publications

This page is not updated frequently. For up to date list of publications please visit TDAlab’s Publication page.

You can also check my publications at DBLP, Google Scholar, Semantic Scholar, or Microsoft Academic Search.

2022

  1. JRNL
    On Symmetric Rectilinear Matrix Partitioning
    Journal of Experimental Algorithmics, 2022.
  2. Conf
    Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning
    Bo Fang, M. Yusuf Özkaya, Ang Li, Ümit V. Çatalyürek, and Sriram Krishnamoorthy
    In IEEE International Conference on Cluster Computing, 2022, Best Paper Nominee. To appear.
  3. Tech
    A Simple and Elegant Mathematical Formulation for the Acyclic DAG Partitioning Problem
    M. Yusuf Özkaya, and Ümit V. Çatalyürek
    ArXiv arXiv:2207.13638, 2022.
  4. Conf
    FIST-HOSVD: Fused In-place Sequentially Truncated Higher Order Singular Value Decomposition
    Benjamin Cobb, Hemanth Kolla, Eric Phipps, and Ümit V. Çatalyürek
    In Platform for Advanced Scientific Computing (PASC), 2022.
  5. Conf
    Batch Dynamic Algorithm to Find k-Core Hierarchies
    Kasimir Gabert, Ali Pınar, and Ümit V. Çatalyürek
    In Proceedings of the 5th ACM SIGMOD Joint International Workshop on Graph Data Management Experiences & Systems (GRADES) and Network Data Analytics (NDA), 2022.
  6. Misc
    BOA: A Partitioned View of Genome Assembly
    Priyanka Ghosh, Xiaojing An, Patrick Keppler, Sureyya Emre Kurt, Ümit V. Çatalyürek, Sriram Krishnamoorthy, P. Sadayappan, Aravind Sukumaran Rajam, and Ananth Kalyanaraman
    Recomb-Seq 2022-12th RECOMB Satellite Workshop on Massively Parallel Sequencing, 2022, non-archival.
  7. Tech
    Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning
    Bo Fang, M. Yusuf Özkaya, Ang Li, Ümit V. Çatalyürek, and Sriram Krishnamoorthy
    ArXiv arXiv:2205.06973, 2022.
  8. Tech
    Batch Dynamic Algorithm to Find k-Cores and Hierarchies
    Kasimir Gabert, Ali Pınar, and Ümit V. Çatalyürek
    ArXiv arXiv:2203.13095, 2022, preprint of Gabert22-GRADES-NDA.
  9. JRNL
    A Block-Based Triangle Counting Algorithm on Heterogeneous Environments
    Abdurrahman Yaşar, Sivasankaran Rajamanickam, Jonathan W. Berry, and Ümit V. Çatalyürek
    IEEE Transactions on Parallel and Distributed Systems, 2022.

2021

  1. Conf
    Column-Segmented Sparse Matrix-Matrix Multiplication
    Xiaojing An, and Ümit V. Çatalyürek
    In HiPC21: 28th IEEE International Conference on High Performance Computing, Data, & Analytics, 2021.
  2. Conf
    ElGA: Elastic and Scalable Dynamic Graph Analysis
    Kasimir Gabert, Kaan Sancak, M. Yusuf Özkaya, Ali Pınar, and Ümit V. Çatalyürek
    In SC21: International Conference for High Performance Computing, Networking, Storage and Analysis, 2021.
  3. Tech
    MG-GCN: Scalable Multi-GPU GCN Training Framework
    Muhammed Fatih Balın, Kaan Sancak, and Ümit V. Çatalyürek
    ArXiv arXiv:2110.08688, 2021.
  4. Conf
    An Evaluation of Task-Parallel Frameworks for Sparse Solvers on Multicore and Manycore CPU Architectures
    Abdullah Alperen, Md Afibuzzaman, Fazlay Rabbi, M. Yusuf Özkaya, Ümit V. Çatalyürek, and Hasan Metin Aktulga
    In Proc. of 50th Int’l. Conf. on Parallel Processing (ICPP), 2021.
  5. Misc
    TRIGGER: TempoRal Interaction Graph GenEratoR
    M. Yusuf Özkaya, Ali Pınar, and Ümit V. Çatalyürek
    The Web Conference 2021, Workshop on Graph Learning Benchmarks (GLB 2021), 2021, non-archival.
  6. Conf
    PIGO: A Parallel Graph Input/Output Library
    Kasimir Gabert, and Ümit V. Çatalyürek
    In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Graphs, Architectures, Programming, and Learning (GrAPL), 2021.
  7. Conf
    Shared-Memory Scalable k-Core Maintenance on Dynamic Graphs and Hypergraphs
    Kasimir Gabert, Ali Pınar, and Ümit V. Çatalyürek
    In 2021 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Parallel and Distributed Processing for Computational Social Systems (ParSocial), 2021.
  8. Misc
    Parallel graph algorithms by blocks: from I/O to algorithms
    Abdurrahman Yaşar, Kasimir Gabert, and Ümit V. Çatalyürek
    Abstract, Proceedings of the 18th ACM International Conference on Computing Frontiers, Big Data Analytics Workshop (BigDAW), 2021.
  9. Conf
    A Unifying Framework to Identify Dense Subgraphs on Streams: Graph Nuclei to Hypergraph Cores
    Kasimir Gabert, Ali Pınar, and Ümit V. Çatalyürek
    In Proceedings of the 14th ACM International Conference on Web Search and Data Mining (WSDM), 2021.

2020

  1. Tech
    A Block-Based Triangle Counting Algorithm on Heterogeneous Environments
    Abdurrahman Yaşar, Sivasankaran Rajamanickam, Jonathan W. Berry, and Ümit V. Çatalyürek
    ArXiv arXiv:2009.12457, 2020.
  2. Tech
    On Symmetric Rectilinear Matrix Partitioning
    ArXiv arXiv:2009.07735, 2020.
  3. JRNL
    Programming strategies for irregular algorithms on the Emu Chick
    Eric Hein, Srinivas Eswar, Abdurrahman Yaşar, Jiajia Li, Jeffrey S Young, Thomas M Conte, Ümit V. Çatalyürek, Rich Vuduc, Jason Riedy, and Bora Uçar
    ACM Transactions on Parallel Computing (TOPC), 2020.
  4. Conf
    A scalable graph generation algorithm to sample over a given shell distribution
    M. Yusuf Özkaya, Muhammed Fatih Balın, Ali Pınar, and Ümit V. Çatalyürek
    In 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (IPDPSW), Workshop on Graphs, Architectures, Programming, and Learning, 2020.

2019

  1. JRNL
    The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features
    Lingling Wang, Anas Abu-Doleh, Johanna Plank, Ümit V. Çatalyürek, Jeffrey Firkins, and Zhongtang Yu
    BMC Genomics, 2019.
  2. Conf
    DeepSparse: A Task-parallel Framework for Sparse Solvers on Deep Memory Architectures
    Md Afibuzzaman, Fazlay Rabbi, M. Yusuf Özkaya, Hasan Metin Aktulga, and Ümit V. Çatalyürek
    In Proceedings of the 26th Annual International Conference on High Performance Computing (HiPC 2019), 2019.
  3. Conf
    Linear Algebra-Based Triangle Counting via Fine-Grained Tasking on Heterogeneous Environments
    Abdurrahman Yaşar, Sivasankaran Rajamanickam, Jonathan W. Berry, Michael M. Wolf, Jeffrey Young, and Ümit V. Çatalyürek
    In IEEE High Performance Extreme Computing Conference (HPEC), 2019.
  4. Tech
    Heuristics for Symmetric Rectilinear Matrix Partitioning
    Abdurrahman Yaşar, and Ümit V. Çatalyürek
    ArXiv arXiv:1909.12209, 2019.
  5. Conf
    Scalable Triangle Counting on Distributed-Memory Systems
    Seher Acer, Abdurrahman Yaşar, Sivasankaran Rajamanickam, Michael M. Wolf, and Ümit V. Çatalyürek
    In High Performance Extreme Computing Conference (HPEC), 2019 IEEE, 2019.
  6. JRNL
    StrainHub: A phylogenetic tool to construct pathogen transmission networks
    Adriano Bernardi Schneider, Colby T Ford, Reilly Hostager, John Williams, Michael Cioce, Ümit V. Çatalyürek, Joel O. Wertheim, and Daniel Janies
    Bioinformatics, 2019.
  7. JRNL
    Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks
    Mehmet Deveci, Karen D. Devine, Kevin Pedretti, Mark A. Taylor, Sivasankaran Rajamanickam, and Ümit V. Çatalyürek
    IEEE Transactions on Parallel and Distributed Systems, 2019.
  8. JRNL
    Multilevel Algorithms for Acyclic Partitioning of Directed Acyclic Graphs
    Julien Herrmann, M. Yusuf Özkaya, Bora Uçar, Kamer Kaya, and Ümit V. Çatalyürek
    SIAM Journal on Scientific Computing (SISC), 2019.
  9. Conf
    Improving Locality-Aware Scheduling with Acyclic Directed Graph Partitioning
    M. Yusuf Özkaya, Anne Benoit, and Ümit V. Çatalyürek
    In Proc. of the 13th International Conf. on Parallel Processing and Applied Mathematics (PPAM), 2019.
  10. Conf
    Efficient and Effective Sparse Tensor Reordering
    Jiajia Li, Bora Uçar, Ümit V. Çatalyürek, Jimeng Sun, Kevin Barker, and Richard Vuduc
    In Proceedings of the ACM International Conference on Supercomputing (ICS), 2019.
  11. Conf
    A scalable clustering-based task scheduler for homogeneous processors using DAG partitioning
    M. Yusuf Özkaya, Anne Benoit, Bora Uçar, Julien Herrmann, and Ümit V. Çatalyürek
    In 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS), 2019.

2018

  1. Conf
    Fast Triangle Counting Using Cilk
    Abdurrahman Yaşar, Sivasankaran Rajamanickam, Michael M. Wolf, Jonathan W. Berry, and Ümit V. Çatalyürek
    In High Performance Extreme Computing Conference (HPEC), 2018 IEEE, 2018.
  2. Conf
    SiNA: A Scalable Iterative Network Aligner
    Abdurrahman Yaşar, Bora Uçar, and Ümit V. Çatalyürek
    In IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2018.
  3. Conf
    Local Detection of Critical Nodes in Active Networks
    M. Yusuf Özkaya, Ahmet Erdem Sarıyüce, Ali Pınar, and Ümit V. Çatalyürek
    In IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2018.
  4. Conf
    An Iterative Global Structure-Assisted Labeled Network Aligner
    Abdurrahman Yaşar, and Ümit V. Çatalyürek
    In Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, 2018.
  5. Conf
    Efficient Sparse-Matrix Multi-Vector Product on GPUs
    Changwan Hong, Aravind Sukumaran-Rajam, Bortik Bandyopadhyay, Jinsung Kim, Süreyya Emre Kurt, Israt Nisa, Shivani Sabhlok, Ümit V. Çatalyürek, Srinivasan Parthasarathy, and P. Sadayappan
    In Proc. 27th International Symposium on High-Performance Parallel and Distributed Computing (HPDC), 2018.
  6. JRNL
    A Resource Provisioning Framework for Bioinformatics Applications in Multi-Cloud Environments
    Izzet F. Senturk, P.Balakrishnan, Anas Abu-Doleh, Kamer Kaya, Qutaibah Malluhi, and Ümit V. Çatalyürek
    The Future Generation Computer Systems Journal, 2018.
  7. Tech
    Acyclic partitioning of large directed acyclic graphs
    Julien Herrmann, M. Yusuf Özkaya, Bora Uçar, Kamer Kaya, and Ümit V. Çatalyürek
    Inria - Research Centre Grenoble – Rhône-Alpes RR-9163, 2018.

2017

  1. Tech
    Active Betweenness Cardinality: Algorithms and Applications
    M. Yusuf Özkaya, Ahmet Erdem Sarıyüce, Ümit V. Çatalyürek, and Ali Pınar
    ArXiv arXiv:1711.10634, 2017.
  2. Conf
    Acyclic Partitioning of Large-Scale Directed Acyclic Graphs
    Julien Herrmann, Jonathan Kho, Bora Uçar, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), 2017.
  3. JRNL
    Graph Manipulations for Fast Centrality Computation
    Ahmet Erdem Sarıyüce, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    ACM Transactions on Knowledge Discovery from Data, 2017.
  4. JRNL
    Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs
    Ahmet Erdem Sarıyüce, C. Seshadhri, Ali Pınar, and Ümit V. Çatalyürek
    ACM Transactions on the Web, 2017.

2016

  1. Misc
    Identification of key mutation signatures from conservation analysis of gene-pseudogene families in human
    Travis Johnson, Jonathan Kho, Ümit V. Çatalyürek, Kun Huang, and Yan Zhang
    Poster, journalF1000Research (ISCB Comm J) (ISMB’16), 2016.
  2. JRNL
    Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States
    Maria Hoffmann, Yan Luo, Steven R. Monday, Narjol Gonzales-Escalona, Andrea R. Ottesen, Tim Muruvanda, Charles Wang, George Kastanis, Christine Keys, Daniel Janies, Izzet F. Senturk, Ümit V. Çatalyürek, Hua Wang, Thomas S. Hammack, William J. Wolfgang, Dianna Schoonmaker-Bopp, Alvina Chu, Robert Myers, Julie Haendiges, Peter S. Evans, Jianghong Meng, Errol A. Strain, Marc W. Allard, and Eric W. Brown
    Journal of Infectious Diseases, 2016.
  3. JRNL
    Multi-jagged: A Scalable Parallel Spatial Partitioning Algorithm
    IEEE Transactions on Parallel and Distributed Systems, 2016.
  4. JRNL
    SONIC: Streaming Overlapping Community Detection
    Ahmet Erdem Sarıyüce, Bugra Gedik, Gabriela Jacques-Silva, Kun-Lung Wu, and Ümit V. Çatalyürek
    Data Mining and Knowledge Discovery (DAMI), 2016.
  5. JRNL
    Incremental k-core Decomposition: Algorithms and Evaluation
    Ahmet Erdem Sarıyüce, Bugra Gedik, Gabriela Jacques-Silva, Kun-Lung Wu, and Ümit V. Çatalyürek
    The VLDB Journal, 2016.
  6. JRNL
    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, James P. Vary, D. Langr, Erik Saule, M. A. Caprio, Ümit V. Çatalyürek, and M. Sosonkina
    Computer Physics Communications, 2016.

2015

  1. JRNL
    Phylogenetic visualization of the spread of H7 influenza A viruses
    Daniel A. Janies, Laura W. Pomeroy, Chris Krueger, Yuqi Zhang, Izzet F. Senturk, Kamer Kaya, and Ümit V. Çatalyürek
    Cladistics, 2015.
  2. Conf
    Spaler: Spark and GraphX based de novo genome assembler
    Anas Abu-Doleh, and Ümit V. Çatalyürek
    In Proc of IEEE Int’l Conference on BigData, 2015.
  3. Conf
    MICA: MicroRNA Integration for Active Module Discovery
    Ayat Hatem, Kamer Kaya, Jeffrey D. Parvin, Kun Huang, and Ümit V. Çatalyürek
    In Proc. of 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB), 2015.
  4. JRNL
    Incremental Closeness Centrality in Distributed Memory
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    Parallel Computing, 2015.
  5. Conf
    Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application
    Daniel Janies, Zachary Witter, Christian Gibson, Thomas Kraft, Izzet F. Senturk, and Ümit V. Çatalyürek
    In MEDINFO’15, 2015.
  6. Conf
    Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions
    Ahmet Erdem Sarıyüce, C. Seshadhri, Ali Pınar, and Ümit V. Çatalyürek
    In 24th International World Wide Web Conference (WWW), 2015, Best Paper Award Nominee.
  7. Conf
    Fast and High Quality Topology-Aware Task Mapping
    Mehmet Deveci, Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    In 29th IEEE International Parallel and Distributed Processing Symposium, 2015.
  8. JRNL
    Hypergraph partitioning for multiple communication cost metrics: Model and methods
    Mehmet Deveci, Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    Journal of Parallel and Distributed Computing, 2015.
  9. JRNL
    Regularizing Graph Centrality Computations
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    Journal of Parallel and Distributed Computing, 2015.
  10. Chap
    An Out-of-Core Task-based Middleware for Data-Intensive Scientific Computing
    Erik Saule, Hasan M. Aktulga, Chao Yang, Esmond G. Ng, and Ümit V. Çatalyürek
    In Handbook on Data Centers, 2015.
  11. JRNL
    Allele-specific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci
    Madelyn M. Gerber, Heather Hampel, Xiao-Ping Zhou, Nathan P. Schulz, Adam Suhy, Mehmet Deveci, Ümit V. Çatalyürek, and Amanda E. Toland
    International Journal of Cancer, 2015.
  12. JRNL
    Mitigating Bias in Planning Two-Color Microarray Experiments
    Nilgun Ferhatosmanoglu, Theodore T. Allen, and Ümit V. Çatalyürek
    International Journal of Data Mining and Bioinformatics, 2015.
  13. Chap
    Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering
    Mehmet Deveci, Onur Küçüktunç, Kemal Eren, Doruk Bozdağ, Kamer Kaya, and Ümit V. Çatalyürek
    In Methods in Molecular Biology, 2015.

2014

  1. JRNL
    Diversifying Citation Recommendations
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    ACM Transactions on Intelligent Systems and Technology, 2014.
  2. Tech
    Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions
    Ahmet Erdem Sarıyüce, C. Seshadhri, Ali Pınar, and Ümit V. Çatalyürek
    ArXiv arXiv:1411.3312, 2014.
  3. Tech
    On Distributed Graph Coloring with Iterative Recoloring
    Ahmet Erdem Sarıyüce, Erik Saule, and Ümit V. Çatalyürek
    ArXiv arXiv:1407.6745, 2014.
  4. Misc
    Computing the Closeness Centrality of Evolving Networks on Clusters
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    Poster, SIAM Workshop on Network Science (NS14), 2014.
  5. Misc
    Partitioning Hypergraphs for Multiple Communication Metrics
    Mehmet Deveci, Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    Abstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14), 2014.
  6. Conf
    Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP), 2014.
  7. Conf
    Exploiting Geometric Partitioning in Task Mapping for Parallel Computers
    Mehmet Deveci, Sivasankaran Rajamanickam, Vitus Leung, Kevin T Pedretti, Stephen L Olivier, David P. Bunde, Ümit V. Çatalyürek, and Karen D. Devine
    In 28th IEEE International Parallel and Distributed Processing Symposium, 2014.
  8. Misc
    Load Balancing and Task Mapping for Exascale Systems
    Mehmet Deveci, and Ümit V. Çatalyürek
    Poster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum, 2014, PhD Forum award
  9. Conf
    Extracting Maximal Exact Matches on GPU
    Anas Abu-Doleh, Kamer Kaya, Mohamed Abouelhoda, and Ümit V. Çatalyürek
    In 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP), 2014.
  10. JRNL
    NUSAP1 influences the DNA damage response by controlling BRCA1 protein levels
    Shweta Kotian, Tapahsama Banerjee, Ainsley Lockhart, Kun Huang, Ümit V. Çatalyürek, and Jeffrey D. Parvin
    Cancer Biology and Therapy, 2014.
  11. Conf
    Wide-area overlay networking to manage science DMZ accelerated flows
    P. Calyam, A. Berryman, Erik Saule, H. Subramoni, P. Schopis, G. Springer, Ümit V. Çatalyürek, and Dhabaleswar K. Panda
    In Computing, Networking and Communications (ICNC), 2014 International Conference on, 2014.
  12. Chap
    High-Performance Computing in High-Throughput Sequencing
    Kamer Kaya, Ayat Hatem, Hatice Gülçin Özer, Kun Huang, and Ümit V. Çatalyürek
    In Biological Knowledge Discovery Handbook, 2014.
  13. JRNL
    Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory
    Myoungsoo Jung, Ellis H. Wilson III, Wonil Choi, John Shalf, Hasan M. Aktulga, Chao Yang, Erik Saule, Ümit V. Çatalyürek, and Mahmut Kandemir
    Scientific Programming, 2014.
  14. JRNL
    mrSNP: Software to detect SNP effects on microRNA binding
    Mehmet Deveci, Ümit V. Çatalyürek, and Amanda E. Toland
    BMC Bioinformatics, 2014.
  15. JRNL
    Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT-2
    Shahid H. Bokhari, Ümit V. Çatalyürek, and Metin N. Gürcan
    Concurrency and Computation: Practice and Experience, 2014, Also available as a <a href=http://www.algopath.com/resources/algopath1.pdf>technical report</a> from Algopath LLC.

2013

  1. JRNL
    Collective Modes in Light Nuclei from First Principles
    T. Dytrych, K. D. Launey, J. P. Draayer, P. Maris, James P. Vary, Erik Saule, Ümit V. Çatalyürek, M. Sosonkina, D. Langr, and M. A. Caprio
    Physical Review Letters, 2013.
  2. JRNL
    Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows
    Lingling Wang, Ayat Hatem, Ümit V. Çatalyürek, Mark Morrison, and Zhongtang Yu
    PLoS ONE, 2013.
  3. Conf
    Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory
    Myoungsoo Jung, Ellis H. Wilson III, Wonil Choi, John Shalf, Hasan M. Aktulga, Chao Yang, Erik Saule, Ümit V. Çatalyürek, and Mahmut Kandemir
    In Proc. of Conference on High Performance Computing Networking, Storage and Analysis (SC ’13), 2013.
  4. Conf
    Incremental Algorithms for Closeness Centrality
    Ahmet Erdem Sarıyüce, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    In Proc of IEEE Int’l Conference on BigData, 2013.
  5. Conf
    A Push-Relabel-based Maximum Cardinality Bipartite Matching Algorithm on GPUs
    Mehmet Deveci, Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    In Proc. of 42nd Int’l. Conf. on Parallel Processing, 2013.
  6. Conf
    Hypergraph Sparsification and Its Application to Partitioning
    Mehmet Deveci, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of 42nd Int’l. Conf. on Parallel Processing, 2013.
  7. Conf
    Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi
    Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of the 10th Int’l Conf. on Parallel Processing and Applied Mathematics (PPAM), 2013.
  8. Conf
    STREAMER: a Distributed Framework for Incremental Closeness Centrality Computation
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of IEEE Cluster 2013, 2013.
  9. Conf
    Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication
    Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    In Proc. of the 10th Int’l Conf. on Parallel Processing and Applied Mathematics (PPAM), 2013.
  10. Conf
    PRASE: PageRank-based Active Subnetwork Extraction
    Ayat Hatem, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB), 2013.
  11. Conf
    Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs
    Anas Abu-Doleh, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB), 2013.
  12. Conf
    Streaming Algorithms for k-core Decomposition
    Ahmet Erdem Sarıyüce, Bugra Gedik, Gabriela Jacques-Silva, Kun-Lung Wu, and Ümit V. Çatalyürek
    In 39th International Conference on Very Large Data Bases (VLDB), 2013.
  13. Conf
    Towards a Personalized, Scalable, and Exploratory Academic Recommendation Service
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2013.
  14. Conf
    GPU accelerated maximum cardinality matching algorithms for bipartite graphs
    Mehmet Deveci, Kamer Kaya, Bora Uçar, and Ümit V. Çatalyürek
    In Proc. of 19th Int’l. Euro-Par Conf. on Parallel Processing, 2013.
  15. JRNL
    A Survey of Pipelined Workflow Scheduling: Models and Algorithms
    Anne Benoit, Ümit V. Çatalyürek, Yves Robert, and Erik Saule
    ACM Computing Surveys, 2013.
  16. Misc
    TheAdvisor: A Webservice for Academic Recommendation
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    Poster, ACM/IEEE Joint Conference on Digital Libraries (JCDL 2013), 2013.
  17. Conf
    Shattering and Compressing Networks for Betweenness centrality
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In SIAM International Conference on Data Mining (SDM), 2013, An extended version is available as a Tech Rep on <a href=http://arxiv.org/abs/1209.6007>ArXiv</a>.
  18. Conf
    Diversified Recommendation on Graphs: Pitfalls, Measures, and Algorithms
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In 22nd International World Wide Web Conference (WWW), 2013.
  19. Tech
    On analysis of partitioning models and metrics in parallel sparse matrix-vector multiplication
    Ümit V. Çatalyürek, Kamer Kaya, and Bora Uçar
    Inria, France RR-8301, 2013.
  20. Conf
    Betweenness Centrality on GPUs and Heterogeneous Architectures
    Ahmet Erdem Sarıyüce, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    In Workshop on General Purpose Processing Using GPUs (GPGPU), in conjunction with ASPLOS, 2013.
  21. Tech
    Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi
    Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    ArXiv arXiv:1302.1078, 2013.
  22. Tech
    Incremental Algorithms for Network Management and Analysis based on Closeness Centrality
    Ahmet Erdem Sarıyüce, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    ArXiv arXiv:1303.0422, 2013.
  23. Conf
    Result Diversification in Automatic Citation Recommendation
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In iConference Workshop on Computational Scientometrics: Theory and Applications, 2013.
  24. JRNL
    No Core CI calculations for light nuclei with chiral 2- and 3-body forces
    Pieter Maris, Hasan M. Aktulga, Sven Binder, Angelo Calci, Ümit V. Çatalyürek, Joachim Langhammer, Esmond G. Ng, Erik Saule, Robert Roth, James P. Vary, and Chao Yang
    Journal of Physics: Conference Series, 2013.
  25. JRNL
    Fast Recommendation on Bibliographic Networks with Sparse-Matrix Ordering and Partitioning
    Onur Küçüktunç, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    Social Network Analysis and Mining (SNAM), 2013.
  26. JRNL
    Benchmarking Short Sequence Mapping Tools
    Ayat Hatem, Doruk Bozdağ, Amanda E. Toland, and Ümit V. Çatalyürek
    BMC Bioinformatics, 2013.
  27. JRNL
    A Comparative Analysis of Biclustering Algorithms for Gene Expression Data
    Kemal Eren, Mehmet Deveci, Onur Küçüktunç, and Ümit V. Çatalyürek
    Briefings in Bioinformatics, 2013.

2012

  1. Conf
    Microarray vs. RNA-Seq: A comparison for active subnetwork discovery
    Ayat Hatem, Kamer Kaya, and Ümit V. Çatalyürek
    In ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB), 2012.
  2. JRNL
    Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures
    Ümit V. Çatalyürek, John Feo, Assefaw H. Gebremedhin, Mahantesh Halappanavar, and Alex Pothen
    Parallel Computing, 2012, Also available as an <a href=http://arxiv.org/abs/1205.3809>arXiv Tech Report</a>.
  3. Conf
    An Out-of-core Eigensolver on SSD-equipped Clusters
    Zheng Zhou, Erik Saule, Hasan M. Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary, and Ümit V. Çatalyürek
    In Proc. of IEEE Cluster, 2012.
  4. Conf
    An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers
    Zheng Zhou, Erik Saule, Hasan M. Aktulga, Chao Yang, Esmond G. Ng, Pieter Maris, James P. Vary, and Ümit V. Çatalyürek
    In 2012 International Conference on Parallel Processing (ICPP) Workshops, Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2), 2012.
  5. Tech
    Shattering and Compressing Networks for Centrality Analysis
    Ahmet Erdem Sarıyüce, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    ArXiv arXiv:1209.6007, 2012.
  6. Tech
    Diversifying Citation Recommendations
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    ArXiv arXiv:1209.5809, 2012.
  7. Conf
    On shared-memory parallelization of a sparse matrix scaling algorithm
    Ümit V. Çatalyürek, Kamer Kaya, and Bora Uçar
    In 2012 International Conference on Parallel Processing (ICPP), 2012.
  8. Conf
    Fast Recommendation on Bibliographic Networks
    Onur Küçüktunç, Kamer Kaya, Erik Saule, and Ümit V. Çatalyürek
    In IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2012.
  9. Conf
    An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture
    Erik Saule, and Ümit V. Çatalyürek
    In 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP), 2012.
  10. Conf
    Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP
    Ahmet Erdem Sarıyüce, Erik Saule, and Ümit V. Çatalyürek
    In 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO), 2012.
  11. Conf
    Multithreaded Clustering for Multi-level Hypergraph Partitioning
    Ümit V. Çatalyürek, Mehmet Deveci, Kamer Kaya, and Bora Uçar
    In 26th IEEE International Parallel and Distributed Processing Symposium, 2012.
  12. JRNL
    Optimizing the maximum stretch of independent tasks on a cluster : From sequential tasks to moldable tasks
    Erik Saule, Doruk Bozdağ, and Ümit V. Çatalyürek
    Journal of Parallel and Distributed Computing, 2012.
  13. Conf
    Algorithms for Offline Tracking of Connected Components in Large Evolving Networks
    Kamer Kaya, Erik Saule, Onur Küçüktunç, and Ümit V. Çatalyürek
    In Workshop on Dynamic Network Analysis (DNA-SDM), 2012.
  14. Tech
    Recommendation on Academic Networks using Direction Aware Citation Analysis
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    ArXiv arXiv:1205.1143, 2012.
  15. Conf
    A divisive clustering technique for maximizing the modularity
    Ümit V. Çatalyürek, Kamer Kaya, Johannes Langguth, and Bora Uçar
    In 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering, 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
  16. Conf
    UMPa: A multi-objective, multi-level partitioner for communication minimization
    Ümit V. Çatalyürek, Mehmet Deveci, Kamer Kaya, and Bora Uçar
    In 10th DIMACS Implementation Challenge Workshop: Graph Partitioning and Graph Clustering, 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
  17. JRNL
    Merging network patterns: a general framework to summarize biomedical network data
    Yang Xiang, David Fuhry, Kamer Kaya, Ruoming Jin, Ümit V. Çatalyürek, and Kun Huang
    Network Modeling and Analysis in Health Informatics and Bioinformatics, 2012.
  18. JRNL
    Optimizing dataflow applications on heterogeneous environments
    George Teodoro, Timothy D. R. Hartley, Ümit V. Çatalyürek, and Renato Ferreira
    Cluster Computing, 2012.
  19. JRNL
    Load-Balancing Spatially Located Computations using Rectangular Partitions
    Erik Saule, Erdeniz O. Bas, and Ümit V. Çatalyürek
    Journal of Parallel and Distributed Computing, 2012.
  20. Misc
    Considerations on Parallel Graph Coloring Algorithms
    Ahmet Erdem Sarıyüce, Erik Saule, and Ümit V. Çatalyürek
    Abstract, SIAM Conference on Parallel Processing for Scientific Computing, 2012.
  21. Conf
    Large-scale ab initio configuration interaction calculations for light nuclei
    Pieter Maris, Hasan M. Aktulga, Mark A Caprio, Ümit V. Çatalyürek, Edmong Ng, Dossay Oryspayev, Hugh Potter, Erik Saule, Masha Sosonkina, James P. Vary, Chao Yang, and Zheng Zhou
    In Journal of Physics: Conference Series. HITES 2012: ’Horizons of Innovative Theories, Experiments, and Supercomputing in Nuclear Physics’, 2012.
  22. JRNL
    Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs
    Enver Kayaaslan, Ali Pınar, Ümit V. Çatalyürek, and Cevdet Aykanat
    SIAM Journal on Scientific Computing (SISC), 2012, A longer version is also available as a <a href=papers/Kayaaslan10-TechRep.pdf>Tech Rep</a>.
  23. Conf
    Direction Awareness in Citation Recommendation
    Onur Küçüktunç, Erik Saule, Kamer Kaya, and Ümit V. Çatalyürek
    In Proceedings of the 6th International Workshop on Ranking in Databases (DBRank), 2012, An extended version is available as a Tech Rep on <a href=http://arxiv.org/abs/1205.1143>ArXiv</a>.
  24. JRNL
    Improving Performance of Adaptive Component-Based Dataflow Middleware
    Timothy D. R. Hartley, Erik Saule, and Ümit V. Çatalyürek
    Parallel Computing, 2012.
  25. Chap
    Parallel Partitioning, Coloring, and Ordering for Scientific Computing
    Ümit V. Çatalyürek Erik G. Boman, Cedric Chevalier, and Karen D. Devine
    In Combinatorial Scientific Computing, 2012.
  26. JRNL
    The Zoltan and Isorropia parallel toolkits for combinatorial scientific computing: Partitioning, ordering and coloring
    Erik G. Boman, Ümit V. Çatalyürek, Cedric Chevalier, and Karen D. Devine
    Scientific Programming, 2012.
  27. Chap
    Two-dimensional approaches to sparse matrix partitioning
    Rob H. Bisseling, Bas O. Fagginger Auer, A.N. Yzelman, Tristan Leeuwen, and Ümit V. Çatalyürek
    In Combinatorial Scientific Computing, 2012.
  28. Misc
    Load-Balancing Spatially Located Computations using Rectangular Partitions
    Erdeniz O. Bas, Erik Saule, and Ümit V. Çatalyürek
    Abstract, SIAM Conference on Parallel Processing for Scientific Computing, 2012.

2011

  1. Conf
    Improving Graph Coloring on Distributed Memory Parallel Computers
    Ahmet Erdem Sarıyüce, Erik Saule, and Ümit V. Çatalyürek
    In Proceedings of the 18th Annual International Conference on High Performance Computing (HiPC 2011), 2011.
  2. Conf
    Benchmarking Short Sequence Mapping Tools
    Ayat Hatem, Doruk Bozdağ, and Ümit V. Çatalyürek
    In IEEE International Conference on Bioinformatics and Biomedicine (BIBM11), 2011, A longer version is also available as a <a href=papers/Hatem11-Bench.pdf>Tech Rep</a>.
  3. JRNL
    Optimizing Latency and Throughput of Application Workflows on Clusters
    Nagavijayalakshmi Vydyanathan, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    Parallel Computing, 2011.
  4. Conf
    Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation
    Lee Cooper, Joel H. Saltz, Ümit V. Çatalyürek, and Kun Huang
    In Proceedings of the IEEE Health Informatics and Systems Biology Conference, 2011.
  5. Conf
    Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds
    Ümit V. Çatalyürek, Kamer Kaya, and Bora Uçar
    In 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), 2011.
  6. JRNL
    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, Ümit V. Çatalyürek, A. Varon, and W. C. Wheeler
    Cladistics, 2011.
  7. JRNL
    Hypergraph Partitioning-Based Fill-Reducing Ordering
    Ümit V. Çatalyürek, Cevdet Aykanat, and Enver Kayaaslan
    SIAM Journal on Scientific Computing (SISC), 2011.
  8. JRNL
    KELVIN: a Software Package for Rigorous Measurement of Statistical Evidence in Human Genetics
    V.J. Vieland, Y. Huang, S.C. Seok, J. Burian, Ümit V. Çatalyürek, J. O’Connell, A. Segre, and W. Valentine-Cooper
    Human Heredity, 2011.
  9. Conf
    Partitioning Spatially Located Computations using Rectangles
    Erik Saule, Erdeniz O. Bas, and Ümit V. Çatalyürek
    In 25th IEEE International Parallel and Distributed Processing Symposium, 2011.
  10. JRNL
    Color and Texture Analysis on Emerging Architectures Parallel Architectures
    F. Igual, R. Mayo, Timothy D. R. Hartley, Ümit V. Çatalyürek, Antonio Ruiz, and M. Ujaldon
    International Journal of High Performance Computing Applications, 2011.
  11. Misc
    A comparison of recent biclustering algorithms
    Mehmet Deveci, Kemal Eren, and Ümit V. Çatalyürek
    Poster, ACM International Conference on Bioinformatics and Computational Biology, 2011, Runner-up of the poster award
  12. Conf
    On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections
    Hasan M. Aktulga, C. Yang, Ümit V. Çatalyürek, P. Maris, James P. Vary, and E. G. Ng
    In Workshop on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (HPSS 2011), in conjunction with the Euro-Par, 2011.
  13. Chap
    Hypergraph Partitioning
    Ümit V. Çatalyürek, Bora Uçar, and Cevdet Aykanat
    In Encyclopedia of Parallel Computing, 2011.
  14. Chap
    PaToH (Partitioning Tool for Hypergraphs)
    Ümit V. Çatalyürek, and Cevdet Aykanat
    In Encyclopedia of Parallel Computing, 2011.
  15. Conf
    Distributed-Memory Parallel Algorithms for Matching and Coloring
    Ümit V. Çatalyürek, Florin Dobrian, Assefaw H. Gebremedhin, Mahantesh Halappanavar, and Alex Pothen
    In 2011 International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO’11), 2011.

2010

  1. Tech
    A Survey of Pipelined Workflow Scheduling: Models and Algorithms
    Anne Benoit, Ümit V. Çatalyürek, Yves Robert, and Erik Saule
    LIP RR-LIP-2010-28, 2010.
  2. Conf
    An Image Analysis Approach for Detecting Malignant Cells in Digitized H amp;E-stained Histology Images of Follicular Lymphoma
    Olcay Sertel, Ümit V. Çatalyürek, G. Lozanski, A. Shanaah, and Metin N. Gürcan
    In 20th International Conference on Pattern Recognition (ICPR), 2010.
  3. JRNL
    A matrix partitioning interface to PaToH in MATLAB
    Bora Uçar, Ümit V. Çatalyürek, and Cevdet Aykanat
    Parallel Computing, 2010.
  4. Conf
    On scalability of hypergraph models for sparse matrix partitioning
    Bora Uçar, and Ümit V. Çatalyürek
    In Proc. of the PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing, 2010.
  5. Conf
    Run-time optimizations for replicated dataflows on heterogeneous environments
    George Teodoro, Timothy D. R. Hartley, Ümit V. Çatalyürek, and Renato Ferreira
    In Proc. of the 19th ACM International Symposium on High Performance Distributed Computing (HPDC), 2010, Best Student Paper Award
  6. Misc
    Optimizing the maximum stretch of online tasks on a parallel system without preemption
    Erik Saule, Doruk Bozdağ, and Ümit V. Çatalyürek
    Abstract, 3rd Scheduling in Aussois Workshop, 2010.
  7. Conf
    A Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence Mapping
    Erik Saule, Doruk Bozdağ, and Ümit V. Çatalyürek
    In Job Scheduling Strategies for Parallel Processing, 2010.
  8. Misc
    Partitioning Spatially Located Load with Rectangles: Algorithms and Simulations
    Erik Saule, Erdeniz O. Bas, and Ümit V. Çatalyürek
    Abstract, New Challenges on Scheduling Theory, Workshop, 2010.
  9. Misc
    Benchmarking Short Sequence Alignment Tools
    Ayat Hatem, Doruk Bozdağ, and Ümit V. Çatalyürek
    Abstract, Bioinformatics, 2010 Ohio Collaborative Conference, 2010.
  10. Conf
    Automatic Dataflow Application Tuning for Heterogeneous Systems
    Timothy D. R. Hartley, Erik Saule, and Ümit V. Çatalyürek
    In Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010), 2010.
  11. Conf
    Comparative Analysis of Biclustering Algorithms
    Doruk Bozdağ, A.S. Kumar, and Ümit V. Çatalyürek
    In ACM International Conference on Bioinformatics and Computational Biology, 2010.
  12. Conf
    Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform
    Doruk Bozdağ, Ayat Hatem, and Ümit V. Çatalyürek
    In 9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS), 2010.
  13. JRNL
    Distributed-memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation
    Doruk Bozdağ, Ümit V. Çatalyürek, Assefaw H. Gebremedhin, F. Manne, Erik G. Boman, and F. Özgüner
    SIAM Journal on Scientific Computing (SISC), 2010.
  14. JRNL
    Development of a code-agnostic computational infrastructure for the dynamic generation of accident progression even trees
    Ümit V. Çatalyürek, B. Rutt, K. Metzroth, Aram Hakobyan, T. Aldemir, R. Denning, S. Dunagan, and D. Kunsman
    Reliability Engineering and System Safety, 2010.
  15. Chap
    Dataflow frameworks for emerging heterogeneous architectures and its application to biomedicine
    Ümit V. Çatalyürek, Renato Ferreira, Timothy D. R. Hartley, Rafael Sachetto, and George Teodoro
    In Scientific Computing with Multicore and Accelerators, 2010.
  16. JRNL
    On Two-Dimensional Sparse Matrix Partitioning: Models, Methods, and a Recipe
    Ümit V. Çatalyürek, Cevdet Aykanat, and Bora Uçar
    SIAM Journal on Scientific Computing (SISC), 2010.

2009

  1. JRNL
    An Integrated Approach to Locality Conscious Processor Allocation and Scheduling of Mixed Parallel Applications
    Nagavijayalakshmi Vydyanathan, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    IEEE Transactions on Parallel and Distributed Systems, 2009.
  2. JRNL
    A Repartitioning Hypergraph Model for Dynamic Load Balancing
    Ümit V. Çatalyürek, Erik G. Boman, K.D. Devine, Doruk Bozdağ, R. Heaphy, and L.A. Fisk
    Journal of Parallel and Distributed Computing, 2009.
  3. JRNL
    Stroma classification for neuroblastoma on graphics processors
    Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Ümit V. Çatalyürek, Joel H. Saltz, and Metin N. Gürcan
    International Journal of Data Mining and Bioinformatics, 2009.
  4. JRNL
    Compaction of Schedules and a Two-Stage Approach for Duplication-Based DAG Scheduling
    Doruk Bozdağ, F. Özgüner, and Ümit V. Çatalyürek
    IEEE Transactions on Parallel and Distributed Systems, 2009.
  5. Conf
    A Component-Based Framework for the Cell Broadband Engine
    Timothy D. R. Hartley, and Ümit V. Çatalyürek
    In Proc. of 23rd Int’l. Parallel and Distributed Processing Symposium, The 18th Heterogeneous Computing Workshop (HCW 2009), 2009.
  6. Conf
    Parallel Short Sequence Mapping for High Throughput Genome Sequencing
    Doruk Bozdağ, C.C. Barbacioru, and Ümit V. Çatalyürek
    In Proc. of 23rd Int’l. Parallel and Distributed Processing Symposium, 2009.
  7. Conf
    Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications
    George Teodoro, Rafael Sachetto, Olcay Sertel, Metin N. Gürcan, Wagner Meira, Ümit V. Çatalyürek, and Renato Ferreira
    In Proc. of the 2009 IEEE International Conference on Cluster Computing, 2009.
  8. JRNL
    Histopathological Image Analysis Using Model-Based Intermediate Representations and Color Texture: Follicular Lymphoma Grading
    Olcay Sertel, Jun Kong, Ümit V. Çatalyürek, Gerard Lozanski, Joel H. Saltz, and Metin N. Gürcan
    Signal Processing Systems, 2009.
  9. JRNL
    Computer-aided prognosis of neuroblastoma on whole-slide images: Classification of stromal development
    Olcay Sertel, Jun Kong, H. Shimada, Ümit V. Çatalyürek, Joel H. Saltz, and Metin N. Gürcan
    Pattern Recognition, 2009.
  10. Conf
    Identification of a Breast Cancer Associated Regulatory Network
    Jeffrey D. Parvin, Zeina Kais, Mansi Arora, Shweta Kotian, Alicia Zha, Derek Ransburgh, Doruk Bozdağ, Ümit V. Çatalyürek, and Kun Huang
    In Bioinformatics, 2009 Ohio Collaborative Conference, 2009.
  11. Conf
    A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments
    Hatice G. Ozer, Doruk Bozdağ, T. Camerlengo, J. Wu, Y.-W. Huang, Timothy D. R. Hartley, Jeffrey D. Parvin, T. Huang, Ümit V. Çatalyürek, and K. Huang
    In Proc. of 1st Int’l. Conf. on Bioinformatics and Computational Biology, 2009.
  12. Conf
    Exploring the GPU for Enhancing Parallelism on Color and Texture Analysis
    Francisco Igual, Rafael Mayo, Timothy D. R. Hartley, Ümit V. Çatalyürek, Antonio Ruiz, and Manuel Ujaldon
    In Proc. of the 2009 International Conference on Parallel Computing (ParCo2009), 2009.
  13. Conf
    Investigating the Use of GPU-Accelerated Nodes for SAR Image Formation
    Timothy D. R. Hartley, Ahmed R. Fasih, Charles A. Berdanier, Füsun Özgüner, and Ümit V. Çatalyürek
    In Proc. of the IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC), 2009.
  14. Misc
    High-Performance Filter-Stream Frameworks for Hierarchical, Heterogeneous, Distributed Supercomputers
    Timothy D. R. Hartley, and Ümit V. Çatalyürek
    Poster, 23rd Int’l. Parallel and Distributed Processing Symposium PhD Forum, 2009.
  15. JRNL
    A Knowledge-Anchored Integrative Image Search and Retrieval System
    Selnur Erdal, Ümit V. Çatalyürek, Philip R. O. Payne, Joel H. Saltz, Jyoti Kamal, and Metin N. Gürcan
    J. Digital Imaging, 2009.
  16. Misc
    Getting Started with Zoltan: A Short Tutorial
    Karen D. Devine, Erik G. Boman, Lee Ann Riesen, Ümit V. Çatalyürek, and Cedric Chevalier
    Abstract, Combinatorial Scientific Computing, 2009.
  17. Conf
    A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets
    Doruk Bozdağ, Jeffrey D. Parvin, and Ümit V. Çatalyürek
    In Proc. of 1st Int’l. Conf. on Bioinformatics and Computational Biology, 2009.
  18. Conf
    Parallel Computing Strategies for Sequence Mapping of NGS Data
    Doruk Bozdağ, Terry Camerlengo, Hatice G. Ozer, Joanne Trgovcich, Tea Meulia, Kun Huang, and Ümit V. Çatalyürek
    In Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis, 2009.
  19. Misc
    Parallelization of Mapping Algorithms for Next Generation Sequencing Applications
    Doruk Bozdağ, Catalin C. Barbacioru, and Ümit V. Çatalyürek
    Abstract, Combinatorial Scientific Computing, 2009.
  20. Misc
    Combinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and Matching
    Doruk Bozdağ, Ümit V. Çatalyürek, F. Dobrian, Assefaw H. Gebremedhin, Mahantesh Halappanavar, and Alex Pothen
    Poster, 21st Supercomputing Conference, 2009.
  21. Misc
    Combinatorial Problems in High-Performance Computing: Partitioning
    Rob Bisseling, Tristan Leeuwen, and Ümit V. Çatalyürek
    Abstract, Combinatorial Scientific Computing, 2009.
  22. Chap
    Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core CPUs and GPUs
    Ümit V. Çatalyürek, Timothy D. R. Hartley, Olcay Sertel, Manuel Ujaldon, Antonio Ruiz, Joel H. Saltz, and Metin Gürcan
    In High Performance and Large Scale Computing, 2009.
  23. Chap
    Hypergraph-based Dynamic Partitioning and Load Balancing
    Ümit V. Çatalyürek, Doruk Bozdağ, Erik G. Boman, K.D. Devine, R. Heaphy, and L.A. Fisk
    In Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, 2009.

2008

  1. Conf
    Using Overlays for Efficient Data Transfer over Shared Wide-Area Networks
    Gaurav Khanna, Ümit V. Çatalyürek, Tahsin M. Kurc, Rajkumar Kettimuthu, P. Sadayappan, Ian Foster, and Joel H. Saltz
    In Proceedings of SC2008 High Performance Computing, Networking, and Storage Conference, 2008.
  2. JRNL
    Large-Scale Biomedical Image Analysis in Grid Environments
    V.S. Kumar, B. Rutt, Tahsin M. Kurc, Ümit V. Çatalyürek, Tony C. Pan, S. Chow, S. Lamont, M. Martone, and Joel H. Saltz
    IEEE Transactions on Information Technology in Biomedicine, 2008.
  3. Conf
    A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows
    N. Vydyanathan, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In 2008 International Conference on Parallel Processing (ICPP), 2008.
  4. JRNL
    Bluegene/L applications: Parallelism on a massive scale
    Bronis R Supinski, Martin Schulz, Vasily V. Bulatov, William Cabot, Bor Chan, Andrew W Cook, Erik W Draegerl, James N Glosli, Jeffrey A Greenough, Keith Henderson, Alison Kubota, Steve Louis, Brian J Miller, Mehul V. Patel, Thomas E Spelce, Frederick H Streitz, Peter L Williams, Robert K Yates, Andy Yoo, George Almasi, Gyan Bhanot, Alan Gara, John A Gunnels, Manish Gupta, Jose Moreira, James Sexton, Bob Walkup, Charles Archer, Francois Gygi, Timothy C Germann, Kai Kadau, Peter S Lomdahl, Charles Rendleman, Michael L Welcome, William McLendon, Bruce Hendrickson, Franz Franchetti, Stefan Kraig, Juergen Lorenz, Christoph W Ueberhuber, Edmond Chow, and Ümit V. Çatalyürek
    International Journal of High Performance Computing, 2008.
  5. Conf
    A Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTP
    Gaurav Khanna, Ümit V. Çatalyürek, Tahsin M. Kurc, Rajkumar Kettimuthu, P. Sadayappan, and Joel H. Saltz
    In Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS), 2008.
  6. Conf
    Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores
    Timothy D. R. Hartley, Ümit V. Çatalyürek, Antonio Ruiz, F. Igual, R. Mayo, and M. Ujaldon
    In Proc. of the 22nd Annual International Conference on Supercomputing, ICS 2008, 2008.
  7. JRNL
    Dynamic generation of accident progression event trees
    Aram Hakobyan, Tunc Aldemir, Richard Denning, Sean Dunagan, David Kunsman, Benjamin Rutt, and Ümit V. Çatalyürek
    Nuclear Engineering and Design, 2008.
  8. Misc
    Parallel Distance-2 Coloring
    Doruk Bozdağ, Ümit V. Çatalyürek, Assefaw H. Gebremedhin, F. Manne, and Erik G. Boman
    Abstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations, 2008.
  9. JRNL
    A framework for scalable greedy coloring on distributed-memory parallel computers
    Doruk Bozdağ, Assefaw H. Gebremedhin, F. Manne, Erik G. Boman, and Ümit V. Çatalyürek
    Journal of Parallel and Distributed Computing, 2008.
  10. Conf
    Combinatorial algorithms for computational science and engineering
    Erik G. Boman, Doruk Bozdağ, Ümit V. Çatalyürek, K. D. Devine, Assefaw H. Gebremedhin, P. D. Hovland, and Alex Pothen
    In Journal of Physics: Conference Series, 2008.

2007

  1. Conf
    Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations
    Ümit V. Çatalyürek, Erik G. Boman, K.D. Devine, Doruk Bozdağ, R. Heaphy, and L.A. Fisk
    In Proc. of 21st Int’l. Parallel and Distributed Processing Symposium, 2007, Best Algorithms Paper Award
  2. Tech
    Zoltan 3.0: Parallel Partitioning, Load-balancing, and Data Management Services; User’s Guide
    Erik Boman, Karen Devine, Lee Ann Fisk, Robert Heaphy, Bruce Hendrickson, Courtenay Vaughan, Ümit V. Çatalyürek, Doruk Bozdağ, William Mitchell, and James Teresco
    Sandia National Laboratories , 2007, Tech. Report SAND2007-4748W \urlhttp://www.cs.sandia.gov/Zoltan/ug_html/ug.html
  3. Tech
    Zoltan 3.0: Parallel Partitioning, Load-balancing, and Data Management Services; Developer’s Guide
    Erik Boman, Karen Devine, Lee Ann Fisk, Robert Heaphy, Bruce Hendrickson, Courtenay Vaughan, Ümit V. Çatalyürek, Doruk Bozdağ, William Mitchell, and James Teresco
    Sandia National Laboratories , 2007, Tech. Report SAND2007-4749W, \urlhttp://www.cs.sandia.gov/Zoltan/dev_html/dev.html
  4. Conf
    Optimizing multiple queries on scientific datasets with partial replicas
    L. Weng, Ümit V. Çatalyürek, Tahsin M. Kurc, G. Agrawal, and Joel H. Saltz
    In Proc. of 8th IEEE/ACM International Conference on Grid Computing (GRID 2007), 2007.
  5. Conf
    Toward Optimizing Latency Under Throughput Constraints for Application Workflows on Clusters
    Nagavijayalakshmi Vydyanathan, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007), 2007.
  6. Conf
    An Efficient and Reliable Scientific Workflow System
    T. Tavares, G. Teodoro, Tahsin M. Kurc, R. Ferreira, D. Neto, W. Meira, Ümit V. Çatalyürek, S. Hastings, S. Oster, S. Langella, and Joel H. Saltz
    In Prof. of Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007), 2007.
  7. Conf
    Pathological image analysis using the GPU: Stroma classification for neuroblastoma
    Antonio Ruiz, Olcay Sertel, Manuel Ujaldon, Ümit V. Çatalyürek, Joel H. Saltz, and M. Gürcan
    In Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine, 2007.
  8. Conf
    Performance vs. accuracy trade-offs for large-scale image analysis applications
    V. S. Kumar, Tahsin M. Kurc, Jun Kong, Ümit V. Çatalyürek, M. N. Gürcan, and Joel H. Saltz
    In Proc. of the 2007 IEEE International Conference on Cluster Computing, 2007.
  9. Conf
    Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters
    G. Khanna, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007), 2007.
  10. Misc
    Storing and Searching Massive Scale-free Graphs
    Timothy D. R. Hartley, Ümit V. Çatalyürek, and Andy Yoo
    Poster, 19th Supercomputing Conference, 2nd Place Student Poster, 2007.
  11. Conf
    Computerized pathological image analysis for neuroblastoma prognosis
    Metin N. Gürcan, Jun Kong., Olcay Sertel, Barla B. Cambazoglu, Joel H. Saltz, and Ümit V. Çatalyürek
    In 2007 AMIA Annual Symposium, 2007.
  12. Conf
    Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma
    Barla B. Cambazoglu, Olcay Sertel, Jun Kong, Joel H. Saltz, Metin N. Gürcan, and Ümit V. Çatalyürek
    In Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07), 2007.
  13. Conf
    Enabling high performance computational science through combinatorial algorithms
    Erik G. Boman, Doruk Bozdağ, Ümit V. Çatalyürek, K. D. Devine, Assefaw H. Gebremedhin, P. D. Hovland, Alex Pothen, and M. M. Strout
    In Journal of Physics: Conference Series, 2007.

2006

  1. Conf
    Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications
    Nagavijayalakshmi Vydyanathan, Sriram Krishnamoorthy, Gerald Sabin, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In Proceedings of 2006 IEEE International Conference on Cluster Computing, 2006.
  2. Conf
    Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs
    D. Ucar, S. Asur, Ümit V. Çatalyürek, and S. Parthasarathy
    In In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), 2006.
  3. Conf
    MSSG: A Framework for Massive Scale Semantic Graphs
    Timothy D. R. Hartley, Ümit V. Çatalyürek, Füsun Özgüner, Andy Yoo, Scott Kohn, and Keith Henderson
    In Proceedings of 2006 IEEE International Conference on Cluster Computing, 2006.
  4. Conf
    Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries
    Li Weng, Ümit V. Çatalyürek, Tahsin M. Kurc, Gagan Agrawal, and Joel H. Saltz
    In 2006 International Conference on Parallel Processing, 2006.
  5. Conf
    On Creating Efficient Object-relational Views of Scientific Datasets
    Sivaramakrishnan Narayanan, Tahsin M. Kurc, Ümit V. Çatalyürek, and Joel H. Saltz
    In 2006 International Conference on Parallel Processing, 2006.
  6. Conf
    Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/O
    Gaurav Khanna, Nagavijayalakshmi Vydyanathan, Ümit V. Çatalyürek, Tahsin M. Kurc, Sriram Krishnamoorthy, P. Sadayappan, and Joel H. Saltz
    In Proceedings of the Fifteen International Symposium on High Performance Distributed Computing (HPDC-15), 2006.
  7. Conf
    A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File Sharing
    Gaurav Khanna, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006, 2006.
  8. Conf
    A task duplication based bottom-up scheduling algorithm for heterogeneous environments
    Doruk Bozdağ, Ümit V. Çatalyürek, and F. Özgüner
    In 15th International Heterogeneous Computing Workshop (in conjunction with IPDPS), 2006.
  9. JRNL
    Supporting Scalable and Distributed Data Subsetting and Aggregation in Large-scale Seismic Data Analysis
    Xi Zhang, Benjamin Rutt, Ümit V. Çatalyürek, Tahsin M. Kurc, and Joel H. Saltz
    The Journal of High Performance Computing Applications, 2006.
  10. Conf
    Scheduling of Tasks with Batch-shared I/O on Heterogeneous Systems
    Nagavijayalakshmi Vydyanathan, Gaurav Khanna, Tahsin M. Kurc, Ümit V. Çatalyürek, Pete Wyckoff, Joel H. Saltz, and P. Sadayappan
    In Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Heterogeneous Computing Workshop (HCW 2006), 2006.
  11. Conf
    An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications
    Nagavijayalakshmi Vydyanathan, Sriram Krishnamoorthy, Gerald Sabin, Ümit V. Çatalyürek, Tahsin M. Kurc, P. Sadayappan, and Joel H. Saltz
    In 2006 International Conference on Parallel Processing, 2006.
  12. Conf
    Large Image Correction and Warping in a Cluster Environment
    Vijay S. Kumar, Benjamin Rutt, Tahsin M. Kurc, Ümit V. Çatalyürek, Sunny Chow, Stephan Lamont, Maryann Martone, and Joel H. Saltz
    In Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006.
  13. Conf
    An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming Model
    Sriram Krishnamoorthy, Ümit V. Çatalyürek, Jarek Nieplocha, and P. Sadayappan
    In Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL 2006), 2006.
  14. Conf
    Hypergraph Partitioning for Automatic Memory Hierarchy Management
    Sriram Krishnamoorthy, Ümit V. Çatalyürek, Jarek Nieplocha, Atanas Rountev, and P. Sadayappan
    In Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006.
  15. Conf
    An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions
    Sriram Krishnamoorthy, Ümit V. Çatalyürek, Jarek Nieplocha, Atanas Rountev, and P. Sadayappan
    In Proc. IPDPS Workshop on Next Generation Software, 2006.
  16. Conf
    Parallel Hypergraph Partitioning for Scientific Computing
    K.D. Devine, Erik G. Boman, R.T. Heaphy, R.H. Bisseling, and Ümit V. Çatalyürek
    In Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), 2006.

2005

  1. Conf
    Distributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying
    Benjamin Rutt, Vijay S. Kumar, Tony C. Pan, Tahsin M. Kurc, Ümit V. Çatalyürek, Yujun Wang, and Joel H. Saltz
    In The 2005 IEEE International Conference on Cluster Computing, 2005.
  2. Conf
    Servicing Seismic and Oil Reservoir Simulation Data through Grid Data Services
    Sivaramakrishnan Narayanan, Tahsin M. Kurc, Ümit V. Çatalyürek, and Joel H. Saltz
    In Proceedings of VLDB Workshop Data Management in Grid 2005 (VLDB DMG’05, 2005.
  3. JRNL
    A Simulation and Data Analysis System for Large Scale,Data-Driven Oil Reservoir Simulation Studies
    Tahsin M. Kurc, Ümit V. Çatalyürek, X. Zhang, Joel H. Saltz, R. Martino, Mary F. Wheeler, M. Peszynska, Alan Sussman, C. Hansen, M. Sen, R. Seifoullaev, P. Stoffa, C. Torres-Verdin, and Manish Parashar
    Concurrency and Computation: Practice and Experience., 2005.
  4. Conf
    A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers
    Doruk Bozdağ, Ümit V. Çatalyürek, Assefaw H. Gebremedhin, F. Manne, Erik G. Boman, and F. Özgüner
    In Proc. of 1st Int’l. Conf. on High Performance Computing and Communications, 2005.
  5. Conf
    A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers
    Erik G. Boman, Doruk Bozdağ, Ümit V. Çatalyürek, Assefaw H. Gebremedhin, and F. Manne
    In Proc. of 11th Int’l. Euro-Par Conf. on Parallel Processing, 2005.
  6. Conf
    A Task Duplication Based Scheduling Algorithm Using Partial Schedules
    Doruk Bozdağ, F. Özgüner, E. Ekici, and Ümit V. Çatalyürek
    In Proc. of 34th Int’l. Conf. on Parallel Processing, 2005.
  7. Conf
    Servicing Range Queries on Multidimensional Datasets with Partial Replicas
    Li Weng, Ümit V. Çatalyürek, Tahsin M. Kurc, Gagan Agrawal, and Joel H. Saltz
    In Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005), 2005.
  8. Conf
    A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batch-shared I/O
    Gaurav Khanna, Nagavijayalakshmi Vydyanathan, Tahsin M. Kurc, Ümit V. Çatalyürek, Pete Wyckoff, Joel H. Saltz, and P. Sadayappan
    In Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005), 2005.
  9. Tech
    Parallel Hypergraph Partitioning for Scientific Computing
    Erik G. Boman, K.D. Devine, R.T. Heaphy, Ümit V. Çatalyürek, and R.H. Bisseling
    Sandia National Laboratories SAND2005-2796C, 2005.
  10. Conf
    A Runtime Framework for Partial Replication and Its Application for On-Demand Data Exploration
    Sivaramakrishnan Narayanan, Ümit V. Çatalyürek, Tahsin M. Kurc, Vijay S. Kumar, and Joel H. Saltz
    In High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, 2005.
  11. Conf
    Design and Implementation of a Data Server Using a Peer-to-Peer Storage System
    Vijay S. Kumar, Tahsin M. Kurc, Ümit V. Çatalyürek, and Joel H. Saltz
    In High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, 2005.
  12. Conf
    A Scalable Distributed Parallel Breadth-First Search Algorithm on BlueGene/L
    Andy Yoo, Edmond Chow, Keith Henderson, William McLendon, Bruce Hendrickson, and Ümit V. Çatalyürek
    In Proceedings of SC2005 High Performance Computing, Networking, and Storage Conference, 2005, Gordon Bell Finalist.
  13. Chap
    Tools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data
    M. Ribeiro, Tahsin M. Kurc, Tony C. Pan, K. Huang, Ümit V. Çatalyürek, X. Zhang, S. Langella, S. Hastings, S. Oster, R. Ferreira, and Joel H. Saltz
    In Grid Computing: The New Frontier Of High Performance Computing, 14, 2005.
  14. Conf
    Towards Dynamic Data-Driven Optimization of Oil Well Placement.
    Manish Parashar, Vincent Matossian, Wolfgang Bangerth, Hector Klie, Benjamin Rutt, Tahsin M. Kurc, Ümit V. Çatalyürek, Joel H. Saltz, and Mary F. Wheeler
    In International Conference on Computational Science (2), 2005.
  15. JRNL
    Application of Grid-enabled technologies for solving optimization problems in data-driven reservoir studies
    Manish Parashar, Hector Klie, Ümit V. Çatalyürek, Tahsin M. Kurc, Vincent Matossian, Joel H. Saltz, and Mary F. Wheeler
    Future Generation Computer Systems, 2005.
  16. JRNL
    XML database support for distributed execution of data-intensive scientific workflows.
    Shannon Hastings, Matheus Ribeiro, Stephen Langella, Scott Oster, Ümit V. Çatalyürek, Tony C. Pan, Kun Huang, Renato Ferreira, Joel H. Saltz, and Tahsin M. Kurc
    SIGMOD Record, 2005.

2004

  1. Conf
    A Distributed Data Management Middleware for Data-Driven Application Systems
    Stephen Langella, Shannon Hastings, Scott Oster, Tahsin M. Kurc, Ümit V. Çatalyürek, and Joel H. Saltz
    In Proceedings of 2004 IEEE International Conference on Cluster Computing, 2004.
  2. Conf
    Strategies for Using Additional Resources in Parallel Hash-based Join Algorithms
    Xi Zhang, Tahsin M. Kurc, Tony C. Pan, Ümit V. Çatalyürek, Sivaramakrishnan Narayanan, Pete Wyckoff, and Joel H. Saltz
    In Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13), 2004.
  3. Conf
    An Approach for Automatic Data Virtualization
    Li Weng, Gagan Agrawal, Ümit V. Çatalyürek, Tahsin M. Kurc, Sivaramakrishnan Narayanan, and Joel H. Saltz
    In Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13), 2004.
  4. Conf
    Application of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies
    Manish Parashar, H. Klie, Ümit V. Çatalyürek, Tahsin M. Kurc, V. Matossian, Joel H. Saltz, and Mary F. Wheeler
    In Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science), 2004.
  5. Conf
    Serving Queries to Multi-Resolution Datasets on Disk-based Storage Clusters
    Xi Zhang, Tony C. Pan, Ümit V. Çatalyürek, Tahsin M. Kurc, and Joel H. Saltz
    In Proceedings of 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004), 2004.
  6. Conf
    Supporting SQL-3 Aggregations on Grid-based Data Repositories
    Li Weng, Gagan Agrawal, Ümit V. Çatalyürek, and Joel H. Saltz
    In Proceedings of the 17th International Workshop on Languages and Compilers for Parallel Computing, 2004.
  7. Conf
    Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O
    Nagavijayalakshmi Vydyanathan, Gaurav Khanna, Tahsin M. Kurc, Ümit V. Çatalyürek, Pete Wyckoff, Joel H. Saltz, and P. Sadayappan
    In Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing (Grid 2004), 2004.
  8. JRNL
    Permuting Sparse Rectangular Matrices into Block-Diagonal Form
    Cevdet Aykanat, Ali Pınar, and Ümit V. Çatalyürek
    SIAM Journal on Scientific Computing (SISC), 2004.

2003

  1. JRNL
    The Virtual Microscope
    Ümit V. Çatalyürek, Michael D. Beynon, Chialin Chang, Tahsin M. Kurc, Alan Sussman, and Joel H. Saltz
    IEEE Transactions on Information Technology in BioMedicine, 2003.
  2. Conf
    Applying Database Support for Large Scale Data Driven Science in Distributed Environments
    Sivaramakrishnan Narayanan, Ümit V. Çatalyürek, Tahsin M. Kurc, Xi Zhang, and Joel H. Saltz
    In Proceedings of the Fourth International Workshop on Grid Computing (Grid 2003), 2003.
  3. Conf
    Optimizing Reduction Computations In a Distributed Environment
    Tahsin M. Kurc, Feng Lee, Gagan Agrawal, Ümit V. Çatalyürek, Renato Ferreira, and Joel H. Saltz
    In ACM/IEEE SC2003, 2003.
  4. Conf
    Driving Scientific Applications by Data in Distributed Environments
    Joel H. Saltz, Ümit V. Çatalyürek, Tahsin M. Kurc, M. Gray, S. Hastings, S. Langella, S. Narayanan, R. Martino, S. Bryant, M. Peszynska, Mary F. Wheeler, Alan Sussman, Michael D. Beynon, C. Hansen, D. Stredney, and D. Sessanna
    In Dynamic Data Driven Application Systems Workshop, held jointly with ICCS 2003, 2003.
  5. Conf
    Impact of High Performance Sockets on Data Intensive Applications
    Pavan Balaji, Jiesheng Wu, Tahsin M. Kurc, Ümit V. Çatalyürek, Dhabaleswar K. Panda, and Joel H. Saltz
    In Proceedings of the Twelfth International Symposium on High Performance Distributed Computing (HPDC-12), 2003.
  6. Conf
    Image Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications.
    Shannon Hastings, Tahsin M. Kurc, Steve Langella, Ümit V. Çatalyürek, Tony C. Pan, and Joel H. Saltz
    In CCGrid: IEEE International Symposium on Cluster Computing and the Grid, 2003.
  7. Conf
    A Component-based Implementation of Multiple Sequence Alignment
    Ümit V. Çatalyürek, Mike Gray, Tahsin M. Kurc, Joel H. Saltz, Eric Stahlberg, and Renato Ferreira
    In 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track, 2003.
  8. JRNL
    Database Support for Data-driven Scientific Applications in the Grid
    Sivaramakrishnan Narayanan, Tahsin M. Kurc, Ümit V. Çatalyürek, and Joel H. Saltz
    Parallel Processing Letters, 2003.
  9. Conf
    A Distributed Execution Environment for Analysis of DCE-MR Image Datasets
    Tahsin M. Kurc, S. Hastings, Ümit V. Çatalyürek, Joel H. Saltz, J. D. Fleig, B. D. Clymer, H. Tengg-Kobligk, K. T. Baudendistel, R. Machiraju, and M. V. Knopp
    In The Society for Computer Applications in Radiology (SCAR 2003), 2003.

2002

  1. Conf
    Executing Multiple Pipelined Data Analysis Operations in the Grid
    Matthew Spencer, Renato Ferreira, Michael Beynon, Tahsin M. Kurc, Ümit V. Çatalyürek, Alan Sussman, and Joel H. Saltz
    In Proceedings of the 2002 ACM/IEEE SC02 Conference, 2002.
  2. Tech
    The Virtual Microscope
    Ümit V. Çatalyürek, Michael D. Beynon, Chialin Chang, Tahsin M. Kurc, Alan Sussman, and Joel H. Saltz
    University of Maryland, Department of Computer Science and UMIACS CS-TR-xxxx and UMIACS-TR-2002-xx, 2002.
  3. JRNL
    Processing Large-Scale Multidimensional Data in Parallel and Distributed Environments
    Michael Beynon, Chialin Chang, Ümit V. Çatalyürek, Tahsin M. Kurc, Alan Sussman, Henrique Andrade, Renato Ferreira, and Joel H. Saltz
    Parallel Computing, 2002, Special Issue on Data Intensive Computing
  4. Conf
    Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems
    Michael D. Beynon, Tahsin M. Kurc, Ümit V. Çatalyürek, Alan Sussman, and Joel H. Saltz
    In Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), 2002.
  5. Conf
    Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
    Ümit V. Çatalyürek, Eric Stahlberg, Renato Ferreira, Tahsin M. Kurc, and Joel H. Saltz
    In Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), First Workshop on High Performance Computational Biology, 2002.
  6. Conf
    Persistent Caching in a Multiple Query Optimization Framework
    Henrique Andrade, Tahsin M. Kurc, Ümit V. Çatalyürek, Alan Sussman, and Joel H. Saltz
    In Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers, 2002.

2001

  1. Conf
    A Hypergraph-Partitioning Approach for Coarse-Grain Decomposition
    Ümit V. Çatalyürek, and Cevdet Aykanat
    In ACM/IEEE SC2001, 2001.
  2. JRNL
    Distributed Processing of Very Large Datasets with DataCutter
    Michael D. Beynon, Tahsin M. Kurc, Ümit V. Çatalyürek, Chialin Chang, Alan Sussman, and Joel H. Saltz
    Parallel Computing, 2001.
  3. Conf
    Performance Optimization for Data Intensive Grid Applications
    Michael D. Beynon, Alan Sussman, Ümit V. Çatalyürek, Tahsin M. Kurc, and Joel H. Saltz
    In Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001), 2001.
  4. JRNL
    Improving the Performance and Functionality of the Virtual Microscope
    Ümit V. Çatalyürek, Tahsin M. Kurc, Alan Sussman, and Joel H. Saltz
    Archives of Pathology and Laboratory Medicine, 2001.
  5. JRNL
    Visualization of Large Datasets with the Active Data Repository
    Tahsin M. Kurc, Ümit V. Çatalyürek, Chialin Chang, Alan Sussman, and Joel H. Saltz
    IEEE Computer Graphics and Applications, 2001.
  6. Tech
    A Component-based Implementation of Iso-surface Rendering for Visualizing Large Datasets
    Michael D. Beynon, Tahsin M. Kurc, Ümit V. Çatalyürek, Alan Sussman, and Joel H. Saltz
    University of Maryland, Department of Computer Science and UMIACS CS-TR-4249 and UMIACS-TR-2001-34, 2001.
  7. Conf
    A Fine-Grain Hypergraph Model for 2D Decomposition of Sparse Matrices
    Ümit V. Çatalyürek, and Cevdet Aykanat
    In Proceedings of 15th International Parallel and Distributed Processing Symposium (IPDPS), 2001.
  8. Conf
    A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregation
    Chialin Chang, Tahsin M. Kurc, Alan Sussman, Ümit V. Çatalyürek, and Joel H. Saltz
    In Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing, 2001.
  9. Tech
    Exploration and Visualization of Very Large Datasets with the Active Data Repository
    Tahsin M. Kurc, Ümit V. Çatalyürek, Chialin Chang, Alan Sussman, and Joel H. Saltz
    University of Maryland, Department of Computer Science and UMIACS CS-TR-4208 and UMIACS-TR-2001-04, 2001, Also appears in IEEE Computer Graphics and Applications, Jul/Aug 2001

1999

  1. PhD
    Hypergraph Models for Sparse Matrix Partitioning and Reordering
    Ümit V. Çatalyürek
    PhD thesis, Bilkent University, Computer Engineering and Information Science , 1999.
  2. JRNL
    Hypergraph-Partitioning Based Decomposition for Parallel Sparse-Matrix Vector Multiplication
    Ümit V. Çatalyürek, and Cevdet Aykanat
    IEEE Transactions on Parallel and Distributed Systems, 1999.
  3. Tech
    PaToH: A Multilevel Hypergraph Partitioning Tool, Version 3.0
    Ümit V. Çatalyürek, and Cevdet Aykanat
    Bilkent University, Department of Computer Engineering , 1999.

1996

  1. JRNL
    Decomposing linear programs for parallel solution
    Ali Pınar, Ümit V. Çatalyürek, Cevdet Aykanat, and M. Pınar
    Lecture notes in Computer Science, 1996.
  2. Conf
    Decomposing irregularly sparse matrices for parallel matrix-vector multiplications
    Ümit V. Çatalyürek, and Cevdet Aykanat
    In Proceedings of 3rd International Symposium on Solving Irregularly Structured Problems in Parallel, Irregular’96, 1996.

1995

  1. Conf
    A Hypergraph Model for Mapping Repeated Sparse Matrix-Vector Product Computations onto Multicomputers
    Ümit V. Çatalyürek, and Cevdet Aykanat
    In Proceedings of International Conference on High Performance Computing, 1995.

1994

  1. MS
    A Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree Ordering
    Ümit V. Çatalyürek
    Master's thesis, Bilkent University, Computer Engineering and Information Science , 1994.