This page is not updated frequently. For up to date list of publications please visit TDAlab’s Publication page.
You can also check my publications at DBLP, Google Scholar, Semantic Scholar, or Microsoft Academic Search.
- ConfPortable Sparse Solver Framework for Large Matrices on Heterogeneous ArchitecturesIn 29th IEEE International Conference on High Performance Computing, Data, & Analytics (HiPC 2022), 2022.
- ConfEfficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph PartitioningIn IEEE International Conference on Cluster Computing, 2022, Best Paper Award
- StrainHub: A phylogenetic tool to construct pathogen transmission networksBioinformatics, 2019.
- ConfAcyclic Partitioning of Large-Scale Directed Acyclic GraphsIn Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), 2017.
- MiscComputing the Closeness Centrality of Evolving Networks on ClustersPoster, SIAM Workshop on Network Science (NS14), 2014.
- MiscPartitioning Hypergraphs for Multiple Communication MetricsAbstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14), 2014.
- MiscLoad Balancing and Task Mapping for Exascale SystemsPoster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum, 2014, PhD Forum award
- ConfResult Diversification in Automatic Citation RecommendationIn iConference Workshop on Computational Scientometrics: Theory and Applications, 2013.
- ConfAlgorithms for Offline Tracking of Connected Components in Large Evolving NetworksIn Workshop on Dynamic Network Analysis (DNA-SDM), 2012.
- ConfA divisive clustering technique for maximizing the modularityIn 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering, 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
- ConfUMPa: A multi-objective, multi-level partitioner for communication minimizationIn 10th DIMACS Implementation Challenge Workshop: Graph Partitioning and Graph Clustering, 2012, Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013.
- MiscConsiderations on Parallel Graph Coloring AlgorithmsAbstract, SIAM Conference on Parallel Processing for Scientific Computing, 2012.
- ChapParallel Partitioning, Coloring, and Ordering for Scientific ComputingIn Combinatorial Scientific Computing, 2012.
- ChapTwo-dimensional approaches to sparse matrix partitioningIn Combinatorial Scientific Computing, 2012.
- MiscA comparison of recent biclustering algorithmsPoster, ACM International Conference on Bioinformatics and Computational Biology, 2011, Runner-up of the poster award
- MiscOptimizing the maximum stretch of online tasks on a parallel system without preemptionAbstract, 3rd Scheduling in Aussois Workshop, 2010.
- ConfA Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence MappingIn Job Scheduling Strategies for Parallel Processing, 2010.
- MiscPartitioning Spatially Located Load with Rectangles: Algorithms and SimulationsAbstract, New Challenges on Scheduling Theory, Workshop, 2010.
- MiscBenchmarking Short Sequence Alignment ToolsAbstract, Bioinformatics, 2010 Ohio Collaborative Conference, 2010.
- ConfAutomatic Dataflow Application Tuning for Heterogeneous SystemsIn Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010), 2010.
- ConfComparative Analysis of Biclustering AlgorithmsIn ACM International Conference on Bioinformatics and Computational Biology, 2010.
- ConfExploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler TransformIn 9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS), 2010.
- ChapDataflow frameworks for emerging heterogeneous architectures and its application to biomedicineIn Scientific Computing with Multicore and Accelerators, 2010.
- JRNLStroma classification for neuroblastoma on graphics processorsInternational Journal of Data Mining and Bioinformatics, 2009.
- ConfA Component-Based Framework for the Cell Broadband EngineIn Proc. of 23rd Int’l. Parallel and Distributed Processing Symposium, The 18th Heterogeneous Computing Workshop (HCW 2009), 2009.
- ConfParallel Short Sequence Mapping for High Throughput Genome SequencingIn Proc. of 23rd Int’l. Parallel and Distributed Processing Symposium, 2009.
- ConfCoordinating the Use of GPU and CPU for Improving Performance of Compute Intensive ApplicationsIn Proc. of the 2009 IEEE International Conference on Cluster Computing, 2009.
- ConfExploring the GPU for Enhancing Parallelism on Color and Texture AnalysisIn Proc. of the 2009 International Conference on Parallel Computing (ParCo2009), 2009.
- ConfInvestigating the Use of GPU-Accelerated Nodes for SAR Image FormationIn Proc. of the IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC), 2009.
- MiscHigh-Performance Filter-Stream Frameworks for Hierarchical, Heterogeneous, Distributed SupercomputersPoster, 23rd Int’l. Parallel and Distributed Processing Symposium PhD Forum, 2009.
- JRNLA Knowledge-Anchored Integrative Image Search and Retrieval SystemJ. Digital Imaging, 2009.
- ConfParallel Computing Strategies for Sequence Mapping of NGS DataIn Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis, 2009.
- MiscCombinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and MatchingPoster, 21st Supercomputing Conference, 2009.
- ChapHypergraph-based Dynamic Partitioning and Load BalancingIn Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications, 2009.
- ConfUsing Overlays for Efficient Data Transfer over Shared Wide-Area NetworksIn Proceedings of SC2008 High Performance Computing, Networking, and Storage Conference, 2008.
- ConfA Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTPIn Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS), 2008.
- MiscParallel Distance-2 ColoringAbstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations, 2008.
- ConfCombinatorial algorithms for computational science and engineeringIn Journal of Physics: Conference Series, 2008.
- ConfHypergraph-based Dynamic Load Balancing for Adaptive Scientific ComputationsIn Proc. of 21st Int’l. Parallel and Distributed Processing Symposium, 2007, Best Algorithms Paper Award
- TechZoltan 3.0: Parallel Partitioning, Load-balancing, and Data Management Services; User’s GuideSandia National Laboratories , 2007, Tech. Report SAND2007-4748W \urlhttp://www.cs.sandia.gov/Zoltan/ug_html/ug.html
- TechZoltan 3.0: Parallel Partitioning, Load-balancing, and Data Management Services; Developer’s GuideSandia National Laboratories , 2007, Tech. Report SAND2007-4749W, \urlhttp://www.cs.sandia.gov/Zoltan/dev_html/dev.html
- ConfPathological image analysis using the GPU: Stroma classification for neuroblastomaIn Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine, 2007.
- MiscStoring and Searching Massive Scale-free GraphsPoster, 19th Supercomputing Conference, 2nd Place Student Poster, 2007.
- ConfComputerized pathological image analysis for neuroblastoma prognosisIn 2007 AMIA Annual Symposium, 2007.
- ConfEfficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of NeuroblastomaIn Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07), 2007.
- ConfEnabling high performance computational science through combinatorial algorithmsIn Journal of Physics: Conference Series, 2007.
- ConfLocality Conscious Processor Allocation and Scheduling for Mixed Parallel ApplicationsIn Proceedings of 2006 IEEE International Conference on Cluster Computing, 2006.
- ConfImproving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced SubgraphsIn In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD), 2006.
- ConfMSSG: A Framework for Massive Scale Semantic GraphsIn Proceedings of 2006 IEEE International Conference on Cluster Computing, 2006.
- ConfUsing Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation QueriesIn 2006 International Conference on Parallel Processing, 2006.
- ConfOn Creating Efficient Object-relational Views of Scientific DatasetsIn 2006 International Conference on Parallel Processing, 2006.
- ConfTask Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/OIn Proceedings of the Fifteen International Symposium on High Performance Distributed Computing (HPDC-15), 2006.
- ConfA Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File SharingIn Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006, 2006.
- JRNLSupporting Scalable and Distributed Data Subsetting and Aggregation in Large-scale Seismic Data AnalysisThe Journal of High Performance Computing Applications, 2006.
- ConfScheduling of Tasks with Batch-shared I/O on Heterogeneous SystemsIn Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Heterogeneous Computing Workshop (HCW 2006), 2006.
- ConfAn Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel ApplicationsIn 2006 International Conference on Parallel Processing, 2006.
- ConfLarge Image Correction and Warping in a Cluster EnvironmentIn Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006.
- ConfAn Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming ModelIn Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL 2006), 2006.
- ConfHypergraph Partitioning for Automatic Memory Hierarchy ManagementIn Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference, 2006.
- ConfAn Extensible Global Address Space Framework with Decoupled Task and Data AbstractionsIn Proc. IPDPS Workshop on Next Generation Software, 2006.
- ConfDistributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient QueryingIn The 2005 IEEE International Conference on Cluster Computing, 2005.
- ConfServicing Seismic and Oil Reservoir Simulation Data through Grid Data ServicesIn Proceedings of VLDB Workshop Data Management in Grid 2005 (VLDB DMG’05, 2005.
- JRNLA Simulation and Data Analysis System for Large Scale,Data-Driven Oil Reservoir Simulation StudiesConcurrency and Computation: Practice and Experience., 2005.
- ConfServicing Range Queries on Multidimensional Datasets with Partial ReplicasIn Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005), 2005.
- TechParallel Hypergraph Partitioning for Scientific ComputingSandia National Laboratories SAND2005-2796C, 2005.
- ConfA Runtime Framework for Partial Replication and Its Application for On-Demand Data ExplorationIn High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, 2005.
- ConfDesign and Implementation of a Data Server Using a Peer-to-Peer Storage SystemIn High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference, 2005.
- ChapTools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image DataIn Grid Computing: The New Frontier Of High Performance Computing, 14, 2005.
- ConfA Distributed Data Management Middleware for Data-Driven Application SystemsIn Proceedings of 2004 IEEE International Conference on Cluster Computing, 2004.
- ConfApplication of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir StudiesIn Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science), 2004.
- ConfDriving Scientific Applications by Data in Distributed EnvironmentsIn Dynamic Data Driven Application Systems Workshop, held jointly with ICCS 2003, 2003.
- ConfImage Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications.In CCGrid: IEEE International Symposium on Cluster Computing and the Grid, 2003.
- ConfA Component-based Implementation of Multiple Sequence AlignmentIn 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track, 2003.
- ConfA Distributed Execution Environment for Analysis of DCE-MR Image DatasetsIn The Society for Computer Applications in Radiology (SCAR 2003), 2003.
- ConfExecuting Multiple Pipelined Data Analysis Operations in the GridIn Proceedings of the 2002 ACM/IEEE SC02 Conference, 2002.
- TechThe Virtual MicroscopeUniversity of Maryland, Department of Computer Science and UMIACS CS-TR-xxxx and UMIACS-TR-2002-xx, 2002.
- JRNLProcessing Large-Scale Multidimensional Data in Parallel and Distributed EnvironmentsParallel Computing, 2002, Special Issue on Data Intensive Computing
- ConfEfficient Manipulation of Large Datasets on Heterogeneous Storage SystemsIn Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), 2002.
- ConfImproving Performance of Multiple Sequence Alignment Analysis in Multi-client EnvironmentsIn Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS), First Workshop on High Performance Computational Biology, 2002.
- ConfPersistent Caching in a Multiple Query Optimization FrameworkIn Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers, 2002.
- ConfPerformance Optimization for Data Intensive Grid ApplicationsIn Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001), 2001.
- JRNLImproving the Performance and Functionality of the Virtual MicroscopeArchives of Pathology and Laboratory Medicine, 2001.
- JRNLVisualization of Large Datasets with the Active Data RepositoryIEEE Computer Graphics and Applications, 2001.
- TechA Component-based Implementation of Iso-surface Rendering for Visualizing Large DatasetsUniversity of Maryland, Department of Computer Science and UMIACS CS-TR-4249 and UMIACS-TR-2001-34, 2001.
- ConfA Hypergraph-Based Workload Partitioning Strategy for Parallel Data AggregationIn Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing, 2001.
- TechExploration and Visualization of Very Large Datasets with the Active Data RepositoryUniversity of Maryland, Department of Computer Science and UMIACS CS-TR-4208 and UMIACS-TR-2001-04, 2001, Also appears in IEEE Computer Graphics and Applications, Jul/Aug 2001
- MSA Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree OrderingMaster's thesis, Bilkent University, Computer Engineering and Information Science , 1994.