Below is a list of my publications by year. This page is not updated frequently. For up to date list of publications please visit TDA Lab's Publication page. Here is another list at DBLP, Google Scholar, Semantic Scholar, or Microsoft Academic Search.
2020:
- Programming Strategies for Irregular Algorithmson the Emu Chick. E.R. Hein, S. Eswar, A. Yasar, J. Li, J.S. Young, T.M. Conte, U.V. Catalyurek, R. Vuduc, J. Riedy, and B. Ucar. ACM Transactions on Parallel Computing. to appear.
- The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features. L. Wang, A. Abu-Doleh, J. Plank, U.V. Catalyurek, J. Firkins, Z. Yu. BMC Genomics, to appear.
2019:
- DeepSparse: A Task-parallel Framework for Sparse Solvers on Deep Memory Architectures. Md Afibuzzaman, F. Rabbi, M.Y. Ozkaya, H.M. Aktulga, and U.V. Catalyurek. Proc. of the 26th Annual International Conference on High Performance Computing (HiPC 2019).
- Linear Algebra-Based Triangle Counting via Fine-Grained Tasking on Heterogeneous Environments. A. Yasar, S. Rajamanickam, J.W. Berry, M.M. Wolf, J. Young, and U.V. Catalyurek. High Performance Extreme Computing Conference (HPEC), Sep 2019. One of the Graph Challenge Innovation Award winners.
- Scalable Triangle Counting on Distributed-Memory Systems. S. Acer, A. Yasar, S. Rajamanickam, M.M. Wolf, and U.V. Catalyurek. High Performance Extreme Computing Conference (HPEC), Sep 2019. One of the Graph Challenge Innovation Award winners.
- StrainHub: A phylogenetic tool to construct pathogen transmission networks. A. de Bernardi Schneider, C.T. Ford, R/ Hostager, J. Williams, M. Cioce, U.V. Catalyurek, J.O. Wertheim, D. Janies. Bioinformatics, Aug 2019.
- Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks. M. Deveci, K.D. Devine, S. Rajamanickam, K. Pedretti, M. A. Taylor, and U.V. Catalyurek. IEEE Transaction on Parallel and Distributed Systems, Vol. 30, No. 9, pp. 2018-2032, Sep 2019.
- Multilevel Algorithms for Acyclic Partitioning of Directed Acyclic Graphs. J. Herrmann, M.Y. Ozkaya, B. Ucar, K. Kaya, and U.V. Catalyurek. SIAM Journal on Scientific Computing, Vol. 41, No. 4, pp. A2117-A2145, 2019.
- Is Acyclic Directed Graph Partitioning Effective for Locality-Aware Scheduling? M.Y. Ozkaya, A. Benoit, U.V. Catalyurek. Proc. of the 13th International Conf. on Parallel Processing and Applied Mathematics (PPAM), 2019, to appear.
- Efficient and Effective Sparse Tensor Reordering. J. Li, B. Ucar, U.V. Catalyurek, J. Sun, K. Baker and R. Vuduc. Proceedings of the ACM International Conference on Supercomputing (ICS), Jun. 2019. Acceptance rate 18%
- A scalable clustering-based task scheduler for homogeneous processors using DAG partitioning. M.Y. Ozkaya, A. Benoit, B. Ucar, J. Herrmann, and U.V. Catalyurek.Proceedings of 33rd IEEE International Parallel and Distributed Processing Symposium (IPDPS), May 2019.
2018:
- Fast Triangle Counting Using Cilk. A. Yasar, S. Rajamanickam, M. M. Wolf, J. W. Berry, and U.V. Catalyurek. High Performance Extreme Computing Conference (HPEC), Sep. 2018. One of the Graph Challenge Champions.
- SiNA: A Scalable Iterative Network Aligner. A. Yasar, B. Ucar, and U.V. Catalyurek. Proceedings of IEEE/ACM International Conference on Social Networks Analysis and Mining (ASONAM), Aug 2018.
- Local Detection of Critical Nodes in Active Networks. M.Y. Ozkaya, A.E. Sariyuce, A. Pınar, and U.V. Catalyurek. Proceedings of IEEE/ACM International Conference on Social Networks Analysis and Mining (ASONAM), Aug 2018.
- An Iterative Global Structure-Assisted Labeled Network Aligner. A. Yasar and U.V. Catalyurek. Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, Aug 2018.
- Efficient Sparse-Matrix Multi-Vector Product on GPUs . C. Hong, A. Sukumaran-Rajam, B. Bandyopadhyay, J. Kim, S. E. Kurt, I. Nisa, S. Sabhlok, U.V. Catalyurek, S. Parthasarathy, P. Sadayappan. the 27th International Symposium on High-Performance Parallel and Distributed Computing (HPDC), Jun 2018.
- 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, Vol. 78, Par 1, pp. 379-391, Jan 2018.
2017:
- Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs. A.E. Sariyuce, C. Seshadhri, A. Pinar, and U.V. Catalyurek. ACM Transactions on the Web (TWEB), Vol. 11, No. 3, Jul 2017.
- Acyclic Partitioning of Large-Scale Directed Acyclic Graphs.J. Herrmann, J. Kho, B. Ucar, K. Kaya, U.V. Catalyurek.Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), May 2017.
- Graph Manipulations for Fast Centrality Computation. A.E. Sariyuce, K. Kaya, E. Saule, and U.V. Catalyurek. ACM Transactions on Knowledge Discovery from Data, Vol 11, No. 3, Apr 2017.
2016:
- 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, Vol. 297, pp. 202-210, 2016.
- Incremental k-core Decomposition: Algorithms and Evaluation. A.E. Sariyuce, G. Gedik, G. Jacques-Silva,The VLDB Journal, Vol. 25, No. 3, pp. 425-447, 2016.
- 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, Vol. 30, No. 4, pp. 819-847, 2016.
- 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.
- 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:
- 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.
- 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.
- 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.
- 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.
- 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.
- Spaler: Spark and GraphX based de novo genome assembler. A. Abu-Doleh and U.V. Catalyurek. IEEE International Conference on BigData, Oct 2015.
- 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.
- 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.
- 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.
- 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%.
- 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.
- 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:
- 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.
- 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.
- 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.
- 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.
- 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%.
- 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.
- 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.
- 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.
- 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:
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- Incremental Algorithms for Closeness Centrality. A.E. Sariyuce, E. Saule, K. Kaya, and U.V. Catalyurek. IEEE International Conference on BigData, Oct 2013.
- 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.
- Hypergraph Sparsification and Its Application to Partitioning. M. Deveci, K. Kaya, and U.V. Catalyurek. 42nd International Conference. on Parallel Processing (ICPP), Oct 2013.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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%.
- 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.
- 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%.
- 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.
- 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
- 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.
- 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:
- 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.
- 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.
- Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs. E. Kayaaslan, A. Pinar, U.V. Catalyurek, and C. Aykanat. SIAM Journal on Scientific Computing, Vol. 34, No. 2, pp. A970-A992, 2012. Also available as technical report.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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%.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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:
- Hypergraph Partitioning. U.V. Catalyurek, B. Ucar, and C. Aykanat. Encyclopedia of Parallel Computing, Springer, Editor-in-chief D. Padua, pp. 871-881, 2011.
- 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.
- Hypergraph Partitioning-Based Fill-Reducing Ordering. U.V. Catalyurek, C. Aykanat and E. Kayaaslan. SIAM Journal on Scientific Computing, Vol. 33, No. 4, pp. 1996-2023, 2011. Also available as Tech Rep.
- 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.
- 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.
- Load-Balancing Spatially Located Computations using Rectangular Partitions. ArXiv, no. arXiv:1104.2566v1, 2011.
- 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%.
- Benchmarking Short Sequence Alignment Tools. A. Hatem, D. Bozdag, and U.V. Catalyurek, IEEE International Conference on Bioinformatics and Biomedicine (BIBM11), Nov 2011.
- 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.
- 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.
- 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.
- 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.
- 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%
- 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.
- 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.
- 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:
- 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 on Scientific Computing, Vol. 32, No. 4, pp. 2418-2446, 2010.
- 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%
- 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.
- Comparative Analysis of Biclustering Algorithms.D. Bozdag, A. Kumar, and U.V. Catalyurek. ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB), 2010.
- 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.
- 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.
- 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.
- On two-dimensional sparse matrix partitioning: Models, Methods, and a Recipe. U. Catalyurek, C. Aykanat and B. Ucar. SIAM Journal on Scientific Computing, Vol. 32, No. 2, pp. 656-683, 2010.
- 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.
- 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.
- 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.
2009:
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
2008:
- 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.
- 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.
- 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.
- 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%
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
2007:
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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.
- 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%.
- 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%.
- 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.
- 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.
- 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.
- 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.
- 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.