, U.V. Catalyurek. Proceedings of IEEE/ACM International Conference on Social Networks Analysis and Mining (ASONAM), Aug, 2012.
  14. Large-scale ab initio configuration interaction calculations for light nuclei. P. Maris, H.M. Aktulga, M.A. Caprio, U.V. Catalyurek, E.G. Ng, D. Oryspayev, H. Potter, E. Saule, M. Sosonkina, J.P. Vary, C. Yang, Z. Zhou. Journal of Physics: Conference Series. HITES 2012: 'Horizons of Innovative Theories, Experiments, and Supercomputing in Nuclear Physics', Vol. 403, No. 012019, 2012.
  15. Multithreaded Clustering for Multi-level Hypergraph Partitioning. U.V. Catalyurek, M. Deveci, K. Kaya, and B. Ucar. Proceedings of 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS'12), May 2012. Acceptance rate 21%.
  16. An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture. E. Saule and U.V. Catalyurek. Proceedings of 26th International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP), May 2012.
  17. Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP. A.E. Sariyuce, E. Saule, and U.V. Catalyurek. Proceedings of 26th International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO'12), May 2012.
  18. Algorithms for Offline Tracking of Connected Components in Large Evolving Networks. K. Kaya, E. Saule, O. Kucukktunc, U.V. Catalyurek. Workshop on Dynamic Network Analysis (DNA-SDM), Apr 2012.
  19. UMPa: A Multi-objective, multi-level partitioner for communication minimization. U.V. Catalyurek, M. Deveci, K. Kaya, and B. Ucar. 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering, Atlanta, GA, February 13-14, 2012. Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
  20. A Divisive clustering technique for maximizing the modularity. U.V. Catalyurek, K. Kaya, J. Langguth, and B. Ucar. 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering, Atlanta, GA, February 13-14, 2012. Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
  21. Two-dimensional approaches to sparse matrix partitioning. R.H. Bisseling, B.O. Fagginger Auer, A.J. N. Yzelman, T. van Leeuwen and U.V. Catalyurek. Combinatorial Scientific Computing, Chapman & Hall / CRC Press, Editors U. Naumann, O. Schenk, 2012.
  22. Parallel Partitioning, Coloring, and Ordering for Scientific Computing. E.G. Boman, U.V. Catalyurek, C. Chevalier, and K.D. Devine. Combinatorial Scientific Computing, Chapman & Hall / CRC Press, Editors U. Naumann, O. Schenk, 2012.

2011:

  1. Hypergraph Partitioning. U.V. Catalyurek, B. Ucar, and C. Aykanat. Encyclopedia of Parallel Computing, Springer, Editor-in-chief D. Padua, pp. 871-881, 2011.
  2. PaToH (Partitioning Tool for Hypegraphs). U.V. Catalyurek and C. Aykanat. Encyclopedia of Parallel Computing, Springer, Editor-in-chief D. Padua, pp. 1479-1487, 2011.
  3. Hypergraph Partitioning-Based Fill-Reducing Ordering. U.V. Catalyurek, C. Aykanat and E. Kayaaslan. SIAM Journal of Scientific Computing, Vol. 33, No. 4, pp. 1996-2023, 2011. Also available as Tech Rep.
  4. Optimizing Latency and Throughput of Application Workflows on Clusters.N. Vydyanathan, U.V. Catalyurek, T.M. Kurc, P. Sadayappan, and J.H. Saltz. Parallel Computing, Vol. 37, No. 10-11, pp. 694-712, Oct 2011.
  5. KELVIN: a Software Package for Rigorous Measurement of Statistical Evidence in Human Genetics. V.J. Vieland, Y. Huang, S.C. Seok, J. Burian, U.V. Catalyurek, J. O'Connell, A. Segre, W. Valentine-Cooper. Human Heredity, Vol 72, No. 5, pp. 276-288, 2011.
  6. Load-Balancing Spatially Located Computations using Rectangular Partitions. ArXiv, no. arXiv:1104.2566v1, 2011.
  7. Improving Graph Coloring on Distributed Memory Parallel Computers. A.E. Sariyuce, E. Saule and U.V. Catalyurek. Proceedings of 18th Annual International Conference on High Performance Computing (HiPC 2011), Dec 2011. Acceptance rate 19%.
  8. Benchmarking Short Sequence Alignment Tools. A. Hatem, D. Bozdag, and U.V. Catalyurek, IEEE International Conference on Bioinformatics and Biomedicine (BIBM11), Nov 2011.
  9. Dynamic Decision and Data-Driven Strategies for the Optimal Management of Subsurface Geo-Systems. M. Parashar, H. Klie, T.M. Kurc, U.V. Catalyurek, J.H. Saltz, and M. Wheeler. Journal of Algorithms & Computational Technology, Vol. 5, No. 4, pp. 645-665, 2011.
  10. On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections. H.M. Aktulga, C. Yang, U.V. Catalyurek, P. Maris, J.P. Vary, and E. G. Ng. Workshop on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (HPSS 2011), in conjunction with the Euro-Par, Aug 29, 2011.
  11. Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation. L. Cooper, J. Saltz, U.V. Catalyurek, K. Huang. Proceedings of the IEEE Health Informatics and Systems Biology Conference, San Jose, CA, Jul 2011.
  12. Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds. U.V. Catalyurek, K. Kaya, and B. Ucar. The Fourth International Workshop on Data Intensive Distributed Computing (DIDC 2011), in conjunction with the 20th International Symposium on High Performance Distributed Computing (HPDC 2011), Jun 8, 2011.
  13. Partitioning Spatially Located Computations using Rectangles. E. Saule, E.O. Bas and U.V. Catalyurek. Proceedings of 25th IEEE International Parallel & Distributed Processing Symposium (IPDPS'11), May 2011. Acceptance rate 20%
  14. Distributed-Memory Parallel Algorithms for Matching and Coloring. U.V. Catalyurek, F. Dobrian, A. Gebremedhin, M. Halappanavar, and A. Pothen. Proceedings of 2011 International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO'11), May 2011.
  15. The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases. D. A. Janies, T. Treseder, B. Alexandrov, F. Habib, J. J. Chen, R. Ferreira, U. Catalyurek, A. Varon, W. C. Wheeler. Cladistics, Vol. 27, No. 1, pp. 61-66, Feb 2011.
  16. Color and Texture Analysis on Emerging Parallel Architectures. F. Igual, R. Mayo, T. Hartley, U.V. Catalyurek, A. Ruiz, and M. Ujaldon. International Journal of High Performance Computing Applications, Vol. 25, No. 4, pp. 404-427, 2011.

2010:

  1. Distributed-memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation. D. Bozdag, U. Catalyurek, A. H. Gebremedhin, F. Manne, E.G. Boman, and F. Ozguner. SIAM Journal of Scientific Computing, Vol. 32, No. 4, pp. 2418-2446, 2010.
  2. Automatic Dataflow Application Tuning for Heterogeneous Systems. T.D.R. Hartley, E. Saule and U.V. Catalyurek. Proceedings of 17th Annual International Conference on High Performance Computing (HiPC 2010), Dec 2010. Acceptance rate 19%
  3. Run-time optimizations for replicated dataflows on heterogeneous environments. G. Teodoro, T. Hartley, U.V. Catalyurek, and R. Ferreira. The ACM International Symposium on High Performance Distributed Computing (HPDC), 2010. Best Student Paper Award.
  4. Comparative Analysis of Biclustering Algorithms.D. Bozdag, A. Kumar, and U.V. Catalyurek. ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB), 2010.
  5. Dataflow Frameworks for Emerging Heterogeneous Architectures and Their Applications to Biomedicine. U.V. Catalyurek, and R. Ferreira, T. D. R. Hartley, R. Sachetto, G. Teodoro. Scientific Computing with Multicore and Accelerators, Chapman & Hall / CRC Press, Editors J. Dongarra, D. A. Bader, and J. Kurzak, 2010.
  6. A Moldable Online Scheduling Algorithm and Its Application to Parallel Short Sequence Mapping. E. Saule, D. Bozdag, and U.V. Catalyurek. Proceedings of the 15th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2010), in conjunction with IPDPS 2010.
  7. Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform. D. Bozdag, A. Hatem, U. Catalyurek. 9th IEEE International Workshop on High Performance Computational Biology (HiCOMB), 2010.
  8. On two-dimensional sparse matrix partitioning: Models, Methods, and a Recipe. U. Catalyurek, C. Aykanat and B. Ucar. SIAM Journal of Scientific Computing, Vol. 32, No. 2, pp. 656-683, 2010.
  9. Development of a code-agnostic computational infrastructure for the dynamic generation of accident progression even trees. U.V. Catalyurek, B. Rutt, K. Metzroth, A. Hakobyan, T. Aldemir, R. Denning, S. Dunagan and D. Kunsman. Reliability Engineering & System Safety, Vol. 95, No. 3, pp. 278-294, 2010.
  10. A matrix partitioning interface to PaToH in MATLAB. B. Ucar, U.V. Catalyurek, and C. Aykanat. Parallel Computing, Vol. 36, No. 5-6, pp. 254 - 272, Jun 2010.
  11. On scalability of hypergraph models for sparse matrix partitioning. B. Ucar and U.V. Catalyurek. Proceedings of the PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing.

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2009:

  1. Hypergraph-based Dynamic Partitioning and Load Balancing U.V. Catalyurek, D. Bozdag, E.G. Boman, K.D. Devine, R. Heaphy and L.A. Riesen. Advanced Computational Infrastructures for Parallel/Distributed Adaptive Applications, Wiley Press, Editors M. Parashar, X. Li, S. Chandra, Dec 2009.
  2. A Repartitioning Hypergraph Model for Dynamic Load Balancing. U.V. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R.T. Heaphy, and L.A. Riesen. Journal of Parallel and Distributed Computing, Vol. 69, No. 8, pp. 711-724, Aug 2009.
  3. Hypergraph Partitioning-Based Fill-Reducing Ordering. U.V. Catalyurek, C. Aykanat and E. Kayaaslan. Technical Report, OSUBMI-TR-2009-n02, The Ohio State University, Department of Biomedical Informatics, also available as BU-CE-0904, Bilkent University, Computer Engineering Department, 2009.
  4. An Integrated Approach to Locality Conscious Processor Allocation and Scheduling of Mixed Parallel Applications. N. Vydyanathan, S. Krishnamoorthy, G. Sabin, U. Catalyurek, T. Kurc, P. Sadayappan, and J. Saltz, IEEE Transaction on Parallel and Distributed Systems, Vol. 20, No. 9, Aug 2009.
  5. Compaction of Schedules and a Two-Stage Approach for Duplication-Based DAG Scheduling. D. Bozdag, F. Ozguner, U.V. Catalyurek. IEEE Transaction on Parallel and Distributed Systems, Vol. 20, No. 6, pp. 857-871, Jun 2009.
  6. Stroma classification for neuroblastoma on graphics processors. A. Ruiz, O. Sertel, M. Ujaldon, U.V. Catalyurek, J. H. Saltz, M. N. Gurcan, International Journal of Data Mining and Bioinformatics, Vol. 3, No. 3, pp. 280-298, Jun 2009.
  7. Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications. G. Teodoro, R. Sachetto, O. Sertel, M. Gurcan, W. Meira Jr., U. Catalyurek and R. Ferreira. Proceedings of the 2009 IEEE International Conference on Cluster Computing, 2009.
  8. Investigating the Use of GPU-Accelerated Nodes for SAR Image Formation. T. D. R. Hartley, A. R. Fasih, C. A. Berdanier, F. Ozguner, and U.V. Catalyurek. Proceedings of the 2009 IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC), 2009.
  9. Parallel Short Sequence Mapping for High Throughput Genome Sequencing. D. Bozdag, C. C. Barbacioru, U.V. Catalyurek. Proceedings of 23rd IEEE International Parallel & Distributed Processing Symposium (IPDPS'09), Acceptance rate 23%, May 2009.
  10. A Component-Based Framework for the Cell Broadband Engine. T. Hartley and U. Catalyurek. Proceedings of 23rd International Parallel and Distributed Processing Symposium (IPDPS'09), The 18th Heterogeneous Computing Workshop (HCW 2009), May 2009.
  11. Combinatorial Problems in High-Performance Computing: Partitioning R. Bisseling, T. van Leeuwen and U.V. Catalyurek. Dagstuhl Seminar Proceedings - Combinatorial Scientific Computing, Editors U. Naumann, O. Schenk, H.D. Simon and S. Toledo, 2009.
  12. Getting Started with Zoltan: A Short Tutorial K.D. Devine, E.G. Boman, L.A Riesen, U.V. Catalyurek and C. Chevalier. Dagstuhl Seminar Proceedings - Combinatorial Scientific Computing, Editors U. Naumann, O. Schenk, H.D. Simon and S. Toledo, 2009.
  13. Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core CPUs and GPUs. U.V. Catalyurek, T. Hartley, O. Sertel, M. Ujaldon. A. Ruiz, J. Saltz, and M. Gurcan. Trends in High Performance and Large Scale Computing, Vol 18, IOS Press, 2009.
  14. High-Performance Signal Processing on Emerging Many-Core Architectures Using CUDA . M. Ujaldon and U. Catalyurek. 2009 IEEE International Conference on Multimedia and Expo (ECME2009), Multimedia Signal Processing and Novel Parallel Computing Workshop, Cancun Mexico, Jul 2009.
  15. A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets. Bozdag, J. D. Parvin, and U.V. Catalyurek. Proceedings of First International Conference on Bioinformatics and Computational Biology (BICoB), 2009.
  16. 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. Parvin, T. Huang, U. Catalyurek, K. Huang. Proceedings of First International Conference on Bioinformatics and Computational Biology (BICoB), 2009.
  17. Computer-aided Prognosis of Neuroblastoma on Whole-slide Images: Classification of Stromal Development. O. Sertel, J. Kong, H. Shimada, U.V. Catalyurek, J. H. Saltz and M. N. Gurcan, Special Issue of Pattern Recognition on Digital Image Processing and Pattern Recognition Techniques for the Detection of Cancer, Vol. 42, No. 6, pp. 1093-1103, 2009.
  18. Histopathological image analysis using model-based intermediate representation and color texture: Follicular Lymphoma grading . O. Sertel, J. Kong, U.V. Catalyurek, G. Lozanski, J. H. Saltz and M. N. Gurcan, Journal of Signal Processing Systems for Signal, Image, and Video Technology, Vol. 55, No. 1, 169-183, Apr 2009.

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2008:

  1. Dynamic Generation of Accident Progression Event Trees. A. Hakobyan, K. Metzroth, T. Aldemir, R. Denning, S. Dunagan, D. Kunsman, B. Rutt, and U. Catalyurek, Nuclear Engineering and Design, Vol. 238, Issue 12, pp. 3457-3467, Dec 2008.
  2. A Framework for Scalable Greedy Coloring on Distributed Memory Parallel Computers. D. Bozdag, A. Gebremedhin, F. Manne, E.G. Boman, U.V. Catalyurek, Journal of Parallel and Distributed Computing, Vol. 68, No. 4, pp. 515-535, 2008.
  3. Large-scale Biomedical Image Analysis in Grid Environments . V. S. Kumar, B. Rutt, T. Kurc, U. Catalyurek, T. Pan, S. Chow, S. Lamont, M. Martone, J. Saltz. IEEE Transactions on Information Technology in Biomedicine, Vol. 12, No. 2, pp. 154-161, Mar 2008.
  4. Using Overlays For Efficient Data Transfer Over Shared Wide-Area Networks. G. Khanna, U. Catalyurek, T.Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, and J. Saltz, Proceedings of SC2008 High Performance Computing, Networking, and Storage Conference, Nov 2008. Acceptance rate 21%
  5. A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows N. Vydyanathan, U. Catalyurek, T. Kurc, J. Saltz, and P. Sadayappan. 2008 International Conference on Parallel Processing, pp. 254-261, Sep 2008.
  6. Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores. T. Hartley, U. Catalyurek, A. Ruiz, M. Ujaldon, F. Igual, R. Mayo, Proceedings of 22nd ACM International Conference on Supercomputing (ICS’08), Jun 2008.
  7. Optimizing co-occurrence matrices on graphics processors using sparse representations. F. Igual, R. Mayo, T. Hartley, U. Catalyurek, A. Ruiz, M. Ujaldon. 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing. Trondheim, Norway, May 2008.
  8. A Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTP. G. Khanna, U. Catalyurek, T.Kurc, R. Kettimuthu, P. Sadayappan, and J. Saltz, Proceedings of 22nd IEEE International Parallel & Distributed Processing Symposium (IPDPS’08), Apr 2008.
  9. Texture classification using non-linear color quantization:Application to histopathological image analysis.O. Sertel, J. Kong, G Lozanski, U. Catalyurek, J. Saltz, M. Gurcan, Proceedings of IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP 2008), 2008.
  10. Computer-aided prognosis of neuroblastoma: classification of stromal development on whole-slide images. O. Sertel, J. Kong, H. Shimada, U. Catalyurek, J. Saltz, M. Gurcan, Proceedings of SPIE Medical Imaging, Feb 2008.
  11. Computerized microscopic image analysis of follicular lymphoma. O. Sertel, J. Kong, U. Catalyurek, J. Saltz, M. Gurcan, G. Lozanski, Proceedings of SPIE Medical Imaging, Feb 2008.

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2007:

  1. A Knowledge-Anchored Integrative Image Search and Retrieval System . S. Erdal, U.V. Catalyurek, P. R. Payne, J. Kamal, J. H. Saltz, M. N. Gurcan, Journal of Digital Imaging, 2007.
  2. 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, pp. 12058, 2007.
  3. Combinatorial Algorithms for Petascale Science. A. Pothen, A. H. Gebremedhin, F. Dobrian, E.G. Boman, K.D. Devine, P.D. Hovland, B. Norris, J. Utke, U.V. Catalyurek, and M. M. Strout. SciDAC Review, No. 5, pp. 26-35, Fall 2007.
  4. Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations. U.V. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R. Heaphy, L.A. Riesen. Proceedings of 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS’07), 2007. Best Paper Award in the Algorithms track.
  5. Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma. A. Ruiz, O. Sertel, M. Ujaldon, U.V. Catalyurek, M. N. Gurcan, J. H. Saltz. Proceedings IEEE Intl. Conference on BioInformation and BioMedicine, 2007.
  6. Computerized Pathological Image Analysis For Neuroblastoma Prognosis. M. N. Gurcan, J. Kong, O. Sertel, B. B. Cambazoglu, J. H. Saltz, U.V. Catalyurek. 2007 AMIA Annual Symposium, 2007.
  7. Performance vs. Accuracy Trade-offs for Large-scale Image Analysis. V. S. Kumar, T. M. Kurc, J. Kong, U.V. Catalyurek, M. N. Gurcan, J. H. Saltz. Proceedings of the IEEE Cluster 2007, 2007.
  8. Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters. G. Khanna, U. Catalyurek, T.Kurc, P. Sadayappan, and J. Saltz. Proceedings of Euro-Par, Aug 2007. Acceptance rate 27%.
  9. Toward Optimizing Latency under Throughput Constraints for Application Workflows on Clusters. N. Vydyanathan, U. Catalyurek, T. Kurc, J. Saltz, and P. Sadayappan. Proceedings of Euro-Par, Aug 2007. Acceptance rate 27%.
  10. Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma. B. B. Cambazoglu, O. Sertel, J. Kong, J. Saltz, M. N. Gurcan, U.V. Catalyurek. Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE’07), Jun 2007.
  11. Intelligent Optimization of Parallel and Distributed Applications. B. Bansal, Ü. V. Çatalyürek, J. Chame, C. Chen, E. Deelman, Y. Gil, M. W. Hall, V. Kumar, T. M. Kurç, K. Lerman, A. Nakano, Yoon-Ju Lee Nelson, J. H. Saltz, A. Sharma, P. Vashishta, IPDPS 2007.
  12. A global address space framework for locality aware scheduling of block-sparse computations. S. Krishnamoorthy, Ü. V. Çatalyürek, J. Nieplocha, A. Rountev, P. Sadayappan, IPDPS 2007.
  13. An Efficient and Reliable Scientific Workflow System. T. Tavares, G. Teodoro, T. M. Kurç, R. Ferreira, D. O. G. Neto, W. Meira Jr., Ü. V. Çatalyürek, S. Hastings, S. Oster, S. Langella, J. H. Saltz. CCGRID 2007, pp. 445-452, May 2007.
  14. Dynamic Data-Driven Systems Approach for Simulation Based Optimizations. T. M. Kurç, X. Zhang, M. Parashar, H. Klie, M. F. Wheeler, Ü. V. Çatalyürek, J. H. Saltz. International Conference on Computational Science (1) 2007, Lecture Notes in Computer Science 4487 Springer 2007, pp. 1213-1221, May 2007.

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2006:

  1. Models, methods and middleware for grid-enabled multiphysics oil reservoir management. H. Klie, W. Bangerth, X. Gai, M.F. Wheeler, P.L. Stoffa, M. Sen, M. Parashar, U. Catalyurek, J. Saltz, and T. Kurc. Engineering with Computers, Springer Verlag, 2006.
  2. Supporting Scalable and Distributed Data Subsetting and Aggregation in Large-Scale Seismic Data Analysis. X. Zhang, B. Rutt, U. Catalyurek, T. Kurc, P. Stoffa, M.Sen, and J. Saltz. The International Journal of High Performance Computing Applications, Vol. 20, No. 3, pp. 423-438, 2006.
  3. An XML-based System for Synthesis of Data from Disparate Databases. T. Kurc, D.A. Janies, A. Johnson, S. Langella, S. Oster, S. L. Hastings, F. Habib, T. Camerlengo, D.W. Ervin, U.V. Catalyurek, and J.H. Saltz. Journal of the American Medical Informatics Association, Vol. 13, No. 3, May/June, 2006
  4. Hypergraph Partitioning for Automatic Memory Hierarchy Management. S. Krishnamoorthy, U. Catalyurek, J. Nieplocha, A. Rountev and P. Sadayappan. Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, Nov 2006. Acceptance rate 23%.
  5. Large Image Correction and Warping in a Cluster Environment. V. S. Kumar, B. Rutt, T. Kurc, U. Catalyurek, S. Chow, S. Lamont, and J. Saltz. Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, Nov 2006. Acceptance rate 23%.
  6. MSSG: A Framework for Massive Scale Semantic Graphs. T. Hartley, U. Catalyurek, F. Özgüner, A. Yoo, S. Kohn and K. Henderson. Proceedings of 2006 IEEE International Conference on Cluster Computing, Sep 2006.
  7. Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs. D. Ucar, S. Asur, U. Catalyurek, and S. Parthasarathy. In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), Sep 2006.
  8. Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications. N. Vydyanathan, S. Krishnamoorthy, G. Sabin, U. Catalyurek, T. Kurc, P. Sadayappan, and Joel Saltz. Proceedings of 2006 IEEE International Conference on Cluster Computing, Sep 2006.
  9. On Creating Efficient Object-relational Views of Scientific Datasets. S. Narayanan, T. Kurc, U. Catalyurek, and J. Saltz. Proceedings of the 2006 International Conference on Parallel Processing (ICPP-06), Aug 2006.
  10. An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications. N. Vydyanathan, S. Krishnamoorthy, G. Sabin, U. Catalyurek, T. Kurc, P. Sadayappan, and J. Saltz. Proceedings of the 2006 International Conference on Parallel Processing (ICPP-06), Aug 2006.
  11. Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries. L. Weng, U. Catalyurek, T. Kurc, G. Agrawal, and J. Saltz. Proceedings of the 2006 International Conference on Parallel Processing (ICPP-06), Aug 2006.
  12. A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File Sharing. G. Khanna, U. Catalyurek, T.Kurc, P. Sadayappan, and J. Saltz. Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006, Saint-Malo, France, Jun 2006.
  13. Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/O. G. Khanna, N. Vydyanathan, U. Catalyurek, T.Kurc, S. Krishnamoorthy, P. Sdayappan, and J. Saltz. Proceedings of the 15th IEEE International Symposium on High-Performance Distributed Computing (HPDC-15), pp. 241-252, Paris, France, Jun 2006. Acceptance rate 15%.
  14. Distributed Dynamic Event Tree Generation for Reliability and Risk Assessment. B. Rutt, U. Catalyurek, A. Hakobyan, K. Metzroth, T. Aldemir, R. Denning, S. Dunagan, and D. Kunsman. Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE’06), pp. 61-70, Jun 2006.
  15. Parallel Hypergraph Partitioning for Scientific Computing. K.D. Devine, E.G. Boman, R.T. Heaphy, R, H. Bisseling, and U.V. Catalyurek. Proceedings of 20th IEEE International Parallel & Distributed Processing Symposium (IPDPS’06), 2006. Acceptance rate 24%.
  16. Scheduling of Tasks with Batch-shared I/O on Heterogeneous Systems. N. Vydyanathan, G. Khanna, U. Catalyurek, T. Kurc, J. Saltz, and P. Sadayappan. Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), The 15th Heterogeneous Computing Workshop (HCW 2006), 2006.
  17. A Task Duplication Based Bottom-Up Scheduling Algorithm for Heterogeneous Environments. D. Bozdag, U. Catalyurek, and F. Ozguner. Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), The 15th Heterogeneous Computing Workshop (HCW 2006), 2006.
  18. An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions. S. Krishnamoorthy, U. Catalyurek, J. Nieplocha, A. Rountev, and P. Sadayappan. Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Next Generation Software (NGS), 2006.
  19. An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming Model. S. Krishnamoorthy, U. Catalyurek, J. Nieplocha, and P. Sadayappan. Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL 2006), 2006.

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2005:

  1. XML database support for distributed execution of data-intensive scientific workflows. S. Hastings, M. Ribeiro, S. Langella, S. Oster, U.V. Catalyurek, T. Pan, K. Huang, R. Ferreira, J. H. Saltz, T. M. Kurc. SIGMOD Record 34(3): 50-55, September 2005.
  2. A Simulation and Data Analysis System for Large Scale, Data-Driven Oil Reservoir Simulation Studies. T. Kurc, U. Catalyurek, X. Zhang, J. Saltz, R. Martino, M. Wheeler, M. Peszynska, A. Sussman, C. Hansen, M. Sen, R. Seifoullaev, P. Stoffa, C. Torres-Verdin, M. Parashar. Concurrency and Computation: Practice and Experience, John Wiley and Sons, Vol. 17, No 11, pp. 1441-1467, September 2005.
  3. A Grid Based Image Archival and Analysis System. S. Hastings, S. Oster, S. Langella, T. M. Kurc, T. Pan, U.V. Catalyurek, and J. H. Saltz. Journal of American Medical Informatics Association, Vol. 12, No. 3, May/June 2005.
  4. Application of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies. M. Parashar, H. Klie, U. Catalyurek, T. Kurc, V. Matossian, J. Saltz and M Wheeler. FGCS – The International Journal of Grid Computing: Theory, Methods and Applications, Elsevier Science Publishers, Vol. 21, Issue 1, pp. 19-26, 2005.
  5. Tools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data. M. Ribeiro, T. Kurc,Tony Pan, K. Huang, U. Catalyurek, X. Zhang, S. Langella, S. Hastings, S. Oster, R. Ferreira and J. Saltz. Grid Computing: The New Frontier Of High Performance Computing, 14, Elseiver, Lucio Grandinetti, 2005.
  6. Virtual Microscopy: Distributed Image Storage, Retrieval, Analysis, and Visualization. T. C Pan, D. Cowden, U. V Catalyurek, S. Jewell, S. Hastings, S. Oster, S. Langella, T. M Kurc, J. H Saltz. Parallel Computing in Bioinformatics, John Wiley & Sons, Albert Zomaya, 2005.
  7. A Scalable Distributed Parallel Breadth-First Search Algorithm on BlueGene/L. A. Yoo, E. Chow, K. Henderson, W. McLendon, B. Hendrickson and U. Catalyurek Proceedings of SC2005 High Performance Computing, Networking, and Storage Conference, Nov 2005, Gordon Bell Finalist.
  8. A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers. D. Bozdag, U. Catalyurek, A. H. Gebremedhin, F. Manne, E.G. Boman, and F. Ozguner. Proceedings of the 2005 International Conference on High Performance Computing and Communications (HPCC-05), Sep 2005.
  9. Servicing Seismic and Oil Reservoir Simulation Data. S. Narayanan, T. Kurc, U. Catalyurek, and J. Saltz. VLDB Workshop on Data Management in Grids, Sep 2005.
  10. Distributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying. B. Rutt, V. S. Kumar, T. Pan, T. Kurc, U. Catalyurek, Y. Wang, J. Saltz. Proceedings of the 2005 IEEE International Conference on Cluster Computing, Sep 2005, appeared in Outstanding Papers Session.
  11. An Efficient Parallel Graph Coloring Algorithm for Distributed Memory Computers. E.G. Boman, D. Bozdag, U. Catalyurek, A. H. Gebremedhin, and F. Manne. Proceedings of Euro-Par, Sep 2005. Acceptance rate 31%.
  12. A Task Duplication Based Scheduling Algorithm Using Partial Schedules. D. Bozdag, F. Ozguner, E. Ekici, and U. Catalyurek. Proceedings of the 2005 International Conference on Parallel Processing (ICPP-05).
  13. Towards Dynamic Data-Driven Optimization of Oil Well Placement. M. Parashar, V. Matossian, W. Bangerth, H. Klie, B. Rutt, T. Kurc, U. Catalyurek, J. Saltz, M. F. Wheeler. Proceedings of the Workshop on Distributed Data Driven Applications and Systems, International Conference on Computational Science 2005 (ICCS 2005), Lecture Notes in Computer Science, Volume 3515, Apr 2005, Pages 656 – 663.
  14. Servicing Range Queries on Multidimensional Datasets with Partial Replicas. L. Weng, U. Catalyurek, T. Kurc, G. Agrawal, and J. Saltz. Proceedings of the Cluster Computing and Grid 2005 (CCGrid05).
  15. A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batch-shared I/O. G. Khanna, N. Vydyanathan, T. Kurc, U. Catalyurek, P. Wyckoff, J. Saltz, and P. Sadayappan. Proceedings of the Cluster Computing and Grid 2005 (CCGrid05).
  16. Design and Implementation of A Data Server using a Peer-to-Peer Storage System. V.S. Kumar, T. Kurc, U. Catalyurek, and J. Saltz. Proceedings of High Performance Computing Symposium (HPC 2005), 2005.
  17. A Runtime Framework for Partial Replication and Its Application for On-Demand Data Exploration. S. Narayanan, U. Catalyurek, T. Kurc, V.S. Kumar, and J. Saltz. Proceedings of High Performance Computing Symposium (HPC 2005), 2005.
  18. Grid-based Management of Biomedical Data using an XML-based Distributed Data Management System. S. Hastings, S. Langella, S. Oster, T. Kurc, T. Pan, U. Catalyurek, D. Janies, and J. Saltz. Proceedings of 20th ACM Symposium on Applied Computing (SAC2005) Bioinformatics Track, Santa Fe, New Mexico, March 2005.

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2004:

  1. Permuting Sparse Rectangular Matrices into Block-Diagonal Form. C. Aykanat, A. Pinar and U.V. Catalyurek. SIAM Journal of Scientific Computing, Vol. 25, No. 6, pp. 1860-1879, 2004.
  2. Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O. N. Vydyanathan, G. Khanna, T. Kurc, U. Catalyurek, P. Wyckoff, J. Saltz, and P. Sadayappan. Proceedings of the Fifth IEEE/ACM International Workshop on Grid Computing (Grid 2004), 2004.
  3. Supporting SQL-3 Aggregations on Grid-based Data. L. Weng, G. Agrawal, U. Catalyurek, and J. Saltz. Proceedings of the 17th International Workshop on Languages and Compilers for Parallel Computing (LCPC 2004), September 2004.
  4. A Distributed Data Management Middleware for Data-Driven Application Systems. S. Langella, S. Hastings, S. Oster, T. Kurc, U. Catalyurek, and J. Saltz. Proceedings of the 2004 IEEE International Conference on Cluster Computing, September 2004.
  5. An Approach for Automatic Data Virtualization.  L. Weng, G. Agrawal, U. Catalyurek, T. Kurc, S. Narayanan, and J. Saltz. Proceedings of the Thirteen IEEE International Symposium on High-Performance Distributed Computing (HPDC-13), June 2004.
  6. Strategies for Using Additional Resources in Parallel Hash-based Join Algorithms. X. Zhang, T. Kurc, T. Pan, U. Catalyurek, S. Narayanan, P. Wyckoff, and J. Saltz.Proceedings of the Thirteen IEEE International Symposium on High-Performance Distributed Computing (HPDC-13), June 2004.
  7. Application of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies. M. Parashar, H. Klie, U. Catalyurek, T. Kurc, V. Matossian, J. Saltz and M Wheeler. Proceedings of the Workshop on Distributed Data Driven Applications and Systems, International Conference on Computational Science 2004 (ICCS 2004) , Krakow, Poland, June 2004.
  8. Serving Queries to Multi-Resolution Datasets on Disk-based Storage Cluster. X. Zhang, T. Pan, U. Catalyurek, T. Kurc and J. Saltz. Proceedings of the 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID 2004), April 2004.

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2003:

  1. The Virtual Microscope. U. Catalyurek, M. D. Beynon, C. Chang, T. Kurc, A. Sussman, and J. Saltz. IEEE Transactions on Information Technology in Biomedicine, Vol. 7, No. 4, pp. 230-248, 2003.Database Support for
  2. Data-driven Scientific Applications in the Grid. S. Narayanan, T. Kurc, U. Catalyurek, J. Saltz. Parallel Processing Letters, Vol. 13, No. 2, pp. 245-271, 2003.
  3. Optimizing Reduction Computations In a Distributed Environment. T. Kurc, F. Lee, G. Agrawal, U. Catalyurek, R. Ferreira and J. Saltz. ACM Press. Proceedings of the 2003 ACM/IEEE SC2003 Conference, Phoenix, AZ, November 2003.
  4. Applying Database Support for Large Scale Data Driven Science in Distributed Environments. S. Narayanan, U. Catalyurek, T. Kurc, X. Zhang and J. Saltz. Proceedings of the Fourth International Workshop on Grid Computing (Grid 2003), pp. 141-148, 2003.
  5. Impact of High Performance Sockets on Data Intensive Applications. P. Balaji, J. Wu, T. Kurc, U. Catalyurek, D. K. Panda, J. Saltz. Proceedings of the Twelfth IEEE International Symposium on High-Performance Distributed Computing (HPDC-12), June 2003.
  6. Driving Scientific Applications by Data in Distributed Environments. J. Saltz, U. Catalyurek, T. Kurc, M. Gray, S. Hastings,  S. Langella, S. Narayanan,  R. Martino, S. Bryant, M. Peszynska, M. Wheeler, A. Sussman,  M. Beynon, C. Hansen, D. Stredney, and D. Sessanna. Workshop on Dynamic Data-Driven Application Systems
    ICCS 2003, Melbourne, Australia, June 2003.
  7. Image Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications. S. Hastings, T. Kurc, S. Langella, U. Catalyurek, T. Pan, and J. Saltz. The 3rd IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGRID 2003), 2003.
  8. A Distributed Execution Environment for Analysis of DCE-MR Image Datasets. T. Kurc, S. Hastings,  U. Catalyurek, J. Saltz, J. D. Fleig, B. D. Clymer, H. von Tengg-Kobligk, K. T. Baudendistel, R. Machiraju, and M. V. Knopp. The Society for Computer Applications in Radiology (SCAR 2003). 2003.
  9. A Component-based Implementation of Multiple Sequence Alignment. U. Catalyurek, M. Gray, T. Kurc, J. Saltz, E. Stahlberg, and R. Ferreira. 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track, Melbourne, FL, March 2003.

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2002:

  1. Processing large-scale multidimensional data in parallel and distributed environments. M. Beynon, C. Chang, U. Catalyurek, T. Kurc, A. Sussman, H. Andrade, R. Ferreira, and J. Saltz. Parallel Computing, Vol. 28, No. 5, pp. 827-859, Special issue on Data Intensive Computing, May 2002.
  2. Executing Multiple Pipelined Data Analysis Operations in the Grid. M. Spencer, R. Ferreira, M. D. Beynon, T. Kurc, U. Catalyurek, A. Sussman, and J. Saltz. ACM Press. Proceedings of the 2002 ACM/IEEE SC2002 Conference, Baltimore, MD, November 2002.
  3. Efficient manipulation of large datasets on heterogeneous storage systems. M. D. Beynon, T. Kurc, U. Catalyurek, A. Sussman, and J. Saltz. Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), The 11th Heterogeneous Computing Workshop (HCW 2002), Fort Lauderdale, Florida, April 2002.
  4. Improving performance of multiple sequence alignment analysis in multi-client environments. U. Catalyurek, E. Stahlberg, R. Ferreira, T. Kurc, and J. Saltz. Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), First Workshop on High Performance Computational Biology, Fort Lauderdale, Florida, April 2002.
  5. Persistent Caching in a Multiple Query Optimization Framework. H. Andrade, T. Kurc, U. Catalyurek, A. Sussman, and J. Saltz. Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers, March 2002. Springer-Verlag.

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2001:

  1. Distributed Processing of Very Large Datasets with DataCutter. M. D. Beynon, T. Kurc, U. Catalyurek, C. Chang, A. Sussman, and J. Saltz. Parallel Computing, Vol. 27, No. 11, pp. 1457-1478, October 2001.
  2. Exploration and Visualization of Very Large Datasets with the Active Data Repository. T. Kurc, U. Catalyurek, C. Chang, A. Sussman, and J. Saltz. IEEE Computer Graphics & Applications, Vol. 21, No. 4, pp. 24–33, July/August, 2001.
  3. A Hypergraph-partitioning Approach for Coarse-Grain Decomposition. U. Catalyurek and C. Aykanat. Proceedings of the 2001 ACM/IEEE SC2001, Denver, CO, November 2001.
  4. Performance Optimization for Data Intensive Grid Applications. M. D. Beynon, A. Sussman, U. Catalyurek, T. Kurc, and J. Saltz. The Third Annual International Workshop on Active Middleware Services (AMS2001), August 2001.
  5. A Fine-Grain Hypergraph Model for 2D Decomposition of Sparse Matrices. U. Catalyurek and C. Aykanat. Proceedings of International Parallel and Distributed Processing Symposium (IPDPS), 8th International Workshop on Solving Irregularly structured Problems in Parallel (Irregular 2001), San Francisco, April 2001.
  6. A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregatiion. C. Chang, T. Kurc, A. Sussman, U. Catalyurek, and J. Saltz. Tenth SIAM Conference on Parallel Processing for Scientific Computing, Portsmouth, Virginia, March 2001.

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2000 and earlier:

  1. Hypergraph Models for Sparse Matrix Partitioning and Reordering. Ü. V. Çatalyürek, Ph.D. Dissertation, Computer Engineering and Information Science Bilkent University, November 1999.
  2. Hypergraph-Partitioning Based Decomposition for Parallel Sparse-Matrix Vector Multiplication. U. Catalyurek and C. Aykanat. IEEE Transaction on Parallel and Distributed Systems, Vol. 10, No. 7, pp. 673-693, 1999.
  3. Decomposing irregularly sparse matrices for parallel matrix-vector multiplications. U. Catalyurek and C. Aykanat. Lecture Notes in Computer Science, vol. 1117, pp. 75-86, 1996.
  4. Decomposing linear programs for parallel solution. A. Pinar, U. Catalyurek, C. Aykanat, and M. Pinar. Lecture Notes in Computer Science, vol. 1041, pp. 473-482, 1996.
  5. A hypergraph model for mapping repeated sparse matrix-vector product computations onto multicomputers. U.V. Catalyurek and C. Aykanat. Proceedings of International Conference on High Performance Computing, HiPC ’95, Goa, India, December 1995.
  6. A Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree Ordering. Ü. V. Çatalyürek, M.S. Thesis, Computer Engineering and Information Science Bilkent University, September 1994.

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©2006 Umit Catalyurek. Last Update: Sep 14th, 2013