Decomposing Linear Programs for Parallel Solution. - Ali Pinar; Ümit V. Çatalyürek; Cevdet Aykanat; Mustafa Ç. Pinar (PARA, 1995)

Decomposing Irregularly Sparse Matrices for Parallel Matrix-Vector Multiplication. - Ümit V. Çatalyürek; Cevdet Aykanat (IRREGULAR, 1996)

Hypergraph-Partitioning-Based Decomposition for Parallel Sparse-Matrix Vector Multiplication. - Ümit V. Çatalyürek; Cevdet Aykanat (IEEE Trans. Parallel Distributed Syst., 1999)

Hypergraph models for sparse matrix partitioning and reordering (Seyrek matris bölümleme ve yeniden-düzenleme için hiperçizge modelleri) - Ümit V. Çatalyürek (1999)

Performance Optimization for Data Intensive Grid Applications. - Michael D. Beynon; Alan Sussman; Ümit V. Çatalyürek; Tahsin M. Kurç; Joel H. Saltz (Active Middleware Services, 2001)

A Fine-Grain Hypergraph Model for 2D Decomposition of Sparse Matrices. - Ümit V. Çatalyürek; Cevdet Aykanat (IPDPS, 2001)

A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregation. - Chialin Chang; Tahsin M. Kurç; Alan Sussman; Ümit V. Çatalyürek; Joel H. Saltz (PP, 2001)

A hypergraph-partitioning approach for coarse-grain decomposition. - Ümit V. Çatalyürek; Cevdet Aykanat (SC, 2001)

Visualization of Large Data Sets with the Active Data Repository. - Tahsin M. Kurç; Ümit V. Çatalyürek; Chialin Chang; Alan Sussman; Joel H. Saltz (IEEE Computer Graphics and Applications, 2001)

Distributed processing of very large datasets with DataCutter. - Michael D. Beynon; Tahsin M. Kurç; Ümit V. Çatalyürek; Chialin Chang; Alan Sussman; Joel H. Saltz (Parallel Comput., 2001)

Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems. - Michael D. Beynon; Tahsin M. Kurç; Ümit V. Çatalyürek; Alan Sussman; Joel H. Saltz (IPDPS, 2002)

Improving Performance of Multiple Sequence Alignment Analysis in Multi-Client Environments. - Ümit V. Çatalyürek; Eric Stahlberg; Renato Ferreira 001; Tahsin M. Kurç; Joel H. Saltz (IPDPS, 2002)

Executing multiple pipelined data analysis operations in the grid. - Matthew Spencer; Renato Ferreira 001; Michael D. Beynon; Tahsin M. Kurç; Ümit V. Çatalyürek; Alan Sussman; Joel H. Saltz (SC, 2002)

Processing large-scale multi-dimensional data in parallel and distributed environments. - Michael D. Beynon; Chialin Chang; Ümit V. Çatalyürek; Tahsin M. Kurç; Alan Sussman; Henrique Andrade; Renato Ferreira 001; Joel H. Saltz (Parallel Comput., 2002)

Image Processing or the Grid: A Toolkit or Building Grid-enabled Image Processing Applications. - Shannon Hastings; Tahsin M. Kurç; Stephen Langella; Ümit V. Çatalyürek; Tony Pan; Joel H. Saltz (CCGRID, 2003)

Applying Database Support for Large Scale Data Driven Science in Distributed Environments. - Sivaramakrishnan Narayanan; Ümit V. Çatalyürek; Tahsin M. Kurç; Xi Zhang; Joel H. Saltz (GRID, 2003)

Impact of High Performance Sockets on Data Intensive Applications. - Pavan Balaji; Jiesheng Wu; Tahsin M. Kurç; Ümit V. Çatalyürek; Dhabaleswar K. Panda 001; Joel H. Saltz (HPDC, 2003)

Driving Scientific Applications by Data in Distributed Environments. - Joel H. Saltz; Ümit V. Çatalyürek; Tahsin M. Kurç; Mike Gray; Shannon Hastings; Stephen Langella; Sivaramakrishnan Narayanan; Ryan Martino; Steven Bryant; Malgorzata Peszynska; Mary F. Wheeler; Alan Sussman; et al. (International Conference on Computational Science, 2003)

A Component-based Implementation of Multiple Sequence Alignment. - Ümit V. Çatalyürek; Mike Gray; Tahsin M. Kurç; Joel H. Saltz; Eric Stahlberg; Renato Ferreira 001 (SAC, 2003)

Optimizing Reduction Computations In a Distributed Environment. - Tahsin M. Kurç; Feng Lee; Gagan Agrawal; Ümit V. Çatalyürek; Renato Ferreira 001; Joel H. Saltz (SC, 2003)

Database Support for Data-Driven Scientific Applications in the Grid. - Sivaramakrishnan Narayanan; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz (Parallel Process. Lett., 2003)

The virtual microscope. - Ümit V. Çatalyürek; Michael D. Beynon; Chialin Chang; Tahsin M. Kurç; Alan Sussman; Joel H. Saltz (IEEE Trans. Inf. Technol. Biomed., 2003)

Serving queries to multi-resolution datasets on disk-based storage clusters. - Xi Zhang; Tony Pan; Ümit V. Çatalyürek; Tahsin M. Kurç; Joel H. Saltz (CCGRID, 2004)

A distributed data management middleware for data-driven application systems. - Stephen Langella; Shannon Hastings; Scott Oster; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz (CLUSTER, 2004)

Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O. - Nagavijayalakshmi Vydyanathan; Gaurav Khanna 002; Tahsin M. Kurç; Ümit V. Çatalyürek; Pete Wyckoff; Joel H. Saltz; P. Sadayappan (GRID, 2004)

Tools for efficient subsetting and pipelined processing of large scale, distributed biomedical image data. - Matheus Ribeiro; Tahsin M. Kurç; Tony Pan; Kun Huang 001; Ümit V. Çatalyürek; Xi Zhang; Stephen Langella; Shannon Hastings; Scott Oster; Renato Ferreira 001; Joel H. Saltz (High Performance Computing Workshop, 2004)

An Approach for Automatic Data Virtualization. - Li Weng; Gagan Agrawal; Ümit V. Çatalyürek; Tahsin M. Kurç; Sivaramakrishnan Narayanan; Joel H. Saltz (HPDC, 2004)

Strategies for Using Additional Resources in Parallel Hash-Based Join Algorithms. - Xi Zhang; Tahsin M. Kurç; Tony Pan; Ümit V. Çatalyürek; Sivaramakrishnan Narayanan; Pete Wyckoff; Joel H. Saltz (HPDC, 2004)

Application of Grid-Enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies. - Manish Parashar; Hector Klie; Ümit V. Çatalyürek; Tahsin M. Kurç; Vincent Matossian; Joel H. Saltz; Mary F. Wheeler (International Conference on Computational Science, 2004)

Supporting SQL-3 Aggregations on Grid-Based Data Repositories. - Li Weng; Gagan Agrawal; Ümit V. Çatalyürek; Joel H. Saltz (LCPC, 2004)

Permuting Sparse Rectangular Matrices into Block-Diagonal Form. - Cevdet Aykanat; Ali Pinar; Ümit V. Çatalyürek (SIAM J. Sci. Comput., 2004)

A hypergraph partitioning based approach for scheduling of tasks with batch-shared I/O. - Gaurav Khanna 002; Nagavijayalakshmi Vydyanathan; Tahsin M. Kurç; Ümit V. Çatalyürek; Pete Wyckoff; Joel H. Saltz; P. Sadayappan (CCGRID, 2005)

Servicing range queries on multidimensional datasets with partial replicas. - Li Weng; Ümit V. Çatalyürek; Tahsin M. Kurç; Gagan Agrawal; Joel H. Saltz (CCGRID, 2005)

Distributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying. - Benjamin Rutt; Vijay S. Kumar; Tony Pan; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz; Yujun Wang (CLUSTER, 2005)

Servicing Seismic and Oil Reservoir Simulation Data Through Grid Data Services. - Sivaramakrishnan Narayanan; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz (DMG, 2005)

A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers. - Erik G. Boman; Doruk Bozdag; Ümit V. Çatalyürek; Assefaw Hadish Gebremedhin; Fredrik Manne (Euro-Par, 2005)

A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers. - Doruk Bozdag; Ümit V. Çatalyürek; Assefaw Hadish Gebremedhin; Fredrik Manne; Erik G. Boman; Füsun Özgüner (HPCC, 2005)

Towards Dynamic Data-Driven Optimization of Oil Well Placement. - Manish Parashar; Vincent Matossian; Wolfgang Bangerth; Hector Klie; Benjamin Rutt; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz; Mary F. Wheeler (International Conference on Computational Science (2), 2005)

A Task Duplication Based Scheduling Algorithm Using Partial Schedules. - Doruk Bozdag; Füsun Özgüner; Eylem Ekici; Ümit V. Çatalyürek (ICPP, 2005)

Supporting Large Scale Medical and Scientific Datasets. - Ümit V. Çatalyürek; Shannon Hastings; Kun Huang 001; Vijay S. Kumar; Tahsin M. Kurç; Stephen Langella; Sivaramakrishnan Narayanan; Scott Oster; Tony Pan; Benjamin Rutt; Xi Zhang; Joel H. Saltz (PARCO, 2005)

Grid-based management of biomedical data using an XML-based distributed data management system. - Shannon Hastings; Stephen Langella; Scott Oster; Tahsin M. Kurç; Tony Pan; Ümit V. Çatalyürek; Daniel Janies; Joel H. Saltz (SAC, 2005)

A Scalable Distributed Parallel Breadth-First Search Algorithm on BlueGene/L. - Andy Yoo; Edmond Chow; Keith W. Henderson; Will McLendon III; Bruce Hendrickson; Ümit V. Çatalyürek (SC, 2005)

A simulation and data analysis system for large-scale, data-driven oil reservoir simulation studies. - Tahsin M. Kurç; Ümit V. Çatalyürek; Xi Zhang; Joel H. Saltz; Ryan Martino; Mary F. Wheeler; Malgorzata Peszynska; Alan Sussman; Christian Hansen 002; Mrinal K. Sen; Roustam Seifoullaev; Paul L. Stoffa; et al. (Concurr. Pract. Exp., 2005)

Application of Grid-enabled technologies for solving optimization problems in data-driven reservoir studies. - Manish Parashar; Hector Klie; Ümit V. Çatalyürek; Tahsin M. Kurç; Wolfgang Bangerth; Vincent Matossian; Joel H. Saltz; Mary F. Wheeler (Future Gener. Comput. Syst., 2005)

Application of Information Technology: A Grid-Based Image Archival and Analysis System. - Shannon Hastings; Scott Oster; Stephen Langella; Tahsin M. Kurç; Tony Pan; Ümit V. Çatalyürek; Joel H. Saltz (J. Am. Medical Informatics Assoc., 2005)

XML database support for distributed execution of data-intensive scientific workflows. - Shannon Hastings; Matheus Ribeiro; Stephen Langella; Scott Oster; Ümit V. Çatalyürek; Tony Pan; Kun Huang 001; Renato Ferreira 001; Joel H. Saltz; Tahsin M. Kurç (SIGMOD Rec., 2005)

Distributed dynamic event tree generation for reliability and risk assessment. - Benjamin Rutt; Ümit V. Çatalyürek; Aram Hakobyan; Kyle Metzroth; Tunc Aldemir; Richard Denning; Sean Dunagan; David Kunsman (CLADE, 2006)

MSSG: A Framework for Massive-Scale Semantic Graphs. - Timothy D. R. Hartley; Ümit V. Çatalyürek; Füsun Özgüner; Andy Yoo; Scott Kohn; Keith W. Henderson (CLUSTER, 2006)

Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications. - Nagavijayalakshmi Vydyanathan; Sriram Krishnamoorthy; Gerald Sabin; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (CLUSTER, 2006)

Service-Based Access to and Processing of Large Scientific Datasets. - Ümit V. Çatalyürek; Sivaramakrishnan Narayanan; Olcay Sertel; Jun Kong 002; Berkant Barla Cambazoglu; Tony Pan; Ashish Sharma 001; Shannon Hastings; Stephen Langella; Scott Oster; Tahsin M. Kurç; Metin Nafi Gürcan; et al. (High Performance Computing Workshop, 2006)

Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared I/O. - Gaurav Khanna 002; Nagavijayalakshmi Vydyanathan; Ümit V. Çatalyürek; Tahsin M. Kurç; Sriram Krishnamoorthy; P. Sadayappan; Joel H. Saltz (HPDC, 2006)

On Creating Efficient Object-relational Views of Scientific Datasets. - Sivaramakrishnan Narayanan; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz (ICPP, 2006)

An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications. - Nagavijayalakshmi Vydyanathan; Sriram Krishnamoorthy; Gerald Sabin; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (ICPP, 2006)

Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries. - Li Weng; Ümit V. Çatalyürek; Tahsin M. Kurç; Gagan Agrawal; Joel H. Saltz (ICPP, 2006)

A task duplication based bottom-up scheduling algorithm for heterogeneous environments. - Doruk Bozdag; Ümit V. Çatalyürek; Füsun Özgüner (IPDPS, 2006)

Parallel hypergraph partitioning for scientific computing. - Karen D. Devine; Erik G. Boman; Robert T. Heaphy; Rob H. Bisseling; Ümit V. Çatalyürek (IPDPS, 2006)

An extensible global address space framework with decoupled task and data abstractions. - Sriram Krishnamoorthy; Ümit V. Çatalyürek; Jarek Nieplocha; Atanas Rountev; P. Sadayappan (IPDPS, 2006)

An approach to locality-conscious load balancing and transparent memory hierarchy management with a global-address-space parallel programming model. - Sriram Krishnamoorthy; Ümit V. Çatalyürek; Jarek Nieplocha; P. Sadayappan (IPDPS, 2006)

A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File Sharing. - Gaurav Khanna 002; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (JSSPP, 2006)

Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-Induced Subgraphs. - Duygu Ucar; Sitaram Asur; Ümit V. Çatalyürek; Srinivasan Parthasarathy 001 (PKDD, 2006)

Data management and query - Hypergraph partitioning for automatic memory hierarchy management. - Sriram Krishnamoorthy; Ümit V. Çatalyürek; Jarek Nieplocha; Atanas Rountev; P. Sadayappan (SC, 2006)

Imaging and visual analysis - Large image correction and warping in a cluster environment. - Vijay S. Kumar; Benjamin Rutt; Tahsin M. Kurç; Ümit V. Çatalyürek; Joel H. Saltz; Sunny K. Chow; Stephan Lamont; Maryann E. Martone (SC, 2006)

Models, methods and middleware for grid-enabled multiphysics oil reservoir management. - Hector Klie; Wolfgang Bangerth; X. Gai; Mary F. Wheeler; Paul L. Stoffa; Mrinal K. Sen; Manish Parashar; Ümit V. Çatalyürek; Joel H. Saltz; Tahsin M. Kurç (Eng. Comput., 2006)

Supporting Scalable and Distributed Data Subsetting and Aggregation in Large-Scale Seismic Data Analysis. - Xi Zhang; Benjamin Rutt; Ümit V. Çatalyürek; Tahsin M. Kurç; Paul L. Stoffa; Mrinal K. Sen; Joel H. Saltz (Int. J. High Perform. Comput. Appl., 2006)

Application of Information Technology: An XML-based System for Synthesis of Data from Disparate Databases. - Tahsin M. Kurç; Daniel Janies; Andrew D. Johnson; Stephen Langella; Scott Oster; Shannon Hastings; Farhat Habib; Terry Camerlengo; David Ervin; Ümit V. Çatalyürek; Joel H. Saltz (J. Am. Medical Informatics Assoc., 2006)

Computerized Pathological Image Analysis For Neuroblastoma Prognosis. - Metin N. Gurcan; Jun Kong 002; Olcay Sertel; Berkant Barla Cambazoglu; Joel H. Saltz; Ümit V. Çatalyürek (AMIA, 2007)

Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma. - Antonio Ruiz; Olcay Sertel; Manuel Ujaldon; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (BIBM, 2007)

An Efficient and Reliable Scientific Workflow System. - Tulio Tavares; George Teodoro; Tahsin M. Kurç; Renato Ferreira 001; Dorgival Olavo Guedes Neto; Wagner Meira Jr.; Ümit V. Çatalyürek; Shannon Hastings; Scott Oster; Stephen Langella; Joel H. Saltz (CCGRID, 2007)

Efficient processing of pathological images using the grid: computer-aided prognosis of neuroblastoma. - Berkant Barla Cambazoglu; Olcay Sertel; Jun Kong 002; Joel H. Saltz; Metin N. Gurcan; Ümit V. Çatalyürek (CLADE@HPDC, 2007)

Performance vs. accuracy trade-offs for large-scale image analysis applications. - Vijay S. Kumar; Tahsin M. Kurç; Jun Kong 002; Ümit V. Çatalyürek; Metin N. Gurcan; Joel H. Saltz (CLUSTER, 2007)

Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters. - Gaurav Khanna 002; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (Euro-Par, 2007)

Toward Optimizing Latency Under Throughput Constraints for Application Workflows on Clusters. - Nagavijayalakshmi Vydyanathan; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (Euro-Par, 2007)

Optimizing multiple queries on scientific datasets with partial replicas. - Li Weng; Ümit V. Çatalyürek; Tahsin M. Kurç; Gagan Agrawal; Joel H. Saltz (GRID, 2007)

Dynamic Data-Driven Systems Approach for Simulation Based Optimizations. - Tahsin M. Kurç; Xi Zhang; Manish Parashar; Hector Klie; Mary F. Wheeler; Ümit V. Çatalyürek; Joel H. Saltz (International Conference on Computational Science (1), 2007)

Intelligent Optimization of Parallel and Distributed Applications. - Bhupesh Bansal; Ümit V. Çatalyürek; Jacqueline Chame; Chun Chen 002; Ewa Deelman; Yolanda Gil; Mary W. Hall; Vijay S. Kumar; Tahsin M. Kurç; Kristina Lerman; Aiichiro Nakano; Yoon-Ju Lee Nelson; et al. (IPDPS, 2007)

Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations. - Ümit V. Çatalyürek; Erik G. Boman; Karen D. Devine; Doruk Bozdag; Robert T. Heaphy; Lee Ann Riesen (IPDPS, 2007)

A global address space framework for locality aware scheduling of block-sparse computations. - Sriram Krishnamoorthy; Ümit V. Çatalyürek; Jarek Nieplocha; Atanas Rountev; P. Sadayappan (IPDPS, 2007)

Processing of Large-Scale Biomedical Images on a Cluster of Multicore CPUs and GPUs. - Ümit V. Çatalyürek; Timothy D. R. Hartley; Olcay Sertel; Manuel Ujaldon; Antonio Ruiz; Joel H. Saltz; Metin N. Gurcan (High Performance Computing Workshop, 2008)

Multi-hop path splitting and multi-pathing optimizations for data transfers over shared wide-area networks using gridFTP. - Gaurav Khanna 002; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz; Rajkumar Kettimuthu; Ian T. Foster (HPDC, 2008)

Texture classification using nonlinear color quantization: Application to histopathological image analysis. - Olcay Sertel; Jun Kong 002; Gerard Lozanski; Arwa Shanaah; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (ICASSP, 2008)

A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows. - Nagavijayalakshmi Vydyanathan; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (ICPP, 2008)

Biomedical image analysis on a cooperative cluster of GPUs and multicores. - Timothy D. R. Hartley; Ümit V. Çatalyürek; Antonio Ruiz; Francisco D. Igual; Rafael Mayo 002; Manuel Ujaldon (ICS, 2008)

A dynamic scheduling approach for coordinated wide-area data transfers using GridFTP. - Gaurav Khanna 002; Ümit V. Çatalyürek; Tahsin M. Kurç; Rajkumar Kettimuthu; P. Sadayappan; Joel H. Saltz (IPDPS, 2008)

Translational research design templates, Grid computing, and HPC. - Joel H. Saltz; Scott Oster; Shannon Hastings; Stephen Langella; Renato Ferreira 001; Justin Permar; Ashish Sharma 001; David Ervin; Tony Pan; Ümit V. Çatalyürek; Tahsin M. Kurç (IPDPS, 2008)

Computerized microscopic image analysis of follicular lymphoma. - Olcay Sertel; Jun Kong 002; Gerard Lozanski; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (Computer-Aided Diagnosis, 2008)

Computer-aided prognosis of neuroblastoma: classification of stromal development on whole-slide images. - Olcay Sertel; Jun Kong 002; Hiroyuki Shimada; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (Computer-Aided Diagnosis, 2008)

Using overlays for efficient data transfer over shared wide-area networks. - Gaurav Khanna 002; Ümit V. Çatalyürek; Tahsin M. Kurç; Rajkumar Kettimuthu; P. Sadayappan; Ian T. Foster; Joel H. Saltz (SC, 2008)

e-Science, caGrid, and Translational Biomedical Research. - Joel H. Saltz; Tahsin M. Kurç; Shannon Hastings; Stephen Langella; Scott Oster; David Ervin; Ashish Sharma 001; Tony Pan; Metin N. Gurcan; Justin Permar; Renato Ferreira 001; Philip R. O. Payne; et al. (Computer, 2008)

BlueGene/L applications: Parallelism On a Massive Scale. - Bronis R. de Supinski; Martin Schulz 001; Vasily V. Bulatov; William H. Cabot; Bor Chan; Andrew W. Cook; Erik W. Draeger; James N. Glosli; Jeffrey A. Greenough; Keith W. Henderson; Alison Kubota; Steve Louis; et al. (Int. J. High Perform. Comput. Appl., 2008)

A framework for scalable greedy coloring on distributed-memory parallel computers. - Doruk Bozdag; Assefaw Hadish Gebremedhin; Fredrik Manne; Erik G. Boman; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2008)

Large-Scale Biomedical Image Analysis in Grid Environments. - Vijay S. Kumar; Benjamin Rutt; Tahsin M. Kurç; Ümit V. Çatalyürek; Tony C. Pan; Sunny K. Chow; Stephan Lamont; Maryann E. Martone; Joel H. Saltz (IEEE Trans. Inf. Technol. Biomed., 2008)

A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets. - Doruk Bozdag; Jeffrey D. Parvin; Ümit V. Çatalyürek (BICoB, 2009)

A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments. - Hatice Gulcin Ozer; Doruk Bozdag; Terry Camerlengo; Jiejun Wu; Yi-Wen Huang; Timothy D. R. Hartley; Jeffrey D. Parvin; Tim Hui-Ming Huang; Ümit V. Çatalyürek; Kun Huang 001 (BICoB, 2009)

Investigating the use of GPU-accelerated nodes for SAR image formation. - Timothy D. R. Hartley; Ahmed Fasih; Charles A. Berdanier; Füsun Özgüner; Ümit V. Çatalyürek (CLUSTER, 2009)

Coordinating the use of GPU and CPU for improving performance of compute intensive applications. - George Teodoro; Rafael Sachetto Oliveira; Olcay Sertel; Metin N. Gurcan; Wagner Meira Jr.; Ümit V. Çatalyürek; Renato Ferreira 001 (CLUSTER, 2009)

Combinatorial Problems in High-Performance Computing: Partitioning. - Rob H. Bisseling; Tristan van Leeuwen; Ümit V. Çatalyürek (Combinatorial Scientific Computing, 2009)

Parallelization of Mapping Algorithms for Next Generation Sequencing Applications. - Doruk Bozdag; Catalin C. Barbacioru; Ümit V. Çatalyürek (Combinatorial Scientific Computing, 2009)

Getting Started with Zoltan: A Short Tutorial. - Karen D. Devine; Erik G. Boman; Lee Ann Riesen; Ümit V. Çatalyürek; Cédric Chevalier (Combinatorial Scientific Computing, 2009)

High-performance signal processing on emerging many-core architectures using cuda. - Manuel Ujaldon; Ümit V. Çatalyürek (ICME, 2009)

Parallel short sequence mapping for high throughput genome sequencing. - Doruk Bozdag; Catalin C. Barbacioru; Ümit V. Çatalyürek (IPDPS, 2009)

A component-based framework for the Cell Broadband Engine. - Timothy D. R. Hartley; Ümit V. Çatalyürek (IPDPS, 2009)

Exploring the GPU for Enhancing Parallelism on Color and Texture Analysis. - Francisco D. Igual; Rafael Mayo 002; Timothy D. R. Hartley; Ümit V. Çatalyürek; Antonio Ruiz; Manuel Ujaldon (PARCO, 2009)

Parallel materialization of large ABoxes. - Sivaramakrishnan Narayanan; Ümit V. Çatalyürek; Tahsin M. Kurç; Joel H. Saltz (SAC, 2009)

Stroma classification for neuroblastoma on graphics processors. - Antonio Ruiz; Olcay Sertel; Manuel Ujaldon; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (Int. J. Data Min. Bioinform., 2009)

A Knowledge-Anchored Integrative Image Search and Retrieval System. - Selnur Erdal; Ümit V. Çatalyürek; Philip R. O. Payne; Joel H. Saltz; Jyoti Kamal; Metin N. Gurcan (J. Digit. Imaging, 2009)

A repartitioning hypergraph model for dynamic load balancing. - Ümit V. Çatalyürek; Erik G. Boman; Karen D. Devine; Doruk Bozdag; Robert T. Heaphy; Lee Ann Riesen (J. Parallel Distributed Comput., 2009)

Computer-aided prognosis of neuroblastoma on whole-slide images: Classification of stromal development. - Olcay Sertel; Jun Kong 002; Hiroyuki Shimada; Ümit V. Çatalyürek; Joel H. Saltz; Metin N. Gurcan (Pattern Recognit., 2009)

Compaction of Schedules and a Two-Stage Approach for Duplication-Based DAG Scheduling. - Doruk Bozdag; Füsun Özgüner; Ümit V. Çatalyürek (IEEE Trans. Parallel Distributed Syst., 2009)

An Integrated Approach to Locality-Conscious Processor Allocation and Scheduling of Mixed-Parallel Applications. - Nagavijayalakshmi Vydyanathan; Sriram Krishnamoorthy; Gerald M. Sabin; Ümit V. Çatalyürek; Tahsin M. Kurç; P. Sadayappan; Joel H. Saltz (IEEE Trans. Parallel Distributed Syst., 2009)

Histopathological Image Analysis Using Model-Based Intermediate Representations and Color Texture: Follicular Lymphoma Grading. - Olcay Sertel; Jun Kong 002; Ümit V. Çatalyürek; Gerard Lozanski; Joel H. Saltz; Metin N. Gurcan (J. Signal Process. Syst., 2009)

Data Flow Frameworks for Emerging Heterogeneous Architectures and Their Application to Biomedicine. - Ümit V. Çatalyürek; Renato Ferreira 001; Timothy D. R. Hartley; George Teodoro; Rafael Sachetto Oliveira (Scientific Computing with Multicore and Accelerators, 2010)

Comparative analysis of biclustering algorithms. - Doruk Bozdag; Ashwin S. Kumar; Ümit V. Çatalyürek (BCB, 2010)

Automatic dataflow application tuning for heterogeneous systems. - Timothy D. R. Hartley; Erik Saule; Ümit V. Çatalyürek (HiPC, 2010)

Run-time optimizations for replicated dataflows on heterogeneous environments. - George Teodoro; Timothy D. R. Hartley; Ümit V. Çatalyürek; Renato Ferreira 001 (HPDC, 2010)

An Image Analysis Approach for Detecting Malignant Cells in Digitized H&E-stained Histology Images of Follicular Lymphoma. - Olcay Sertel; Ümit V. Çatalyürek; Gerard Lozanski; Arwa Shanaah; Metin N. Gurcan (ICPR, 2010)

Exploring parallelism in short sequence mapping using Burrows-Wheeler Transform. - Doruk Bozdag; Ayat Hatem; Ümit V. Çatalyürek (IPDPS Workshops, 2010)

Message from the Workshops Chair. - Ümit V. Çatalyürek (IPDPS Workshops, 2010)

A Moldable Online Scheduling Algorithm and Its Application to Parallel Short Sequence Mapping. - Erik Saule; Doruk Bozdag; Ümit V. Çatalyürek (JSSPP, 2010)

On the Scalability of Hypergraph Models for Sparse Matrix Partitioning. - Bora Uçar; Ümit V. Çatalyürek (PDP, 2010)

A Matrix Partitioning Interface to PaToH in MATLAB. - Bora Uçar; Ümit V. Çatalyürek; Cevdet Aykanat (Parallel Comput., 2010)

Development of a code-agnostic computational infrastructure for the dynamic generation of accident progression event trees. - Ümit V. Çatalyürek; Benjamin Rutt; Kyle Metzroth; Aram Hakobyan; Tunc Aldemir; Richard Denning; Sean Dunagan; David Kunsman (Reliab. Eng. Syst. Saf., 2010)

Distributed-Memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation. - Doruk Bozdag; Ümit V. Çatalyürek; Assefaw H. Gebremedhin; Fredrik Manne; Erik G. Boman; Füsun Özgüner (SIAM J. Sci. Comput., 2010)

On Two-Dimensional Sparse Matrix Partitioning: Models, Methods, and a Recipe. - Ümit V. Çatalyürek; Cevdet Aykanat; Bora Uçar (SIAM J. Sci. Comput., 2010)

Benchmarking Short Sequence Mapping Tools. - Ayat Hatem; Doruk Bozdag; Ümit V. Çatalyürek (BIBM, 2011)

On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections. - Hasan Metin Aktulga; Chao Yang 001; Ümit V. Çatalyürek; Pieter Maris; James P. Vary; Esmond G. Ng (Euro-Par Workshops (1), 2011)

Improving graph coloring on distributed-memory parallel computers. - Ahmet Erdem Sariyüce; Erik Saule; Ümit V. Çatalyürek (HiPC, 2011)

Acceleration of Two Point Correlation Function Calculation for Pathology Image Segmentation. - Lee A. D. Cooper; Joel H. Saltz; Ümit V. Çatalyürek; Kun Huang 001 (HISB, 2011)

Integrated data placement and task assignment for scientific workflows in clouds. - Ümit V. Çatalyürek; Kamer Kaya; Bora Uçar (DICT@HPDC, 2011)

Distributed-Memory Parallel Algorithms for Matching and Coloring. - Ümit V. Çatalyürek; Florin Dobrian; Assefaw Hadish Gebremedhin; Mahantesh Halappanavar; Alex Pothen (IPDPS Workshops, 2011)

Partitioning Spatially Located Computations Using Rectangles. - Erik Saule; Erdeniz Ö. Bas; Ümit V. Çatalyürek (IPDPS, 2011)

Petascale kinetic simulation of the magnetosphere. - Homa Karimabadi; Burlen Loring; H. X. Vu; Yuri A. Omelchenko; Vadim Roytershteyn; William S. Daughton; Tamara B. Sipes; Mahidhar Tatineni; Amitava Majumdar 001; Ümit V. Çatalyürek; Alper Yilmaz (TG, 2011)

Hypergraph Partitioning through Vertex Separators on Graphs - Enver Kayaaslan; Ali Pinar; Ümit V. Çatalyürek; Cevdet Aykanat (CoRR, 2011)

Color and texture analysis using emerging parallel architectures. - Francisco D. Igual; Rafael Mayo 002; Timothy D. R. Hartley; Ümit V. Çatalyürek; Antonio Ruiz; Manuel Ujaldon (Int. J. High Perform. Comput. Appl., 2011)

Optimizing latency and throughput of application workflows on clusters. - Naga Vydyanathan; Ümit V. Çatalyürek; Tahsin M. Kurç; Ponnuswamy Sadayappan; Joel H. Saltz (Parallel Comput., 2011)

Hypergraph Partitioning-Based Fill-Reducing Ordering for Symmetric Matrices. - Ümit V. Çatalyürek; Cevdet Aykanat; Enver Kayaaslan (SIAM J. Sci. Comput., 2011)

PaToH (Partitioning Tool for Hypergraphs). - Ümit V. Çatalyürek; Cevdet Aykanat (Encyclopedia of Parallel Computing, 2011)

Hypergraph Partitioning. - Ümit V. Çatalyürek; Bora Uçar; Cevdet Aykanat (Encyclopedia of Parallel Computing, 2011)

Fast Recommendation on Bibliographic Networks. - Onur Kucuktunc; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (ASONAM, 2012)

Microarray vs. RNA-Seq: a comparison for active subnetwork discovery. - Ayat Hatem; Kamer Kaya; Ümit V. Çatalyürek (BCB, 2012)

An Out-of-Core Eigensolver on SSD-equipped Clusters. - Zheng Zhou 003; Erik Saule; Hasan Metin Aktulga; Chao Yang 001; Esmond G. Ng; Pieter Maris; James P. Vary; Ümit V. Çatalyürek (CLUSTER, 2012)

UMPa: A multi-objective, multi-level partitioner for communication minimization. - Ümit V. Çatalyürek; Mehmet Deveci; Kamer Kaya; Bora Uçar (Graph Partitioning and Graph Clustering, 2012)

A partitioning-based divisive clustering technique for maximizing the modularity. - Ümit V. Çatalyürek; Kamer Kaya; Johannes Langguth; Bora Uçar (Graph Partitioning and Graph Clustering, 2012)

On Shared-Memory Parallelization of a Sparse Matrix Scaling Algorithm. - Ümit V. Çatalyürek; Kamer Kaya; Bora Uçar (ICPP, 2012)

An Out-of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers. - Zheng Zhou 003; Erik Saule; Hasan Metin Aktulga; Chao Yang 001; Esmond G. Ng; Pieter Maris; James P. Vary; Ümit V. Çatalyürek (ICPP Workshops, 2012)

Multithreaded Clustering for Multi-level Hypergraph Partitioning. - Ümit V. Çatalyürek; Mehmet Deveci; Kamer Kaya; Bora Uçar (IPDPS, 2012)

Scalable Hybrid Implementation of Graph Coloring Using MPI and OpenMP. - Ahmet Erdem Sariyüce; Erik Saule; Ümit V. Çatalyürek (IPDPS Workshops, 2012)

An Early Evaluation of the Scalability of Graph Algorithms on the Intel MIC Architecture. - Erik Saule; Ümit V. Çatalyürek (IPDPS Workshops, 2012)

Optimizing dataflow applications on heterogeneous environments. - George Teodoro; Timothy D. R. Hartley; Ümit V. Çatalyürek; Renato Ferreira 001 (Clust. Comput., 2012)

Recommendation on Academic Networks using Direction Aware Citation Analysis - Onur Küçüktunç; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (CoRR, 2012)

Graph Coloring Algorithms for Muti-core and Massively Multithreaded Architectures - Ümit V. Çatalyürek; John Feo; Assefaw Hadish Gebremedhin; Mahantesh Halappanavar; Alex Pothen (CoRR, 2012)

Shattering and Compressing Networks for Centrality Analysis - Ahmet Erdem Sariyüce; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (CoRR, 2012)

Color and texture analysis on emerging parallel architectures. - Francisco D. Igual; Rafael Mayo 002; Timothy D. R. Hartley; Ümit V. Çatalyürek; Antonio Ruiz; Manuel Ujaldon (Int. J. High Perform. Comput. Appl., 2012)

Optimizing the stretch of independent tasks on a cluster: From sequential tasks to moldable tasks. - Erik Saule; Doruk Bozdag; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2012)

Load-balancing spatially located computations using rectangular partitions. - Erik Saule; Erdeniz Ö. Bas; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2012)

Merging network patterns: a general framework to summarize biomedical network data. - Yang Xiang; David Fuhry; Kamer Kaya; Ruoming Jin; Ümit V. Çatalyürek; Kun Huang 001 (Netw. Model. Anal. Health Informatics Bioinform., 2012)

Graph coloring algorithms for multi-core and massively multithreaded architectures. - Ümit V. Çatalyürek; John Feo; Assefaw Hadish Gebremedhin; Mahantesh Halappanavar; Alex Pothen (Parallel Comput., 2012)

Improving performance of adaptive component-based dataflow middleware. - Timothy D. R. Hartley; Erik Saule; Ümit V. Çatalyürek (Parallel Comput., 2012)

Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs. - Enver Kayaaslan; Ali Pinar; Ümit V. Çatalyürek; Cevdet Aykanat (SIAM J. Sci. Comput., 2012)

The Zoltan and Isorropia parallel toolkits for combinatorial scientific computing: Partitioning, ordering and coloring. - Erik G. Boman; Ümit V. Çatalyürek; Cédric Chevalier; Karen D. Devine (Sci. Program., 2012)

Betweenness centrality on GPUs and heterogeneous architectures. - Ahmet Erdem Sariyüce; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (GPGPU@ASPLOS, 2013)

Towards a personalized, scalable, and exploratory academic recommendation service. - Onur Küçüktunç; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (ASONAM, 2013)

Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on GPUs. - Anas Abu-Doleh; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (BCB, 2013)

PRASE: PageRank-based Active Subnetwork Extraction. - Ayat Hatem; Kamer Kaya; Ümit V. Çatalyürek (BCB, 2013)

Incremental algorithms for closeness centrality. - Ahmet Erdem Sariyüce; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (IEEE BigData, 2013)

STREAMER: A distributed framework for incremental closeness centrality computation. - Ahmet Erdem Sariyüce; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (CLUSTER, 2013)

GPU Accelerated Maximum Cardinality Matching Algorithms for Bipartite Graphs. - Mehmet Deveci; Kamer Kaya; Bora Uçar; Ümit V. Çatalyürek (Euro-Par, 2013)

Hypergraph Sparsification and Its Application to Partitioning. - Mehmet Deveci; Kamer Kaya; Ümit V. Çatalyürek (ICPP, 2013)

A Push-Relabel-Based Maximum Cardinality Bipartite Matching Algorithm on GPUs. - Mehmet Deveci; Kamer Kaya; Bora Uçar; Ümit V. Çatalyürek (ICPP, 2013)

TheAdvisor: a webservice for academic recommendation. - Onur Küçüktunç; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (JCDL, 2013)

Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication. - Kamer Kaya; Bora Uçar; Ümit V. Çatalyürek (PPAM (2), 2013)

Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi. - Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (PPAM (1), 2013)

Shattering and Compressing Networks for Betweenness Centrality. - Ümit V. Çatalyürek; Kamer Kaya; Ahmet Erdem Sariyüce; Erik Saule (SDM, 2013)

Diversified recommendation on graphs: pitfalls, measures, and algorithms. - Onur Küçüktunç; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (WWW, 2013)

A comparative analysis of biclustering algorithms for gene expression data. - Kemal Eren; Mehmet Deveci; Onur Küçüktunç; Ümit V. Çatalyürek (Briefings Bioinform., 2013)

Benchmarking short sequence mapping tools. - Ayat Hatem; Doruk Bozdag; Amanda E. Toland; Ümit V. Çatalyürek (BMC Bioinform., 2013)

Incremental Algorithms for Network Management and Analysis based on Closeness Centrality - Ahmet Erdem Sariyüce; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (CoRR, 2013)

A survey of pipelined workflow scheduling: Models and algorithms. - Anne Benoit; Ümit V. Çatalyürek; Yves Robert; Erik Saule (ACM Comput. Surv., 2013)

Streaming Algorithms for k-core Decomposition. - Ahmet Erdem Sariyüce; Bugra Gedik; Gabriela Jacques-Silva; Kun-Lung Wu; Ümit V. Çatalyürek (Proc. VLDB Endow., 2013)

Fast recommendation on bibliographic networks with sparse-matrix ordering and partitioning. - Onur Küçüktunç; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (Soc. Netw. Anal. Min., 2013)

Wide-area overlay networking to manage science DMZ accelerated flows. - Prasad Calyam; Alex Berryman; Erik Saule; Hari Subramoni; Paul Schopis; Gordon Springer; Ümit V. Çatalyürek; Dhabaleswar K. Panda 001 (ICNC, 2014)

Author's retrospective for biomedical image analysis on a cooperative cluster of gpus and multicores. - Timothy D. R. Hartley; Ümit V. Çatalyürek; Antonio Ruiz; Francisco D. Igual; Rafael Mayo 002; Manuel Ujaldon (ICS 25th Anniversary, 2014)

Extracting Maximal Exact Matches on GPU. - Anas Abu-Doleh; Kamer Kaya; Mohamed Abouelhoda; Ümit V. Çatalyürek (IPDPS Workshops, 2014)

Exploiting Geometric Partitioning in Task Mapping for Parallel Computers. - Mehmet Deveci; Sivasankaran Rajamanickam; Vitus J. Leung; Kevin T. Pedretti; Stephen L. Olivier; David P. Bunde; Ümit V. Çatalyürek; Karen D. Devine (IPDPS, 2014)

HiCOMB Keynote and Invited Talks. - Stephen Larson; Ümit V. Çatalyürek; Ananth Kalyanaraman (IPDPS Workshops, 2014)

Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures. - Ahmet Erdem Sariyüce; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (IPDPS Workshops, 2014)

mrSNP: Software to detect SNP effects on microRNA binding. - Mehmet Deveci; Ümit V. Çatalyürek; Amanda E. Toland (BMC Bioinform., 2014)

Massively multithreaded maxflow for image segmentation on the Cray XMT-2. - Shahid H. Bokhari; Ümit V. Çatalyürek; Metin Nafi Gürcan (Concurr. Comput. Pract. Exp., 2014)

On Distributed Graph Coloring with Iterative Recoloring. - Ahmet Erdem Sariyüce; Erik Saule; Ümit V. Çatalyürek (CoRR, 2014)

Exploring the future of out-of-core computing with compute-local non-volatile memory. - Myoungsoo Jung; Ellis Herbert Wilson III; Wonil Choi; John Shalf; Hasan Metin Aktulga; Chao Yang 001; Erik Saule; Ümit V. Çatalyürek; Mahmut T. Kandemir (Sci. Program., 2014)

Diversifying Citation Recommendations. - Onur Küçüktunç; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (ACM Trans. Intell. Syst. Technol., 2014)

A Novel Multiple Choice Question Generation Strategy: Alternative Uses for Controlled Vocabulary Thesauri in Biomedical-Sciences Education. - Marcelo A. Lopetegui; Barbara A. Lara; Po-Yin Yen; Ümit V. Çatalyürek; Philip R. O. Payne (AMIA, 2015)

MICA: MicroRNA integration for active module discovery. - Ayat Hatem; Kamer Kaya; Jeffrey D. Parvin; Kun Huang 001; Ümit V. Çatalyürek (BCB, 2015)

Spaler: Spark and GraphX based de novo genome assembler. - Anas Abu-Doleh; Ümit V. Çatalyürek (IEEE BigData, 2015)

Fast and High Quality Topology-Aware Task Mapping. - Mehmet Deveci; Kamer Kaya; Bora Uçar; Ümit V. Çatalyürek (IPDPS, 2015)

Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application. - Daniel Janies; Zachary L. Witter; Christian Gibson; Thomas Kraft; Izzet F. Senturk; Ümit V. Çatalyürek (MedInfo, 2015)

Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions. - Ahmet Erdem Sariyüce; C. Seshadhri 001; Ali Pinar; Ümit V. Çatalyürek (WWW, 2015)

Mitigating bias in planning two-colour microarray experiments. - Nilgun Ferhatosmanoglu; Theodore T. Allen; Ümit V. Çatalyürek (Int. J. Data Min. Bioinform., 2015)

Hypergraph partitioning for multiple communication cost metrics: Model and methods. - Mehmet Deveci; Kamer Kaya; Bora Uçar; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2015)

Regularizing graph centrality computations. - Ahmet Erdem Sariyüce; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2015)

Incremental closeness centrality in distributed memory. - Ahmet Erdem Sariyüce; Erik Saule; Kamer Kaya; Ümit V. Çatalyürek (Parallel Comput., 2015)

An Out-of-Core Task-based Middleware for Data-Intensive Scientific Computing. - Erik Saule; Hasan Metin Aktulga; Chao Yang 001; Esmond G. Ng; Ümit V. Çatalyürek (Handbook on Data Centers, 2015)

Visual analytics on the spread of pathogens. - Julien Herrmann; Zachary L. Witter; Nakul Patel; Jonathan Kho; Daniel A. Janies; Ümit V. Çatalyürek (BCB, 2016)

Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei. - Tomás Dytrych; Pieter Maris; Kristina D. Launey; Jerry P. Draayer; James P. Vary; Daniel Langr; Erik Saule; Mark A. Caprio; Ümit V. Çatalyürek; Masha Sosonkina (Comput. Phys. Commun., 2016)

SONIC: streaming overlapping community detection. - Ahmet Erdem Sariyüce; Bugra Gedik; Gabriela Jacques-Silva; Kun-Lung Wu; Ümit V. Çatalyürek (Data Min. Knowl. Discov., 2016)

Multi-Jagged: A Scalable Parallel Spatial Partitioning Algorithm. - Mehmet Deveci; Sivasankaran Rajamanickam; Karen D. Devine; Ümit V. Çatalyürek (IEEE Trans. Parallel Distributed Syst., 2016)

Incremental k-core decomposition: algorithms and evaluation. - Ahmet Erdem Sariyüce; Bugra Gedik; Gabriela Jacques-Silva; Kun-Lung Wu; Ümit V. Çatalyürek (VLDB J., 2016)

Acyclic Partitioning of Large Directed Acyclic Graphs. - Julien Herrmann; Jonathan Kho; Bora Uçar; Kamer Kaya; Ümit V. Çatalyürek (CCGrid, 2017)

GABB Keynote. - Ümit V. Çatalyürek (IPDPS Workshops, 2017)

Active Betweenness Cardinality: Algorithms and Applications. - Yusuf Özkaya; Ahmet Erdem Sariyüce; Ümit V. Çatalyürek; Ali Pinar (CoRR, 2017)

Guest Editor's Introduction: Selected Papers from ACM-BCB 2014. - Ümit V. Çatalyürek (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Graph Manipulations for Fast Centrality Computation. - Ahmet Erdem Sariyüce; Kamer Kaya; Erik Saule; Ümit V. Çatalyürek (ACM Trans. Knowl. Discov. Data, 2017)

Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs. - Ahmet Erdem Sariyüce; C. Seshadhri 001; Ali Pinar; Ümit V. Çatalyürek (ACM Trans. Web, 2017)

Local Detection of Critical Nodes in Active Graphs. - M. Yusuf Özkaya; Ahmet Erdem Sanyuce; Ali Pinar; Ümit V. Çatalyürek (ASONAM, 2018)

SiNA: A Scalable Iterative Network Aligner. - Abdurrahman Yasar; Bora Uçar; Ümit V. Çatalyürek (ASONAM, 2018)

Efficient sparse-matrix multi-vector product on GPUs. - Changwan Hong; Aravind Sukumaran-Rajam; Bortik Bandyopadhyay; Jinsung Kim; Süreyya Emre Kurt; Israt Nisa; Shivani Sabhlok; Ümit V. Çatalyürek; Srinivasan Parthasarathy 001; P. Sadayappan (HPDC, 2018)

Fast Triangle Counting Using Cilk. - Abdurrahman Yasar; Sivasankaran Rajamanickam; Michael M. Wolf; Jonathan W. Berry; Ümit V. Çatalyürek (HPEC, 2018)

HCW 2018 Keynote Talk 2. - Ümit V. Çatalyürek (IPDPS Workshops, 2018)

An Iterative Global Structure-Assisted Labeled Network Aligner. - Abdurrahman Yasar; Ümit V. Çatalyürek (KDD, 2018)

Geometric Partitioning and Ordering Strategies for Task Mapping on Parallel Computers. - Mehmet Deveci; Karen D. Devine; Kevin T. Pedretti; Mark A. Taylor; Sivasankaran Rajamanickam; Ümit V. Çatalyürek (CoRR, 2018)

A resource provisioning framework for bioinformatics applications in multi-cloud environments. - Izzet F. Senturk; Ponnuraman Balakrishnan; Anas Abu-Doleh; Kamer Kaya; Qutaibah M. Malluhi; Ümit V. Çatalyürek (Future Gener. Comput. Syst., 2018)

DeepSparse: A Task-Parallel Framework for SparseSolvers on Deep Memory Architectures. - Md. Afibuzzaman; Fazlay Rabbi; M. Yusuf Özkaya; Hasan Metin Aktulga; Ümit V. Çatalyürek (HiPC, 2019)

Scalable Triangle Counting on Distributed-Memory Systems. - Seher Acer; Abdurrahman Yasar; Sivasankaran Rajamanickam; Michael M. Wolf; Ümit V. Çatalyürek (HPEC, 2019)

Linear Algebra-Based Triangle Counting via Fine-Grained Tasking on Heterogeneous Environments : (Update on Static Graph Challenge). - Abdurrahman Yasar; Sivasankaran Rajamanickam; Jonathan W. Berry; Michael M. Wolf; Jeffrey S. Young 001; Ümit V. Çatalyürek (HPEC, 2019)

Efficient and effective sparse tensor reordering. - Jiajia Li 001; Bora Uçar; Ümit V. Çatalyürek; Jimeng Sun 001; Kevin J. Barker; Richard W. Vuduc (ICS, 2019)

A Scalable Clustering-Based Task Scheduler for Homogeneous Processors Using DAG Partitioning. - M. Yusuf Özkaya; Anne Benoit; Bora Uçar; Julien Herrmann; Ümit V. Çatalyürek (IPDPS, 2019)

Improving Locality-Aware Scheduling with Acyclic Directed Graph Partitioning. - M. Yusuf Özkaya; Anne Benoit; Ümit V. Çatalyürek (PPAM (1), 2019)

Heuristics for Symmetric Rectilinear Matrix Partitioning. - Abdurrahman Yasar; Ümit V. Çatalyürek (CoRR, 2019)

Special issue: Selected papers from IPDPS'18. - Anne Benoit; Ümit V. Çatalyürek (J. Parallel Distributed Comput., 2019)

Multilevel Algorithms for Acyclic Partitioning of Directed Acyclic Graphs. - Julien Herrmann; M. Yusuf Özkaya; Bora Uçar; Kamer Kaya; Ümit V. Çatalyürek (SIAM J. Sci. Comput., 2019)

Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks. - Mehmet Deveci; Karen D. Devine; Kevin T. Pedretti; Mark A. Taylor; Sivasankaran Rajamanickam; Ümit V. Çatalyürek (IEEE Trans. Parallel Distributed Syst., 2019)

A scalable graph generation algorithm to sample over a given shell distribution. - M. Yusuf Özkaya; Muhammed Fatih Balin; Ali Pinar; Ümit V. Çatalyürek (IPDPS Workshops, 2020)

StrainHub: a phylogenetic tool to construct pathogen transmission networks. - Adriano de Bernardi Schneider; Colby T. Ford; Reilly Hostager; John Williams; Michael Cioce; Ümit V. Çatalyürek; Joel O. Wertheim; Daniel Janies (Bioinform., 2020)

On Symmetric Rectilinear Matrix Partitioning. - Abdurrahman Yasar; Muhammed Fatih Balin; Xiaojing An; Kaan Sancak; Ümit V. Çatalyürek (CoRR, 2020)

Programming Strategies for Irregular Algorithms on the Emu Chick. - Eric R. Hein; Srinivas Eswar; Abdurrahman Yasar; Jiajia Li 001; Jeffrey S. Young 001; Thomas M. Conte; Ümit V. Çatalyürek; Richard W. Vuduc; E. Jason Riedy; Bora Uçar (ACM Trans. Parallel Comput., 2020)

Parallel graph algorithms by blocks: from I/O to algorithms. - Abdurrahman Yasar; Kasimir Gabert; Ümit V. Çatalyürek (CF, 2021)

Column-Segmented Sparse Matrix-Matrix Multiplication on Multicore CPUs. - Xiaojing An; Ümit V. Çatalyürek (HiPC, 2021)

An Evaluation of Task-Parallel Frameworks for Sparse Solvers on Multicore and Manycore CPU Architectures. - Abdullah Alperen; Md. Afibuzzaman; Fazlay Rabbi; M. Yusuf Özkaya; Ümit V. Çatalyürek; Hasan Metin Aktulga (ICPP, 2021)

PIGO: A Parallel Graph Input/Output Library. - Kasimir Gabert; Ümit V. Çatalyürek (IPDPS Workshops, 2021)

Shared-Memory Scalable k-Core Maintenance on Dynamic Graphs and Hypergraphs. - Kasimir Gabert; Ali Pinar; Ümit V. Çatalyürek (IPDPS Workshops, 2021)

Implementing Performance Portable Graph Algorithms Using Task-Based Execution. - Ümit V. Çatalyürek (IA3@SC, 2021)

EIGA: elastic and scalable dynamic graph analysis. - Kasimir Gabert; Kaan Sancak; M. Yusuf Özkaya; Ali Pinar; Ümit V. Çatalyürek (SC, 2021)

A Unifying Framework to Identify Dense Subgraphs on Streams: Graph Nuclei to Hypergraph Cores. - Kasimir Gabert; Ali Pinar; Ümit V. Çatalyürek (WSDM, 2021)

Efficient Hierarchical State Vector Simulation of Quantum Circuits via Acyclic Graph Partitioning. - Bo Fang 002; M. Yusuf Özkaya; Ang Li 006; Ümit V. Çatalyürek; Sriram Krishnamoorthy (CLUSTER, 2022)

Batch dynamic algorithm to find k-core hierarchies. - Kasimir Gabert; Ali Pinar; Ümit V. Çatalyürek (GRADES-NDA@SIGMOD, 2022)

A Portable Sparse Solver Framework for Large Matrices on Heterogeneous Architectures. - Fazlay Rabbi; Christopher S. Daley; Ümit V. Çatalyürek; Hasan Metin Aktulga (HIPC, 2022)

MG-GCN: A Scalable multi-GPU GCN Training Framework. - Muhammed Fatih Balin; Kaan Sancak; Ümit V. Çatalyürek (ICPP, 2022)

FIST-HOSVD: fused in-place sequentially truncated higher order singular value decomposition. - Benjamin Cobb; Hemanth Kolla; Eric T. Phipps; Ümit V. Çatalyürek (PASC, 2022)

Batch Dynamic Algorithm to Find k-Cores and Hierarchies. - Kasimir Gabert; Ali Pinar; Ümit V. Çatalyürek (CoRR, 2022)

A Simple and Elegant Mathematical Formulation for the Acyclic DAG Partitioning Problem. - M. Yusuf Özkaya; Ümit V. Çatalyürek (CoRR, 2022)

PGAbB: A Block-Based Graph Processing Framework for Heterogeneous Platforms. - Abdurrahman Yasar; Sivasankaran Rajamanickam; Jonathan W. Berry; Ümit V. Çatalyürek (CoRR, 2022)

(LA)yer-neigh(BOR) Sampling: Defusing Neighborhood Explosion in GNNs. - Muhammed Fatih Balin; Ümit V. Çatalyürek (CoRR, 2022)

On Symmetric Rectilinear Partitioning. - Abdurrahman Yasar; Muhammed Fatih Balin; Xiaojing An; Kaan Sancak; Ümit V. Çatalyürek (ACM J. Exp. Algorithmics, 2022)

A Block-Based Triangle Counting Algorithm on Heterogeneous Environments. - Abdurrahman Yasar; Sivasankaran Rajamanickam; Jonathan W. Berry; Ümit V. Çatalyürek (IEEE Trans. Parallel Distributed Syst., 2022)

Optimizing Irregular Dense Operators of Heterogeneous GNN Models on GPU. - Israt Nisa; Minjie Wang; Da Zheng; Qiang Fu; Ümit V. Çatalyürek; George Karypis (IPDPS Workshops, 2023)

Layer-Neighbor Sampling - Defusing Neighborhood Explosion in GNNs. - Muhammed Fatih Balin; Ümit V. Çatalyürek (NeurIPS, 2023)

SGORP: A Subgradient-based Method for d-Dimensional Rectilinear Partitioning. - Muhammed Fatih Balin; Xiaojing An; Abdurrahman Yasar; Ümit V. Çatalyürek (CoRR, 2023)

Open Problems in (Hyper)Graph Decomposition. - Deepak Ajwani; Rob H. Bisseling; Katrin Casel; Ümit V. Çatalyürek; Cédric Chevalier; Florian Chudigiewitsch; Marcelo Fonseca Faraj; Michael R. Fellows; Lars Gottesbüren; Tobias Heuer; George Karypis; Kamer Kaya; et al. (CoRR, 2023)

Recent Trends in Graph Decomposition (Dagstuhl Seminar 23331). - George Karypis; Christian Schulz 003; Darren Strash; Deepak Ajwani; Rob H. Bisseling; Katrin Casel; Ümit V. Çatalyürek; Cédric Chevalier; Florian Chudigiewitsch; Marcelo Fonseca Faraj; Michael R. Fellows; Lars Gottesbüren; et al. (Dagstuhl Reports, 2023)

More Recent Advances in (Hyper)Graph Partitioning. - Ümit V. Çatalyürek; Karen D. Devine; Marcelo Fonseca Faraj; Lars Gottesbüren; Tobias Heuer; Henning Meyerhenke; Peter Sanders 001; Sebastian Schlag; Christian Schulz 003; Daniel Seemaier; Dorothea Wagner (ACM Comput. Surv., 2023)

Do We Really Need Complicated Graph Learning Models? - A Simple but Effective Baseline. - Kaan Sancak; Muhammed Fatih Balin; Ümit V. Çatalyürek (LoG, 2024)

A Scalable and Effective Alternative to Graph Transformers. - Kaan Sancak; Zhigang Hua; Jin Fang; Yan Xie; Andrey Malevich; Bo Long; Muhammed Fatih Balin; Ümit V. Çatalyürek (AAAI, 2025)

Cooperative Minibatching in Graph Neural Networks. - Muhammed Fatih Balin; Dominique LaSalle; Ümit V. Çatalyürek (Trans. Mach. Learn. Res., 2025)