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Ümit V. Çatalyürek

  • Adjunct Professor, SBS-Biomedical Informatics
  • 266 Ferst Drive
    Georgia Institute of Technology
    Atlanta, GA 30332

About

Education

PhD 2000, Bilkent University, Turkey

Areas of interest

High-performance computing, runtime systems for data-intensive computing, parallel algorithms for scientific and engineering applications, combinatorial scientific computing and biomedical informatics.

Biography

Ümit V. Çatalyürek is a Professor in the Departments of Biomedical Informatics, Electrical & Computer Engineering, and Computer Science & Engineering at the Ohio State University. Dr. Çatalyürek received his Ph.D. in 2000 from Bilkent University, and prior to joining the Ohio State University in 2001, he worked at Johns Hopkins University as a Research Associate and at the University of Maryland as a Visiting Research Scientist. Dr. Çatalyürek is a recipient of NSF CAREER award and primary investigator of several awards from Department of Energy, National Institute of Health, and National Science Foundation. Dr. Çatalyürek currently serves as an Associate Editor for Parallel Computing, an as an editorial board member for IEEE Transactions on Parallel and Distributed Computing, Journal of Parallel and Distributed Computing, and Network Modeling and Analysis in Health Informatics and Bioinformatics. In the past, he also served on the editorial board of SIAM Journal of Scientific Computing. Dr. Çatalyürek was the founding General Chair of 1st ACM International Health Informatics Symposium 2010, Program Chair of 5th ACM Conference on Bioinformatics, Computational Biology and Health Informatics 2014, and Workshops Chair of IPDPS 2010-2014. He also serves on the program committees and organizing committees of several international conferences. He is a member of ACM, SIAM and senior member of IEEE. Dr. Çatalyürek has co-authored more than 200 peer-reviewed articles, invited book chapters and papers. His main research areas are in high performance computing, combinatorial scientific computing and biomedical informatics.

Office

310A Lincoln Tower, ph: 614.292.0914, fax: 614.688.6600, or 316 Dreese Labs, fax: 614-292-7596

Alternate address

Department of Biomedical Informatics, 250 Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210

Honors

  • January, 2011

    The runner-up of the poster award.

  • January, 2010

    Best Student Paper Award.

  • January, 2008

    SBS Excellence in Teaching and Research Award.

  • January, 2007

    NSF CAREER Award.

  • January, 2007

    Best paper award in Algorithms track of the 2007 International Parallel and Distributed Processing Symposium (IPDPS 2007)..

  • January, 1992

    Bilkent University Scholarship.

  • January, 1987

    Third Place in High School Chemistry Contest, Marmara Region.

  • January, 1987

    Bilkent University Scholarship.

  • January, 1987

    Second Place in High School Math Contest, Marmara Region.

  • SBS Excellence in Teaching and Research Award.

  • NSF CAREER Award.

  • Best Student Paper Award.

  • Second Place in High School Math Contest, Marmara Region.

  • Third Place in High School Chemistry Contest, Marmara Region.

  • Best paper award in Algorithms track of the 2007 International Parallel and Distributed Processing Symposium (IPDPS 2007)..

Books

1999

  • Ü.V. Çatalyürek. 1999. "Hypergraph Models for Sparse Matrix Partitioning and Reordering." Computer Engineering and Information Science, Bilkent University.

1994

  • Ü.V. Çatalyürek. 1994. "A Constructive Multi-way circuit Partitioning Algorithm Based on Minimum Degree Ordering." Computer Engineering and Information Science, Bilkent University.

Edited Books

2011

  • 2011. "Contemporary Computing, Proceedings of 4th International Conference, IC3." Springer.

2010

  • 2010. "Proceedings of ACM International Health Informatics Symposium (IHI 2010)." ACM.

Chapters

2012

  • 2012. "Two-dimensional approaches to sparse matrix partitioning." In Combinatorial Scientific Computing, edited by U. Naumann, O. Schenk,
  • 2012. "Parallel Partitioning, Coloring, and Ordering for Scientific Computing." In Combinatorial Scientific Computing, edited by U. Naumann, O. Schenk,

2011

  • 2011. "PaToH (Partitioning Tool for Hypegraphs)." In Encyclopedia of Parallel Computing, edited by D. Padua,
  • 2011. "Hypergraph Partitioning." In Encyclopedia of Parallel Computing,

Journal Articles

2017

  • Çatalyürek, Ü.V., 2017, "Guest Editor's Introduction: Selected Papers from ACM-BCB 2014." IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, no. 5, 1000-1001 - 1000-1001.

2013

  • Sariyüce, A.E.; Gedik, B.; Jacques-Silva, G.; Wu, K.L. et al., 2013, "Streaming algorithms for k-core decomposition." Proceedings of the VLDB Endowment 6, no. 6, 433-444 - 433-444.

2011

  • Ãœ.V. Çatalyürek, C. Aykanat and E. Kayaaslan, 2011, "Hypergraph Partitioning-Based Fill-Reducing Ordering." SIAM Journal of Scientific Computing 33, no. 4, 1996-2023 - 1996-2023.
  • N. Vydyanathan, Ü.V. Çatalyürek, T.M. Kurç, P. Sadayappan and J.H. Saltz, 2011, "Optimizing latency and Throughput of application workflows on clusters." Parallel Computing 37, no. 10-11, 694-712 - 694-712.

2010

  • D. Bozdag, Ü.V. Çatalyürek, A. H. Gebremedhin, F. Manne, E.G. Boman, and F. Özgüner, 2010, "Distributed-memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation." SIAM Journal of Scientific Computing 4, no. 32, 2418-2446 - 2418-2446.

2009

  • O. Sertel, J. Kong, H. Shimada, Ãœ.V. Çatalyürek, J.H. Saltz, M.N. Gurcan, 2009, "Computer-aided Prognosis of Neuroblastoma on Whole-slide Images: Classification of Stromal Development." Special Issue of Pattern Recognition on Digital Image Processing and Pattern Recognition Techniques for the Detection of Cancer 42, no. 6, 1093-1103 - 1093-1103.
  • Ruiz,Antonio; Sertel,Olcay; Ujaldon,Manuel; Catalyurek,Umit; Saltz,Joel; Gurcan,Metin,N, 2009, "Stroma classification for neuroblastoma on graphics processors." INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS 3, no. 3, 280-298 - 280-298.
  • S. Erdal, Ü.V. Çatalyürek, P.R. Payne, J. Kamal, J.H. Saltz, M.N. Gurcan, 2009, "A Knowledge-Anchored Integrative Image Search and Retrieval System." Journal of Digital Imaging 22, no. 2, 166-182 - 166-182.
  • O. Sertel, J. Kong, Ãœ.V. Çatalyürek, G. Lozanski, J.H. Saltz, M.N. Gurcan, 2009, "Histopathological image analysis using model-based intermediate representations and color texture: Follicular lymphoma grading." The Journal of Signal Processing Systems for Signal, Image, and Video Technology 55, no. 1, 169-183 - 169-183.
  • Bozdag,Doruk; Oezguener,Fuesun; Catalyurek,Umit,V, 2009, "Compaction of Schedules and a Two-Stage Approach for Duplication-Based DAG Scheduling." IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 20, no. 6, 857-871 - 857-871.

2008

  • Kumar,Vijay,S; Rutt,Benjamin; Kurc,Tahsin; Catalyurek,Umit,V; Pan,Tony,C; Chow,Sunny; Lamont,Stephan; Martone,Maryann; Saltz,Joel,H, 2008, "Large-scale biomedical image analysis in grid environments." IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE 12, no. 2, 154-161 - 154-161.
  • de Supinski,Bronis,R; Schulz,Martin; Bulatov,Vasily,V; Cabot,William; Chan,Bor; Cook,Andrew,W; Draegerl,Erik,W; Glosli,James,N; Greenough,Jeffrey,A; Henderson,Keith; Kubota,Alison; Louis,Steve; Miller,Brian,J; Patel,Mehul,V; Spelce,Thomas,E; Streitz,Frederick,H; Williams,Peter,L; Yates,Robert,K; Yoo,Andy; Almasi,George; Bhanot,Gyan; Gara,Alan; Gunnels,John,A; Gupta,Manish; Moreira,Jose; Sexton,James; Walkup,Bob; Archer,Charles; Gygi,Francois; Germann,Timothy,C; Kadau,Kai; Lomdahl,Peter,S; Rendleman,Charles; Welcome,Michael,L; McLendon,William; Hendrickson,Bruce; Franchetti,Franz; Kraig,Stefan; Lorenz,Juergen; Ueberhuber,Christoph,W; Chow,Edmond; Catalyuerek,Uemit, 2008, "Bluegene/L applications: Parallelism on a massive scale." INTERNATIONAL JOURNAL OF HIGH PERFORMANCE COMPUTING APPLICATIONS 22, no. 1, 33-51 - 33-51.
  • A. Hakobyan, K. Metzroth, T. Aldemir, R. Denning, S. Dunagan, D. Kunsman, B. Rutt, Ü.V. Çatalyürek, 2008, "Dynamic Generation of Accident Progression Event Trees." Nuclear Engineering and Design 12, no. 238, 3457-3467 - 3457-3467.
  • J. Saltz, T. Kurc, S. Hastings, S. Langella, S. Oster, D. Ervin, A. Sharma, T. Pan, M. Gurcan, J. Permar, R. Ferreira, P. Payne, Ãœ.V. Çatalyürek, E. Caserta, G. Leone, M.C. Ostrowski, R. Madduri, I. Foster, S. Madhavan, K. Buetow, K. Shanbhag, E. Siegel, 2008, "e-Science, caGrid, and Translational Biomedical Research." Computer 41, no. 11, 58-66 - 58-66.
  • D. Bozdag, A.H. Gebremedhin, F. Manne, E.G. Boman, Ãœ.V. Çatalyürek, 2008, "A Framework for Scalable Greedy Coloring on Distributed Memory Parallel Computers." Journal of Parallel and Distributed Computing 4, no. 68, 515-535 - 515-535.

2007

  • Cambazoglu, B.B.; Sertel, O.; Kong, J.; Saltz, J. et al., 2007, "Efficient processing of pathological images using the grid: Computer-aided prognosis of neuroblastoma." Proceedings of the 5th IEEE Workshop on Challenges of Large Applications in Distributed Environments, CLADE'07 35-41 - 35-41.
  • A. Pothen, A.H. Gebremedhin, F. Dobrian, E.G. Boman, K.D. Devine, P.D. Hovland, B. Norris, J. Utke, Ãœ.V. Çatalyürek, and M.M. Strout, 2007, "Combinatorial Algorithms for Petascale Science." SciDAC Review

2006

  • Kurc,Tahsin; Janies,Daniel,A; Johnson,Andrew,D; Langella,Stephen; Oster,Scott; Hastings,Shannon; Habib,Farhat; Camerlengo,Terry; Ervin,David; Catalyurek,Umit,V; Saltz,Joel,H, 2006, "An XML-based system for synthesis of data from disparate databases." JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 13, no. 3, 289-301 - 289-301.
  • H. Klie, W. Bangerth, X. Gai, M.F. Wheeler, P.L. Stoffa, M. Sen, M. Prashar, Ü.V. Çatalyürek, J.H. Saltz, T.M. Kurc, 2006, "Models, Methods and Middleware for Grid-enabled Multiphysics Oil Reservoir Management." Engineering with Computers 22, no. 3, 349-370 - 349-370.

2005

  • S. Hastings, S. Oster, S. Langella, T.M. Kurc, T. Pan, Ü.V. Çatalyürek, J.H. Saltz, 2005, "A grid-based image archival and analysis system.." Journal of the American Medical Informatics Association : JAMIA 12, no. 3, 286-95 - 286-95.
  • Hastings,S; Ribeiro,M; Langella,S; Oster,S; Catalyurek,U; Pan,T; Huang,K; Ferreira,R; Saltz,J; Kurc,T, 2005, "XML database support for distributed execution of data-intensive scientific workflows." SIGMOD RECORD 34, no. 3, 50-55 - 50-55.
  • Kurc,T; Catalyurek,U; Zhang,X; Saltz,J; Martino,R; Wheeler,M; Peszynska,M; Sussman,A; Hansen,C; Sen,M; Seifoullaev,R; Stoffa,P; Torres-Verdin,C; Parashar,M, 2005, "A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies." CONCURRENCY AND COMPUTATION-PRACTICE & EXPERIENCE 17, no. 11, 1441-1467 - 1441-1467.

2004

  • Aykanat,C; Pinar,A; Catalyurek,U,V, 2004, "Permuting sparse rectangular matrices into block-diagonal form." SIAM JOURNAL ON SCIENTIFIC COMPUTING 25, no. 6, 1860-1879 - 1860-1879.

2003

  • Kurc, T.; Hastings, S.; Catalyurek, U.V.; Saltz, J. et al., 2003, "A distributed execution environment for analysis of DCE-MR image datasets." Journal of Digital Imaging 16, no. SUPPL., 4-8 - 4-8.
  • Catalyurek,U; Beynon,M,D; Chang,C,L; Kurc,T; Sussman,A; Saltz,J, 2003, "The virtual microscope." IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE 7, no. 4, 230-248 - 230-248.
  • S. Narayanan, T.M. Kurc, Ü.V. Çatalyürek, J.H. Saltz, 2003, "Database support for data-driven scientific applications in the grid." Parallel Processing Letters 13, no. 2, 245-271 - 245-271.
  • Ü.V. Çatalyürek, M.D. Beynon, C. Chang, T.M. Kurc, A. Sussman, J.H. Saltz, 2003, "The virtual microscope." IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society 7, no. 4, 230-48 - 230-48.

2002

  • M. Beynon, C. Chialin, Ü.V. Çatalyürek, T.M. Kurc, A. Sussman, H. Andrade, R.A. Ferreira, J.H. Saltz, 2002, "Processing large-scale multi-dimensional data in parallel and distributed environments." Parallel Computing 28, no. 5, 827-859 - 827-859.

2001

  • T.M. Kurc, Ãœ.V. Çatalyürek, C. Chang, A. Sussman, J.H. Saltz, 2001, "Exploration and Visualization of large data sets with the Active Data Repository." IEEE Computer Graphics and Applications 21, no. 4, 24-33 - 24-33.

1999

  • Catalyurek,U,V; Aykanat,C, 1999, "Hypergraph-partitioning-based decomposition for parallel sparse-matrix vector multiplication." IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 10, no. 7, 673-693 - 673-693.

Presentations

  • "Middleware Infastructure for Large-Scale Data Management." 2004, Presented at ASC VIEWS Alliance Forum,
  • "Use of the Teragrid for Sub-surface Modeling and Oil Reservoir Management Studies." 2006, Presented at Teragrid 2006,
  • "Dynamic Load Balancing & Matrix Partitioning." 2008, Presented at Work on Combinatorial Scientific Computing & Petascale Simulations,
  • "How Scalable is Your Load Balancer?." 2007, Presented at SIAM Conference on Computational Science and Engineering (SIAM CSE'07),
  • "Dataflow Frameworks for Heterogeneous systems." 2010,
  • "Exploiting Geometry and Adjacencies in Mesh Partitioning." 2012, Presented at SIAM Conference on Parallel Processing for Scientific Computing,
  • "Combinatorial Scientific Computing on Petascale Machines." 2007, Presented at Petascale Applications Symposium,
  • "Partitioning Spatially Located Load with Rectangles: Algorithms and Simulations." 2010, Presented at New Challenges on Scheduling Theory Workshop,
  • "Partitioning Sparse Matrices." 2009, Presented at Minisymposium on Combinatorial Scientific Computing and CS&E, SIAM Conference on Computational Science & Engineering (CSE09),
  • "Parallel Distance-2 Coloring." 2008, Presented at Workshop on Combinatorial Scientific Computing and Petascale Simulations,
  • "Optimizing the maximum stretch of online tasks on a parallel system without preemption." 2010, Presented at 3rd 'Scheduling in Aussois' Workshop,
  • "Benchmarking Short Sequence Alignment Tools." 2010, Presented at Bioinformatics, 2010 Ohio Collaborative Conference,
  • "Considerations on Parallel Graph Coloring Algorithms." 2012, Presented at SIAM Conference on Parallel Processing for Scientific Computing,
  • "Hypergraph-Partitioning Approaches for Workload Decomposition." 2002,
  • "Runtime and Compiler Support for Large Scale Data Driven Science." 2004,
  • "Service-oriented Bioscience Cluster at OSC." 2008, Presented at Software Applications and Codes Meeting for the Ohio Supercomputer Center Bioscience Cluster Expansion,
  • "Multi-Objective Scheduling of Streaming Workflows." 2008, Presented at 2nd Scheduling in Aussois Workshop,
  • "Tutorial: The Zoltan Toolkit." 2008, Presented at Workshop on Combinatorial Scientific Computing & Petascale Simulations,
  • "Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core CPUs and GPUs." 2008, Presented at International Advanced Research Workshop on High Performance Computing and Grids,
  • "Parallel Computing Strategies for Sequence Mapping of NGS Data." 2009, Presented at 9th International Conference for the Critical Assesment of Massive Data Analysis,
  • "Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core CPUs and GPUs." 2009, Presented at Ohio Supercomputer Center Workshop on Accelerating simulations with NVIDIA GPU hardware,
  • "Load-Balancing Spatially Located Computations using Rectangular Partitions." 2012, Presented at SIAM Conference on Parallel Processing & Scientific Computing (PP12),
  • "Supporting Large Scale Data Driven Science in Distributed Environments." 2005, Presented at Minisymposium on Distributed Data Management Infrastructures for Scalable Computational Science and Engineering Applications, SIAM Conference on Computational Science and Engineering,
  • "Hypergraph Models for Load Balancing Irregular Applications." 2004, Presented at Mini-Symposium on Load Balancing for Emerging Applications, in SIAM Conference of Parallel Processing for Scientific Computing,
  • "STORM (Overview)." 2005, Presented at First DIALOGUE Workshop: Applications-Driven Issues in Data Grids,
  • "Application of Grid Technology in Cancer Research: Middleware and Tools." 2006, Presented at International Advance Research Workshop on High Performance Computing and Grids,
  • "Service Oriented Access to HPC Resources: A Case Study- OSC Bioscience Cluster." 2008, Presented at SC08 Workshop on Supercomputing, Multicore Architectures, and Biomedical Informatics, in conjunction with Supercomputing 2008,
  • "Combinatorial Problems in High-Performance Computing: Partitioning." 2009, Presented at Dagstuhl Combinatorial Scientific Computing Seminar,
  • "Getting Started with Zoltan: A Short Tutorial." 2009, Presented at Dagstuhl Combinatorial Scientific Computing Seminar,
  • "Combinatorial Scientific Computing & ADAPT & Scientific Computinng on Emerging Architectures." 2009,
  • "Partitioning Spatially Located Load with Rectangles." 2010,
  • "Task Scheduling for Data-Intensive Tasks with Batch-shared I/O." 2007,

Papers in Proceedings

2018

  • Ozkaya, M.Y.; Sanyuce, A.E.; Pinar, A.; Catalyurek, U.V. "Local detection of critical nodes in active graphs." (10 2018).
  • Hong, C.; Sukumaran-Rajam, A.; Bandyopadhyay, B.; Kim, J. et al. "Efficient sparse-matrix multi-vector product on GPUs." (6 2018).
  • Yasar, A.; Ucar, B.; Catalyurek, U.V. "Sina: A scalable iterative network aligner." (10 2018).
  • Yasar, A.; Catalyürek, U.V. "An iterative global structure-assisted labeled network aligner." (7 2018).
  • Çatalyürek, Ü.V. "Message from the Program Chair." (2 2018).

2017

  • Kaya, K.; Gedik, B.; Catalyurek, U.V. "HPC4BD 2017 Workshop Foreword and Program Committee." (9 2017).
  • El Baz, D.; Catalyurek, U.; Bourgeois, J. "Message from the ScalCom 2016 General Chairs." (1 2017).
  • Herrmann, J.; Kho, J.; Ucar, B.; Kaya, K. et al. "Acyclic Partitioning of Large Directed Acyclic Graphs." (1 2017).
  • Sariyüce, A.E.; Seshadhri, C.; Pinar, A.; Çatalyürek, Ü.V. "Nucleus decompositions for identifying hierarchy of dense subgraphs." (7 2017).
  • Herrmann, J.; Kho, J.; Ucar, B.; Kaya, K. et al. "Acyclic Partitioning of Large Directed Acyclic Graphs." in 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGRID). (1 2017).
  • Herrmann, J.; Kho, J.; Ucar, B.; Kaya, K. et al. "Acyclic Partitioning of Large Directed Acyclic Graphs." (7 2017).

2016

  • Herrmann, J.; Witter, Z.L.; Patel, N.; Kho, J. et al. "Visual analytics on the spread of pathogens." (10 2016).
  • Kaya, K.; Gedik, B.; Çatalyürek, Ü.V. "HPC4BD 2016 Workshop Foreword and Program Committee." (9 2016).

2015

  • Hatem, A, Kaya, K, Parvin, J, Huang, K, Catalyurek, U "MICA: MicroRNA Integration for Active Module Discovery." in ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB). (9 2015).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. "Fast and high quality topology-aware task mapping." in 29th IEEE International Parallel and Distributed Processing Symposium (IPDPS). (1 2015).
  • Abu-Doleh, A.; Catalyurek, U.V. "Spaler: Spark and GraphX based de novo genome assembler." (12 2015).
  • Kaya, K.; Gedik, B.; Çatalyürek, Ü.V. "Foreword: 1st International Workshop on High Performance Computing for Big Data." (1 2015).
  • Hatem, A.; Kaya, K.; Parvin, J.; Huang, K. et al. "MICA: MicroRNA Integration for active module discovery." (9 2015).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. "Fast and High Quality Topology-Aware Task Mapping." (7 2015).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. et al. "Fast and high quality topology-aware task mapping." (1 2015).
  • Kaya, K.; Gedik, B.; Catalyurek, U.V. "HPC4BD 2015 Workshop Foreword." (12 2015).
  • Cątalyürek, Ü.V. "Message from the Workshops Chair." (7 2015).
  • Çatalyürek, Ü.V. "Message from the Workshops Chair." (9 2015).

2014

  • Sariyuce, A.E.; Saule, E.; Kaya, K.; Catalyurek, U.V. "Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures." in 28th IEEE International Parallel & Distributed Processing Symposium Workshops (IPDPSW). (1 2014).
  • Kaya, K.; Ucar, B.; Catalyuerek, U.V. "Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication." in 10th International Conference on Parallel Processing and Applied Mathematics (PPAM). (1 2014).
  • Abu-Doleh, A.; Kaya, K.; Abouelhoda, M.; Catalyurek, U.V. "Extracting Maximal Exact Matches on GPU." in 28th IEEE International Parallel & Distributed Processing Symposium Workshops (IPDPSW). (1 2014).
  • Sariyuce, A.E.; Saule, E.; Kaya, K.; Catalyurek, U.V. et al. "Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures." (1 2014).
  • Abu-Doleh, A.; Kaya, K.; Abouelhoda, M.; Catalyurek, U.V. et al. "Extracting Maximal Exact Matches on GPU." (1 2014).
  • Calyam, P.; Berryman, A.; Saule, E.; Subramoni, H. et al. "Wide-area Overlay Networking to Manage Science DMZ Accelerated Flows." in International Conference on Computing, Networking and Communications (ICNC). (1 2014).
  • Deveci, M.; Rajamanickam, S.; Leung, V.J.; Pedretti, K. et al. "Exploiting Geometric Partitioning in Task Mapping for Parallel Computers." (1 2014).
  • Calyam, P.; Berryman, A.; Saule, E.; Subramoni, H. et al. "Wide-area Overlay Networking to Manage Science DMZ Accelerated Flows." (1 2014).
  • Çatalyürek, U.V. "Message from the workshops chair." (1 2014).
  • Kaya, K.; Ucar, B.; Catalyuerek, U.V. "Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication." (1 2014).
  • Sariyüce, A.E.; Saule, E.; Kaya, K.; Çatalyürek, Ü.V. "Hardware/software vectorization for closeness centrality on multi-/many-core architectures." (1 2014).
  • Abu-Doleh, A.; Kaya, K.; Abouelhoda, M.; Çatalyurek, Ü.V. "Extracting maximal exact matches on GPU." (1 2014).
  • Çatalyürek, Ü.V. "Message from the workshops chair." (1 2014).
  • Hartley, T.D.R.; Catalyurek, U.; Ruiz, A.; Igual, F. et al. "Biomedical image analysis on a cooperative cluster of GPUs and multicores." (1 2014).
  • Calyam, P.; Berryman, A.; Saule, E.; Subramoni, H. et al. "Wide-area overlay networking to manage science DMZ accelerated flows." (1 2014).
  • Hartley, T.D.R.; Çatalyürek, Ü.V.; Ruiz, A.; Igual, F. et al. "Author's retrospective for: Biomedical image analysis on a cooperative cluster of GPUs and multicores." (1 2014).
  • Kaya, K.; Uçar, B.; Çatalyürek, U.V. "Analysis of partitioning models and metrics in parallel sparse matrix-vector multiplication." (1 2014).
  • Deveci, M.; Rajamanickam, S.; Leung, V.J.; Pedretti, K. et al. "Exploiting geometric partitioning in task mapping for parallel computers." (1 2014).

2013

  • Sariyuece, A.E.; Saule, E.; Kaya, K.; Catalyuerek, U.V. "STREAMER: a Distributed Framework for Incremental Closeness Centrality Computation." in 15th IEEE International Conference on Cluster Computing (CLUSTER). (1 2013).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. "A Push-Relabel-Based Maximum Cardinality Bipartite Matching Algorithm on GPUs." in 42nd Annual International Conference on Parallel Processing (ICPP). (1 2013).
  • Catalyuerek, U.V.; Deveci, M.; Kaya, K.; Ucar, B. "UMPa: A multi-objective, multi-level partitioner for communication minimization." in 10th DIMACS Implementation Challenge Workshop. (1 2013).
  • Catalyuerek, U.V.; Deveci, M.; Kaya, K.; Ucar, B. "UMPa: A multi-objective, multi-level partitioner for communication minimization." (1 2013).
  • Sariyuece, A.E.; Saule, E.; Kaya, K.; Catalyuerek, U.V. et al. "STREAMER: a Distributed Framework for Incremental Closeness Centrality Computation." (1 2013).
  • Deveci, M.; Kaya, K.; Catalyurek, U.V.; IEEE, "Hypergraph Sparsification and Its Application to Partitioning." (1 2013).
  • Jung, M.; III, W.E.H.; Choil, W.; Shalf, J. et al. "Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory." (1 2013).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. et al. "A Push-Relabel-Based Maximum Cardinality Bipartite Matching Algorithm on GPUs." (1 2013).
  • Maris, P.; Aktulga, H.M.; Binder, S.; Calci, A. et al. "No Core CI calculations for light nuclei with chiral 2-and 3-body forces." (1 2013).
  • Maris, P.; Aktulga, H.M.; Binder, S.; Calci, A. et al. "No Core CI calculations for light nuclei with chiral 2- and 3-body forces." (8 2013).
  • Deveci, M.; Kaya, K.; Catalyurek, U.V. "Hypergraph Sparsification and Its Application to Partitioning." in 42nd Annual International Conference on Parallel Processing (ICPP). (1 2013).
  • Deveci, M.; Kaya, K.; Ucar, B.; Catalyurek, U.V. "A push-Relabel-based maximum cardinality bipartite matching algorithm on GPUs." (1 2013).
  • Jung, M.; Wilson, E.H.; Choi, W.; Shalf, J. et al. "Exploring the future of out-of-core computing with compute-local non-volatile memory." (1 2013).
  • Abu-Doleh, A.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "Masher: Mapping long(er) reads with hash-based genome indexing on GPUs." (11 2013).
  • Maris, P.; Aktulga, H.M.; Binder, S.; Calci, A. et al. "No Core CI calculations for light nuclei with chiral 2- and 3-body forces." (10 2013).
  • Küçüktunç, O.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "TheAdvisor: A webservice for ac ademic recommendation." (8 2013).
  • Sariyüce, A.E.; Kaya, K.; Saule, E.; Çatalyürek, U.V. "Betweenness centrality on GPUs and heterogeneous architectures." (4 2013).
  • Sariyüce, A.E.; Saule, E.; Kaya, K.; Çatalyürek, Ü.V. "Shattering and compressing networks for betweenness centrality." (1 2013).
  • Sanyüce, A.E.; Saule, E.; Kaya, K.; Çatalyürek, Ü.V. "Shattering and compressing networks for betweenness centrality." (1 2013).
  • Küçüktunç, O.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "Towards a personalized, scalable, and exploratory academic recommendation service." (1 2013).
  • Küçüktunç, O.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "Diversified recommendation on graphs: Pitfalls, measures, and algorithms." (12 2013).
  • Çatalyürek, U.V. "Message from the workshops chair." (1 2013).
  • Hatem, A.; Kaya, K.; Çatalyürek, U.V. "PRASE: PageRank-based active subnetwork extraction." (11 2013).
  • Sariyuce, A.E.; Saule, E.; Kaya, K.; Catalyurek, U.V. "STREAMER: A distributed framework for incremental closeness centrality computation." (12 2013).
  • Deveci, M.; Kaya, K.; Çatalyürek, U.V. "Hypergraph sparsification and its application to partitioning." (1 2013).

2012

  • Saule, E.; Catalyuerek, U.V.; IEEE, "An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture." (1 2012).
  • E. Saule and Ü.V. Çatalyürek "An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture." in 26th International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP). (5 2012).
  • Ü.V. Çatalyürek, M. Deveci, K. Kaya, and B. Uçar "Multithreaded Clustering for Multi-level Hypergraph Partitioning." in 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS’12). (5 2012).
  • Igual, F.D.; Mayo, R.; Hartley, T.D.R.; Catalyuerek, U.V. et al. "Color and texture analysis on emerging parallel architectures." (8 2012).
  • Igual, F.D.; Mayo, R.; Hartley, T.D.R.; Çatalyürek, Ü.V. et al. "RETRACTED: Color and texture analysis on emerging parallel architectures." (8 2012).
  • Osborn, D.M.; Mandelli, D.; Metzroth, K.; Aldemir, T. et al. "A dynamic level 2 PRA using ADAPT-MELCOR." in European Safety And Reliability Conference (ESREL). (1 2012).
  • Kuecuektunc, O.; Kaya, K.; Saule, E.; Catalyuerek, U.V. et al. "Fast Recommendation on Bibliographic Networks." (1 2012).
  • K. Kaya, E. Saule, O. Küçüktunç, Ü.V. Çatalyürek "Algorithms for Offline Tracking of Connected Components in Large Evolving Networks." in Workshop on Dynamic Network Analysis (DNA-SDM). (4 2012).
  • Saule, E.; Çatalyürek, U.V. "An early evaluation of the scalability of graph algorithms on the Intel MIC architecture." (10 2012).
  • Küçüktunç, O.; Kaya, K.; Saule, E.; Çatalyürek, U.V. "Fast recommendation on bibliographic networks." (12 2012).
  • Sariyuece, A.E.; Saule, E.; Catalyuerek, U.V.; IEEE, "Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP." (1 2012).
  • Aktulga, H.M.; Yang, C.; Catalyurek, U.V.; Maris, P. et al. "On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections." (1 2012).
  • Kuecuektunc, O.; Kaya, K.; Saule, E.; Catalyuerek, U.V. "Fast Recommendation on Bibliographic Networks." in IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining. (1 2012).
  • Catalyuerek, U.V.; Deveci, M.; Kaya, K.; Ucar, B. "Multithreaded Clustering for Multi-level Hypergraph Partitioning." in 26th IEEE International Parallel and Distributed Processing Symposium (IPDPS) / Workshop on High Performance Data Intensive Computing. (1 2012).
  • Sariyüce, A.E.; Saule, E.; Çatalyürek, U.V. "Scalable hybrid implementation of graph coloring using MPI and OpenMP." (10 2012).
  • A.E. Sariyüce, E. Saule and Ü.V. Çatalyürek "Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP." in 26th International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO’12). (5 2012).
  • Ü.V. Çatalyürek, K. Kaya, J. Langguth, and B. Uçar "A Divisive clustering technique for maximizing the modularity." in 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering. (2 2012).
  • Osborn, D.M.; Mandelli, D.; Metzroth, K.; Aldemir, T. et al. "A dynamic level 2 PRA using ADAPT-MELCOR." (2 2012).
  • Catalyuerek, U.V.; Deveci, M.; Kaya, K.; Ucar, B. et al. "Multithreaded Clustering for Multi-level Hypergraph Partitioning." (1 2012).
  • Çatalyürek, U.V. "Message from the workshops chair." (10 2012).
  • Hatem, A.; Kaya, K.; Çatalyürek, U.V. "Microarray vs. RNA-Seq: A comparison for active subnetwork discovery." (11 2012).
  • Zhou, Z.; Saule, E.; Aktulga, H.M.; Yang, C. et al. "An out-of-core eigensolver on SSD-equipped clusters." (12 2012).
  • Çatalyürek, U.V.; Deveci, M.; Kaya, K.; Uçar, B. "Multithreaded clustering for multi-level hypergraph partitioning." (10 2012).
  • Zhou, Z.; Saule, E.; Aktulga, H.M.; Yang, C. et al. "An out-of-core dataflow middleware to reduce the cost of large scale iterative solvers." (12 2012).
  • Igual, F.D.; Mayo, R.; Hartley, T.D.R.; Çatalyürek, U.V. et al. "Color and texture analysis on emerging parallel architectures." (8 2012).
  • Zhou, Z.; Saule, E.; Aktulga, H.M.; Yang, C. et al. "An Out-of-core Eigensolver on SSD-equipped Clusters." (1 2012).
  • Çatalyürek, U.V.; Kaya, K.; Uçar, B. "On shared-memory parallelization of a sparse matrix scaling algorithm." (12 2012).
  • Osborn, D.M.; Mandelli, D.; Metzroth, K.; Aldemir, T. et al. "A dynamic level 2 PRA using ADAPT-MELCOR." (1 2012).
  • Ü.V. Çatalyürek, M. Deveci, K. Kaya, and B. Uçar "UMPa: A Multi-objective, multi-level partitioner for communication minimization." in 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering. (2 2012).
  • Aktulga, H.M.; Yang, C.; Çatalyürek, U.V.; Maris, P. et al. "On reducing I/O overheads in large-scale invariant subspace projections." (12 2012).

2011

  • Çatalyürek, U.V.; Kaya, K.; Uçar, B. "Integrated data placement and task assignment for scientific workflows in Clowds." (7 2011).
  • Cooper, L.A.D.; Saltz, J.H.; Catalyurek, U.; Huang, K. "Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation.." (7 2011).
  • Cooper, L.A.D.; Saltz, J.H.; Catalyurek, U.; Huang, K. "Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation.." (7 2011).
  • Saule, E.; Baş, E.O.; Çatalyürek, U.V. "Partitioning spatially located computations using rectangles." (10 2011).
  • Karimabadi, H.; Loring, B.; Vu, H.X.; Omelchenko, Y. et al. "Petascale kinetic simulation of the magnetosphere." (9 2011).
  • U.V. Catalyurek, F. Dobrian, A. Gebremedhin, M. Halappanavar, and A. Pothen "Distributed-Memory Parallel Algorithms for Matching and Coloring." in 2011 International Symposium on Parallel and Distributed Processing, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO’11). (5 2011).
  • U.V. Catalyurek, K. Kaya, and B. Ucar "Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds." in 20th International Symposium on High Performance Distributed Computing (HPDC 2011), The Fourth International Workshop on Data Intensive Distributed Computing (DIDC 2011). (1 2011).
  • Kosar, T.; Raicu, I.; Foster, I.; Fox, G. et al. "Workshop on data intensive computing in the clouds - DataCloud." (12 2011).
  • A.E. Sariyuce, E. Saule and U.V. Catalyurek "Improving Graph Coloring on Distributed Memory Parallel Computers." in Proceedings of 18th Annual International Conference on High Performance Computing (HiPC 2011). (1 2011).
  • Çatalyürek, U.V.; Dobrian, F.; Gebremedhin, A.; Halappanavar, M. et al. "Distributed-memory parallel algorithms for matching and coloring." (12 2011).
  • H.M. Aktulga, C. Yang, U.V. Catalyurek, P. Maris, J.P. Vary, and E. G. Ng "On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections." in Workshop on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (HPSS 2011), in conjunction with the Euro-Par. (1 2011).
  • Aldemir, T.; Catalyurek, U.; Denning, R.; Smidts, C. et al. "Method and tool development to support systematic quantification of uncertainties, invited." (12 2011).
  • E. Saule, E.Ö. Bas and Ü.V. Çatalyürek "Partitioning Spatially Located Computations using Rectangles." in Proceedings of 25th IEEE International Parallel & Distributed Processing Symposium (IPDPS’11). (5 2011).
  • L. Cooper, J. Saltz, U.V. Catalyurek, K. Huang "Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation." in IEEE Health Informatics and Systems Biology Conference. (7 2011).
  • Hatem, A.; Bozdaǧ, D.; Çatalyürek, U.V. "Benchmarking short sequence mapping tools." (12 2011).
  • Cooper, L.A.D.; Saltz, J.H.; Catalyurek, U.; Huang, K. "Acceleration of two point correlation function calculation for pathology image segmentation." (11 2011).
  • D.M. Osborn, D. Mandelli, K. Metzroth, T. Aldemir, R. Denning and Ü.V. Çatalyürek "A dynamic level 2 PRA using ADAPT-MELCOR." in Advances in Safety, Reliability and Risk Managemen, Proceedings of the 20th European Safety and Reliability (ESREL). (9 2011).
  • A. Hatem, D. Bozdag, and Ü.V. Çatalyürek "Benchmarking Short Sequence Mapping Tools." in IEEE International Conference on Bioinformatics and Biomedicine (BIBM11). (1 2011).
  • El Baz, D.; Baker, J.; Boukerche, A.; Boyer, V. et al. "Workshop on parallel computing and optimization - PCO." (12 2011).
  • Çatalyürek, U.V. "Message from the workshops chair." (12 2011).
  • Aluru, S.; Bader, D.A.; Kalyanaraman, A.; Agarwal, G. et al. "Message from the workshop chairs." (12 2011).

2010

  • Çatalyürek, U.V. "General chair's welcome." (12 2010).
  • Hartley, T.D.R.; Saule, E.; Catalyurek, U.V. "Automatic dataflow application tuning for heterogeneous systems." (12 2010).
  • Bozdaǧ, D.; Kumar, A.S.; Catalyurek, U.V. "Comparative analysis of biclustering algorithms." (10 2010).
  • F. Igual, R. Mayo, T. Hartley, Ü.V. Çatalyürek, A. Ruiz, and M. Ujaldón "Exploring the GPU for Enhancing Parallelism on Color and Texture Analysis." in 14th International Conference on Parallel Computing (ParCo2009). (1 2010).
  • D. Bozdag, A. Kumar, and Ü.V. Çatalyürek "Comparative Analysis of Biclustering Algorithms." in ACM International Conference On Bioinformatics and Computational Biology (ACM-BCB). (8 2010).
  • Igual, F.; Mayo, R.; Hartley, T.D.R.; Catalyurek, U. et al. "Exploring the GPU for enhancing parallelism on color and texture analysis." (1 2010).
  • Çatalyürek, U.V. "Message from the workshops chair." (7 2010).
  • Saule, E.; Bozdag, D.; Catalyurek, U.V. "A Moldable Online Scheduling Algorithm and Its Application to Parallel Short Sequence Mapping." (1 2010).
  • Teodoro, G.; Hartley, T.D.R.; Catalyurek, U.; Ferreira, R. "Run-time optimizations for replicated dataflows on heterogeneous environments." (12 2010).
  • Saule, E.; Bozdaǧ, D.; Catalyurek, U.V. "A moldable online scheduling algorithm and its application to parallel short sequence mapping." (11 2010).
  • Bozdaǧ, D.; Hatem, A.; Catalyurek, U.V. "Exploring parallelism in short sequence mapping using burrows-wheeler transform." (7 2010).
  • Uçar, B.; Çatalyürek, U.V. "On the scalability of hypergraph models for sparse matrix partitioning." (5 2010).
  • T.D.R. Hartley, E. Saule and U.V. Catalyurek "Automatic Dataflow Application Tuning for Heterogeneous Systems." in Proceedings of 17th Annual International Conference on High Performance Computing (HiPC 2010). (12 2010).
  • O. Sertel, Ü.V. Çatalyürek, G. Lozanski, A. Shanaah, and M.N. Gurcan "An Image Analysis Approach for Detecting Malignant Cells in Digitized H&E-stained Histology Images of Follicular Lymphoma." in 20th International Conference on Pattern Recognition (ICPR). (8 2010).
  • G. Teodoro, T. Hartley, Ü.V. Çatalyürek, and R. Ferreira "Run-time optimizations for replicated dataflows on heterogeneous environments." in The ACM International Symposium on High Performance Distributed Computing (HPDC). (6 2010).
  • D. Bozdag, A. Hatem, U.V. Catalyurek "Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform." in 24th International Parallel and Distributed Processing Symposium (IPDPS), 9th IEEE International Workshop on High Performance Computational Biology. (4 2010).
  • E. Saule, D. Bozdag, U.V. Catalyurek "A Moldable Online Scheduling Algorithm and Its Application to Parallel Short Sequence Mapping." in 15th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2010), in conjunction with IPDPS. (4 2010).
  • B. Ucar, U.V. Catalyurek "On scalability of hypergraph models for sparse matrix partitioning." in PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing. (1 2010).
  • Sertel, O.; Catalyurek, U.V.; Lozanski, G.; Shanaah, A. et al. "An image analysis approach for detecting malignant cells in digitized H&E-stained histology images of follicular lymphoma." (11 2010).

2009

  • Hartley, T.D.R.; Catalyurek, U.V. "A component-based framework for the cell broadband engine." (11 2009).
  • Bozdaǧ, D.; Barbacioru, C.C.; Catalyurek, U.V. "Parallel short sequence mapping for high throughput genome sequencing." (11 2009).
  • Teodoro, G.; Sachetto, R.; Sertel, O.; Gurcan, M.N. et al. "Coordinating the use of GPU and CPU for improving performance of compute intensive applications." (12 2009).
  • N. Vydyanathan, S. Krishnamoorthy, G. Sabin, Ãœ.V. Çatalyürek, T. Kurc, P. Sadayappan, J. Saltz "An Integrated Approach to Locality Conscious PRocessor Allocation and Scheduling of Mixed Parallel Applications." (8 2009).
  • Bozdag,Doruk; Parvin,Jeffrey,D; Catalyurek,Umit,V "A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).
  • G. Teodoro, R. Sachetto, O. Sertel, M.N. Gurcan, W. Meira Jr., U.V. Catalyurek, R. Ferreira "Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications." in 2009 IEEE International Conference on Cluster Computing. (1 2009).
  • H.G. Ozer, D. Bozdag, T. Camerlengo, J. Wu, Y.W. Huang, T. Hartley, J.D. Parvin, T. Huang, U.V. Catalyurek, K. Huang "A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments." in First International Conference on Bioinformatics and Computational Biology (BICoB). (1 2009).
  • Boman, E.G.; Catalyurek, U.V.; Chevalier, C.; Devine, K.D. et al. "Advances in parallel partitioning, load balancing and matrix ordering for scientific computing." (7 2009).
  • Bozdag, D.; Parvin, J.D.; Catalyurek, U.V. "A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets." (1 2009).
  • Boman, E.G.; Catalyurek, U.V.; Chevalier, C.; Devine, K.D. et al. "Advances in parallel partitioning, load balancing and matrix ordering for scientific computing." (1 2009).
  • D. Bozdag, J.D. Parvin, U.V. Catalyurek "A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets." in First International Conference on Bioinformatics and Computational Biology (BICoB). (1 2009).
  • Ozer, H.G.; Bozdag, D.; Camerlengo, T.; Wu, J. et al. "A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments." (1 2009).
  • Hartley, T.D.R.; Fasih, A.R.; Berdanier, C.A.; Oezguener, F. et al. "Investigating the Use of GPU-Accelerated Nodes for SAR Image Formation." (1 2009).
  • Ozer,Hatice,Gulcin; Bozdag,Doruk; Camerlengo,Terry; Wu,Jiejun; Huang,Yi-Wen; Hartley,Tim; Parvin,Jeffrey,D; Huang,Tim; Catalyurek,Umit,V; Huang,Kun "A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).
  • S. Naranayan, U.V. Catalyurek, T.M. Kurc, J.H. Saltz "Parallel materialization of large ABoxes." in ACM Symposium on Applied Computing (SAC). (1 2009).
  • T. Hartley, A.R. Fasih, C.A. Berdanier, F. Ozguner, U.V. Catalyurek "Investigating the Use of GPU-Accelerated Nodes for SAR Image Formation." in 2009 IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC). (1 2009).
  • Catalyurek,Umit,V; Boman,Erik,G; Devine,Karen,D; Bozdag,Doruk; Heaphy,Robert,T; Riesen,Lee,Ann "A repartitioning hypergraph model for dynamic load balancing." in 21st IEEE International Parallel and Distributed Processing Symposium (IPDPS 2007). (8 2009).
  • D. Bozdag, C.C. Barbacioru, U.V. Catalyurek "Parallel Short Sequence Mapping for High Throughput Genome Sequencing." in 23rd IEEE International PArallel & Distributed Processing Symposium (IPDPS09). (5 2009).
  • T. Hartley, U.V. Catalyurek "A Component-Based Framework for the Cell Broadband Engine." in 23rd International Parallel and Distributed Processing Symposium (IPDPS09); the 18th Heterogeneous Computing Workshop. (5 2009).
  • Ozer, H.G.; Bozdaǧ, D.; Camerlengo, T.; Wu, J. et al. "A comprehensive analysis workflow for genome-wide screening data from ChIP-sequencing experiments." (8 2009).
  • Hartley, T.D.R.; Fasih, A.R.; Berdanier, C.A.; Özgüner, F. et al. "Investigating the use of GPU-accelerated nodes for SAR image formation." (12 2009).
  • Ujaldon, M.; Catalyurek, U.V. "High-performance signal processing on emerging many-core architectures using CUDA." (11 2009).
  • Bozdaǧ, D.; Parvin, J.D.; Catalyurek, U.V. "A biclustering method to discover co-regulated genes using diverse gene expression datasets." (8 2009).
  • Hartley, T.D.R.; Fasih, A.R.; Berdanier, C.A.; Oezguener, F. et al. "Investigating the Use of GPU-Accelerated Nodes for SAR Image Formation." in IEEE International Conference on Cluster Computing (Cluster 2009). (1 2009).
  • Ozer,Hatice,Gulcin; Bozdag,Doruk; Camerlengo,Terry; Wu,Jiejun; Huang,Yi-Wen; Hartley,Tim; Parvin,Jeffrey,D; Huang,Tim; Catalyurek,Umit,V; Huang,Kun "A comprehensive analysis workflow for genome-wide screening data from ChIP-sequencing experiments." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).
  • Bozdag, D.; Parvin, J.D.; Catalyurek, U.V. "A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).
  • Teodoro, G.; Sachetto, R.; Sertel, O.; Gurcan, M.N. et al. "Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications." in IEEE International Conference on Cluster Computing (Cluster 2009). (1 2009).
  • Boman, E.G.; Catalyurek, U.V.; Chevalier, C.; Devine, K.D. et al. "Advances in parallel partitioning, load balancing and matrix ordering for scientific computing." (12 2009).
  • Parvin, J.D.; Kais, Z.; Arora, M.; Kotian, S. et al. "Identification of a breast cancer associated regulatory network." (11 2009).
  • Parvin, J.D.; Kais, Z.; Arora, M.; Kotian, S. et al. "Identification of a breast cancer associated regulatory network." (1 2009).
  • Metzroth, K.; Winningham, R.; Catalyurek, U.; Denning, R. et al. "Linking of the RELAP5-3D thermal-hydraulic code with the ADAPT PRA tool." (12 2009).
  • Sussman, A.; Catalyurek, U. "IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium: Message from the workshops chairs." (11 2009).
  • Teodoro, G.; Sachetto, R.; Sertel, O.; Gurcan, M.N. et al. "Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications." (1 2009).
  • Bozdag D, Parvin JD, and Catalyurek UV. "A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets." (1 2009).
  • Parvin,Jeffrey,D; Kais,Zeina; Arora,Mansi; Kotian,Shweta; Zha,Alicia; Ransburgh,Derek; Bozdag,Doruk; Catalyurek,Umit; Huang,Kun "Identification of a breast cancer associated regulatory network." in 4th Annual Ohio Collaborative Conference on Bioinformatics. (1 2009).
  • Ozer, H.G.; Bozdag, D.; Camerlengo, T.; Wu, J. et al. "A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).

2008

  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "Using Overlays For Efficient Data Transfer Over Shared Wide-Area Networks." (1 2008).
  • Sertel, O.; Kong, J.; Lozanski, G.; Shana'ah, A. et al. "Texture classification using nonlinear color quantization: Application to histopathological image analysis." (1 2008).
  • Sertel, O.; Kong, J.; Lozanski, G.; Shanaah, A. et al. "Computer-assisted grading of follicular lymphoma: High grade differentiation." (1 2008).
  • Sertel, O.; Kong, J.; Lozanski, G.; Shana'ah, A. et al. "Texture classification using nonlinear color quantization: Application to histopathological image analysis." in 33rd IEEE International Conference on Acoustics, Speech and Signal Processing. (1 2008).
  • Sertel, O.; Kong, J.; Lozanski, G.; Shanaah, A. et al. "Computer-assisted grading of follicular lymphoma: High grade differentiation." in 97th Annual Meeting of the United-States-and-Canadian-Academy-of-Pathology. (1 2008).
  • Saltz,Joel; Oster,Scott; Hastings,Shannon; Langella,Stephen; Ferreira,Renato; Permar,Justin; Sharma,Ashish; Ervin,David; Pan,Tony; Catalyurek,Umit; Kurc,Tahsin "Translational research design templates, Grid computing, and HPC." in 10th Workshop on Advances in Parallel and Distributed Computational Models/22nd IEEE International Parallel and Distributed Processing Symposium. (1 2008).
  • G. Khanna, Ü.V. Çatalyürek, T. Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, J. Saltz "Multi-Hop Path Splitting and Multi-Pathing Optimizations for Data Transfers Over Shared Wide-Area Networks Using GridFTP." (1 2008).
  • Vydyanathant, N.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "A duplication based algorithm for optimizing latency under throughput constraints for streaming workflows." (11 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP." in 10th Workshop on Advances in Parallel and Distributed Computational Models/22nd IEEE International Parallel and Distributed Processing Symposium. (1 2008).
  • G. Khanna, U.V. Catalyurek, T. Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, J. Saltz "Using Overlays for Efficient Data Transfer Over Shared Wide-Area Networks." in SC2008 High Performance Computing, Networking, and Storage Conference. (11 2008).
  • Sertel,Olcay; Kong,Jun; Lozanski,Gerard; Catalyurek,Umit; Saltz,Joel,H; Gurcan,Metin,N "Computerized microscopic image analysis of follicular lymphoma." in Medical Imaging 2008 Conference. (1 2008).
  • Sertel,Olcay; Kong,Jun; Lozanski,Gerard; Shana'ah,Anva; Catalyurek,Umit; Saltz,Joel; Gurcan,Metin "Texture classification using nonlinear color quantization: Application to histopathological image analysis." in 33rd IEEE International Conference on Acoustics, Speech and Signal Processing. (1 2008).
  • Hartley, T.D.R.; Catalyurek, U.; Ruiz, A.; Igual, F. et al. "Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores." in 22nd ACM International Conference on Supercomputing. (1 2008).
  • N. Vydyanathan, U.V. Catalyurek, T.M. Kurc, J.H. Saltz, P. Sadayappan "A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows." in 2008 International Conference on Parallel Processing. (9 2008).
  • Hartley, T.D.R.; Catalyurek, U.; Ruiz, A.; Igual, F. et al. "Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores." (1 2008).
  • Sertel,Olcay; Kong,Jun; Shimada,Hiroyuki; Catalyurek,Umit; Saltz,Joel,H; Gurcan,Metin "Computer-aided prognosis of neuroblastoma: Classification of stromal development on whole-slide images." in Medical Imaging 2008 Conference. (1 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "Using overlays for efficient data transfer over shared wide-area networks." (12 2008).
  • Sertel, O.; Kong, J.; Lozanski, G.; Shana 'Ah, A. et al. "Texture classification using nonlinear color quantization: Application to histopathological image analysis." (9 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP." (9 2008).
  • F. Igual, R. Mayo, T. Hartley, U.V. Catalyurek, A. Ruiz, M. Ujaldon "Optimizing co-occurrence matrices on graphics processors using sparse representations." in 9th International Workshop on State-of-the-Art in Scientific and Parallel Computing. (5 2008).
  • Hartley, T.D.R.; Catalyurek, U.; Ruiz, A.; Igual, F. et al. "Biomedical image analysis on a cooperative cluster of GPUs and multicores." (12 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "Multi-hop path splitting and multi-pathing optimizations for data transfers over shared wide-area networks using GridFTP." (12 2008).
  • G. Khanna, U.V. Catalyurek, T. Kurc, R. Kettimuthu, P. Sadayappan, J. Saltz "A Dynamic Scheduling Approach for Coordinated Wide-Area Data Trasnfers Using GridFTP." in 22nd IEEE International Parallel & Distributed Processing Symposium (IPDPS08). (4 2008).
  • T. Hartley, U.V. Catalyurek, A. Ruiz, M. Ujaldon, F. Igual, R. Mayo "Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores." in Proceedings of 22nd ACM International Conference on Supercomputing (ICS'08). (6 2008).
  • G. Khanna, U. Catalyurek, T. Kurc, R. Kettimuthu, P. Sadayappan, and J. H. Saltz "“A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP,”." in Proc. 22nd IEEE International Parallel and Distributed Processing Symposium (IPDPS). (4 2008).
  • J.H. Saltz, S. Oster, S. Hastings, S. Langella, R. Ferreira, J. Permar, A. Sharma, D. Ervin, T. Pan, Ü.V. Çatalyürek, and T.M. Kurç "Translational research design templates, Grid computing, and HPC." in IEEE International Symposium on Parallel and Distributed Processing 2008 (IPDPS 2008). (4 2008).
  • O. Sertel, J. Kong, H. Shimada, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan "Computer-aided prognosis of neuroblastoma: classification of stromal development on whole-slide images." in Proceedings of SPIE Medical Imaging. (2 2008).
  • O. Sertel, J. Kong, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan, G. Lozanski "Computerized microscopic image analysis of follicular lymphoma." in SPIE Medical Imaging. (2 2008).
  • Boman,Erik,G; Bozdag,Doruk; Catalyurek,Umit,V; Devine,Karen,D; Gebremedhin,Assefaw,H; Hovland,Paul,D; Pothen,Alex "Combinatorial algorithms for computational science and engineering." in 4th Annual Scientific Discovery Through Advanced Computing Conference (SciDAC 2008). (1 2008).
  • Hartley,Timothy,DR; Catalyurek,Umit; Ruiz,Antonio; Igual,Francisco; Mayo,Rafael; Ujaldon,Manuel "Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores." in 22nd ACM International Conference on Supercomputing. (1 2008).
  • Khanna,Gaurav; Catalyurek,Umit; Kurc,Tahsin; Kettimuthu,Rajkumar; Sadayappan,P; Saltz,Joel "A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP." in 10th Workshop on Advances in Parallel and Distributed Computational Models/22nd IEEE International Parallel and Distributed Processing Symposium. (1 2008).
  • O. Sertel, J. Kong, G. Lozanski, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan "Texture classification using non-linear color quantization: Application to histopathological image analysis." in Proceedings of IEEE Int. Conf. on Acoustics, Speech, and Signal Processing (ICASSP '08). (1 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP." (1 2008).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Kettimuthu, R. et al. "Using Overlays For Efficient Data Transfer Over Shared Wide-Area Networks." in International Conference for High Performance Computing, Networking, Storage and Analysis. (1 2008).

2007

  • U.V. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R. Heaphy, L.A. Riesen "Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations." in 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS '07). (1 2007).
  • T.M. Kurc, X. Zhang, M. Parashar, H. Klie, M.F. Wheeler, U.V. Catalyurek, J.H. Saltz "Dynamic Data-Driven Systems Approach for Simulation Based Optimizations." in International Conference on Computation Science (1). (1 2007).
  • Ruiz,Antonio; Sertel,Olcay; Ujaldon,Manuel; Catalyurek,Umit; Saltz,Joel; Gurcan,Metin "Pathological image analysis using the GPU: Stroma classification for neuroblastoma." in IEEE International Conference on Bioinformatics and Biomedicine. (1 2007).
  • S. Erdal, U.V. Catalyurek, J.H. Saltz, J. Kamal, M.N. Gurcan "Flexible patient information search and retrieval framework: Pilot Implementation." in PACS and Imaging Informatics, SPIE Symposium on Medical Imaging. (1 2007).
  • 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, and J.H. Saltz, "An Efficient and Reliable Scientific Workflow System." in CCGRID 2007. (1 2007).
  • N. Vydyanathan, U.V. Catalyurek, T.M. Kurc, J.H. Saltz, P. Sadayappan "Toward Optimizing Latency under Throughput Constraints for Application Workflows on Clusters." in Proceedings of Euro-Par, 2007. (1 2007).
  • M.N. Gurcan, J. Kong, O. Sertel, B.B. Cambazoglu, J.H. Saltz, U.V. Catalyurek "Computerized Pathological Image Analysis for Neuroblastoma Prognosis." in 2007 AMIA Annual Symposium. (1 2007).
  • Weng,Li; Catalyurek,Umit; Kurc,Tahsin; Agrawal,Gagan; Saltz,Joel "Optimizing multiple queries on scientific datasets with partial replicas." in 8th IEEE/ACM International Conference on Grid Computing. (1 2007).
  • L. Weng, U.V. Catalyurek, T.M. Kurc, G. Agrawal, J.H. Saltz "Optimizing Multiple Queries on Scientific Datasets with Partial Replicas." in Proceedings of the 8th IEEE/ACM International Conference on Grid Computing (GRID 2007). (1 2007).
  • Kurc,Tahsin; Zhang,Xi; Parashar,Manish; Klie,Hector; Wheeler,Mar,F; Catalyurek,Umit; Saltz,Joel "Dynamic data-driven systems approach for simulation based optimizations." in 7th International Conference on Computational Science (ICCS 2007). (1 2007).
  • Khanna,Gaurav; Catalyurek,Umit; Kurc,Tahsin; Sadayappan,P; Saltz,Joel "Scheduling file transfers for data-intensive jobs on heterogeneous clusters." in 13th International Euro-Par Conference on Parallel Processing. (1 2007).
  • Khanna,Gaurav; Catalyurek,Umit; Kurc,Tahsin; Sadayappan,P; Saltz,Joel "A data locality aware online scheduling approach for I/O-intensive jobs with file sharing." in 12th International Workshop on Job Scheduling Strategies for Parallel Processing. (1 2007).
  • G. Khanna, U.V. Catalyurek, T.M. Kurc, P. Sadayappan, J.H. Saltz "Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters." in Proceedings of Euro-Par, 2007. (1 2007).
  • Erdal,Selnur; Catalyurek,Umit,V; Saltz,Joel; Kamal,Jyoti; Gurcan,Metin,N "Flexible patient information search and retrieval framework: Pilot implementation." in Medical Imaging 2007 Conference. (1 2007).
  • Boman,Erik,G; Bozdag,Doruk; Catalyurek,Umit,V; Devine,Karen,D; Gebremedhin,Assefaw,H; Hovland,Paul,D; Pothen,Alex; Strout,Michelle,Mills "Enabling high performance computational science through combinatorial algorithms." in 3rd Annual Scientific Discovery through Advanced Computing Conference (SciDAC 2007). (1 2007).
  • B.B. Cambazoglu, O. Sertel, J. Kong, J.H. Saltz, M.N. Gurcan, U.V. Catalyurek "Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma." in Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE'07). (1 2007).
  • A. Ruiz, O. Sertel, M. Ujaldon, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan "Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma." in Proceedings IEEE International Conference on Bioinformatics and BioMedicine (BIBM'07). (1 2007).
  • S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, A. Rountev, P. Sadayappan "A global address space framework for locality aware scheduling of block-sparse computations." in IPDPS 2007. (4 2007).
  • B. Bansal, U.V. Catalyurek, J. Chame, C. Chen, E. Deelman, Y. Gil, M. Hall, V. Kumar, T.M. Kurc, K. Lerman, A. Nakano, Y. Nelson, J.H. Saltz, A. Sharma, P. Vashishta "Intelligent Optimization of Parallel and Distributed Applications." in 2007 IEEE International Parallel and Distributed Processing Symposium. (4 2007).
  • Tavares,Tulio; Teodoro,George; Kurc,Tahsin; Ferreira,Renato; Guedes,Dorgival; Meira,Wagner; Catalyurek,Umit; Hastings,Shannon; Oster,Scott; Langella,Steve; Saltz,Joel "An efficient and reliable scientific workflow system." in 7th IEEE International Symposium on Cluster Computing and the Grid. (1 2007).
  • Khanna, G.; Catalyurek, U.; Kure, T.; Sadayappan, P. et al. "Scheduling file transfers for data-intensive jobs on heterogeneous clusters." (12 2007).
  • Vydyanathan,Nagavijayalakshmi; Catalyurek,Umit,V; Kurc,Tahsin,M; Sadayappan,Ponnuswamy; Saltz,Joel,H "Toward optimizing latency under throughput constraints for application workflows on clusters." in 13th International Euro-Par Conference on Parallel Processing. (1 2007).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Optimizing multiple queries on scientific datasets with partial replicas." (1 2007).
  • Bansal, B.; Catalyurek, U.; Chame, J.; Chen, C. et al. "Intelligent optimization of parallel and distributed applications." (9 2007).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "A data locality aware online scheduling approach for I/O-intensive jobs with file sharing." in 12th International Workshop on Job Scheduling Strategies for Parallel Processing. (1 2007).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "Scheduling file transfers for data-intensive jobs on heterogeneous clusters." in 13th International Euro-Par Conference on Parallel Processing. (1 2007).
  • Vydyanathan, N.; Catalyurek, U.V.; Kurc, T.M.; Sadayappan, P. et al. "Toward optimizing latency under throughput constraints for application workflows on clusters." in 13th International Euro-Par Conference on Parallel Processing. (1 2007).
  • Weng, L.; Catalyurek, U.; Kurct, T.; Agrawal, G. et al. "Optimizing multiple queries on scientific datasets with partial replicas." (12 2007).
  • Kong, J.; Sertel, O.; Gewirtz, A.; Shana'ah, A. et al. "Development of computer based system to aid pathologists in histological grading of follicular lymphomas." in 49th Annual Meeting of the American-Society-of-Hematology. (11 2007).
  • Tavares, T.; Teodoro, G.; Kurc, T.; Ferreira, R. et al. "An efficient and reliable scientific workflow system." (1 2007).
  • Tavares, T.; Teodoro, G.; Kurc, T.; Ferreira, R. et al. "An efficient and reliable scientific workflow system." in 7th IEEE International Symposium on Cluster Computing and the Grid. (1 2007).
  • Kurc, T.; Zhang, X.; Parashar, M.; Klie, H. et al. "Dynamic data-driven systems approach for simulation based optimizations." in 7th International Conference on Computational Science (ICCS 2007). (1 2007).
  • Ruiz, A.; Sertel, O.; Ujaldon, M.; Catalyurek, U. et al. "Pathological image analysis using the GPU: Stroma classification for neuroblastoma." in IEEE International Conference on Bioinformatics and Biomedicine. (1 2007).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Optimizing multiple queries on scientific datasets with partial replicas." in 8th IEEE/ACM International Conference on Grid Computing. (1 2007).
  • Ruiz, A.; Sertel, O.; Ujaldon, M.; Catalyurek, U. et al. "Pathological image analysis using the GPU: Stroma classification for neuroblastoma." (1 2007).
  • Kure, T.; Zhang, X.; Parashar, M.; Klie, H. et al. "Dynamic data-driven systems approach for simulation based optimizations." (12 2007).
  • Khanna, G.; Catalyurek, U.; Kure, T.; Sadayappan, P. et al. "A data locality aware online scheduling approach for I/O-intensive jobs with file sharing." (12 2007).
  • Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Rountev, A. et al. "A global address space framework for locality aware scheduling of block-sparse computations." (9 2007).
  • Erdal, S.; Catalyurek, U.V.; Saltz, J.; Kamal, J. et al. "Flexible patient information search and retrieval framework: Pilot implementation." in Medical Imaging 2007 Conference. (1 2007).
  • Vydyanathan, N.; Catalyurek, U.V.; Kure, T.M.; Sadayappan, P. et al. "Toward optimizing latency under throughput constraints for application workflows on clusters." (12 2007).
  • Catalyurek, U.V.; Boman, E.G.; Devine, K.D.; Bozdaǧ, D. et al. "Hypergraph-based dynamic load balancing for adaptive scientific computations." (9 2007).
  • Erdal, S.; Catalyurek, U.V.; Saltz, J.; Kamal, J. et al. "Flexible patient information search and retrieval framework: Pilot implementation." (10 2007).
  • V. Kumar, T. Kurc, J. Kong, U.V. Catalyurek, M.N. Gurcan, J.H. Saltz "Performance vs. Accuracy Trade-offs for Large-scale Image Analysis Applications." in Proceedings of the IEEE Cluster 2007. (1 2007).
  • Kurc, T.; Zhang, X.; Parashar, M.; Klie, H. et al. "Dynamic data-driven systems approach for simulation based optimizations." (1 2007).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "Scheduling file transfers for data-intensive jobs on heterogeneous clusters." (1 2007).
  • Kong, J.; Sertel, O.; Gewirtz, A.; Shana'ah, A. et al. "Development of computer based system to aid pathologists in histological grading of follicular lymphomas." (11 2007).
  • Erdal, S.; Catalyurek, U.V.; Kamal, J.; Gurcan, M.N. "Flexible Patient Information Search and Retrieval Framework: Pilot Implementation." in PACS and Imaging Informatics, SPIE Symposium on Medical Imaging. (2 2007).
  • Ruiz, A.; Sertel, O.; Ujaldon, M.; Catalyurek, U. et al. "Pathological image analysis using the GPU: Stroma classification for neuroblastoma." (12 2007).
  • Erdal, S.; Catalyurek, U.V.; Saltz, J.; Kamal, J. et al. "Flexible patient information search and retrieval framework: Pilot implementation." (1 2007).
  • Vydyanathan, N.; Catalyurek, U.V.; Kurc, T.M.; Sadayappan, P. et al. "Toward optimizing latency under throughput constraints for application workflows on clusters." (1 2007).
  • G. Khanna, Ü.V. Çatalyürek, T. Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, J. Saltz "Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters." (1 2007).
  • Khanna, G.; Catalyurek, U.; Kurc, T.; Sadayappan, P. et al. "A data locality aware online scheduling approach for I/O-intensive jobs with file sharing." (1 2007).

2006

  • Rutt, B.; Kumar, V.S.; Pan, T.; Kurc, T. et al. "Distributed out-of-core preprocessing of very large microscopy images for efficient querying." in IEEE International Conference on Cluster Computing. (1 2006).
  • D. Bozdag, U.V. Catalyurek, F. Ozguner "A Task Duplication Based Bottom-Up Scheduling Algorithm for Heterogeneous Environments." in The 15th Heterogeneous Computing Workshop (HCW '06). (1 2006).
  • Rutt, B.; Catalyurek, U.; Hakobyan, A.; Metzroth, K. et al. "Distributed dynamic event tree generation for reliability and risk assessment." in 4th International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 2006). (1 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "An integrated approach for processor allocation and scheduling of mixed-parallel applications." in 35th International Conference on Parallel Processing. (1 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "Locality conscious processor allocation and scheduling for mixed parallel applications." in IEEE International Conference on Cluster Computing. (1 2006).
  • G. Khanna, U.V. Catalyurek, T. Kurc, P. Sadayappan, J. Saltz "A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs With File Sharing." in 12th International Workshop on Job Scheduling Strategies. (6 2006).
  • Hartley, T.D.R.; Catalyurek, U.; Ozguner, F.; Yoo, A. et al. "MSSG: A framework for massive-scale semantic graphs." in IEEE International Conference on Cluster Computing. (1 2006).
  • Ucar, D.; Asur, S.; Catalyurek, U.; Parthasarathy, S. "Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs." in 10th European Conference on Principle and Practice of Knowledge Discovery in Databases. (1 2006).
  • Sriram Krishnamoorthy, Umit Catalyurek, Jarek Nieplocha, Atanas Rountev, and P. Sadayappan "Hypergraph Partitioning for Automated Memory Management." in International Conference for High Performance Computing, Networking, Storage and Analysis (SC'06). (11 2006).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Using space and attribute partitioned partial replicas for data subsetting and aggregation queries." in 35th International Conference on Parallel Processing. (1 2006).
  • Vydyanathan,N; Krishnamoorthy,S; Sabin,G; Catalyurek,U; Kurc,T; Sadayappan,P; Saltz,J "Locality conscious processor allocation and scheduling for mixed parallel applications." in IEEE International Conference on Cluster Computing. (1 2006).
  • S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, A. Rountev, P. Sadayappan "Hypergraph Partitioning for Automatic Memory Hierarchy Management." in 2006 ACM/IEEE conference on Supercomputing (SC2006). (11 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications." (12 2006).
  • S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, P. Sadayappan "An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management With a Global-Address-Space Parallel Program Model." in 20th International Parallel and Distributed Processing Symposium (IPDPS '06). (1 2006).
  • V. Kumar, B. Rutt, T.M. Kurc, U.V. Catalyurek, J.H. Saltz, S. Chow, S. Lamont, M. Martone Large Image Correction and Warping in a Cluster Environment. in Proceedings of the ACM/IEEE SC2006 Conference on High Performance Networking and Computing. http://portal.acm.org/citation.cfmid=1188539, (1 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "An integrated approach for processor allocation and scheduling of mixed-parallel applications." (1 2006).
  • Hartley, T.D.R.; Catalyurek, U.; Özgüner, F.; Yoo, A. et al. "MSSG: A framework for massive-scale semantic graphs." (12 2006).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Using space and attribute partitioned partial replicas for data subsetting and aggregation queries." (1 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "Locality conscious processor allocation and scheduling for mixed parallel applications." (1 2006).
  • Rutt, B.; Catalyurek, U.; Hakobyan, A.; Metzroth, K. et al. "Distributed dynamic event tree generation for reliability and risk assessment." (12 2006).
  • Ucar, D.; Asur, S.; Catalyurek, U.; Parthasarathy, S. "Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs." (1 2006).
  • D. Ucar, S. Asur, U.V. Catalyurek, S. Parthasarathy "Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs." in Knowledge Discovery in Databases: PKDD 2006. (9 2006).
  • Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Rountev, A. et al. "Hypergraph partitioning for automatic memory hierarchy management." (12 2006).
  • Rutt, B.; Hakobyan, A.; Metzroth, K.; Catalyurek, U. et al. "A softwaretool for the creation and analysis of dynamic event trees." (12 2006).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "On creating efficient object-relational views of scientific datasets." (12 2006).
  • Hartley, T.D.R.; Catalyurek, U.; Ozguner, F.; Yoo, A. et al. "MSSG: A framework for massive-scale semantic graphs." (1 2006).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Using space and attribute partitioned partial replicas for data subsetting and aggregation queries." (12 2006).
  • Vydyanathan, N.; Khanna, G.; Catalyurek, U.; Kurc, T. et al. "Scheduling of tasks with batch-shared I/O on heterogeneous systems." (1 2006).
  • Bozdaǧ, D.; Catalyurek, U.; Özgüner, F. "A task duplication based bottom-up scheduling algorithm for heterogeneous environments." (1 2006).
  • Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Sadayappan, P. "An approach to locality-conscious load balancing and transparent memory hierarchy management with a global-address-space parallel programming model." (1 2006).
  • Metzroth, K.; Catalyurek, U.; Aldemir, T.; Dunagan, S. et al. "A graphical tool for the analysis of event trees." (7 2006).
  • Kumar, V.S.; Rutt, B.; Kurc, T.; Catalyurek, U. et al. "Large image correction and warping in a cluster environment." (12 2006).
  • Khanna, G.; Vydyanathan, N.; Catalyurek, U.; Kurc, T. et al. "Task scheduling and file replication for data-intensive jobs with batch-shared I/O." (12 2006).
  • Ucar, D.; Asur, S.; Catalyurek, U.; Parthasarathy, S. "Improving functional modularity in protein-protein interactions graphs using hub-induced subgraphs." (1 2006).
  • Devine, K.D.; Boman, E.G.; Heaphy, R.T.; Bisseling, R.H. et al. "Parallel hypergraph partitioning for scientific computing." (1 2006).
  • Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Rountev, A. et al. "An extensible global address space framework with decoupled task and data abstractions." (1 2006).
  • Rutt, B.; Catalyurek, U.; Hakobyan, A.; Metzroth, K. et al. "Distributed dynamic event tree generation for reliability and risk assessment." (1 2006).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "On creating efficient object-relational views of scientific datasets." (1 2006).
  • Vydyanathan, N.; Krishnamoorthy, S.; Sabin, G.; Catalyurek, U. et al. "Locality conscious processor allocation and scheduling for mixed parallel applications." (12 2006).
  • Rutt, B.; Kumar, V.S.; Pan, T.; Kurc, T. et al. "Distributed out-of-core preprocessing of very large microscopy images for efficient querying." (1 2006).
  • S. Narayan, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "On Creating Efficient Object-relational Views of Scientific Datasets." in Proceedings of the 2006 International Conference on Parallel Processing (ICPP-06). (8 2006).
  • S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, A. Rountev, P. Sadayappan "An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions." in 20th International Parallel and Distributed Processing Symposium (IPDPS). (1 2006).
  • Rutt,Benjamin; Kumar,Vijay,S; Pan,Tony; Kurc,Tahsin; Catalyurek,Umit; Saltz,Joel; Wang,Yujun "Distributed out-of-core preprocessing of very large microscopy images for efficient querying." in IEEE International Conference on Cluster Computing. (1 2006).
  • Rutt,Benjamin; Catalyurek,Umit; Hakobyan,Aram; Metzroth,Kyle; Aldemir,Tunc; Denning,Richard; Dunagan,Sean; Kunsman,David "Distributed dynamic event tree generation for reliability and risk assessment." in 4th International Workshop on the Challenges of Large Applications in Distributed Environments (CLADE 2006). (1 2006).
  • N. Vydyanathan, S. Krishnamoorthy, G. Sabin, U.V. Catalyurek, T.M. Kurc, P. Sadayappan, J.H. Saltz "An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications." in Proceedings of the 2006 International Conference on Parallel Processing (ICPP-06). (1 2006).
  • N. Vydyanathan, G. Khanna, U.V. Catalyurek, T.M. Kurc, J.H. Saltz, P. Sadayappan "Scheduling of Tasks with Batch-Shared I/O on Heterogeneous Systems." in The 15th Heterogeneous Computing Workshop (HCW 2006). (1 2006).
  • Hartley,Timothy,DR; Catalyurek,Umit; Ozguner,Fusun; Yoo,Andy; Kohn,Scott; Henderson,Keith "MSSG: A framework for massive-scale semantic graphs." in IEEE International Conference on Cluster Computing. (1 2006).
  • G. Khanna, N. Vydyanathan, U.V. Catalyurek, T.M. Kurc, S. Krishnamoorthy, P. Sadayappan, J.H. Saltz "Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/O." in 15th IEEE International Symposium on High-Performance Distributed Computing (HPDC-15). (6 2006).
  • B. Rutt, U.V. Catalyurek, A. Hakobyan, K. Mezroth, T. Aldemir, R. Denning, S. Dunagan, D. Kunsman "Distributed Dynamic Event Tree Generation for Reliabilty and Risk Assesment." in International Workshop on Challenges of Large Applications in Distributed Environments (CLADE '06). (6 2006).
  • K.D. Devine, E.G. Boman, R.T. Heaphy, R.H. Bisseling, U.V. Catalyurek "Parallel Hypergraph Partitioning for Scientific Computing." in 20th IEEE International Parallel and Distributed Processing Symposium (IPDPS '06). (1 2006).
  • L. Weng, U.V. Catalyurek, T.M. Kurc, G. Agrawal, J.H. Saltz "Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries." in 2006 International Conference on Parallel Processing (ICPP-06). (8 2006).
  • T. Hartley, U.V. Catalyurek, F. Ozguner, A. Yoo, S. Kohn, K. Henderson "MSSG: A Framework for Massive Scale Semantic Graphs." in Proceedings of 2006 IEEE International Conference on Cluster Computing. (9 2006).
  • N. Vydyanathan, S. Krishnamoorthy, G. Sabin, U.V. Catalyurek, T.M. Kurc, P. Sadayappan, J.H. Saltz "Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications." in 2006 IEEE International Conference on Cluster Computing. (9 2006).

2005

  • Parashar, M.; Matossian, V.; Bangerth, W.; Klie, H. et al. "Towards dynamic data-driven optimization of oil well placement." (1 2005).
  • M. Parashar, H. Klie, Ãœ.V. Çatalyürek, T. Kurc, W. Bangerth, V. Matossian, J. Saltz, M.F. Wheeler "Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies." (1 2005).
  • Parashar,M; Matossian,V; Bangerth,W; Klie,H; Rutt,B; Kurc,T; Catalyurek,U; Saltz,J; Wheeler,M,F "Towards dynamic data-driven optimization of oil well placement." in 5th International Conference on Computational Science (ICCS 2005). (1 2005).
  • Narayanan,S; Kurc,T; Catalyurek,U; Saltz,J "Servicing seismic and oil reservoir simulation data through Grid data services." in 1st VLDB Workshop on Data Management in Grids. (1 2005).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Saltz, J. "Supporting SQL-3 aggregations on grid-based data repositories." (1 2005).
  • Parashar, M.; Matossian, V.; Bangerth, W.; Klie, H.; Rutt, B.; Kurc, T.; Catalyurek, U.; Saltz, J.; Wheeler, M. F. "Towards dynamic data-driven optimization of oil well placement." (1 2005).
  • Hastings, S.; Langella, S.; Oster, S.; Kurc, T. et al. "G-based management of biomedical data using an XML-based distributed data management system." (12 2005).
  • Khanna, G.; Vydyanathan, N.; Catalyurek, U.; Kurc, T. et al. "Task scheduling and file replication for data-intensive jobs with batch-shared I/O." in 15th IEEE International Symposium on High Performance Distributed Computing. (1 2005).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "Servicing seismic and oil reservoir simulation data through grid data services." (1 2005).
  • Gaurav Khanna; Nagavijayalakshmi Vydyanathan; Kurc, T.; Catalyurek, U.; Wyckoff, P.; Saltz, J.; Sadayappan, P. "A hypergraph partitioning based approach for scheduling of tasks with batch-shared I/O." (1 2005).
  • Bozdaǧ, D.; Catalyurek, U.; Gebremedhin, A.H.; Manne, F. et al. "A parallel distance-2 graph coloring algorithm for distributed memory computers." (12 2005).
  • Khanna, G.; Vydyanathan, N.; Kurc, T.; Catalyurek, U. et al. "A hypergraph partitioning based approach for scheduling of tasks with batch-shared I/O." (1 2005).
  • Khanna, G.; Vydyanathan, N.; Kurc, T.; Catalyurek, U. et al. "A hypergraph partitioning based approach for scheduling of tasks with batch-shared I/O." in 5th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2005). (1 2005).
  • Rutt, B.; Kumar, V.S.; Pan, T.; Kurc, T. et al. "Distributed out-of-core preprocessing of very large microscopy images for efficient querying." (12 2005).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "Servicing seismic and oil reservoir simulation data through grid data services." (12 2005).
  • Parashar, M.; Matossian, V.; Bangerth, W.; Klie, H. et al. "Towards dynamic data-driven optimization of oil well placement." (9 2005).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Saltz, J. "Supporting SQL-3 aggregations on grid-based data repositories." in 17th International Workshop on Languages and Compilers for High Performance Computing. (1 2005).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Servicing range queries on multidimensional datasets with partial replicas." in 5th IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2005). (1 2005).
  • Bozdaǧ, D.; Özgüner, F.; Ekici, E.; Catalyurek, U. "A task duplication based scheduling algorithm using partial schedules." (12 2005).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Servicing range queries on multidimensional datasets with partial replicas." (12 2005).
  • S. Narayanan, U.V. Catalyurek, T.M. Kurc, V. Kumar, J.H. Saltz "A Runtime Framework for Partial Replication and Its Application for On-Demand Data Exploration." in High Performance Computing Symposium (HPC '05). (1 2005).
  • Yoo, A.; Chow, E.; Henderson, K.; McLendon, W. et al. "A scalable distributed parallel breadth-first search algorithm on BlueGene/L." (12 2005).
  • Bozdag, D.; Ozguner, F.; Ekici, E.; Catalyurek, U. "A task duplication based scheduling algorithm using partial schedules." in 34th International Conference on Parallel Processing (ICPP). (1 2005).
  • Bozdag, D.; Catalyurek, U.; Gebremedhin, A.H.; Manne, F. et al. "parallel distance-2 graph coloring algorithm for distributed memory computers." in 1st International on High Performance Computing and Communications (HPCC 2005). (1 2005).
  • Boman, E.G.; Bozdag, D.; Catalyurek, U.; Gebremedhin, A.H. et al. "A scalable parallel graph coloring algorithm for distributed memory computers." (1 2005).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "Servicing seismic and oil reservoir simulation data through Grid data services." (1 2005).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Agrawal, G. et al. "Servicing range queries on multidimensional datasets with partial replicas." (1 2005).
  • Khanna, G.; Vydyanathan, N.; Kurc, T.; Catalyurek, U. et al. "A hypergraph partitioning based approach for scheduling of tasks with batch-shared I/O." (12 2005).
  • S. Hastings, S. Langella, S. Oster, T.M. Kurc, T. Pan, U.V. Catalyurek, D.A. Janies, J.H. Saltz "Grid-based Management of Biomedical Data using an XML-based Distributed Data Management System." in Proceedings of the 19th Annual ACM Symposium on Applied Computing. (1 2005).
  • Weng, L.; Catalyurek, U.; Kurc, T.; Gagan Agrawal; Saltz, J. "Servicing range queries on multidimensional datasets with partial replicas." (1 2005).
  • Bozdag,D; Catalyurek,U; Gebremedhin,A,H; Manne,F; Boman,E,G; Ozguner,F "parallel distance-2 graph coloring algorithm for distributed memory computers." in 1st International on High Performance Computing and Communications (HPCC 2005). (1 2005).
  • G. Khanna, N. Vydyanathan, T.M. Kurc, U.V. Catalyurek, P. Wyckoff, J.H. Saltz, P. Sadayappan "A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batch-Shared I/O." in Cluster Computing and Grid 2005 (CCGrid '05). (1 2005).
  • Boman,E,G; Bozdag,D; Catalyurek,U; Gebremedhin,A,H; Manne,F "A scalable parallel graph coloring algorithm for distributed memory computers." in 11th International Euro-Par Conference. (1 2005).
  • B. Rutt, V.S. Kumar, T. Pan, T.M. Kurc, U.V. Catalyurek, Y. Wang, and J.H. Saltz "Distributed Out-of-core Preprocessing of Very Large Microscopy Images for Efficient Querying." in 2005 IEEE International Conference on Cluster Computing. (1 2005).
  • M. Parashar, V. Matossian, W. Bangerth, H. Klie, B. Rutt, T.M. Kurc, U.V. Catalyurek, J.H. Saltz, M.F. Wheeler "Towards Dynamic Data-Driven Optimization of Oil Well Placement." in ICCS '05. (4 2005).
  • S. Narayanan, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "Servicing Seismic and Oil Reservoir Simulation Data." in VLBD Workshop on Data Management in Grids. (9 2005).
  • E.G. Boman, D. Bozdag, U.V. Catalyurek, A.H. Gebremedhin, F. Manne "An Efficient Parallel Graph Coloring Algorithm for Distributed Memory Computers." in Proceedings of Euro-Par 2005 Parallel Processing: 11th International Euro-Par Conference. (1 2005).
  • D. Bozdag, U.V. Catalyurek, A.H. Gebremedhin, F. Manne, E.G. Boman, F. Ozguner "A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers." in 2005 International Conference on High Performance Computing and Communications (HPCC-05). (9 2005).
  • Boman, E.G.; Bozdag, D.; Catalyurek, U.; Gebremedhin, A.H. et al. "A scalable parallel graph coloring algorithm for distributed memory computers." in 11th International Euro-Par Conference. (1 2005).
  • Narayanan, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "Servicing seismic and oil reservoir simulation data through Grid data services." in 1st VLDB Workshop on Data Management in Grids. (1 2005).
  • Weng,L; AGRAWAL,G; Catalyurek,U; Saltz,J "Supporting SQL-3 aggregations on grid-based data repositories." in 17th International Workshop on Languages and Compilers for High Performance Computing. (1 2005).
  • L. Weng, U.V. Catalyurek, T.M. Kurc, G. Agrawal, J.H. Saltz "Servicing Range Queries on Multidimensional Datasets with Partial Replicas." in Cluster Computing and Grid 2005 (CCGrid05). (1 2005).
  • D. Bozdag, F. Ozguner, E. Ekici, U.V. Catalyurek "A Task Duplication Based Scheduling Algorithm Using Partial Schedules." in 2005 International Conference on Parallel Processing (ICPP-05). (1 2005).
  • A. Yoo, E. Chow, K. Henderson, W. McLendon, B. Hendrickson, U.V. Catalyurek "A Scalable Distributed Parallel Breadth-First Search Algorithm on BlueGene/L." in International Conference for High Performance Computing, Networking, and Storage (SC2005). (11 2005).
  • Bozdag, D.; Ozguner, F.; Ekici, E.; Catalyurek, U. "A task duplication based scheduling algorithm using partial schedules." (1 2005).
  • V. Kumar, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "Design and Implementation of a Data Server Using a Peer-to-Peer Storage System." in High Performance Computing Symposium (HPC '05). (1 2005).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Saltz, J. "Supporting SQL-3 aggregations on grid-based data repositories." (1 2005).
  • Parashar, M.; Matossian, V.; Bangerth, W.; Klie, H. et al. "Towards dynamic data-driven optimization of oil well placement." in 5th International Conference on Computational Science (ICCS 2005). (1 2005).
  • Bozdag, D.; Catalyurek, U.; Gebremedhin, A.H.; Manne, F. et al. "parallel distance-2 graph coloring algorithm for distributed memory computers." (1 2005).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Saltz, J. "Supporting SQL-3 aggregations on grid-based data repositories." (10 2005).
  • Boman, E.G.; Bozdaǧ, D.; Catalyurek, U.; Gebremedhin, A.H. et al. "A scalable parallel graph coloring algorithm for distributed memory computers." (10 2005).
  • Ü.V. Çatalyürek, S. Hastings, K. Huang, V. S. Kumar, T.M. Kurç, S. Langella, S. Narayanan, S. Oster, T. Pan, B. Rutt, X. Zhang, and J.H. Saltz "Supporting Large-Scale Medical and Scientific Datasets." in International Conference ParCO. (1 2005).
  • Khanna, G.; Vydyanathan, N.; Catalyurek, U.; Kurc, T. et al. "Task scheduling and file replication for data-intensive jobs with batch-shared I/O." (1 2005).

2004

  • Parashar, M.; Klie, H.; Catalyurek, U.; Kurc, T. et al. "Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies." (12 2004).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Kurc, T. et al. "An approach for automatic data virtualization." (10 2004).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Kurc, T. et al. "An approach for automatic data virtualization." (1 2004).
  • Zhang, X.; Pan, T.; Catalyurek, U.; Kurc, T. et al. "Serving queries to multi-resolution datasets on disk-based storage clusters." (1 2004).
  • Zhang, X.; Kurc, T.; Pan, T.; Catalyurek, U. et al. "Strategies for using additional resources in parallel hash-based join algorithms." (10 2004).
  • Zhang, X.; Kurc, T.; Pan, T.; Catalyurek, U. et al. "Strategies for using additional resources in parallel hash-based join algorithms." (1 2004).
  • Vydyanathan, N.; Khanna, G.; Kurc, T.; Catalyurek, U. et al. "Use of PVFS for efficient execution of jobs with pipeline-shared I/O." (12 2004).
  • Weng, L.; Agrawal, G.; Catalyurek, U.; Kurc, T. et al. "An approach for automatic data virtualization." in 13th IEEE International Symposium on High Performance Distributed Computing (HPDC-13). (1 2004).
  • Parashar, M.; Klie, H.; Catalyurek, U.; Kurc, T. et al. "Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies." in 4th International Conference on Computational Science (ICCS 2004). (1 2004).
  • Vydyanathan, N.; Khanna, G.; Kurc, T.; Catalyurek, U. et al. "Use of PVFS for efficient execution of jobs with pipeline-shared I/O." in 5th International Workshop on Grid Computing. (1 2004).
  • Vydyanathan, N.; Khanna, G.; Kurc, T.; Catalyurek, U. et al. "Use of PVFS for efficient execution of jobs with pipeline-shared I/O." (1 2004).
  • S. Langella, S. Hastings, S. Oster, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "A Distributed Data Management Middleware for Data-Driven Application Systems." in 2004 IEEE International Conference on Cluster Computing. (9 2004).
  • Langella, S.; Hastings, S.; Oster, S.; Kurc, T. et al. "A distributed data management middleware for data-driven application systems." (1 2004).
  • Langella, S.; Hastings, S.; Oster, S.; Kurc, T. et al. "A distributed data management middleware for data-driven application systems." (12 2004).
  • Parashar, M.; Klie, H.; Catalyurek, U.; Kurc, T. et al. "Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies." (1 2004).
  • Zhang, Xi; Pan, Tony; Catalyurek, Umit; Kurc, Tahsin; Saltz, Joel "Serving queries to multi-resolution datasets on disk-based storage clusters." (1 2004).
  • Xi Zhang; Kurc, T.; Pan, T.; Catalyurek, U.; Narayanan, S.; Wyckoff, P.; Saltz, J. "Strategies for using additional resources in parallel hash-based join algorithms." (1 2004).
  • Weng, L.; Gagan Agrawal; Catalyurek, U.; Kur, T.; Narayanan, S.; Saltz, J. "An approach for automatic data virtualization." (1 2004).
  • Vydyanathan, N.; Gaurav Khanna; Kurc, T.; Catalyurek, U.; Wyckoff, P.; Saltz, J.; Sadayappan, P. "Use of PVFS for efficient execution of jobs with pipeline-shared I/O." (1 2004).
  • Langella, S.; Hastings, S.; Oster, S.; Kurc, T.; Catalyurek, U.; Saltz, J. "A distributed data management middleware for data-driven application systems." (1 2004).
  • Zhang, X.; Pan, T.; Catalyurek, U.; Kurc, T. et al. "Serving queries to multi-resolution datasets on disk-based storage clusters." in 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCG 2004). (1 2004).
  • L. Weng, G. Agrawal, U.V. Catalyurek, J.H. Saltz "Supporting SQL-3 Aggregations on Grid-based Data Repositories." in Languages and Compilers for High Performance Computing (LLPC '04). (9 2004).
  • L. Weng, G. Agrawal, U.V. Catalyurek, T.M. Kurc, S. Narayanan, J.H. Saltz "An Approach for Automatic Data Virtualization." in Proceedings of the 13th IEEE International Symposium on High-Performance Distributed Computing (HPDC-13). (6 2004).
  • M. Parashar, H. Klie, U.V. Catalyurek, T.M. Kurc, V. Matossian, J.H Saltz, M.F. Wheeler "Applications of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservior Studies." in Workshop on Distributed Data Driven Applications and Systems (ICCS 2004). (6 2004).
  • X. Zhang, T.M. Kurc, T. Pan, U.V. Catalyurek, S. Narayanan, P. Wyckoff, J.H. Saltz "Strategies for Using Additional Resources in Parallel." in 13th IEEE International Symposium on High Performance Distributed Computing (HPDC-13). (6 2004).
  • X. Zhang, T. Pan, U.V. Catalyurek, T.M Kurc, J.H. Saltz "Serving queries to multi-resolution datasets on disk-based storage clusters." in Proceedings of the 4th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2004 (CCGrid 2004). (4 2004).
  • N. Vydyanathan, G. Khanna, T.M. Kurc, U.V. Catalyurek, P. Wyckoff, J.H. Saltz, P. Sadayappan "Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O." in Fifth IEEE/ACM International Workshop on Grid Computing, 2004. (1 2004).
  • Parashar,M; Klie,H; Catalyurek,U; Kurc,T; Matossian,V; Saltz,J; Wheeler,M,F "Application of grid-enabled technologies for solving optimization problems in data-driven reservoir studies." in 4th International Conference on Computational Science (ICCS 2004). (1 2004).
  • Zhang,X; Kurc,T; Pan,T; Catalyurek,U; Narayanan,S; Wyckoff,P; Saltz,J "Strategies for using additional resources in parallel hash-based join algorithms." in 13th IEEE International Symposium on High Performance Distributed Computing (HPDC-13). (1 2004).
  • Zhang,X; Pan,T; Catalyurek,U; Kurc,T; Saltz,J "Serving queries to multi-resolution datasets on disk-based storage clusters." in 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCG 2004). (1 2004).
  • Zhang, X.; Pan, T.; Catalyurek, U.; Kurc, T. et al. "Serving queries to multi-resolution datasets on disk-based storage clusters." (9 2004).
  • Zhang, X.; Kurc, T.; Pan, T.; Catalyurek, U. et al. "Strategies for using additional resources in parallel hash-based join algorithms." in 13th IEEE International Symposium on High Performance Distributed Computing (HPDC-13). (1 2004).

2003

  • Hastings, S.; Kurc, T.; Langella, S.; Catalyurek, U. et al. "Image processing for the grid: A toolkit for building grid-enabled image processing applications." (1 2003).
  • Saltz, J.; Catalyurek, U.; Kurc, T.; Gray, M. et al. "Driving scientific applications by data in distributed environments." in International Conference on Computational Science (ICCS 2003). (1 2003).
  • Kurc, T.; Lee, F.; Agrawal, G.; Catalyurek, U. et al. "Optimizing reduction computations in a distributed environment." (12 2003).
  • Narayanan, S.; Catalyurek, U.; Kurc, T.; Zhang, X. et al. "Applying database support for large scale data driven science in distributed environments." (1 2003).
  • Saltz, J.; Catalyurek, U.; Kurc, T.; Gray, M. et al. "Driving scientific applications by data in distributed environments." (1 2003).
  • Balaji, P.; Jiesheng Wu; Kurc, T.; Catalyurek, U.; Panda, D. K.; Saltz, J. "Impact of high performance sockets on data intensive applications." (1 2003).
  • Balaji, P.; Wu, J.S.; Kurc, T.; Catalyurek, U. et al. "Impact of high performance sockets on data intensive applications." (1 2003).
  • Saltz,J; Catalyurek,U; Kurc,T; Gray,M; Hastings,S; Langella,S; Narayanan,S; Martino,R; Bryant,S; Peszynska,M; Wheeler,M; Sussman,A; Beynon,M; Hansen,C; Stredney,D; Sessanna,D "Driving scientific applications by data in distributed environments." in International Conference on Computational Science (ICCS 2003). (1 2003).
  • P. Balaji, J. Wu, T.M. Kurc, U.V. Catalyurek, D.K. Panda, J.H. Saltz "Impact of High Performance Sockets on Data Intensive Applications." in Proceedings of the 12th IEEE International Symposium on High Performance Distributed Computing (HPDC-12). (6 2003).
  • T.M. Kurc, F. Lee, G. Agrawal, U.V. Catalyurek, R. Ferreira, J.H. Saltz "Optimizing Reduction Computations Distributed Environment." in ACM/IEEE SC2003 Conference. (11 2003).
  • Ü.V. Çatalyürek, M. Gray, T.M. Kurç, J.H. Saltz, E. Stahlberg, and R. Ferreira "A Component-based Implementation of Multiple Sequence Alignment." in Proceedings of the 2003 ACM Symposium on Applied Computing, SAC2003. (1 2003).
  • Sivaramakrishnan Narayanan; Catalyurek, U.; Kurc, T.; Zhang, X.; Saltz, J. "Applying database support for large scale data driven science in distributed environments." (1 2003).
  • T. Kurc, S. Hastings, U.V. Catalyurek, J.H. Saltz, J.D. Fleig, B.D. Clymer, H. von Tengg-Kobligk, K.T. Baudendistel, R. Machiraju, M.V Knopp "A Disdtributed Execution Environment for Analysis of DCE-MR Image Datasets." in The Society for Computer Applications in Radiology (SCAR 2003). (1 2003).
  • Hastings, S.; Kurc, T.; Langella, S.; Catalyurek, U. et al. "Image processing for the grid: A toolkit for building grid-enabled image processing applications." (12 2003).
  • Hastings, S.; Kurc, T.; Langella, S.; Catalyurek, U.; Pan, T.; Saltz, J. "Image processing for the grid: a toolkit for building grid-enabled image processing applications." (1 2003).
  • S. Narayanan, U.V. Catalyurek, T.M. Kurc, X. Zhang, J.H. Saltz "Applying Database Support for Large Scale Data Driven Science in Distributed Environments." in Proceedings of the Fourth International Workshop on Grid Computing. (1 2003).
  • S. Hastings, T.M. Kurc, S. Langella, U.V. Catalyurek, T. Pan, J.H. Saltz "Image Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications." in Proceedings of the 3rd International Symposium on Cluster Computing and the Grid (CCGrid '03). (1 2003).
  • Saltz, J.; Catalyurek, U.; Kurc, T.; Gray, M. et al. "Driving scientific applications by data in distributed environments." (12 2003).
  • Balaji, P.; Wu, J.S.; Kurc, T.; Catalyurek, U. et al. "Impact of high performance sockets on data intensive applications." in 12th IEEE International Symposium on High-Performance Distributed Computing. (1 2003).
  • Catalyurek, U.; Gray, M.; Kurc, T.; Saltzt, J. et al. "A component-based implementation of multiple sequence alignment." (7 2003).
  • Balaji, P.; Wu, J.; Kurc, T.; Catalyurek, U. et al. "Impact of high performance sockets on data intensive applications." (1 2003).
  • Narayanan, S.; Catalyurek, U.; Kurc, T.; Zhang, X. et al. "Applying database support for large scale data driven science in distributed environments." (1 2003).
  • J.H. Saltz, U.V. Catalyurek, T.M. Kurc, M. Gray, S. Hastings, S. Langella, S. Narayan, R. Martino, K. Bryant, M. Peszynska, M.F. Wheeler, A. Sussman, M. Beynon, C. Hansen, D. Stredney, D. Sessana "Driving Scientific Applications by Data in Distributed Environments." in Proceedings of the Workshop on Dynamic Data-Driven Application Systems. (6 2003).

2002

  • M. Spencer, R. Ferreira, M. Beynon, T.M. Kurc, U.V. Catalyurek, A. Sussman, J.H. Saltz "Executing Multiple Pipelined Data Analysis Operations in the Grid." in Proceedings of the 2002 ACM/IEEE SC02 Conference. (11 2002).
  • M. Beynon, T.M. Kurc, U.V. Catalyurek, A. Sussman, J.H. Saltz "Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems." in Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS),The 11th Heterogeneous Computing Workshop. (4 2002).
  • U.V. Catalyurek, E.A. Stahlberg, R.A. Ferreira, J.H. Saltz "Improving Performance of Multiple Sequence Alignment Analysis in Multi-Client Environments." in Proceedings of the First International Workshop on High Performance Computational Biology. (4 2002).
  • H. Andrade, T.M. Kurc, U.V. Catalyurek, A. Sussman, J.H. Saltz "Persistent Caching in a Multiple Query Optimization Framework." in Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers. (3 2002).
  • Beynon, M.D.; Kurc, T.; Catalyurek, U.; Sussman, A. et al. "Efficient manipulation of large datasets on heterogeneous storage systems." (1 2002).
  • Catalyurek, U.; Stahlberg, E.; Ferreira, R.; Kurc, T. et al. "Improving performance of multiple sequence alignment analysis in multi-client environments." (1 2002).
  • Beynon, M. D.; Sussman, A.; Catalyurek, U.; Kurc, T.; Saltz, J. "Performance optimization for data intensive grid applications." (1 2002).
  • Beynon, M.D.; Sussman, A.; Catalyurek, U.; Kurc, T. et al. "Performance optimization for data intensive grid applications." (1 2002).

2001

  • U.V. Catalyurek, C. Aykanat "A Hypergraph-Partitioning Approach for Coarse-Grain Decomposition." in Proceedings of the ACM/IEEE SC2001 Conference (SC'01). (11 2001).
  • Beynon, M.D.; Sussman, A.; Çatalyürek, ; Kurc, T. et al. "Performance optimization for data intensive grid applications." (1 2001).
  • Beynon,M,D; Kurc,T; Catalyurek,U; Chang,C,L; Sussman,A; Saltz,J "Distributed processing of very large datasets with DataCutter." in Workshop on Clusters and Computational Grids for Scientific Computing. (10 2001).
  • C. Chang, T.M. Kurc, A. Sussman, U.V. Catalyurek, J.H. Saltz "A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregation." in Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing. (3 2001).
  • Çatalyürek, V.; Aykanat, C. "A fine-grain hypergraph model for 2D decomposition of sparse matrices." (1 2001).
  • U.V. Catalyurek, C. Aykanat "A Fine-Grain Hypergraph Model for 2D Decomposition of Sparse Matrices." in Proceedings of International Parallel and Distributed Processing Symposium (IPDPS), 8th International Workshop on Solving Irregularly structured Problems in Parallel (Irregular 2001). (11 2001).
  • M. Beynon, A. Sussman, U.V. Catalyurek, T.M. Kurc, J.H. Saltz "Performance Optimization for Data Intensive Grid Applications." in Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001). (8 2001).

1996

  • Pınar, A.; Çatalyürek, Ü.V.; Aykanat, C.; Pınarnar, M. "Decomposing linear programs for parallel solution." (1 1996).
  • Çatalyürek, Ü.V.; Aykanat, C. "Decomposing irregularly sparse matrices for parallel matrix-vector multiplication." (1 1996).
  • Ü.V. Çatalyürek and C. Aykanat "Decomposing irregularly sparse matrices for parallel matrix-vector multiplications." in Proceedings of the Third International Workshop on Parallel Algorithms for Irregularly Structured Problems. (1 1996).
  • A. Pinar, U.V. Catalyurek, C. Aykanat, M. Pinar "Decomposing Linear Programs for Parallel Solution." in Lecture Notes in Computer Science. (1 1996).

1995

  • U.V. Catalyurek, C. Aykanat "A hypergraph model for mapping repeated sparse matrix-vector product computations onto multicomputers." in Proceedings of the International Conference on High Performance Computing (HiPC' 95). (12 1995).

Unknown

  • "Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments." in Medical Informatics Group.
  • "Parallel Hypergraph Partitioning for Scientific Computing."
  • "Hypergraph-Based Dynamic Load Balancing for Adaptive Scientific Computations." in Minisymposium on Combinatorial Scientific Computing, 6th International Congress on Industrial and Applied Mathematics (ICIAM'07).
  • "Parallel Short Sequence Mapping for High Throughput Genome Sequencing." in Dagstuhl Combinatorial Scientific Computing Seminar.
  • "Texture Classification Using Nonlinear color Quantization: Application to Histopathological Image Analysis.." in IEEEICASSP 2008.
  • "An Image Analysis Approach for Detecting Malignant Cells in Digitized H&E-stained Histology Images of Follicular Lymphoma.." in Submitted to ICPR.
  • "Development of Computer Based System to Aid Pathologists in Histological Grading of Follicular Lymphomas.." in 49th Annual Meeting and Exposition of the American Society of Hematology`.