HPC Lab
Publications
Sorted by publication year  Sort by project category  Journal/Book Conference Report Abstract/Poster 
2018

A Resource Provisioning Framework for Bioinformatics Applications in MultiCloud Environments
I. F. Senturk, P.Balakrishnan, A. AbuDoleh, K. Kaya, Q. Malluhi, Ü. V. Çatalyürek
The Future Generation Computer Systems Journal, vol. 78, no. 1, Jan 2018 Online

Acyclic partitioning of large directed acyclic graphs
J. Herrmann, M. Y. Özkaya, B. U. car, K. Kaya, Ü. V. Çatalyürek
Tech. Report, Inria  Research Centre Grenoble  Rh\^oneAlpes, no. RR9163, Mar 2018 Online
2017

Graph Manipulations for Fast Centrality Computation
A. E. Sarıyüce, K. Kaya, E. Saule, Ü. V. Çatalyürek
ACM Transactions on Knowledge Discovery from Data, vol. 11, no. 3, pg. 26:126:25, Apr 2017 Online

Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs
A. E. Sarıyüce, C. Seshadhri, A. Pınar, Ü. V. Çatalyürek
ACM Transactions on the Web, vol. 11, no. 3, Jul 2017

Acyclic Partitioning of LargeScale Directed Acyclic Graphs
J. Herrmann, J. Kho, B. Uçar, K. Kaya, Ü. V. Çatalyürek
Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), May 2017
2016

Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States
M. Hoffmann, Y. Luo, S. R. Monday, N. GonzalesEscalona, A. R. Ottesen, T. Muruvanda, C. Wang, G. Kastanis, C. Keys, D. Janies, I. F. Senturk, Ü. V. Çatalyürek, H. Wang, T. S. Hammack, W. J. Wolfgang, D. SchoonmakerBopp, A. Chu, R. Myers, J. Haendiges, P. S. Evans, J. Meng, E. A. Strain, M. W. Allard, E. W. Brown
Journal of Infectious Diseases, vol. 213, no. 4, pg. 502508, Apr 2016 Online

Multijagged: A Scalable Parallel Spatial Partitioning Algorithm
M. Deveci, S. Rajamanickam, K. D. Devine, Ü. V. Çatalyürek
IEEE Transactions on Parallel and Distributed Systems, vol. 27, no. 3, pg. 803817, Mar 2016 Online

SONIC: Streaming Overlapping Community Detection
A. E. Sarıyüce, B. Gedik, G. JacquesSilva, K. Wu, Ü. V. Çatalyürek
Data Mining and Knowledge Discovery (DAMI), vol. 30, no. 4, pg. 819847, 2016 Online

Incremental kcore Decomposition: Algorithms and Evaluation
A. E. Sarıyüce, B. Gedik, G. JacquesSilva, K. Wu, Ü. V. Çatalyürek
The VLDB Journal, vol. 25, no. 3, pg. 425447, 2016 Online

Efficacy of the SU(3) scheme for ab initio largescale calculations beyond the lightest nuclei
T. Dytrych, P. Maris, K. D. Launey, J. P. Draayer, J. P. Vary, D. Langr, E. Saule, M. A. Caprio, Ü. V. Çatalyürek, M. Sosonkina
Computer Physics Communications, vol. 207, pg. 202  210, 2016 Online

Identification of key mutation signatures from conservation analysis of genepseudogene families in human
T. Johnson, J. Kho, Ü. V. Çatalyürek, K. Huang, Y. Zhang
Poster, journalF1000Research (ISCB Comm J) (ISMB'16), Jul 2016 Online
2015

Phylogenetic visualization of the spread of H7 influenza A viruses
D. A. Janies, L. W. Pomeroy, C. Krueger, Y. Zhang, I. F. Senturk, K. Kaya, Ü. V. Çatalyürek
Cladistics, vol. 31, no. 6, pg. 679691, Dec 2015 Online

Incremental Closeness Centrality in Distributed Memory
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
Parallel Computing, vol. 47, pg. 318, Aug 2015 Online

Hypergraph partitioning for multiple communication cost metrics: Model and methods
M. Deveci, K. Kaya, B. Uçar, Ü. V. Çatalyürek
Journal of Parallel and Distributed Computing, vol. 77, pg. 6983, Mar 2015 Online

Regularizing Graph Centrality Computations
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
Journal of Parallel and Distributed Computing, vol. 76, pg. 106119, Feb 2015 Online

An OutofCore Taskbased Middleware for DataIntensive Scientific Computing
E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, Ü. V. Çatalyürek
Handbook on Data Centers, Springer, Editors S. U. Khan, A. Y. Zomoya, pg. 647667, 2015, ISBN 9781493920914 Online

Allelespecific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci
M. M. Gerber, H. Hampel, X. Zhou, N. P. Schulz, A. Suhy, M. Deveci, Ü. V. Çatalyürek, A. E. Toland
International Journal of Cancer, vol. 137, no. 10, pg. 23232331, 2015 Online

Mitigating Bias in Planning TwoColor Microarray Experiments
N. Ferhatosmanoglu, T. T. Allen, Ü. V. Çatalyürek
International Journal of Data Mining and Bioinformatics, vol. 13, no. 1, pg. 3149, 2015

Querying Coregulated Genes on Diverse Gene Expression Datasets Via Biclustering
M. Deveci, O. Küçüktunç, K. Eren, a. D. Bozdağ, K. Kaya, Ü. V. Çatalyürek
Methods in Molecular Biology, Springer, Editors P.H. Guzzi, 2015 Online

Spaler: Spark and GraphX based de novo genome assembler
A. AbuDoleh, Ü. V. Çatalyürek
Proc of IEEE Int'l Conference on BigData, Oct 2015

MICA: MicroRNA Integration for Active Module Discovery
A. Hatem, K. Kaya, J. Parvin, K. Huang, Ü. V. Çatalyürek
Proc. of 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACMBCB), Sep 2015

Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application
D. Janies, Z. Witter, C. Gibson, T. Kraft, I. F. Senturk, Ü. V. Çatalyürek
MEDINFO'15, Aug 2015

Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions
A. E. Sarıyüce, C. Seshadhri, A. Pınar, Ü. V. Çatalyürek
24th International World Wide Web Conference (WWW), May 2015, Also available as a Tech Rep on ArXiv\". Best Paper Award Nominee.

Fast and High Quality TopologyAware Task Mapping
M. Deveci, K. Kaya, B. Uçar, Ü. V. Çatalyürek
29th IEEE International Parallel and Distributed Processing Symposium, May 2015
2014

Diversifying Citation Recommendations
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
ACM Transactions on Intelligent Systems and Technology, vol. 5, no. 4, pg. 55:155:21, Dec 2014

NUSAP1 influences the DNA damage response by controlling BRCA1 protein levels
S. Kotian, T. Banerjee, A. Lockhart, K. Huang, Ü. V. Çatalyürek, J. D. Parvin
Cancer Biology and Therapy, vol. 15, no. 5, pg. 533543, Feb 2014 Online

HighPerformance Computing in HighThroughput Sequencing
K. Kaya, A. Hatem, H. G. Özer, K. Huang, Ü. V. Çatalyürek
Biological Knowledge Discovery Handbook, John Wiley & Sons, Editors M. Elloumi, A. Y. Zomaya, 2014

Exploring the Future of OutOfCore Computing with ComputeLocal NonVolatile Memory
M. Jung, E. H. W. III, W. Choi, J. Shalf, H. M. Aktulga, C. Yang, E. Saule, Ü. V. Çatalyürek, M. Kandemir
Scientific Programming, vol. 22, no. 2, pg. 125139, 2014 Online

mrSNP: Software to detect SNP effects on microRNA binding
M. Deveci, Ü. V. Çatalyürek, A. E. Toland
BMC Bioinformatics, vol. 15, pg. 73, 2014 Online

Massively Multithreaded Maxflow for Image Segmentation on the Cray XMT2
S. H. Bokhari, Ü. V. Çatalyürek, M. N. Gürcan
Concurrency and Computation: Practice and Experience, vol. 26, no. 18, pg. 28362855, 2014, Also available as a technical report from Algopath LLC. Online

Hardware/Software Vectorization for Closeness Centrality on Multi/ManyCore Architectures Paper
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP), May 2014

Randomized matching heuristics with quality guarantees on shared memory parallel computers
F. Dufossé, K. Kaya, B. Uçar
28th IEEE International Parallel and Distributed Processing Symposium, May 2014

Exploiting Geometric Partitioning in Task Mapping for Parallel Computers Paper
M. Deveci, S. Rajamanickam, V. Leung, K. T. Pedretti, S. L. Olivier, D. P. Bunde, Ü. V. Çatalyürek, K. D. Devine
28th IEEE International Parallel and Distributed Processing Symposium, May 2014

Extracting Maximal Exact Matches on GPU Paper
A. AbuDoleh, K. Kaya, M. Abouelhoda, Ü. V. Çatalyürek
28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP), May 2014

Widearea overlay networking to manage science DMZ accelerated flows
P. Calyam, A. Berryman, E. Saule, H. Subramoni, P. Schopis, G. Springer, Ü. V. Çatalyürek, D.K. Panda
Computing, Networking and Communications (ICNC), 2014 International Conference on, pg. 269275, Feb 2014

Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions
A. E. Sarıyüce, C. Seshadhri, A. Pınar, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1411.3312, Nov 2014 Online

On Distributed Graph Coloring with Iterative Recoloring Paper
A. E. Sarıyüce, E. Saule, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1407.6745, Jul 2014 Online

Computing the Closeness Centrality of Evolving Networks on Clusters Paper
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
Poster, SIAM Workshop on Network Science (NS14), July 2014

Partitioning Hypergraphs for Multiple Communication Metrics Paper
M. Deveci, K. Kaya, B. Uçar, Ü. V. Çatalyürek
Abstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14), July 2014

Load Balancing and Task Mapping for Exascale Systems Paper
M. Deveci, Ü. V. Çatalyürek
Poster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum, May 2014, PhD Forum award
2013

Collective Modes in Light Nuclei from First Principles
T. Dytrych, K. D. Launey, J. P. Draayer, P. Maris, J. P. Vary, E. Saule, Ü. V. Çatalyürek, M. Sosonkina, D. Langr, M. A. Caprio
Physical Review Letters, vol. 111, no. 25, pg. 252501, Dec 2013 Online

Metagenomic Insights into the CarbohydrateActive Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows
L. Wang, A. Hatem, Ü. V. Çatalyürek, M. Morrison, Z. Yu
PLoS ONE, Public Library of Science, vol. 8, no. 11, pg. e78507, Nov 2013 Online

A Survey of Pipelined Workflow Scheduling: Models and Algorithms
A. Benoit, Ü. V. Çatalyürek, Y. Robert, E. Saule
ACM Computing Surveys, vol. 45, no. 4, pg. 50:150:36, Aug 2013 Online

No Core CI calculations for light nuclei with chiral 2 and 3body forces
P. Maris, H. M. Aktulga, S. Binder, A. Calci, Ü. V. Çatalyürek, J. Langhammer, E. G. Ng, E. Saule, R. Roth, J. P. Vary, C. Yang
Journal of Physics: Conference Series, vol. 454, no. 1, pg. 012063, 2013 Online

Pushrelabel based Algorithms for the Maximum Transversal Problem
K. Kaya, J. Langguth, F. Manne, B. Uçar
Computers & Operations Research, vol. 40, no. 5, pg. 12661275, 2013

Constructing Elimination Trees for Sparse Unsymmetric Matrices
K. Kaya, B. Uçar
SIAM Journal on Matrix Analysis and Applications, vol. 34, no. 2, pg. 345354, 2013

Fast Recommendation on Bibliographic Networks with SparseMatrix Ordering and Partitioning
O. Küçüktunç, K. Kaya, E. Saule, Ü. V. Çatalyürek
Social Network Analysis and Mining (SNAM), vol. 3, no. 4, pg. 10971111, 2013 Online

Benchmarking Short Sequence Mapping Tools
A. Hatem, D. Bozdağ, A. E. Toland, Ü. V. Çatalyürek
BMC Bioinformatics, vol. 14, no. 1, 2013 Online

A Comparative Analysis of Biclustering Algorithms for Gene Expression Data Paper
K. Eren, M. Deveci, O. Küçüktunç, Ü. V. Çatalyürek
Briefings in Bioinformatics, vol. 14, no. 3, pg. 279292, 2013 Online

Preconditioners based on Strong Subgraphs
I. S. Duff, K. Kaya
Electronic Transactions on Numerical Analysis, 2013

Exploring the Future of OutOfCore Computing with ComputeLocal NonVolatile Memory
M. Jung, E. H. W. III, W. Choi, J. Shalf, H. M. Aktulga, C. Yang, E. Saule, Ü. V. Çatalyürek, M. Kandemir
Proc. of Conference on High Performance Computing Networking, Storage and Analysis (SC '13), Nov 2013

Incremental Algorithms for Closeness Centrality Paper Slides
A. E. Sarıyüce, K. Kaya, E. Saule, Ü. V. Çatalyürek
Proc of IEEE Int'l Conference on BigData, Oct 2013

A PushRelabelbased Maximum Cardinality Bipartite Matching Algorithm on GPUs Paper
M. Deveci, K. Kaya, B. Uçar, Ü. V. Çatalyürek
Proc. of 42nd Int'l. Conf. on Parallel Processing, Oct 2013

Hypergraph Sparsification and Its Application to Partitioning Paper
M. Deveci, K. Kaya, Ü. V. Çatalyürek
Proc. of 42nd Int'l. Conf. on Parallel Processing, Oct 2013

Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi
E. Saule, K. Kaya, Ü. V. Çatalyürek
Proc. of the 10th Int'l Conf. on Parallel Processing and Applied Mathematics (PPAM), Sep 2013

STREAMER: a Distributed Framework for Incremental Closeness Centrality Computation Paper Slides
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
Proc. of IEEE Cluster 2013, Sep 2013

Analysis of Partitioning Models and Metrics in Parallel Sparse MatrixVector Multiplication
K. Kaya, B. Uçar, Ü. V. Çatalyürek
Proc. of the 10th Int'l Conf. on Parallel Processing and Applied Mathematics (PPAM), Sep 2013

PRASE: PageRankbased Active Subnetwork Extraction
A. Hatem, K. Kaya, Ü. V. Çatalyürek
Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB), Sep 2013

Masher: Mapping Long(er) Reads with Hashbased Genome Indexing on GPUs Paper
A. AbuDoleh, E. Saule, K. Kaya, Ü. V. Çatalyürek
Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB), Sep 2013

Streaming Algorithms for kcore Decomposition
A. E. Sarıyüce, B. Gedik, G. JacquesSilva, K. Wu, Ü. V. Çatalyürek
39th International Conference on Very Large Data Bases (VLDB), Aug 2013

Towards a Personalized, Scalable, and Exploratory Academic Recommendation Service
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), Aug 2013

GPU accelerated maximum cardinality matching algorithms for bipartite graphs Paper Slides
M. Deveci, K. Kaya, B. Uçar, Ü. V. Çatalyürek
Proc. of 19th Int'l. EuroPar Conf. on Parallel Processing, Aug 2013

Shattering and Compressing Networks for Betweenness Centrality Paper
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
SIAM International Conference on Data Mining (SDM), May 2013, An extended version is available as a Tech Rep on ArXiv.

Diversified Recommendation on Graphs: Pitfalls, Measures, and Algorithms Paper Slides
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
22nd International World Wide Web Conference (WWW), May 2013

Betweenness Centrality on GPUs and Heterogeneous Architectures Paper
A. E. Sarıyüce, K. Kaya, E. Saule, Ü. V. Çatalyürek
Workshop on General Purpose Processing Using GPUs (GPGPU), in conjunction with ASPLOS, Mar 2013

Result Diversification in Automatic Citation Recommendation
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
iConference Workshop on Computational Scientometrics: Theory and Applications, Feb 2013

On analysis of partitioning models and metrics in parallel sparse matrixvector multiplication
Ü. V. Çatalyürek, K. Kaya, B. Uçar
Tech. Report, Inria, France, no. RR8301, May 2013 Online

Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi
E. Saule, K. Kaya, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1302.1078, Feb 2013 Online

Incremental Algorithms for Network Management and Analysis based on Closeness Centrality
A. E. Sarıyüce, K. Kaya, E. Saule, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1303.0422, Feb 2013 Online

TheAdvisor: A Webservice for Academic Recommendation
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
Poster, ACM/IEEE Joint Conference on Digital Libraries (JCDL 2013), Jul 2013
2012

Graph Coloring Algorithms for Multicore and Massively Multithreaded Architectures
Ü. V. Çatalyürek, J. Feo, A. H. Gebremedhin, M. Halappanavar, A. Pothen
Parallel Computing, vol. 38, no. 1011, pg. 576594, OctNov 2012, Also available as an arXiv Tech Report. Online

Optimizing the maximum stretch of independent tasks on a cluster : From sequential tasks to moldable tasks
E. Saule, D. Bozdağ, Ü. V. Çatalyürek
Journal of Parallel and Distributed Computing, vol. 72, no. 4, pg. 489503, Apr 2012 Online

Optimizing Performance and Reliability on Heterogeneous Parallel Systems: Approximation Algorithms and Heuristics
E. Jeannot, E. Saule, D. Trystram
Journal of Parallel and Distributed Computing, vol. 72, no. 2, pg. 268  280, Feb 2012 Online

Merging network patterns: a general framework to summarize biomedical network data
Y. Xiang, D. Fuhry, K. Kaya, R. Jin, Ü. V. Çatalyürek, K. Huang
Network Modeling and Analysis in Health Informatics and Bioinformatics, Springer, vol. 1, no. 3, pg. 103116, 2012 Online

Optimizing dataflow applications on heterogeneous environments
G. Teodoro, T. D. R. Hartley, Ü. V. Çatalyürek, R. Ferreira
Cluster Computing, vol. 15, no. 2, pg. 125144, 2012 Online

LoadBalancing Spatially Located Computations using Rectangular Partitions
E. Saule, E. O. Bas, Ü. V. Çatalyürek
Journal of Parallel and Distributed Computing, vol. 72, no. 10, pg. 12011214, 2012, Also available as a Tech Rep on arXiv. Online

Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs
E. Kayaaslan, A. Pınar, Ü. V. Çatalyürek, C. Aykanat
SIAM Journal of Scientific Computing, vol. 34, no. 2, pg. A970A992, 2012, A longer version is also available as a Tech Rep. Online

Improving Performance of Adaptive ComponentBased Dataflow Middleware
T. D. R. Hartley, E. Saule, Ü. V. Çatalyürek
Parallel Computing, vol. 38, no. 67, pg. 289309, 2012 Online

Parallel Partitioning, Coloring, and Ordering for Scientific Computing
E. G. Boman, Ü. V. Çatalyürek, C. Chevalier, K. D. Devine
Combinatorial Scientific Computing, Chapman & Hall / CRC Press, Editors U. Naumann, O. Schenk, Computational Science, 2012

The Zoltan and Isorropia parallel toolkits for combinatorial scientific computing: Partitioning, ordering and coloring
E. G. Boman, Ü. V. Çatalyürek, C. Chevalier, K. D. Devine
Scientific Programming, vol. 20, no. 2, pg. 129150, 2012 Online

Twodimensional approaches to sparse matrix partitioning
R. H. Bisseling, B. O. F. Auer, A.N. Yzelman, T. van Leeuwen, Ü. V. Çatalyürek
Combinatorial Scientific Computing, Chapman & Hall / CRC Press, Editors U. Naumann, O. Schenk, Computational Science, 2012

Microarray vs. RNASeq: A comparison for active subnetwork discovery
A. Hatem, K. Kaya, Ü. V. Çatalyürek
ACM Conference on Bioinformatics, Computational Biology and Biomedicine (BCB), Oct 2012

An Outofcore Eigensolver on SSDequipped Clusters Paper
Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, Ü. V. Çatalyürek
Proc. of IEEE Cluster, Sep 2012

An OutOfCore Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers Paper
Z. Zhou, E. Saule, H. M. Aktulga, C. Yang, E. G. Ng, P. Maris, J. P. Vary, Ü. V. Çatalyürek
2012 International Conference on Parallel Processing (ICPP) Workshops, Fifth International Workshop on Parallel Programming Models and Systems Software for HighEnd Computing (P2S2), Sep 2012

On sharedmemory parallelization of a sparse matrix scaling algorithm Paper
Ü. V. Çatalyürek, K. Kaya, B. Uçar
2012 International Conference on Parallel Processing (ICPP), Sep 2012

Fast Recommendation on Bibliographic Networks Paper
O. Küçüktunç, K. Kaya, E. Saule, Ü. V. Çatalyürek
IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), Aug 2012

An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture Paper Slides
E. Saule, Ü. V. Çatalyürek
26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP), May 2012

Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP Paper
A. E. Sarıyüce, E. Saule, Ü. V. Çatalyürek
26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO), May 2012

Multithreaded Clustering for Multilevel Hypergraph Partitioning Paper
Ü. V. Çatalyürek, M. Deveci, K. Kaya, B. Uçar
26th IEEE International Parallel and Distributed Processing Symposium, May 2012

Algorithms for Offline Tracking of Connected Components in Large Evolving Networks Paper
K. Kaya, E. Saule, O. Küçüktunç, Ü. V. Çatalyürek
Workshop on Dynamic Network Analysis (DNASDM), Apr 2012

A divisive clustering technique for maximizing the modularity
Ü. V. Çatalyürek, K. Kaya, J. Langguth, B. Uçar
10th DIMACS Implementation Challenge  Graph Partitioning and Graph Clustering, Feb 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.

UMPa: A multiobjective, multilevel partitioner for communication minimization Paper
Ü. V. Çatalyürek, M. Deveci, K. Kaya, B. Uçar
10th DIMACS Implementation Challenge Workshop: Graph Partitioning and Graph Clustering, Feb 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.

Largescale ab initio configuration interaction calculations for light nuclei
P. Maris, H. M. Aktulga, M. A. Caprio, Ü. V. Çatalyürek, E. Ng, D. Oryspayev, H. Potter, E. Saule, M. Sosonkina, J. P. Vary, C. Yang, Z. Zhou
Journal of Physics: Conference Series. HITES 2012: 'Horizons of Innovative Theories, Experiments, and Supercomputing in Nuclear Physics', vol. 403, no. 012019, 2012 Online

Direction Awareness in Citation Recommendation
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
Proceedings of the 6th International Workshop on Ranking in Databases (DBRank), pg. 6, 2012, An extended version is available as a Tech Rep on ArXiv.

Shattering and Compressing Networks for Centrality Analysis Paper
A. E. Sarıyüce, E. Saule, K. Kaya, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1209.6007, Sep 2012 Online

Diversifying Citation Recommendations
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1209.5809, Sep 2012 Online

Recommendation on Academic Networks using Direction Aware Citation Analysis
O. Küçüktunç, E. Saule, K. Kaya, Ü. V. Çatalyürek
Tech. Report, ArXiv, no. arXiv:1205.1143, Apr 2012 Online

Considerations on Parallel Graph Coloring Algorithms Slides
A. E. Sarıyüce, E. Saule, Ü. V. Çatalyürek
Abstract, SIAM Conference on Parallel Processing for Scientific Computing, 2012

LoadBalancing Spatially Located Computations using Rectangular Partitions Slides
E. Bas, E. Saule, Ü. V. Çatalyürek
Abstract, SIAM Conference on Parallel Processing for Scientific Computing, 2012
2011

Optimizing Latency and Throughput of Application Workflows on Clusters
N. Vydyanathan, Ü. V. Çatalyürek, T. M. Kurc, P. Sadayappan, J. H. Saltz
Parallel Computing, vol. 37, no. 1011, pg. 694712, OctNov 2011 Online

The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases
D. A. Janies, T. Treseder, B. Alexandrov, F. Habib, J. J. Chen, R. Ferreira, Ü. V. Çatalyürek, A. Varon, W. C. Wheeler
Cladistics, vol. 27, no. 1, pg. 6166, Feb 2011 Online

Hypergraph PartitioningBased FillReducing Ordering
Ü. V. Çatalyürek, C. Aykanat, E. Kayaaslan
SIAM Journal of Scientific Computing, vol. 33, no. 4, pg. 19962023, Feb 2011 Online

KELVIN: a Software Package for Rigorous Measurement of Statistical Evidence in Human Genetics
V.J. Vieland, Y. Huang, S.C. Seok, J. Burian, Ü. V. Çatalyürek, J. O'Connell, A. Segre, W. ValentineCooper
Human Heredity, vol. 72, no. 5, pg. 276288, 2011 Online

Color and Texture Analysis on Emerging Architectures Parallel Architectures
F. Igual, R. Mayo, T. D. R. Hartley, Ü. V. Çatalyürek, A. Ruiz, M. Ujaldon
International Journal of High Performance Computing Applications, vol. 25, no. 4, pg. 404427, 2011 Online

Hypergraph Partitioning
Ü. V. Çatalyürek, B. Uçar, C. Aykanat
Encyclopedia of Parallel Computing, Springer, Editors D. Padua, pg. 871881, 2011 Online

PaToH (Partitioning Tool for Hypergraphs)
Ü. V. Çatalyürek, C. Aykanat
Encyclopedia of Parallel Computing, Springer, Editors D. Padua, pg. 14791487, 2011 Online

Improving Graph Coloring on Distributed Memory Parallel Computers
A. E. Sarıyüce, E. Saule, Ü. V. Çatalyürek
Proceedings of the 18th Annual International Conference on High Performance Computing (HiPC 2011), Dec 2011

Benchmarking Short Sequence Mapping Tools
A. Hatem, D. Bozdağ, Ü. V. Çatalyürek
IEEE International Conference on Bioinformatics and Biomedicine (BIBM11), Nov 2011, A longer version is also available as a Tech Rep.

Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation
L. Cooper, J. H. Saltz, Ü. V. Çatalyürek, K. Huang
Proceedings of the IEEE Health Informatics and Systems Biology Conference, Jul 2011

Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds
Ü. V. Çatalyürek, K. Kaya, B. Uçar
The Fourth International Workshop on Data Intensive Distributed Computing (DIDC 2011), in conjunction with the 20th International Symposium on High Performance Distributed Computing (HPDC 2011), Jun 2011

Partitioning Spatially Located Computations using Rectangles Paper Slides
E. Saule, E. O. Bas, Ü. V. Çatalyürek
25th IEEE International Parallel and Distributed Processing Symposium, 2011

On Reducing I/O Overheads in LargeScale Invariant Subspace Projections
H. M. Aktulga, C. Yang, Ü. V. Çatalyürek, P. Maris, J.P. Vary, E. G. Ng
Workshop on Algorithms and Programming Tools for NextGeneration HighPerformance Scientific Software (HPSS 2011), in conjunction with the EuroPar, 2011

DistributedMemory Parallel Algorithms for Matching and Coloring
Ü. V. Çatalyürek, F. Dobrian, A. H. Gebremedhin, M. Halappanavar, A. Pothen
2011 International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO'11), pg. 19661975, 2011

A comparison of recent biclustering algorithms Paper
M. Deveci, K. Eren, Ü. V. Çatalyürek
Poster, ACM International Conference on Bioinformatics and Computational Biology, 2011, Runnerup of the poster award
2010

A matrix partitioning interface to PaToH in MATLAB Paper
B. Uçar, Ü. V. Çatalyürek, C. Aykanat
Parallel Computing, vol. 36, no. 56, pg. 254  272, 2010

Distributedmemory Parallel Algorithms for Distance2 Coloring and Related Problems in Derivative Computation
D. Bozdağ, Ü. V. Çatalyürek, A. H. Gebremedhin, F. Manne, E. G. Boman, F. Özgüner
SIAM Journal of Scientific Computing, vol. 32, no. 4, pg. 24182446, 2010 Online

Development of a codeagnostic computational infrastructure for the dynamic generation of accident progression even trees
Ü. V. Çatalyürek, B. Rutt, K. Metzroth, A. Hakobyan, T. Aldemir, R. Denning, S. Dunagan, D. Kunsman
Reliability Engineering and System Safety, vol. 95, no. 3, pg. 278  294, 2010 Online

Dataflow frameworks for emerging heterogeneous architectures and its application to biomedicine
Ü. V. Çatalyürek, R. Ferreira, T. D. R. Hartley, R. Sachetto, G. Teodoro
Scientific Computing with Multicore and Accelerators, Chapman and Hall / CRC Press, Editors J. Dongarra, D. A. Bader, J. Kurzak, 2010

On TwoDimensional Sparse Matrix Partitioning: Models, Methods, and a Recipe Paper
Ü. V. Çatalyürek, C. Aykanat, B. Uçar
SIAM Journal on Scientific Computing, SIAM, vol. 32, no. 2, pg. 656683, 2010 Online

An Image Analysis Approach for Detecting Malignant Cells in Digitized H amp;Estained Histology Images of Follicular Lymphoma
O. Sertel, Ü. V. Çatalyürek, G. Lozanski, A. Shanaah, M.N. Gürcan
20th International Conference on Pattern Recognition (ICPR), pg. 273 276, Aug 2010

On scalability of hypergraph models for sparse matrix partitioning Paper
B. Uçar, Ü. V. Çatalyürek
Proc. of the PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and NetworkBased Computing, 2010

Runtime optimizations for replicated dataflows on heterogeneous environments
G. Teodoro, T. D. R. Hartley, Ü. V. Çatalyürek, R. Ferreira
Proc. of the 19th ACM International Symposium on High Performance Distributed Computing (HPDC), pg. 1324, 2010, Best Student Paper Award Online

A Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence Mapping Paper Slides
E. Saule, D. Bozdağ, Ü. V. Çatalyürek
Job Scheduling Strategies for Parallel Processing, Springer, Lecture Notes in Computer Science, vol. 6253, 2010

Automatic Dataflow Application Tuning for Heterogeneous Systems
T. D. R. Hartley, E. Saule, Ü. V. Çatalyürek
Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010), 2010

Comparative Analysis of Biclustering Algorithms Paper Slides
D. Bozdağ, A.S. Kumar, Ü. V. Çatalyürek
ACM International Conference on Bioinformatics and Computational Biology, 2010

Exploring Parallelism in Short Sequence Mapping Using BurrowsWheeler Transform Slides
D. Bozdağ, A. Hatem, Ü. V. Çatalyürek
9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS), 2010

A Survey of Pipelined Workflow Scheduling: Models and Algorithms Paper
A. Benoit, Ü. V. Çatalyürek, Y. Robert, E. Saule
Tech. Report, LIP, no. RRLIP201028, Sep 2010 Online

Optimizing the maximum stretch of online tasks on a parallel system without preemption Slides
E. Saule, D. Bozdağ, Ü. V. Çatalyürek
Abstract, 3rd Scheduling in Aussois Workshop, 2010

Partitioning Spatially Located Load with Rectangles: Algorithms and Simulations Slides
E. Saule, E. Bas, Ü. V. Çatalyürek
Abstract, New Challenges on Scheduling Theory, Workshop, 2010

Benchmarking Short Sequence Alignment Tools
A. Hatem, D. Bozdağ, Ü. V. Çatalyürek
Abstract, Bioinformatics, 2010 Ohio Collaborative Conference, 2010
2009

An Integrated Approach to Locality Conscious Processor Allocation and Scheduling of Mixed Parallel Applications
N. Vydyanathan, Ü. V. Çatalyürek, T. M. Kurc, P. Sadayappan, J. H. Saltz
IEEE Transactions on Parallel and Distributed Systems, vol. 20, no. 8, Aug 2009 Online

A Repartitioning Hypergraph Model for Dynamic Load Balancing
Ü. V. Çatalyürek, E. G. Boman, K.D. Devine, D. Bozdağ, R. Heaphy, L.A. Fisk
Journal of Parallel and Distributed Computing, vol. 69, no. 8, pg. 711724, Aug 2009

Stroma classification for neuroblastoma on graphics processors
A. Ruiz, O. Sertel, M. Ujaldon, Ü. V. Çatalyürek, J. H. Saltz, M. N. Gürcan
International Journal of Data Mining and Bioinformatics, vol. 3, pg. 280298, Jun 2009 Online

Compaction of Schedules and a TwoStage Approach for DuplicationBased DAG Scheduling
D. Bozdağ, F. Özgüner, Ü. V. Çatalyürek
IEEE Transactions on Parallel and Distributed Systems, vol. 20, no. 6, pg. 857871, Jun 2009 Online

Histopathological Image Analysis Using ModelBased Intermediate Representations and Color Texture: Follicular Lymphoma Grading
O. Sertel, J. Kong, Ü. V. Çatalyürek, G. Lozanski, J. H. Saltz, M. N. Gürcan
Signal Processing Systems, vol. 55, no. 13, pg. 169183, 2009 Online

Computeraided prognosis of neuroblastoma on wholeslide images: Classification of stromal development
O. Sertel, J. Kong, H. Shimada, Ü. V. Çatalyürek, J. H. Saltz, M. N. Gürcan
Pattern Recognition, vol. 42, no. 6, pg. 10931103, 2009 Online

A KnowledgeAnchored Integrative Image Search and Retrieval System
S. Erdal, Ü. V. Çatalyürek, P. R. O. Payne, J. H. Saltz, J. Kamal, M. N. Gürcan
J. Digital Imaging, vol. 22, no. 2, pg. 166182, 2009

Processing of LargeScale Biomedical Images on a Cluster of MultiCore CPUs and GPUs
Ü. V. Çatalyürek, T. Hartley, O. Sertel, M. Ujaldon, A. Ruiz, J. Saltz, M. Gürcan
High Performance and Large Scale Computing, IOS Press, Editors W. Gentzsch, L. Grandinetti, G. Joubert, vol. 18, pg. 341364, 2009 Online

Hypergraphbased Dynamic Partitioning and Load Balancing
Ü. V. Çatalyürek, D. Bozdağ, E. G. Boman, K.D. Devine, R. Heaphy, L.A. Fisk
Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, Wiley Publishing, Editors M. Parashar, X. Li, S. Chandra, 2009

A ComponentBased Framework for the Cell Broadband Engine Paper Slides
T. D. R. Hartley, Ü. V. Çatalyürek
Proc. of 23rd Int'l. Parallel and Distributed Processing Symposium, The 18th Heterogeneous Computing Workshop (HCW 2009), May 2009

Parallel Short Sequence Mapping for High Throughput Genome Sequencing
D. Bozdağ, C.C. Barbacioru, Ü. V. Çatalyürek
Proc. of 23rd Int'l. Parallel and Distributed Processing Symposium, pg. 110, May 2009

Coordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications Slides
G. Teodoro, R. Sachetto, O. Sertel, M. Gürcan, W. Meira, Ü. V. Çatalyürek, R. Ferreira
Proc. of the 2009 IEEE International Conference on Cluster Computing, 2009

Identification of a Breast Cancer Associated Regulatory Network
J. D. Parvin, Z. Kais, M. Arora, S. Kotian, A. Zha, D. Ransburgh, D. Bozdağ, Ü. V. Çatalyürek, K. Huang
Bioinformatics, 2009 Ohio Collaborative Conference, IEEE Computer Society, pg. 7175, 2009 Online

A Comprehensive Analysis Workflow for GenomeWide Screening Data from ChIPSequencing Experiments
H. G. Ozer, D. Bozdağ, T. Camerlengo, J. Wu, Y.W. Huang, T. Hartley, J. D. Parvin, T. Huang, Ü. V. Çatalyürek, K. Huang
Proc. of 1st Int'l. Conf. on Bioinformatics and Computational Biology, Springer, Lecture Notes in Computer Science, vol. 5462, pg. 320330, 2009 Online

Exploring the GPU for Enhancing Parallelism on Color and Texture Analysis
F. Igual, R. Mayo, T. D. R. Hartley, Ü. V. Çatalyürek, A. Ruiz, M. Ujaldon
Proc. of the 2009 International Conference on Parallel Computing (ParCo2009), 2009

Investigating the Use of GPUAccelerated Nodes for SAR Image Formation Paper Slides
T. D. R. Hartley, A. R. Fasih, C. A. Berdanier, F. Özgüner, Ü. V. Çatalyürek
Proc. of the IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC), 2009

A Biclustering Method to Discover Coregulated Genes Using Diverse Gene Expression Datasets Paper
D. Bozdağ, J. D. Parvin, Ü. V. Çatalyürek
Proc. of 1st Int'l. Conf. on Bioinformatics and Computational Biology, Springer, Lecture Notes in Computer Science, vol. 5462, pg. 151163, 2009 Online

HighPerformance FilterStream Frameworks for Hierarchical, Heterogeneous, Distributed Supercomputers Slides
T. D. R. Hartley, Ü. V. Çatalyürek
Poster, 23rd Int'l. Parallel and Distributed Processing Symposium PhD Forum, 2009

Getting Started with Zoltan: A Short Tutorial
K. D. Devine, E. G. Boman, L. A. Riesen, Ü. V. Çatalyürek, C. Chevalier
Abstract, Combinatorial Scientific Computing, Schloss Dagstuhl  LeibnizZentrum fuer Informatik, Dagstuhl Seminar Proceedings, no. 09061, 2009 Online

Parallel Computing Strategies for Sequence Mapping of NGS Data Slides
D. Bozdağ, T. Camerlengo, H. G. Ozer, J. Trgovcich, T. Meulia, K. Huang, Ü. V. Çatalyürek
Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis, 2009

Parallelization of Mapping Algorithms for Next Generation Sequencing Applications
D. Bozdağ, C. C. Barbacioru, Ü. V. Çatalyürek
Abstract, Combinatorial Scientific Computing, Schloss Dagstuhl  LeibnizZentrum fuer Informatik, Dagstuhl Seminar Proceedings, no. 09061, 2009 Online

Combinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and Matching
D. Bozdağ, Ü. V. Çatalyürek, F. Dobrian, A. H. Gebremedhin, M. Halappanavar, A. Pothen
Poster, 21st Supercomputing Conference, 2009

Combinatorial Problems in HighPerformance Computing: Partitioning
R. Bisseling, T. van Leeuwen, Ü. V. Çatalyürek
Abstract, Combinatorial Scientific Computing, Schloss Dagstuhl  LeibnizZentrum fuer Informatik, Dagstuhl Seminar Proceedings, no. 09061, 2009 Online
2008

LargeScale Biomedical Image Analysis in Grid Environments
V.S. Kumar, B. Rutt, T. Kurc, Ü. V. Çatalyürek,, T.C. Pan, S. Chow, S. Lamont, M. Martone, J. H. Saltz
IEEE Transactions on Information Technology in Biomedicine, vol. 12, no. 2, pg. 154161, Mar 2008

Bluegene/L applications: Parallelism on a massive scale
B. R. d. Supinski, M. Schulz, V. V. Bulatov, W. Cabot, B. Chan, A. W. Cook, E. W. Draegerl, J. N. Glosli, J. A. Greenough, K. Henderson, A. Kubota, S. Louis, B. J. Miller, M. V. Patel, T. E. Spelce, F. H. Streitz, P. L. Williams, R. K. Yates, A. Yoo, G. Almasi, G. Bhanot, A. Gara, J. A. Gunnels, M. Gupta, J. Moreira, J. Sexton, B. Walkup, C. Archer, F. Gygi, T. C. Germann, K. Kadau, P. S. Lomdahl, C. Rendleman, M. L. Welcome, W. McLendon, B. Hendrickson, F. Franchetti, S. Kraig, J. Lorenz, C. W. Ueberhuber, E. Chow, Ü. V. Çatalyürek
International Journal of High Performance Computing, vol. 22, no. 1, pg. 3351, Jan 2008

Dynamic generation of accident progression event trees
A. Hakobyan, T. Aldemir, R. Denning, S. Dunagan, D. Kunsman, B. Rutt, Ü. V. Çatalyürek
Nuclear Engineering and Design, vol. 238, no. 12, pg. 3457  3467, 2008 Online

A framework for scalable greedy coloring on distributedmemory parallel computers
D. Bozdağ, A. H. Gebremedhin, F. Manne, E. G. Boman, Ü. V. Çatalyürek
Journal of Parallel and Distributed Computing, vol. 68, no. 4, pg. 515535, 2008 Online

Using Overlays for Efficient Data Transfer over Shared WideArea Networks
G. Khanna, Ü. V. Çatalyürek, T. Kurc, R. Kettimuthu, P. Sadayappan, I. Foster, J. H. Saltz
Proceedings of SC2008 High Performance Computing, Networking, and Storage Conference, Nov 2008

A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows
N. Vydyanathan, Ü. V. Çatalyürek, T. M. Kurc, P. Sadayappan, J. H. Saltz
2008 International Conference on Parallel Processing (ICPP), pg. 254261, 2008 Online

A Dynamic Scheduling Approach for Coordinated WideArea Data Transfers using GridFTP
G. Khanna, Ü. V. Çatalyürek, T. Kurc, R. Kettimuthu, P. Sadayappan, J. H. Saltz
Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS), 2008

Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores Paper
T. D. R. Hartley, Ü. V. Çatalyürek, A. Ruiz, F. Igual, R. Mayo, M. Ujaldon
Proc. of the 22nd Annual International Conference on Supercomputing, ICS 2008, pg. 1525, 2008 Online

Combinatorial algorithms for computational science and engineering
E. G. Boman, D. Bozdağ, Ü. V. Çatalyürek, K. D. Devine, A. H. Gebremedhin, P. D. Hovland, A. Pothen
Journal of Physics: Conference Series, vol. 125, 2008

Parallel Distance2 Coloring
D. Bozdağ, Ü. V. Çatalyürek, A. H. Gebremedhin, F. Manne, E. G. Boman
Abstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations, 2008
2007

Hypergraphbased Dynamic Load Balancing for Adaptive Scientific Computations Paper
Ü. V. Çatalyürek, E. G. Boman, K.D. Devine, D. Bozdağ, R. Heaphy, L.A. Fisk
Proc. of 21st Int'l. Parallel and Distributed Processing Symposium, pg. 111, Mar 2007, Best Algorithms Paper Award

Optimizing multiple queries on scientific datasets with partial replicas
L. Weng, Ü. V. Çatalyürek, T. M. Kurc, G. Agrawal, J. H. Saltz
Proc. of 8th IEEE/ACM International Conference on Grid Computing (GRID 2007), pg. 259266, 2007 Online

Toward Optimizing Latency Under Throughput Constraints for Application Workflows on Clusters
N. Vydyanathan, Ü. V. Çatalyürek, T. Kurc, P. Sadayappan, J. H. Saltz
Proceedings of the 13th International EuroPar Conference (EuroPar 2007), pg. 173183, 2007 Online

An Efficient and Reliable Scientific Workflow System
T. Tavares, G. Teodoro, T. M. Kurc, R. Ferreira, D. Neto, W. Meira, Ü. V. Çatalyürek, S. Hastings, S. Oster, S. Langella, J. H. Saltz
Prof. of Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007), pg. 445452, 2007 Online

Pathological image analysis using the GPU: Stroma classification for neuroblastoma
A. Ruiz, O. Sertel, M. Ujaldon, Ü. V. Çatalyürek, J. Saltz, M. Gürcan
Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine, pg. 7885, 2007

Performance vs. accuracy tradeoffs for largescale image analysis applications
V. S. Kumar, T. M. Kurc, J. Kong, Ü. V. Çatalyürek, M. N. Gürcan, J. H. Saltz
Proc. of the 2007 IEEE International Conference on Cluster Computing, pg. 100109, 2007 Online

Scheduling File Transfers for DataIntensive Jobs on Heterogeneous Clusters
G. Khanna, Ü. V. Çatalyürek, T. Kurc, P. Sadayappan, J. Saltz
Proceedings of the 13th International EuroPar Conference (EuroPar 2007), pg. 214223, 2007 Online

Computerized pathological image analysis for neuroblastoma prognosis
M. N. Gurcan, J. Kong., O. Sertel, B. B. Cambazoglu, J. H. Saltz, Ü. V. Çatalyürek
2007 AMIA Annual Symposium, 2007

Efficient Processing of Pathological Images Using the Grid: ComputerAided Prognosis of Neuroblastoma
B. B. Cambazoglu, O. Sertel, J. Kong, J. H. Saltz, M. N. Gurcan, Ü. V. Çatalyürek
Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07), 2007

Enabling high performance computational science through combinatorial algorithms
E. G. Boman, D. Bozdağ, Ü. V. Çatalyürek, K. D. Devine, A. H. Gebremedhin, P. D. Hovland, A. Pothen, M. M. Strout
Journal of Physics: Conference Series, vol. 78, pg. 012058 (10pp), 2007

Storing and Searching Massive Scalefree Graphs Slides
T. D. R. Hartley, Ü. V. Çatalyürek, A. Yoo
Poster, 19th Supercomputing Conference, 2nd Place Student Poster, 2007
2006

Supporting Scalable and Distributed Data Subsetting and Aggregation in Largescale Seismic Data Analysis
X. Zhang, B. Rutt, Ü. V. Çatalyürek, T. Kurc, J. H. Saltz
The Journal of High Performance Computing Applications, vol. 20, no. 3, pg. 423438, 2006

Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications
N. Vydyanathan, S. Krishnamoorthy, G. Sabin, Ü. V. Çatalyürek, T. Kurc, P. Sadayappan, J. H. Saltz
Proceedings of 2006 IEEE International Conference on Cluster Computing, Sep 2006

Improving Functional Modularity in ProteinProtein Interactions Graphs Using Hubinduced Subgraphs
D. Ucar, S. Asur, Ü. V. Çatalyürek, S. Parthasarathy
In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), Sep 2006

MSSG: A Framework for Massive Scale Semantic Graphs Paper Slides
T. D. R. Hartley, Ü. V. Çatalyürek, F. Özgüner, A. Yoo, S. Kohn, K. Henderson
Proceedings of 2006 IEEE International Conference on Cluster Computing, Sep 2006

Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries
L. Weng, Ü. V. Çatalyürek, T. Kurc, G. Agrawal, J. H. Saltz
2006 International Conference on Parallel Processing, Aug 2006

On Creating Efficient Objectrelational Views of Scientific Datasets
S. Narayanan, T. Kurc, Ü. V. Çatalyürek, J. H. Saltz
2006 International Conference on Parallel Processing, Aug 2006

Task Scheduling and File Replication for DataIntensive Jobs with Batchshared I/O
G. Khanna, N. Vydyanathan, Ü. V. Çatalyürek, T. Kurc, S. Krishnamoorthy, P. Sadayappan, J. H. Saltz
Proceedings of the Fifteen International Symposium on High Performance Distributed Computing (HPDC15), pg. 241252, Jun 2006

A Data Locality Aware Online Scheduling Approach for I/OIntensive Jobs with File Sharing
G. Khanna, Ü. V. Çatalyürek, T. Kurc, P. Sadayappan, J. H. Saltz
Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006, Jun 2006

A task duplication based bottomup scheduling algorithm for heterogeneous environments
D. Bozdağ, Ü. V. Çatalyürek, F. Özgüner
15th International Heterogeneous Computing Workshop (in conjunction with IPDPS), Apr 2006 Online

Scheduling of Tasks with Batchshared I/O on Heterogeneous Systems
N. Vydyanathan, G. Khanna, T. Kurc, Ü. V. Çatalyürek, P. Wyckoff, J. H. Saltz, P. Sadayappan
Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Heterogeneous Computing Workshop (HCW 2006), 2006

An Integrated Approach for Processor Allocation and Scheduling of MixedParallel Applications
N. Vydyanathan, S. Krishnamoorthy, G. Sabin, Ü. V. Çatalyürek, T. Kurc, P. Sadayappan, J. H. Saltz
2006 International Conference on Parallel Processing, 2006

Large Image Correction and Warping in a Cluster Environment
V. S. Kumar, B. Rutt, T. Kurc, Ü. V. Çatalyürek, S. Chow, S. Lamont, M. Martone, J. H. Saltz
Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006

An Approach to LocalityConscious Load Balancing and Transparent Memory Hierarchy Management with a GlobalAddressSpace Parallel Programming Model
S. Krishnamoorthy, Ü. V. Çatalyürek, J. Nieplocha, P. Sadayappan
Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for HighLevel Languages and Libraries (POHLL 2006), 2006

Hypergraph Partitioning for Automatic Memory Hierarchy Management
S. Krishnamoorthy, Ü. V. Çatalyürek, J. Nieplocha, A. Rountev, P. Sadayappan
Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006

An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions
S. Krishnamoorthy, Ü. V. Çatalyürek, J. Nieplocha, A. Rountev, P. Sadayappan
Proc. IPDPS Workshop on Next Generation Software, 2006

Parallel Hypergraph Partitioning for Scientific Computing
K.D. Devine, E. G. Boman, R.T. Heaphy, R.H. Bisseling, Ü. V. Çatalyürek
Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), IEEE, 2006
2005

A Simulation and Data Analysis System for Large Scale,DataDriven Oil Reservoir Simulation Studies
T. Kurc, Ü. V. Çatalyürek, X. Zhang, J. Saltz, R. Martino, M. Wheeler, M. Peszynska, A. Sussman, C. Hansen, M. Sen, R. Seifoullaev, P. Stoffa, C. TorresVerdin, M. Parashar
Concurrency and Computation: Practice and Experience., vol. 17, no. 11, pg. 14411467, Sep 2005

Tools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data
M. Ribeiro, T. Kurc, T. Pan, K. Huang, Ü. V. Çatalyürek, X. Zhang, S. Langella, S. Hastings, S. Oster, R. Ferreira, J. Saltz
Grid Computing: The New Frontier Of High Performance Computing, 14, Elsevier, Editors L. Grandinetti, 2005

Application of Gridenabled technologies for solving optimization problems in datadriven reservoir studies
M. Parashar, H. Klie, Ü. V. Çatalyürek, T. M. Kurc, V. Matossian, J. H. Saltz, M. F. Wheeler
Future Generation Computer Systems, vol. 21, no. 1, pg. 1926, Jan 2005

XML database support for distributed execution of dataintensive scientific workflows.
S. Hastings, M. Ribeiro, S. Langella, S. Oster, Ü. V. Çatalyürek, T. Pan, K. Huang, R. Ferreira, J. H. Saltz, T. M. Kurc
SIGMOD Record, vol. 34, no. 3, pg. 5055, 2005 Online

Distributed OutofCore Preprocessing of Very Large Microscopy Images for Efficient Querying
B. Rutt, V. S. Kumar, T. Pan, T. Kurc, Ü. V. Çatalyürek, Y. Wang, J. H. Saltz
The 2005 IEEE International Conference on Cluster Computing, Sep 2005

Servicing Seismic and Oil Reservoir Simulation Data through Grid Data Services
S. Narayanan, T. M. Kurc, Ü. V. Çatalyürek, J. H. Saltz
Proceedings of VLDB Workshop Data Management in Grid 2005 (VLDB DMG'05, pg. 98109, Sep 2005

A Parallel Distance2 Graph Coloring Algorithm for Distributed Memory Computers
D. Bozdağ, Ü. V. Çatalyürek, A. H. Gebremedhin, F. Manne, E. G. Boman, F. Özgüner
Proc. of 1st Int'l. Conf. on High Performance Computing and Communications, Springer, Lecture Notes in Computer Science, vol. 3726, pg. 796806, Sep 2005 Online

A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers
E. G. Boman, D. Bozdağ, Ü. V. Çatalyürek, A. H. Gebremedhin, F. Manne
Proc. of 11th Int'l. EuroPar Conf. on Parallel Processing, Springer, Lecture Notes in Computer Science, vol. 3648, pg. 241251, Aug 2005 Online

A Task Duplication Based Scheduling Algorithm Using Partial Schedules
D. Bozdağ, F. Özgüner, E. Ekici, Ü. V. Çatalyürek
Proc. of 34th Int'l. Conf. on Parallel Processing, pg. 630637, Jun 2005 Online

Servicing Range Queries on Multidimensional Datasets with Partial Replicas
L. Weng, Ü. V. Çatalyürek, T. Kurc, G. Agrawal, J. H. Saltz
Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005), May 2005

A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batchshared I/O
G. Khanna, N. Vydyanathan, T. Kurc, Ü. V. Çatalyürek, P. Wyckoff, J. H. Saltz, P. Sadayappan
Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005), May 2005

A Runtime Framework for Partial Replication and Its Application for OnDemand Data Exploration
S. Narayanan, Ü. V. Çatalyürek, T. Kurc, V. S. Kumar, J. H. Saltz
High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, Mar 2005

Design and Implementation of a Data Server Using a PeertoPeer Storage System
V. S. Kumar, T. M. Kurc, Ü. V. Çatalyürek, J. H. Saltz
High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, Mar 2005

A Scalable Distributed Parallel BreadthFirst Search Algorithm on BlueGene/L
A. Yoo, E. Chow, K. Henderson, W. McLendon, B. Hendrickson, Ü. V. Çatalyürek
Proceedings of SC2005 High Performance Computing, Networking, and Storage Conference, 2005, Gordon Bell Finalist.

Towards Dynamic DataDriven Optimization of Oil Well Placement.
M. Parashar, V. Matossian, W. Bangerth, H. Klie, B. Rutt, T. M. Kurc, Ü. V. Çatalyürek, J. H. Saltz, M. F. Wheeler
International Conference on Computational Science (2), pg. 656663, 2005 Online

Parallel Hypergraph Partitioning for Scientific Computing
E. G. Boman, K.D. Devine, R.T. Heaphy, Ü. V. Çatalyürek, R.H. Bisseling
Tech. Report, Sandia National Laboratories, no. SAND20052796C, Apr 2005
2004

Permuting Sparse Rectangular Matrices into BlockDiagonal Form
C. Aykanat, A. Pınar, Ü. V. Çatalyürek
SIAM Journal on Scientific Computing, vol. 26, no. 6, pg. 18601879, 2004

A Distributed Data Management Middleware for DataDriven Application Systems
S. Langella, S. Hastings, S. Oster, T. Kurc, Ü. V. Çatalyürek, J. H. Saltz
Proceedings of 2004 IEEE International Conference on Cluster Computing, Sep 2004

Strategies for Using Additional Resources in Parallel Hashbased Join Algorithms
X. Zhang, T. Kurc, T. Pan, Ü. V. Çatalyürek, S. Narayanan, P. Wyckoff, J. H. Saltz
Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC13), IEEE Press, Jun 2004

An Approach for Automatic Data Virtualization
L. Weng, G. Agrawal, Ü. V. Çatalyürek, T. Kurc, S. Narayanan, J. H. Saltz
Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC13), IEEE Press, Jun 2004

Application of Gridenabled Technologies for Solving Optimization Problems in DataDriven Reservoir Studies
M. Parashar, H. Klie, Ü. V. Çatalyürek, T. Kurc, V. Matossian, J. Saltz, M.F. Wheeler
Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science), pg. 805812, Jun 2004

Serving Queries to MultiResolution Datasets on Diskbased Storage Clusters
X. Zhang, T. Pan, Ü. V. Çatalyürek, T. Kurc, J. H. Saltz
Proceedings of 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004), Apr 2004

Supporting SQL3 Aggregations on Gridbased Data Repositories
L. Weng, G. Agrawal, Ü. V. Çatalyürek, J. H. Saltz
Proceedings of the 17th International Workshop on Languages and Compilers for Parallel Computing, 2004

Use of PVFS for Efficient Execution of Jobs with PipelineShared I/O
N. Vydyanathan, G. Khanna, T. Kurc, Ü. V. Çatalyürek, P. Wyckoff, J. H. Saltz, P. Sadayappan
Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing (Grid 2004), 2004
2003

The Virtual Microscope
Ü. V. Çatalyürek, M. D. Beynon, C. Chang, T. Kurc, A. Sussman, J. H. Saltz
IEEE Transactions on Information Technology in BioMedicine, vol. 7, no. 4, pg. 230248, Dec 2003

Database Support for Datadriven Scientific Applications in the Grid
S. Narayanan, T. Kurc, Ü. V. Çatalyürek, J. H. Saltz
Parallel Processing Letters, vol. 13, no. 2, pg. 245271, 2003

Applying Database Support for Large Scale Data Driven Science in Distributed Environments
S. Narayanan, Ü. V. Çatalyürek, T. Kurc, X. Zhang, J. H. Saltz
Proceedings of the Fourth International Workshop on Grid Computing (Grid 2003), pg. 141148, Nov 2003

Optimizing Reduction Computations In a Distributed Environment
T. Kurc, F. Lee, G. Agrawal, Ü. V. Çatalyürek, R. Ferreira, J. H. Saltz
ACM/IEEE SC2003, Nov 2003

Driving Scientific Applications by Data in Distributed Environments
J. Saltz, Ü. V. Çatalyürek, T. Kurc, M. Gray, S. Hastings, S. Langella, S. Narayanan, R. Martino, S. Bryant, M. Peszynska, M. Wheeler, A. Sussman, M. Beynon, C. Hansen, D. Stredney, a. D. Sessanna
Dynamic Data Driven Application Systems Workshop, held jointly with ICCS 2003, Jun 2003

Impact of High Performance Sockets on Data Intensive Applications
P. Balaji, J. Wu, T. Kurc, Ü. V. Çatalyürek, D. K. Panda, J. H. Saltz
Proceedings of the Twelfth International Symposium on High Performance Distributed Computing (HPDC12), IEEE Press, Jun 2003

Image Processing for the Grid: A Toolkit for Building Gridenabled Image Processing Applications.
S. Hastings, T. Kurc, S. Langella, Ü. V. Çatalyürek, T. Pan, J. H. Saltz
CCGrid: IEEE International Symposium on Cluster Computing and the Grid, IEEE Press, May 2003

A Componentbased Implementation of Multiple Sequence Alignment
Ü. V. Çatalyürek, M. Gray, T. Kurc, J. H. Saltz, E. Stahlberg, R. Ferreira
18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track, Mar 2003

A Distributed Execution Environment for Analysis of DCEMR Image Datasets
T. Kurc, S. Hastings, Ü. V. Çatalyürek, J. Saltz, J. D. Fleig, B. D. Clymer, H. von TenggKobligk, K. T. Baudendistel, R. Machiraju, M. V. Knopp
The Society for Computer Applications in Radiology (SCAR 2003), 2003
2002

Processing LargeScale Multidimensional Data in Parallel and Distributed Environments
M. Beynon, C. Chang, Ü. V. Çatalyürek, T. Kurc, A. Sussman, H. Andrade, R. Ferreira, J. H. Saltz
Parallel Computing, vol. 28, no. 5, pg. 827859, May 2002, Special Issue on Data Intensive Computing

Executing Multiple Pipelined Data Analysis Operations in the Grid
M. Spencer, R. Ferreira, M. Beynon, T. Kurc, Ü. V. Çatalyürek, A. Sussman, J. H. Saltz
Proceedings of the 2002 ACM/IEEE SC02 Conference, ACM Press, Nov 2002

Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems
M. D. Beynon, T. Kurc, Ü. V. Çatalyürek, A. Sussman, J. H. Saltz
Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), Apr 2002

Improving Performance of Multiple Sequence Alignment Analysis in Multiclient Environments
Ü. V. Çatalyürek, E. Stahlberg, R. Ferreira, T. Kurc, J. H. Saltz
Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), First Workshop on High Performance Computational Biology, Apr 2002

Persistent Caching in a Multiple Query Optimization Framework
H. Andrade, T. Kurc, Ü. V. Çatalyürek, A. Sussman, J. H. Saltz
Proceedings of the Sixth Workshop on Languages, Compilers and Runtime Systems for Scalable Computers, SpringerVerlag, Mar 2002

The Virtual Microscope
Ü. V. Çatalyürek, M. D. Beynon, C. Chang, T. Kurc, A. Sussman, J. H. Saltz
Tech. Report, University of Maryland, Department of Computer Science and UMIACS, no. CSTRxxxx and UMIACSTR2002xx, Oct 2002
2001

Distributed Processing of Very Large Datasets with DataCutter
M. D. Beynon, T. Kurc, Ü. V. Çatalyürek, C. Chang, A. Sussman, J. H. Saltz
Parallel Computing, vol. 27, no. 11, pg. 14571478, Oct 2001 Online

Improving the Performance and Functionality of the Virtual Microscope
Ü. V. Çatalyürek, T. Kurc, A. Sussman, J. H. Saltz
Archives of Pathology and Laboratory Medicine, vol. 125, no. 8, Aug 2001

Visualization of Large Datasets with the Active Data Repository
T. Kurc, Ü. V. Çatalyürek, C. Chang, A. Sussman, J. H. Saltz
IEEE Computer Graphics and Applications, vol. 21, no. 4, pg. 2433, Jul/Aug 2001

A HypergraphPartitioning Approach for CoarseGrain Decomposition
Ü. V. Çatalyürek, C. Aykanat
ACM/IEEE SC2001, Nov 2001

Performance Optimization for Data Intensive Grid Applications
M. D. Beynon, A. Sussman, Ü. V. Çatalyürek, T. Kurc, J. H. Saltz
Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001), Aug 2001

A FineGrain Hypergraph Model for 2D Decomposition of Sparse Matrices
Ü. V. Çatalyürek, C. Aykanat
Proceedings of 15th International Parallel and Distributed Processing Symposium (IPDPS), Apr 2001

A HypergraphBased Workload Partitioning Strategy for Parallel Data Aggregation
C. Chang, T. Kurc, A. Sussman, Ü. V. Çatalyürek, J. H. Saltz
Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing, Mar 2001

A Componentbased Implementation of Isosurface Rendering for Visualizing Large Datasets
M. D. Beynon, T. Kurc, Ü. V. Çatalyürek, A. Sussman, J. H. Saltz
Tech. Report, University of Maryland, Department of Computer Science and UMIACS, no. CSTR4249 and UMIACSTR200134, May 2001

Exploration and Visualization of Very Large Datasets with the Active Data Repository
T. Kurc, Ü. V. Çatalyürek, C. Chang, A. Sussman, J. H. Saltz
Tech. Report, University of Maryland, Department of Computer Science and UMIACS, no. CSTR4208 and UMIACSTR200104, Jan 2001, Also appears in IEEE Computer Graphics and Applications, Jul/Aug 2001
1999

HypergraphPartitioning Based Decomposition for Parallel SparseMatrix Vector Multiplication
Ü. V. Çatalyürek, C. Aykanat
IEEE Transactions on Parallel and Distributed Systems, vol. 10, no. 7, pg. 673693, 1999

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

PaToH: A Multilevel Hypergraph Partitioning Tool, Version 3.0
Ü. V. Çatalyürek, C. Aykanat
Tech. Report, Bilkent University, Department of Computer Engineering, 1999, PaToH is available Online
1996

Decomposing linear programs for parallel solution
A. Pınar, Ü. V. Çatalyürek, C. Aykanat, M. Pınar
Lecture Notes in Computer Science, vol. 1041, pg. 473482, 1996

Decomposing irregularly sparse matrices for parallel matrixvector multiplications
Ü. V. Çatalyürek, C. Aykanat
Proceedings of 3rd International Symposium on Solving Irregularly Structured Problems in Parallel, Irregular'96, SpringerVerlag, Lecture Notes in Computer Science, vol. 1117, pg. 7586, 1996
1995

A Hypergraph Model for Mapping Repeated Sparse MatrixVector Product Computations onto Multicomputers
Ü. V. Çatalyürek, C. Aykanat
Proceedings of International Conference on High Performance Computing, Dec 1995
1994

A Constructive Multiway Circuit Partitioning Algorithm Based on Minimum Degree Ordering
Ü. V. Çatalyürek
Master's Thesis, Bilkent University, Computer Engineering and Information Science, Sep 1994