Ümit V. Çatalyürek
 Adjunct Professor, SBSBiomedical Informatics

266 Ferst Drive
Georgia Institute of Technology
Atlanta, GA 30332
About
Education
PhD 2000, Bilkent University, Turkey
Areas of interest
Highperformance computing, runtime systems for dataintensive 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 20102014. 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 coauthored more than 200 peerreviewed 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: 6142927596
Alternate address
Department of Biomedical Informatics, 250 Lincoln Tower, 1800 Cannon Dr., Columbus, OH 43210
Honors

January, 2011
The runnerup 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 Multiway 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. "Twodimensional 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,
Journal Articles
2019
 Benoit, A.; Çatalyürek, Ü.V., 2019, "Special issue: Selected papers from IPDPS’18." Journal of Parallel and Distributed Computing 133, 174175  174175.
2017
 Çatalyürek, Ü.V., 2017, "Guest Editor's Introduction: Selected Papers from ACMBCB 2014." IEEE/ACM Transactions on Computational Biology and Bioinformatics 14, no. 5, 10001001  10001001.
2013
 Sariyüce, A.E.; Gedik, B.; JacquesSilva, G.; Wu, K.L. et al., 2013, "Streaming algorithms for kcore decomposition." Proceedings of the VLDB Endowment 6, no. 6, 433444  433444.
2011
 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. 1011, 694712  694712.
 Ãœ.V. Ã‡atalyÃ¼rek, C. Aykanat and E. Kayaaslan, 2011, "Hypergraph PartitioningBased FillReducing Ordering." SIAM Journal of Scientific Computing 33, no. 4, 19962023  19962023.
2010
 D. Bozdag, Ü.V. Çatalyürek, A. H. Gebremedhin, F. Manne, E.G. Boman, and F. Özgüner, 2010, "Distributedmemory Parallel Algorithms for Distance2 Coloring and Related Problems in Derivative Computation." SIAM Journal of Scientific Computing 4, no. 32, 24182446  24182446.
2009
 O. Sertel, J. Kong, H. Shimada, Ãœ.V. Ã‡atalyÃ¼rek, J.H. Saltz, M.N. Gurcan, 2009, "Computeraided Prognosis of Neuroblastoma on Wholeslide 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, 10931103  10931103.
 O. Sertel, J. Kong, Ãœ.V. Ã‡atalyÃ¼rek, G. Lozanski, J.H. Saltz, M.N. Gurcan, 2009, "Histopathological image analysis using modelbased intermediate representations and color texture: Follicular lymphoma grading." The Journal of Signal Processing Systems for Signal, Image, and Video Technology 55, no. 1, 169183  169183.
 Bozdag,Doruk; Oezguener,Fuesun; Catalyurek,Umit,V, 2009, "Compaction of Schedules and a TwoStage Approach for DuplicationBased DAG Scheduling." IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 20, no. 6, 857871  857871.
 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, 280298  280298.
 S. Erdal, Ü.V. Çatalyürek, P.R. Payne, J. Kamal, J.H. Saltz, M.N. Gurcan, 2009, "A KnowledgeAnchored Integrative Image Search and Retrieval System." Journal of Digital Imaging 22, no. 2, 166182  166182.
2008
 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, 3351  3351.
 D. Bozdag, A.H. Gebremedhin, F. Manne, E.G. Boman, Ãœ.V. Ã‡atalyÃ¼rek, 2008, "A Framework for Scalable Greedy Coloring on Distributed Memory Parallel Computers." Journal of Parallel and Distributed Computing 4, no. 68, 515535  515535.
 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, 34573467  34573467.
 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. Ã‡atalyÃ¼rek, E. Caserta, G. Leone, M.C. Ostrowski, R. Madduri, I. Foster, S. Madhavan, K. Buetow, K. Shanbhag, E. Siegel, 2008, "eScience, caGrid, and Translational Biomedical Research." Computer 41, no. 11, 5866  5866.
 Kumar,Vijay,S; Rutt,Benjamin; Kurc,Tahsin; Catalyurek,Umit,V; Pan,Tony,C; Chow,Sunny; Lamont,Stephan; Martone,Maryann; Saltz,Joel,H, 2008, "Largescale biomedical image analysis in grid environments." IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE 12, no. 2, 154161  154161.
2007
 Cambazoglu, B.B.; Sertel, O.; Kong, J.; Saltz, J. et al., 2007, "Efficient processing of pathological images using the grid: Computeraided prognosis of neuroblastoma." Proceedings of the 5th IEEE Workshop on Challenges of Large Applications in Distributed Environments, CLADE'07 3541  3541.
 A. Pothen, A.H. Gebremedhin, F. Dobrian, E.G. Boman, K.D. Devine, P.D. Hovland, B. Norris, J. Utke, Ãœ.V. Ã‡atalyÃ¼rek, 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 XMLbased system for synthesis of data from disparate databases." JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION 13, no. 3, 289301  289301.
 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 Gridenabled Multiphysics Oil Reservoir Management." Engineering with Computers 22, no. 3, 349370  349370.
2005
 S. Hastings, S. Oster, S. Langella, T.M. Kurc, T. Pan, Ü.V. Çatalyürek, J.H. Saltz, 2005, "A gridbased image archival and analysis system.." Journal of the American Medical Informatics Association : JAMIA 12, no. 3, 28695  28695.
 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 dataintensive scientific workflows." SIGMOD RECORD 34, no. 3, 5055  5055.
 Kurc,T; Catalyurek,U; Zhang,X; Saltz,J; Martino,R; Wheeler,M; Peszynska,M; Sussman,A; Hansen,C; Sen,M; Seifoullaev,R; Stoffa,P; TorresVerdin,C; Parashar,M, 2005, "A simulation and data analysis system for largescale, datadriven oil reservoir simulation studies." CONCURRENCY AND COMPUTATIONPRACTICE & EXPERIENCE 17, no. 11, 14411467  14411467.
2004
 Aykanat,C; Pinar,A; Catalyurek,U,V, 2004, "Permuting sparse rectangular matrices into blockdiagonal form." SIAM JOURNAL ON SCIENTIFIC COMPUTING 25, no. 6, 18601879  18601879.
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, 230248  230248.
 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, 23048  23048.
 Kurc, T.; Hastings, S.; Catalyurek, U.V.; Saltz, J. et al., 2003, "A distributed execution environment for analysis of DCEMR image datasets." Journal of Digital Imaging 16, no. SUPPL., 48  48.
 S. Narayanan, T.M. Kurc, Ü.V. Çatalyürek, J.H. Saltz, 2003, "Database support for datadriven scientific applications in the grid." Parallel Processing Letters 13, no. 2, 245271  245271.
2002
 M. Beynon, C. Chialin, Ü.V. Çatalyürek, T.M. Kurc, A. Sussman, H. Andrade, R.A. Ferreira, J.H. Saltz, 2002, "Processing largescale multidimensional data in parallel and distributed environments." Parallel Computing 28, no. 5, 827859  827859.
2001
 T.M. Kurc, Ãœ.V. Ã‡atalyÃ¼rek, 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, 2433  2433.
1999
 Catalyurek,U,V; Aykanat,C, 1999, "Hypergraphpartitioningbased decomposition for parallel sparsematrix vector multiplication." IEEE TRANSACTIONS ON PARALLEL AND DISTRIBUTED SYSTEMS 10, no. 7, 673693  673693.
Presentations
 "Middleware Infastructure for LargeScale Data Management." 2004, Presented at ASC VIEWS Alliance Forum,
 "Use of the Teragrid for Subsurface 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 Distance2 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,
 "HypergraphPartitioning Approaches for Workload Decomposition." 2002,
 "Runtime and Compiler Support for Large Scale Data Driven Science." 2004,
 "Serviceoriented Bioscience Cluster at OSC." 2008, Presented at Software Applications and Codes Meeting for the Ohio Supercomputer Center Bioscience Cluster Expansion,
 "MultiObjective 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 LargeScale Biomedical Images on a Cluster of MultiCore 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 LargeScale Biomedical Images on a Cluster of MultiCore CPUs and GPUs." 2009, Presented at Ohio Supercomputer Center Workshop on Accelerating simulations with NVIDIA GPU hardware,
 "LoadBalancing 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 MiniSymposium on Load Balancing for Emerging Applications, in SIAM Conference of Parallel Processing for Scientific Computing,
 "STORM (Overview)." 2005, Presented at First DIALOGUE Workshop: ApplicationsDriven 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 HighPerformance 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 DataIntensive Tasks with Batchshared I/O." 2007,
Papers in Proceedings
2020
 Özkaya, M.Y.; Benoit, A.; Çatalyürek, Ü.V. "Improving localityaware scheduling with acyclic directed graph partitioning." (1 2020).
2019
 Yasar, A.; Rajamanickam, S.; Berry, J.; Wolf, M. et al. "Linear algebrabased triangle counting via finegrained tasking on heterogeneous environments : ((Update on Static Graph Challenge)." (9 2019).
 Yusuf Özkaya, M.; Benoit, A.; Uçar, B.; Herrmann, J. et al. "A scalable clusteringbased task scheduler for homogeneous processors using DAG partitioning." (5 2019).
 Li, J.; Uçar, B.; Çatalyürek, V.; Sun, J. et al. "Efficient and effective sparse tensor reordering." (6 2019).
 Afibuzzaman, M.; Rabbi, F.; Ozkaya, M.Y.; Aktulga, H.M. et al. "DeepSparse: A TaskParallel Framework for SparseSolvers on Deep Memory Architectures." (12 2019).
 Acer, S.; Yasar, A.; Rajamanickam, S.; Wolf, M. et al. "Scalable triangle counting on distributedmemory systems." (9 2019).
2018
 Yasar, A.; Ucar, B.; Catalyurek, U.V. "Sina: A scalable iterative network aligner." (10 2018).
 Yasar, A.; Rajamanickam, S.; Wolf, M.; Berry, J. et al. "Fast Triangle Counting Using Cilk." (11 2018).
 Ozkaya, M.Y.; Sanyuce, A.E.; Pinar, A.; Catalyurek, U.V. "Local detection of critical nodes in active graphs." (10 2018).
 Çatalyürek, Ü.V. "Message from the Program Chair." (2 2018).
 Yasar, A.; Catalyürek, U.V. "An iterative global structureassisted labeled network aligner." (7 2018).
2017
 Sariyüce, A.E.; Seshadhri, C.; Pinar, A.; Çatalyürek, Ü.V. "Nucleus decompositions for identifying hierarchy of dense subgraphs." (7 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).
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
 Cątalyürek, Ü.V. "Message from the Workshops Chair." (7 2015).
 AbuDoleh, 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).
 Kaya, K.; Gedik, B.; Catalyurek, U.V. "HPC4BD 2015 Workshop Foreword." (12 2015).
 Çatalyürek, Ü.V. "Message from the Workshops Chair." (9 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
 Sanyüce, A.E.; Saule, E.; Kaya, K.; Çatalyürek, Ü.V. "Shattering and compressing networks for betweenness centrality." (1 2013).
 Sariyüce, A.E.; Saule, E.; Kaya, K.; Çatalyürek, Ü.V. "Shattering and compressing networks for betweenness centrality." (1 2013).
 AbuDoleh, A.; Saule, E.; Kaya, K.; Çatalyürek, U.V. "Masher: Mapping long(er) reads with hashbased genome indexing on GPUs." (11 2013).
 Hatem, A.; Kaya, K.; Çatalyürek, U.V. "PRASE: PageRankbased active subnetwork extraction." (11 2013).
 Çatalyürek, U.V. "Message from the workshops chair." (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).
 Sariyüce, A.E.; Kaya, K.; Saule, E.; Çatalyürek, U.V. "Betweenness centrality on GPUs and heterogeneous architectures." (4 2013).
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).
 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 Multilevel Hypergraph Partitioning." in 26th IEEE International Parallel & Distributed Processing Symposium (IPDPS’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 (DNASDM). (4 2012).
 Çatalyürek, U.V.; Kaya, K.; Uçar, B. "On sharedmemory parallelization of a sparse matrix scaling algorithm." (12 2012).
 Zhou, Z.; Saule, E.; Aktulga, H.M.; Yang, C. et al. "An outofcore dataflow middleware to reduce the cost of large scale iterative solvers." (12 2012).
 Hatem, A.; Kaya, K.; Çatalyürek, U.V. "Microarray vs. RNASeq: A comparison for active subnetwork discovery." (11 2012).
 Çatalyürek, U.V. "Message from the workshops chair." (10 2012).
2011
 El Baz, D.; Baker, J.; Boukerche, A.; Boyer, V. et al. "Workshop on parallel computing and optimization  PCO." (12 2011).
 Aluru, S.; Bader, D.A.; Kalyanaraman, A.; Agarwal, G. et al. "Message from the workshop chairs." (12 2011).
 D.M. Osborn, D. Mandelli, K. Metzroth, T. Aldemir, R. Denning and Ü.V. Çatalyürek "A dynamic level 2 PRA using ADAPTMELCOR." in Advances in Safety, Reliability and Risk Managemen, Proceedings of the 20th European Safety and Reliability (ESREL). (9 2011).
 Çatalyürek, U.V. "Message from the workshops chair." (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).
 A. Hatem, D. Bozdag, and Ü.V. Çatalyürek "Benchmarking Short Sequence Mapping Tools." in IEEE International Conference on Bioinformatics and Biomedicine (BIBM11). (1 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).
 Çatalyürek, U.V.; Kaya, K.; Uçar, B. "Integrated data placement and task assignment for scientific workflows in Clowds." (7 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).
 Çatalyürek, U.V.; Dobrian, F.; Gebremedhin, A.; Halappanavar, M. et al. "Distributedmemory parallel algorithms for matching and coloring." (12 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).
 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).
 H.M. Aktulga, C. Yang, U.V. Catalyurek, P. Maris, J.P. Vary, and E. G. Ng "On Reducing I/O Overheads in LargeScale Invariant Subspace Projections." in Workshop on Algorithms and Programming Tools for NextGeneration HighPerformance Scientific Software (HPSS 2011), in conjunction with the EuroPar. (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).
 U.V. Catalyurek, F. Dobrian, A. Gebremedhin, M. Halappanavar, and A. Pothen "DistributedMemory 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).
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 NetworkBased Computing. (1 2010).
 D. Bozdag, A. Hatem, U.V. Catalyurek "Exploring Parallelism in Short Sequence Mapping Using BurrowsWheeler 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).
 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).
 Teodoro, G.; Hartley, T.D.R.; Catalyurek, U.; Ferreira, R. "Runtime optimizations for replicated dataflows on heterogeneous environments." (12 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 (ACMBCB). (8 2010).
 G. Teodoro, T. Hartley, Ü.V. Çatalyürek, and R. Ferreira "Runtime optimizations for replicated dataflows on heterogeneous environments." in The ACM International Symposium on High Performance Distributed Computing (HPDC). (6 2010).
 Bozdaǧ, D.; Hatem, A.; Catalyurek, U.V. "Exploring parallelism in short sequence mapping using burrowswheeler transform." (7 2010).
 Bozdaǧ, D.; Kumar, A.S.; Catalyurek, U.V. "Comparative analysis of biclustering algorithms." (10 2010).
 Çatalyürek, U.V. "Message from the workshops chair." (7 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).
 O. Sertel, Ü.V. Çatalyürek, G. Lozanski, A. Shanaah, and M.N. Gurcan "An Image Analysis Approach for Detecting Malignant Cells in Digitized H&Estained Histology Images of Follicular Lymphoma." in 20th International Conference on Pattern Recognition (ICPR). (8 2010).
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 ComponentBased Framework for the Cell Broadband Engine." in 23rd International Parallel and Distributed Processing Symposium (IPDPS09); the 18th Heterogeneous Computing Workshop. (5 2009).
 Bozdag,Doruk; Parvin,Jeffrey,D; Catalyurek,Umit,V "A Biclustering Method to Discover Coregulated Genes Using Diverse Gene Expression Datasets." in 1st International Conference on Bioinformatics and Computational Biology. (1 2009).
 D. Bozdag, J.D. Parvin, U.V. Catalyurek "A Biclustering Method to Discover Coregulated 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 GenomeWide Screening Data from ChIPSequencing Experiments." in First International Conference on Bioinformatics and Computational Biology (BICoB). (1 2009).
 T. Hartley, A.R. Fasih, C.A. Berdanier, F. Ozguner, U.V. Catalyurek "Investigating the Use of GPUAccelerated Nodes for SAR Image Formation." in 2009 IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC). (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).
 Ozer,Hatice,Gulcin; Bozdag,Doruk; Camerlengo,Terry; Wu,Jiejun; Huang,YiWen; Hartley,Tim; Parvin,Jeffrey,D; Huang,Tim; Catalyurek,Umit,V; Huang,Kun "A Comprehensive Analysis Workflow for GenomeWide Screening Data from ChIPSequencing Experiments." 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).
 Hartley, T.D.R.; Catalyurek, U.V. "A componentbased framework for the cell broadband engine." (11 2009).
 Ujaldon, M.; Catalyurek, U.V. "Highperformance signal processing on emerging manycore architectures using CUDA." (11 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).
 Metzroth, K.; Winningham, R.; Catalyurek, U.; Denning, R. et al. "Linking of the RELAP53D thermalhydraulic code with the ADAPT PRA tool." (12 2009).
2008
 O. Sertel, J. Kong, G. Lozanski, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan "Texture classification using nonlinear 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 widearea 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).
 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).
 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).
 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).
 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).
 O. Sertel, J. Kong, H. Shimada, U.V. Catalyurek, J.H. Saltz, M.N. Gurcan "Computeraided prognosis of neuroblastoma: classification of stromal development on wholeslide images." in Proceedings of SPIE Medical Imaging. (2 2008).
 Sertel,Olcay; Kong,Jun; Shimada,Hiroyuki; Catalyurek,Umit; Saltz,Joel,H; Gurcan,Metin "Computeraided prognosis of neuroblastoma: Classification of stromal development on wholeslide images." in Medical Imaging 2008 Conference. (1 2008).
 G. Khanna, U.V. Catalyurek, T. Kurc, R. Kettimuthu, P. Sadayappan, J. Saltz "A Dynamic Scheduling Approach for Coordinated WideArea Data Trasnfers Using GridFTP." in 22nd IEEE International Parallel & Distributed Processing Symposium (IPDPS08). (4 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).
 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).
 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).
 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).
 F. Igual, R. Mayo, T. Hartley, U.V. Catalyurek, A. Ruiz, M. Ujaldon "Optimizing cooccurrence matrices on graphics processors using sparse representations." in 9th International Workshop on StateoftheArt in Scientific and Parallel Computing. (5 2008).
 G. Khanna, U.V. Catalyurek, T. Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, J. Saltz "Using Overlays for Efficient Data Transfer Over Shared WideArea Networks." in SC2008 High Performance Computing, Networking, and Storage Conference. (11 2008).
2007
 Kurc,Tahsin; Zhang,Xi; Parashar,Manish; Klie,Hector; Wheeler,Mar,F; Catalyurek,Umit; Saltz,Joel "Dynamic datadriven systems approach for simulation based optimizations." in 7th International Conference on Computational Science (ICCS 2007). (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).
 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).
 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 EuroPar, 2007. (1 2007).
 Khanna,Gaurav; Catalyurek,Umit; Kurc,Tahsin; Sadayappan,P; Saltz,Joel "A data locality aware online scheduling approach for I/Ointensive jobs with file sharing." in 12th International Workshop on Job Scheduling Strategies for Parallel Processing. (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).
 Khanna,Gaurav; Catalyurek,Umit; Kurc,Tahsin; Sadayappan,P; Saltz,Joel "Scheduling file transfers for dataintensive jobs on heterogeneous clusters." in 13th International EuroPar Conference on Parallel Processing. (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).
 G. Khanna, U.V. Catalyurek, T.M. Kurc, P. Sadayappan, J.H. Saltz "Scheduling File Transfers for DataIntensive Jobs on Heterogeneous Clusters." in Proceedings of EuroPar, 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: ComputerAided Prognosis of Neuroblastoma." in Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE'07). (1 2007).
 Bansal, B.; Catalyurek, U.; Chame, J.; Chen, C. et al. "Intelligent optimization of parallel and distributed applications." (9 2007).
 Weng, L.; Catalyurek, U.; Kurct, T.; Agrawal, G. et al. "Optimizing multiple queries on scientific datasets with partial replicas." (12 2007).
 T.M. Kurc, X. Zhang, M. Parashar, H. Klie, M.F. Wheeler, U.V. Catalyurek, J.H. Saltz "Dynamic DataDriven Systems Approach for Simulation Based Optimizations." in International Conference on Computation Science (1). (1 2007).
 S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, A. Rountev, P. Sadayappan "A global address space framework for locality aware scheduling of blocksparse 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).
 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).
 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).
 Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Rountev, A. et al. "A global address space framework for locality aware scheduling of blocksparse computations." (9 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).
 U.V. Catalyurek, E.G. Boman, K.D. Devine, D. Bozdag, R. Heaphy, L.A. Riesen "Hypergraphbased Dynamic Load Balancing for Adaptive Scientific Computations." in 21st IEEE International Parallel & Distributed Processing Symposium (IPDPS '07). (1 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 EuroPar Conference on Parallel Processing. (1 2007).
 V. Kumar, T. Kurc, J. Kong, U.V. Catalyurek, M.N. Gurcan, J.H. Saltz "Performance vs. Accuracy Tradeoffs for Largescale Image Analysis Applications." in Proceedings of the IEEE Cluster 2007. (1 2007).
2006
 D. Bozdag, U.V. Catalyurek, F. Ozguner "A Task Duplication Based BottomUp Scheduling Algorithm for Heterogeneous Environments." in The 15th Heterogeneous Computing Workshop (HCW '06). (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).
 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).
 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 MixedParallel Applications." in Proceedings of the 2006 International Conference on Parallel Processing (ICPP06). (1 2006).
 G. Khanna, U.V. Catalyurek, T. Kurc, P. Sadayappan, J. Saltz "A Data Locality Aware Online Scheduling Approach for I/OIntensive Jobs With File Sharing." in 12th International Workshop on Job Scheduling Strategies. (6 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.; Hakobyan, A.; Metzroth, K.; Catalyurek, U. et al. "A softwaretool for the creation and analysis of dynamic event trees." (12 2006).
 Vydyanathan, N.; Khanna, G.; Catalyurek, U.; Kurc, T. et al. "Scheduling of tasks with batchshared I/O on heterogeneous systems." (1 2006).
 Bozdaǧ, D.; Catalyurek, U.; Özgüner, F. "A task duplication based bottomup scheduling algorithm for heterogeneous environments." (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 outofcore preprocessing of very large microscopy images for efficient querying." in IEEE International Conference on Cluster Computing. (1 2006).
 S. Krishnamoorthy, U.V. Catalyurek, J. Nieplocha, P. Sadayappan "An Approach to LocalityConscious Load Balancing and Transparent Memory Hierarchy Management With a GlobalAddressSpace Parallel Program Model." in 20th International Parallel and Distributed Processing Symposium (IPDPS '06). (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, G. Khanna, U.V. Catalyurek, T.M. Kurc, J.H. Saltz, P. Sadayappan "Scheduling of Tasks with BatchShared 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 massivescale semantic graphs." in IEEE International Conference on Cluster Computing. (1 2006).
 Krishnamoorthy, S.; Catalyurek, U.; Nieplocha, J.; Sadayappan, P. "An approach to localityconscious load balancing and transparent memory hierarchy management with a globaladdressspace 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).
 G. Khanna, N. Vydyanathan, U.V. Catalyurek, T.M. Kurc, S. Krishnamoorthy, P. Sadayappan, J.H. Saltz "Task Scheduling and File Replication for DataIntensive Jobs with Batchshared I/O." in 15th IEEE International Symposium on HighPerformance Distributed Computing (HPDC15). (6 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).
 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).
 S. Narayan, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "On Creating Efficient Objectrelational Views of Scientific Datasets." in Proceedings of the 2006 International Conference on Parallel Processing (ICPP06). (8 2006).
 D. Ucar, S. Asur, U.V. Catalyurek, S. Parthasarathy "Improving Functional Modularity in ProteinProtein Interactions Graphs Using Hubinduced Subgraphs." in Knowledge Discovery in Databases: PKDD 2006. (9 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).
 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).
 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).
 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 (ICPP06). (8 2006).
2005
 Bozdag,D; Catalyurek,U; Gebremedhin,A,H; Manne,F; Boman,E,G; Ozguner,F "parallel distance2 graph coloring algorithm for distributed memory computers." in 1st International on High Performance Computing and Communications (HPCC 2005). (1 2005).
 V. Kumar, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "Design and Implementation of a Data Server Using a PeertoPeer Storage System." in High Performance Computing Symposium (HPC '05). (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 (ICPP05). (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 EuroPar 2005 Parallel Processing: 11th International EuroPar Conference. (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 BatchShared I/O." in Cluster Computing and Grid 2005 (CCGrid '05). (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).
 Yoo, A.; Chow, E.; Henderson, K.; McLendon, W. et al. "A scalable distributed parallel breadthfirst search algorithm on BlueGene/L." (12 2005).
 Hastings, S.; Langella, S.; Oster, S.; Kurc, T. et al. "Gbased management of biomedical data using an XMLbased distributed data management system." (12 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 EuroPar Conference. (1 2005).
 B. Rutt, V.S. Kumar, T. Pan, T.M. Kurc, U.V. Catalyurek, Y. Wang, and J.H. Saltz "Distributed Outofcore 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 DataDriven Optimization of Oil Well Placement." in ICCS '05. (4 2005).
 A. Yoo, E. Chow, K. Henderson, W. McLendon, B. Hendrickson, U.V. Catalyurek "A Scalable Distributed Parallel BreadthFirst Search Algorithm on BlueGene/L." in International Conference for High Performance Computing, Networking, and Storage (SC2005). (11 2005).
 Weng,L; AGRAWAL,G; Catalyurek,U; Saltz,J "Supporting SQL3 aggregations on gridbased data repositories." in 17th International Workshop on Languages and Compilers for High Performance Computing. (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 LargeScale Medical and Scientific Datasets." in International Conference ParCO. (1 2005).
 S. Narayanan, U.V. Catalyurek, T.M. Kurc, V. Kumar, J.H. Saltz "A Runtime Framework for Partial Replication and Its Application for OnDemand Data Exploration." in High Performance Computing Symposium (HPC '05). (1 2005).
 S. Hastings, S. Langella, S. Oster, T.M. Kurc, T. Pan, U.V. Catalyurek, D.A. Janies, J.H. Saltz "Gridbased Management of Biomedical Data using an XMLbased Distributed Data Management System." in Proceedings of the 19th Annual ACM Symposium on Applied Computing. (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).
 Parashar,M; Matossian,V; Bangerth,W; Klie,H; Rutt,B; Kurc,T; Catalyurek,U; Saltz,J; Wheeler,M,F "Towards dynamic datadriven 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).
 D. Bozdag, U.V. Catalyurek, A.H. Gebremedhin, F. Manne, E.G. Boman, F. Ozguner "A Parallel Distance2 Graph Coloring Algorithm for Distributed Memory Computers." in 2005 International Conference on High Performance Computing and Communications (HPCC05). (9 2005).
2004
 Zhang,X; Kurc,T; Pan,T; Catalyurek,U; Narayanan,S; Wyckoff,P; Saltz,J "Strategies for using additional resources in parallel hashbased join algorithms." in 13th IEEE International Symposium on High Performance Distributed Computing (HPDC13). (1 2004).
 Parashar,M; Klie,H; Catalyurek,U; Kurc,T; Matossian,V; Saltz,J; Wheeler,M,F "Application of gridenabled technologies for solving optimization problems in datadriven reservoir studies." in 4th International Conference on Computational Science (ICCS 2004). (1 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 PipelineShared I/O." in Fifth IEEE/ACM International Workshop on Grid Computing, 2004. (1 2004).
 X. Zhang, T. Pan, U.V. Catalyurek, T.M Kurc, J.H. Saltz "Serving queries to multiresolution datasets on diskbased storage clusters." in Proceedings of the 4th IEEE/ACM International Symposium on Cluster Computing and the Grid, 2004 (CCGrid 2004). (4 2004).
 M. Parashar, H. Klie, U.V. Catalyurek, T.M. Kurc, V. Matossian, J.H Saltz, M.F. Wheeler "Applications of Gridenabled Technologies for Solving Optimization Problems in DataDriven Reservior Studies." in Workshop on Distributed Data Driven Applications and Systems (ICCS 2004). (6 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 HighPerformance Distributed Computing (HPDC13). (6 2004).
 S. Langella, S. Hastings, S. Oster, T.M. Kurc, U.V. Catalyurek, J.H. Saltz "A Distributed Data Management Middleware for DataDriven Application Systems." in 2004 IEEE International Conference on Cluster Computing. (9 2004).
 L. Weng, G. Agrawal, U.V. Catalyurek, J.H. Saltz "Supporting SQL3 Aggregations on Gridbased Data Repositories." in Languages and Compilers for High Performance Computing (LLPC '04). (9 2004).
 Zhang,X; Pan,T; Catalyurek,U; Kurc,T; Saltz,J "Serving queries to multiresolution datasets on diskbased storage clusters." in 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCG 2004). (1 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 (HPDC13). (6 2004).
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 Gridenabled Image Processing Applications." in Proceedings of the 3rd International Symposium on Cluster Computing and the Grid (CCGrid '03). (1 2003).
 Kurc, T.; Lee, F.; Agrawal, G.; Catalyurek, U. et al. "Optimizing reduction computations in a distributed environment." (12 2003).
 Catalyurek, U.; Gray, M.; Kurc, T.; Saltzt, J. et al. "A componentbased implementation of multiple sequence alignment." (7 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).
 Ü.V. Çatalyürek, M. Gray, T.M. Kurç, J.H. Saltz, E. Stahlberg, and R. Ferreira "A Componentbased Implementation of Multiple Sequence Alignment." in Proceedings of the 2003 ACM Symposium on Applied Computing, SAC2003. (1 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).
 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 (HPDC12). (6 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 DataDriven Application Systems. (6 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).
 T. Kurc, S. Hastings, U.V. Catalyurek, J.H. Saltz, J.D. Fleig, B.D. Clymer, H. von TenggKobligk, K.T. Baudendistel, R. Machiraju, M.V Knopp "A Disdtributed Execution Environment for Analysis of DCEMR Image Datasets." in The Society for Computer Applications in Radiology (SCAR 2003). (1 2003).
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 Runtime Systems for Scalable Computers. (3 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).
 Beynon, M.D.; Kurc, T.; Catalyurek, U.; Sussman, A. et al. "Efficient manipulation of large datasets on heterogeneous storage systems." (1 2002).
 U.V. Catalyurek, E.A. Stahlberg, R.A. Ferreira, J.H. Saltz "Improving Performance of Multiple Sequence Alignment Analysis in MultiClient Environments." in Proceedings of the First International Workshop on High Performance Computational Biology. (4 2002).
2001
 U.V. Catalyurek, C. Aykanat "A HypergraphPartitioning Approach for CoarseGrain 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 HypergraphBased Workload Partitioning Strategy for Parallel Data Aggregation." in Proceedings of the Tenth SIAM Conference on Parallel Processing for Scientific Computing. (3 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).
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 matrixvector 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).
 Çatalyürek, Ü.V.; Aykanat, C. "Decomposing irregularly sparse matrices for parallel matrixvector multiplication." (1 1996).
1995
 U.V. Catalyurek, C. Aykanat "A hypergraph model for mapping repeated sparse matrixvector product computations onto multicomputers." in Proceedings of the International Conference on High Performance Computing (HiPC' 95). (12 1995).