# publications

*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.

## 2022

- ConfEfficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning
*In IEEE International Conference on Cluster Computing*, 2022,*Best Paper Nominee. To appear.*

## 2021

## 2020

## 2019

- StrainHub: A phylogenetic tool to construct pathogen transmission networks
*Bioinformatics*, 2019.

## 2018

## 2017

- ConfAcyclic Partitioning of Large-Scale Directed Acyclic Graphs
*In Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid)*, 2017.

## 2016

## 2015

## 2014

- MiscComputing the Closeness Centrality of Evolving Networks on Clusters
*Poster, SIAM Workshop on Network Science (NS14)*, 2014. - MiscPartitioning Hypergraphs for Multiple Communication Metrics
*Abstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14)*, 2014. - MiscLoad Balancing and Task Mapping for Exascale Systems
*Poster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum*, 2014,*PhD Forum award*

## 2013

- ConfResult Diversification in Automatic Citation Recommendation
*In iConference Workshop on Computational Scientometrics: Theory and Applications*, 2013.

## 2012

- ConfAlgorithms for Offline Tracking of Connected Components in Large Evolving Networks
*In Workshop on Dynamic Network Analysis (DNA-SDM)*, 2012. - ConfA divisive clustering technique for maximizing the modularity
*In 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 minimization
*In 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 Algorithms
*Abstract, SIAM Conference on Parallel Processing for Scientific Computing*, 2012. - ChapParallel Partitioning, Coloring, and Ordering for Scientific Computing
*In Combinatorial Scientific Computing*, 2012. - ChapTwo-dimensional approaches to sparse matrix partitioning
*In Combinatorial Scientific Computing*, 2012.

## 2011

- MiscA comparison of recent biclustering algorithms
*Poster, ACM International Conference on Bioinformatics and Computational Biology*, 2011,*Runner-up of the poster award*

## 2010

- MiscOptimizing the maximum stretch of online tasks on a parallel system without preemption
*Abstract, 3rd Scheduling in Aussois Workshop*, 2010. - ConfA Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence Mapping
*In Job Scheduling Strategies for Parallel Processing*, 2010. - MiscPartitioning Spatially Located Load with Rectangles: Algorithms and Simulations
*Abstract, New Challenges on Scheduling Theory, Workshop*, 2010. - MiscBenchmarking Short Sequence Alignment Tools
*Abstract, Bioinformatics, 2010 Ohio Collaborative Conference*, 2010. - ConfAutomatic Dataflow Application Tuning for Heterogeneous Systems
*In Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010)*, 2010. - ConfComparative Analysis of Biclustering Algorithms
*In ACM International Conference on Bioinformatics and Computational Biology*, 2010. - ConfExploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform
*In 9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS)*, 2010. - ChapDataflow frameworks for emerging heterogeneous architectures and its application to biomedicine
*In Scientific Computing with Multicore and Accelerators*, 2010.

## 2009

- JRNLStroma classification for neuroblastoma on graphics processors
*International Journal of Data Mining and Bioinformatics*, 2009. - ConfA Component-Based Framework for the Cell Broadband Engine
*In 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 Sequencing
*In Proc. of 23rd Int’l. Parallel and Distributed Processing Symposium*, 2009. - ConfCoordinating the Use of GPU and CPU for Improving Performance of Compute Intensive Applications
*In Proc. of the 2009 IEEE International Conference on Cluster Computing*, 2009. - ConfExploring the GPU for Enhancing Parallelism on Color and Texture Analysis
*In Proc. of the 2009 International Conference on Parallel Computing (ParCo2009)*, 2009. - ConfInvestigating the Use of GPU-Accelerated Nodes for SAR Image Formation
*In 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 Supercomputers
*Poster, 23rd Int’l. Parallel and Distributed Processing Symposium PhD Forum*, 2009. - JRNLA Knowledge-Anchored Integrative Image Search and Retrieval System
*J. Digital Imaging*, 2009. - ConfParallel Computing Strategies for Sequence Mapping of NGS Data
*In 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 Matching
*Poster, 21st Supercomputing Conference*, 2009. - ChapHypergraph-based Dynamic Partitioning and Load Balancing
*In Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications*, 2009.

## 2008

- ConfUsing Overlays for Efficient Data Transfer over Shared Wide-Area Networks
*In Proceedings of SC2008 High Performance Computing, Networking, and Storage Conference*, 2008. - ConfA Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTP
*In Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS)*, 2008. - MiscParallel Distance-2 Coloring
*Abstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations*, 2008. - ConfCombinatorial algorithms for computational science and engineering
*In Journal of Physics: Conference Series*, 2008.

## 2007

- ConfHypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations
*In 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 neuroblastoma
*In Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine*, 2007. - MiscStoring and Searching Massive Scale-free Graphs
*Poster, 19th Supercomputing Conference, 2nd Place Student Poster*, 2007. - ConfComputerized pathological image analysis for neuroblastoma prognosis
*In 2007 AMIA Annual Symposium*, 2007. - ConfEfficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma
*In Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07)*, 2007. - ConfEnabling high performance computational science through combinatorial algorithms
*In Journal of Physics: Conference Series*, 2007.

## 2006

- ConfLocality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications
*In Proceedings of 2006 IEEE International Conference on Cluster Computing*, 2006. - ConfImproving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs
*In In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD)*, 2006. - ConfMSSG: A Framework for Massive Scale Semantic Graphs
*In Proceedings of 2006 IEEE International Conference on Cluster Computing*, 2006. - ConfUsing Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries
*In 2006 International Conference on Parallel Processing*, 2006. - ConfOn Creating Efficient Object-relational Views of Scientific Datasets
*In 2006 International Conference on Parallel Processing*, 2006. - ConfTask Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/O
*In 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 Sharing
*In 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 Analysis
*The Journal of High Performance Computing Applications*, 2006. - ConfScheduling of Tasks with Batch-shared I/O on Heterogeneous Systems
*In 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 Applications
*In 2006 International Conference on Parallel Processing*, 2006. - ConfLarge Image Correction and Warping in a Cluster Environment
*In 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 Model
*In 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 Management
*In Proceedings of SC2006 High Performance Computing, Networking, and Storage Conference*, 2006. - ConfAn Extensible Global Address Space Framework with Decoupled Task and Data Abstractions
*In Proc. IPDPS Workshop on Next Generation Software*, 2006.

## 2005

- ConfDistributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying
*In The 2005 IEEE International Conference on Cluster Computing*, 2005. - ConfServicing Seismic and Oil Reservoir Simulation Data through Grid Data Services
*In 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 Studies
*Concurrency and Computation: Practice and Experience.*, 2005. - ConfServicing Range Queries on Multidimensional Datasets with Partial Replicas
*In 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 Exploration
*In High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference*, 2005. - ConfDesign and Implementation of a Data Server Using a Peer-to-Peer Storage System
*In High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference*, 2005. - ChapTools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data
*In Grid Computing: The New Frontier Of High Performance Computing, 14*, 2005.

## 2004

- ConfA Distributed Data Management Middleware for Data-Driven Application Systems
*In Proceedings of 2004 IEEE International Conference on Cluster Computing*, 2004. - ConfApplication of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies
*In Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science)*, 2004.

## 2003

- ConfDriving Scientific Applications by Data in Distributed Environments
*In 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 Alignment
*In 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track*, 2003. - ConfA Distributed Execution Environment for Analysis of DCE-MR Image Datasets
*In The Society for Computer Applications in Radiology (SCAR 2003)*, 2003.

## 2002

- ConfExecuting Multiple Pipelined Data Analysis Operations in the Grid
*In 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 Environments
*Parallel Computing*, 2002,*Special Issue on Data Intensive Computing* - ConfEfficient Manipulation of Large Datasets on Heterogeneous Storage Systems
*In Proceedings of 16th International Parallel and Distributed Processing Symposium (IPDPS)*, 2002. - ConfImproving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
*In 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 Framework
*In Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers*, 2002.

## 2001

- ConfPerformance Optimization for Data Intensive Grid Applications
*In Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001)*, 2001. - JRNLImproving the Performance and Functionality of the Virtual Microscope
*Archives of Pathology and Laboratory Medicine*, 2001. - JRNLVisualization of Large Datasets with the Active Data Repository
*IEEE 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 Aggregation
*In 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*

## 1999

## 1996

## 1995

## 1994

- MSA Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree Ordering
*Master's thesis*, Bilkent University, Computer Engineering and Information Science , 1994.