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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

  • 20110101

    The runner-up of the poster award.

  • 20100101

    Best Student Paper Award.

  • 20080101

    SBS Excellence in Teaching and Research Award.

  • 20070101

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

  • 20070101

    NSF CAREER Award.

  • 19920101

    Bilkent University Scholarship.

  • 19870101

    Second Place in High School Math Contest, Marmara Region.

  • 19870101

    Bilkent University Scholarship.

  • 19870101

    Third Place in High School Chemistry Contest, Marmara Region.

  • Best Student Paper Award.

  • NSF CAREER 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)..

  • SBS Excellence in Teaching and Research Award.

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

2010

  • 2010. "Dataflow Frameworks for Emerging Heterogeneous Architectures and Their Applications to Biomedicine." In Scientific Computing with Multicore and Accelerators, edited by J. Dongarra, D. A. Bader, and J. Kurzak,

Journal Articles

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, 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.
  • 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.
  • 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.
  • 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.

2008

  • 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.
  • 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.
  • 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.
  • 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.
  • 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.

2007

  • 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
  • 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.

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

  • 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.
  • 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.
  • 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.
  • 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.

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,
  • "STORM." 2006, Presented at Second DIALOGUE Workshop: Applications-Driven Issues in Data Grids,
  • "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

2017

  • El Baz, D.; Catalyurek, U.; Bourgeois, J. "Message from the ScalCom 2016 General Chairs." (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." (7 2017).

2016

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

2015

  • Kaya, K.; Gedik, B.; Çatalyürek, Ü.V. "Foreword: 1st International Workshop on High Performance Computing for Big Data." (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).
  • Abu-Doleh, A.; Catalyurek, U.V. "Spaler: Spark and GraphX based de novo genome assembler." (12 2015).

2014

  • Çatalyürek, U.V. "Message from the workshops chair." (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).
  • 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).
  • Çatalyürek, Ü.V. "Message from the workshops chair." (1 2014).

2013

  • Küçüktunç, O.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "TheAdvisor: A webservice for ac ademic recommendation." (8 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).
  • 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).
  • Hatem, A.; Kaya, K.; Çatalyürek, U.V. "PRASE: PageRank-based active subnetwork extraction." (11 2013).
  • Çatalyürek, U.V. "Message from the workshops chair." (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. "Diversified recommendation on graphs: Pitfalls, measures, and algorithms." (12 2013).
  • Küçüktunç, O.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "Towards a personalized, scalable, and exploratory academic recommendation service." (1 2013).

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).
  • 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).
  • 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).
  • 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).
  • Çatalyürek, U.V.; Kaya, K.; Uçar, B. "On shared-memory parallelization of a sparse matrix scaling algorithm." (12 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).
  • 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).
  • Hatem, A.; Kaya, K.; Çatalyürek, U.V. "Microarray vs. RNA-Seq: A comparison for active subnetwork discovery." (11 2012).
  • Çatalyürek, U.V. "Message from the workshops chair." (10 2012).

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).
  • 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.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).
  • Karimabadi, H.; Loring, B.; Vu, H.X.; Omelchenko, Y. et al. "Petascale kinetic simulation of the magnetosphere." (9 2011).
  • Çatalyürek, U.V.; Kaya, K.; Uçar, B. "Integrated data placement and task assignment for scientific workflows in Clowds." (7 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).
  • A. Hatem, D. Bozdag, and Ü.V. Çatalyürek "Benchmarking Short Sequence Mapping Tools." in IEEE International Conference on Bioinformatics and Biomedicine (BIBM11). (1 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).
  • 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).
  • 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).
  • Saule, E.; Baş, E.O.; Çatalyürek, U.V. "Partitioning spatially located computations using rectangles." (10 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).
  • El Baz, D.; Baker, J.; Boukerche, A.; Boyer, V. et al. "Workshop on parallel computing and optimization - PCO." (12 2011).
  • Çatalyürek, U.V.; Dobrian, F.; Gebremedhin, A.; Halappanavar, M. et al. "Distributed-memory parallel algorithms for matching and coloring." (12 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).
  • Kosar, T.; Raicu, I.; Foster, I.; Fox, G. et al. "Workshop on data intensive computing in the clouds - DataCloud." (12 2011).
  • Aldemir, T.; Catalyurek, U.; Denning, R.; Smidts, C. et al. "Method and tool development to support systematic quantification of uncertainties, invited." (12 2011).

2010

  • Hartley, T.D.R.; Saule, E.; Catalyurek, U.V. "Automatic dataflow application tuning for heterogeneous systems." (12 2010).
  • Bozdaǧ, D.; Hatem, A.; Catalyurek, U.V. "Exploring parallelism in short sequence mapping using burrows-wheeler transform." (7 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).
  • 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).
  • Uçar, B.; Çatalyürek, U.V. "On the scalability of hypergraph models for sparse matrix partitioning." (5 2010).
  • Çatalyürek, U.V. "Message from the workshops chair." (7 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).
  • 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).
  • 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).
  • Bozdaǧ, D.; Kumar, A.S.; Catalyurek, U.V. "Comparative analysis of biclustering algorithms." (10 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).
  • Çatalyürek, U.V. "General chair's welcome." (12 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).
  • 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).
  • 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).
  • Teodoro, G.; Hartley, T.D.R.; Catalyurek, U.; Ferreira, R. "Run-time optimizations for replicated dataflows on heterogeneous environments." (12 2010).

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).
  • 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).
  • 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).
  • 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, 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).
  • 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).
  • Sussman, A.; Catalyurek, U. "IPDPS 2009 - Proceedings of the 2009 IEEE International Parallel and Distributed Processing Symposium: Message from the workshops chairs." (11 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).
  • Hartley, T.D.R.; Catalyurek, U.V. "A component-based framework for the cell broadband engine." (11 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).
  • 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).
  • 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).
  • 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).
  • Ujaldon, M.; Catalyurek, U.V. "High-performance signal processing on emerging many-core architectures using CUDA." (11 2009).

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).
  • 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).
  • 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,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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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,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, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan, G. Lozanski "Computerized microscopic image analysis of follicular lymphoma." in SPIE Medical Imaging. (2 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).
  • 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).
  • 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).
  • 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).
  • 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).

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).
  • Bansal, B.; Catalyurek, U.; Chame, J.; Chen, C. et al. "Intelligent optimization of parallel and distributed applications." (9 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • Weng, L.; Catalyurek, U.; Kurct, T.; Agrawal, G. et al. "Optimizing multiple queries on scientific datasets with partial replicas." (12 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).

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).
  • 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).
  • 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).
  • Rutt, B.; Hakobyan, A.; Metzroth, K.; Catalyurek, U. et al. "A softwaretool for the creation and analysis of dynamic event trees." (12 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).
  • 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).
  • 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).
  • 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.; Rountev, A. et al. "An extensible global address space framework with decoupled task and data abstractions." (1 2006).
  • Kumar, V.S.; Rutt, B.; Kurc, T.; Catalyurek, U. et al. "Large image correction and warping in a cluster environment." (12 2006).
  • Metzroth, K.; Catalyurek, U.; Aldemir, T.; Dunagan, S. et al. "A graphical tool for the analysis of event trees." (7 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).

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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • Yoo, A.; Chow, E.; Henderson, K.; McLendon, W. et al. "A scalable distributed parallel breadth-first search algorithm on BlueGene/L." (12 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).
  • 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).
  • 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).
  • 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).

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. 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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).
  • 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; 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).

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).
  • 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).
  • 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).
  • 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).
  • Catalyurek, U.; Gray, M.; Kurc, T.; Saltzt, J. et al. "A component-based implementation of multiple sequence alignment." (7 2003).
  • Kurc, T.; Lee, F.; Agrawal, G.; Catalyurek, U. et al. "Optimizing reduction computations in a distributed environment." (12 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).
  • 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).
  • 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).

2002

  • Beynon, M.D.; Kurc, T.; Catalyurek, U.; Sussman, A. et al. "Efficient manipulation of large datasets on heterogeneous storage systems." (1 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).
  • 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).
  • 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).

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).
  • 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).
  • 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).
  • 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).

1996

  • A. Pinar, U.V. Catalyurek, C. Aykanat, M. Pinar "Decomposing Linear Programs for Parallel Solution." in Lecture Notes in Computer Science. (1 1996).
  • Pınar, A.; Çatalyürek, Ü.V.; Aykanat, C.; Pınarnar, M. "Decomposing linear programs for parallel solution." (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).
  • Çatalyürek, Ü.V.; Aykanat, C. "Decomposing irregularly sparse matrices for parallel matrix-vector multiplication." (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).