Journal/Book Conference Report Abstract/Poster |
@article { Hein20-TOPC,
title = { Programming strategies for irregular algorithms on the {E}mu {C}hick },
author = { Eric Hein and Srinivas Eswar and Abdurrahman Ya{\c{s}}ar and Jiajia Li and Jeffrey S Young and Thomas M Conte and {\"U}mit V {\c{C}}ataly{\"u}rek and Rich Vuduc and Jason Riedy and Bora U{\c{c}}ar },
journal = { ACM Transactions on Parallel Computing (TOPC) },
year = { 2020 },
}
@inproceedings { Ozkaya20-GrAPL,
author = { M. Yusuf {\"O}zkaya and M. Fatih Bal{\i}n and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 2020 IEEE International Parallel and Distributed Processing Symposium Workshops (GrAPL) },
title = { A scalable graph generation algorithm to sample over a given shell distribution },
year = { 2020 },
}
@article { Wang19-BMCGenomics,
title = { The transcriptome of the rumen ciliate Entodinium caudatum reveals some of its metabolic features },
author = { Lingling Wang and Anas Abu-Doleh and Johanna Plank and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Jeffrey Firkins and Zhongtang Yu },
journal = { BMC Genomics },
year = { 2019 },
}
@inproceedings { Afibuzzaman19-HiPC,
author = { Md Afibuzzaman and Fazlay Rabbi and M. Yusuf \"Ozkaya and Hasan Metin Aktulga and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { DeepSparse: A Task-parallel Framework for Sparse Solvers on Deep Memory Architectures },
booktitle = { Proceedings of the 26th Annual International Conference on High Performance Computing (HiPC 2019) },
month = { Dec },
year = { 2019 },
}
@inproceedings { Yasar19-HPEC,
title = { Linear Algebra-Based Triangle Counting via Fine-Grained Tasking on Heterogeneous Environments },
author = { Abdurrahman Ya{\c{s}}ar and Sivasankaran Rajamanickam and Jonathan W. Berry and Michael M. Wolf and Jeffrey Young and {\"U}mit V. {\c{C}}ataly{\"u}rek },
booktitle = { IEEE High Performance Extreme Computing Conference (HPEC) },
year = { 2019 },
optnote = { One of the Graph Challenge Innovation Award winners. },
}
@techreport { Yasar19-ARXIV,
title = { Heuristics for Symmetric Rectilinear Matrix Partitioning },
author = { Abdurrahman Ya{\c{s}}ar and, {\"U}mit V. {\c{C}}ataly{\"u}rek },
year = { 2019 },
institution = { ArXiv },
month = { Oct },
number = { arXiv:1909.12209 },
link = { https://arxiv.org/abs/1909.12209 },
}
@inproceedings { Acer19-HPEC,
title = { Scalable Triangle Counting on Distributed-Memory Systems },
author = { Seher Acer and Abdurrahman Ya{\c{s}}ar and Sivasankaran Rajamanickam and Michael M. Wolf and {\"U}mit V. {\c{C}}ataly{\"u}rek },
booktitle = { High Performance Extreme Computing Conference (HPEC), 2019 IEEE },
year = { 2019 },
optnote = { One of the Graph Challenge Innovation Award winners. },
organization = { IEEE },
}
@article { Scheider19-BIONF,
author = { Adriano de Bernardi Schneider and Colby T Ford and Reilly Hostager and John Williams and Michael Cioce and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel O. Wertheim and Daniel Janies },
title = { StrainHub: A phylogenetic tool to construct pathogen transmission networks },
journal = { Bioinformatics },
year = { 2019 },
month = { 08 },
abstract = { In exploring the epidemiology of infectious diseases, networks have been used to reconstruct contacts among individuals and/or populations. Summarizing networks using pathogen metadata (e.g., host species and place of isolation) and a phylogenetic tree is a nascent, alternative approach. In this paper, we introduce a tool for reconstructing transmission networks in arbitrary space from phylogenetic information and metadata. Our goals are to provide a means of deriving new insights and infection control strategies based on the dynamics of the pathogen lineages derived from networks and centrality metrics. We created a web-based application, called StrainHub, in which a user can input a phylogenetic tree based on genetic or other data along with characters derived from metadata using their preferred tree search method. StrainHub generates a transmission network based on character state changes in metadata, such as place or source of isolation, mapped on the phylogenetic tree. The user has the option to calculate centrality metrics on the nodes including betweenness, closeness, degree, and a new metric, the source/hub ratio. The outputs include the network with values for metrics on its nodes and the tree with characters reconstructed. All of these results can be exported for further analysis.strainhub.io and https://github.com/abschneider/StrainHub },
issn = { 1367-4803 },
doi = { 10.1093/bioinformatics/btz646 },
link = { https://doi.org/10.1093/bioinformatics/btz646 },
opteprint = { http://oup.prod.sis.lan/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz646/29171171/btz646.pdf },
}
@article { Deveci19-TPDS,
author = { Mehmet Deveci and Karen D. Devine and Kevin Pedretti and Mark A. Taylor and Sivasankaran Rajamanickam and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks },
journal = { IEEE Transactions on Parallel and Distributed Systems },
year = { 2019 },
volume = { 30 },
number = { 9 },
pages = { 2018-2032 },
doi = { 10.1109/TPDS.2019.2900043 },
link = { https://doi.org/10.1109/TPDS.2019.2900043 },
}
@article { Herrmann19-SISC,
author = { Julien Herrmann and M. Yusuf {\"O}zkaya and Bora U{\c{c}}ar and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { Multilevel Algorithms for Acyclic Partitioning of Directed Acyclic Graphs },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
keyword = { directed graph ; acyclic partitioning ; multilevel partitioning },
year = { 2019 },
volume = { 41 },
number = { 4 },
pages = { A2117-A2145 },
doi = { 10.1137/18M1176865 },
link = { https://doi.org/10.1137/18M1176865 },
}
@inproceedings { Ozkaya19-PPAM,
author = { M. Yusuf {\"O}zkaya and Anne Benoit and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { Improving Locality-Aware Scheduling with Acyclic Directed Graph Partitioning },
booktitle = { Proc. of the 13th International Conf. on Parallel Processing and Applied Mathematics (PPAM) },
month = { Sep },
pages = { 211--223 },
year = { 2019 },
organization = { Springer },
}
@inproceedings { Li19-ICS,
author = { Jiajia Li and Bora U\c{c}ar and \"{U}mit V. \c{C}ataly\"{u}rek and Jimeng Sun and Kevin Barker and Richard Vuduc },
title = { Efficient and Effective Sparse Tensor Reordering },
booktitle = { Proceedings of the ACM International Conference on Supercomputing (ICS) },
series = { ICS \'19 },
year = { 2019 },
isbn = { 978-1-4503-6079-1 },
location = { Phoenix, Arizona },
pages = { 227--237 },
numpages = { 11 },
link = { http://doi.acm.org/10.1145/3330345.3330366 },
doi = { 10.1145/3330345.3330366 },
acmid = { 3330366 },
publisher = { ACM },
address = { New York, NY, USA },
keyword = { HiCOO, hierarchical coordinate, reordering, sparse tensor, tensor decomposition },
}
@inproceedings { Ozkaya19-IPDPS,
author = { M. Yusuf \"Ozkaya and Anne Benoit and Bora U{\c{c}}ar and Julien Herrmann and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { A scalable clustering-based task scheduler for homogeneous processors using DAG partitioning },
booktitle = { 2019 IEEE International Parallel and Distributed Processing Symposium (IPDPS) },
pages = { 155--165 },
year = { 2019 },
organization = { IEEE },
}
@inproceedings { Yasar18-HPEC,
title = { Fast Triangle Counting Using Cilk },
author = { Abdurrahman Ya{\c{s}}ar and Sivasankaran Rajamanickam and Michael M. Wolf and Jonathan W. Berry and {\"U}mit V. {\c{C}}ataly{\"u}rek },
booktitle = { High Performance Extreme Computing Conference (HPEC), 2018 IEEE },
pages = { 1--7 },
year = { 2018 },
link = { http://ieeexplore.ieee.org/document/8547563 },
organization = { IEEE },
optnote = { One of the Graph Challenge Champions. },
}
@inproceedings { Yasar18-ASONAM,
author = { Abdurrahman Ya{\c{s}}ar and Bora U{\c{c}}ar and {\"U}mit V. {\c{C}}ataly{\"u}rek },
title = { SiNA: A Scalable Iterative Network Aligner },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
month = { Aug },
year = { 2018 },
}
@inproceedings { Ozkaya18-ASONAM,
author = { M. Yusuf {\"O}zkaya and Ahmet Erdem Sar{\i}y{\"{u}}ce and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { Local Detection of Critical Nodes in Active Networks },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
month = { Aug },
year = { 2018 },
optnote = { Extended version is available at {ArXiv}. },
}
@inproceedings { Yasar2018-KDD,
author = { Abdurrahman Ya{\c{s}}ar and {\"U}mit V. {\c{C}}ataly{\"u}rek },
title = { An Iterative Global Structure-Assisted Labeled Network Aligner },
booktitle = { Proceedings of the 24th ACM SIGKDD International Conference on\nKnowledge Discovery and Data Mining },
month = { Aug },
year = { 2018 },
link = { http://www.kdd.org/kdd2018/accepted-papers/view/an-iterative-global-structure-assisted-labeled-network-aligner },
optnote = { Also available as a Tech Rep on {ArXiv}. },
}
@inproceedings { Hong18-HPDC,
author = { Changwan Hong and Aravind Sukumaran-Rajam and Bortik Bandyopadhyay and Jinsung Kim\nand S\"{u}reyya Emre Kurt and Israt Nisa and Shivani Sabhlok and\n{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Srinivasan Parthasarathy and\nP. Sadayappan },
title = { Efficient Sparse-Matrix Multi-Vector Product on GPUs },
booktitle = { Proc. 27th International Symposium on High-Performance Parallel and Distributed Computing (HPDC) },
month = { June },
year = { 2018 },
link = { https://dl.acm.org/citation.cfm?id=3208062 },
}
@article { Senturk18-FGCS,
author = { Izzet F. Senturk and P.Balakrishnan and Anas Abu-Doleh and Kamer Kaya and Qutaibah Malluhi and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
title = { A Resource Provisioning Framework for Bioinformatics Applications in Multi-Cloud Environments },
journal = { The Future Generation Computer Systems Journal },
link = { http://dx.doi.org/10.1016/j.future.2016.06.008 },
year = { 2018 },
volume = { 78 },
number = { 1 },
month = { Jan },
}
@techreport { Herrmann18-HAL,
title = { Acyclic partitioning of large directed acyclic graphs },
author = { Julien Herrmann and M. Yusuf {\"O}zkaya and Bora U{\c c}ar and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
link = { https://hal.inria.fr/hal-01744603 },
type = { Research Report },
number = { RR-9163 },
institution = { Inria - Research Centre Grenoble -- Rh{\^o}ne-Alpes },
year = { 2018 },
month = { Mar },
keyword = { directed graph ; acyclic partitioning ; multilevel partitioning ; partitionnement acyclic ; partitionnement multiniveau ; graphes orient{\\'e}s },
pdf = { https://hal.inria.fr/hal-01744603/file/RR-9163.pdf },
}
@techreport { Ozkaya17-arXiv,
title = { Active Betweenness Cardinality: Algorithms and Applications },
institution = { ArXiv },
author = { M. Yusuf {\"O}zkaya and Ahmet Erdem Sar{\i}y{\"{u}}ce and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Ali P{\i}nar },
year = { 2017 },
month = { Nov },
number = { arXiv:1711.10634 },
link = { http://arxiv.org/abs/1711.10634 },
}
@inproceedings { Herrmann17-CCGrid,
title = { Acyclic Partitioning of Large-Scale Directed Acyclic Graphs },
author = { Julien Herrmann and Jonathan Kho and Bora U{\c{c}}ar and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of the 17th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid) },
month = { May },
year = { 2017 },
}
@article { Sariyuce17-TKDD,
title = { Graph Manipulations for Fast Centrality Computation },
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { ACM Transactions on Knowledge Discovery from Data },
link = { http://doi.acm.org/10.1145/3022668 },
month = { Apr },
number = { 3 },
optdoi = { 10.1145/3022668 },
pages = { 26:1--26:25 },
volume = { 11 },
year = { 2017 },
}
@article { Sariyuce17-TWEB,
title = { Nucleus Decompositions for Identifying Hierarchy of Dense Subgraphs },
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and C. Seshadhri and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { ACM Transactions on the Web },
month = { Jul },
volume = { 11 },
number = { 3 },
optdoi = { 10.1145/3022668 },
pages = { 26:1--26:25 },
link = { https://dl.acm.org/citation.cfm?id=3057742 },
year = { 2017 },
}
@inproceedings { Johnson16-ISCB,
author = { Travis Johnson and Jonathan Kho and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kun Huang and Yan Zhang },
booktitle = { Poster, journalF1000Research (ISCB Comm J) (ISMB\'16) },
link = { http://dx.doi.org/10.7490/f1000research.1112733.1 },
month = { Jul },
title = { Identification of key mutation signatures from conservation analysis of gene-pseudogene families in human },
year = { 2016 },
}
@article { Hoffmann16-JID,
author = { Maria Hoffmann and Yan Luo and Steven R. Monday and Narjol Gonzales-Escalona and Andrea R. Ottesen and Tim Muruvanda and Charles Wang and George Kastanis and Christine Keys and Daniel Janies and Izzet F. Senturk and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Hua Wang and Thomas S. Hammack and William J. Wolfgang and Dianna Schoonmaker-Bopp and Alvina Chu and Robert Myers and Julie Haendiges and Peter S. Evans and Jianghong Meng and Errol A. Strain and Marc W. Allard and Eric W. Brown },
doi = { 10.1093/infdis/jiv297 },
journal = { Journal of Infectious Diseases },
link = { http://jid.oxfordjournals.org/content/213/4/502.abstract },
month = { Apr },
number = { 4 },
pages = { 502-508 },
title = { Tracing Origins of the Salmonella Bareilly strain causing a Foodborne Outbreak in the United States },
volume = { 213 },
year = { 2016 },
}
@article { Deveci16-TPDS,
author = { Mehmet Deveci and Sivasankaran Rajamanickam and Karen D. Devine and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { IEEE Transactions on Parallel and Distributed Systems },
link = { http://dx.doi.org/10.1109/TPDS.2015.2412545 },
month = { Mar },
number = { 3 },
pages = { 803-817 },
title = { Multi-jagged: A Scalable Parallel Spatial Partitioning Algorithm },
volume = { 27 },
year = { 2016 },
}
@article { Sariyuce16-DAMI,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Data Mining and Knowledge Discovery (DAMI) },
link = { http://dx.doi.org/10.1007/s10618-015-0440-z },
number = { 4 },
pages = { 819--847 },
title = { SONIC: Streaming Overlapping Community Detection },
volume = { 30 },
year = { 2016 },
}
@article { Sariyuce16-VLDBJ,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { The VLDB Journal },
link = { http://link.springer.com/article/10.1007/s00778-016-0423-8 },
number = { 3 },
pages = { 425--447 },
title = { Incremental k-core Decomposition: Algorithms and Evaluation },
volume = { 25 },
year = { 2016 },
}
@article { Dytrych16-CRC,
author = { T. Dytrych and P. Maris and K. D. Launey and J. P. Draayer and James P. Vary and D. Langr and Erik Saule and M. A. Caprio and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and M. Sosonkina },
journal = { Computer Physics Communications },
link = { http://www.sciencedirect.com/science/article/pii/S0010465516301680 },
pages = { 202 - 210 },
title = { Efficacy of the SU(3) scheme for ab initio large-scale calculations beyond the lightest nuclei },
volume = { 207 },
year = { 2016 },
}
@phdthesis { AbuDoleh16-PhD,
author = { Anas Abu-Doleh },
institution = { The Ohio State University, Electrical and Computer Engineering },
key = { AbuDoleh16-PhD },
month = { May },
title = { High Performance and Scalable Matching and Assembly of Biological Sequences },
year = { 2016 },
}
@phdthesis { Sariyuce15-PhD,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce },
institution = { The Ohio State University, Computer Science and Engineering },
key = { Sariyuce15-PhD },
month = { May },
title = { Fast Algorithms for Large-Scale Network Analytics },
year = { 2015 },
}
@phdthesis { Deveci15-PhD,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce },
institution = { The Ohio State University, Computer Science and Engineering },
key = { Deveci15-PhD },
month = { May },
title = { Load-Balancing and Task Mapping for Exascale Systems },
year = { 2015 },
}
@article { Janies15-Cladistics,
author = { Daniel A. Janies and Laura W. Pomeroy and Chris Krueger and Yuqi Zhang and Izzet F. Senturk and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Cladistics },
link = { http://onlinelibrary.wiley.com/doi/10.1111/cla.12107/abstract },
month = { Dec },
number = { 6 },
pages = { 679--691 },
title = { Phylogenetic visualization of the spread of H7 influenza A viruses },
volume = { 31 },
year = { 2015 },
}
@inproceedings { AbuDoleh15-BigData,
author = { Anas Abu-Doleh and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc of IEEE Int\'l Conference on BigData },
month = { Oct },
title = { Spaler: Spark and GraphX based de novo genome assembler },
year = { 2015 },
}
@inproceedings { Hatem15-BCB,
author = { Ayat Hatem and Kamer Kaya and Jeffrey D. Parvin and Kun Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 6th ACM Conference on Bioinformatics, Computational Biology and Health Informatics (ACM-BCB) },
month = { Sep },
title = { {MICA: MicroRNA} Integration for Active Module Discovery },
year = { 2015 },
}
@article { Sariyuce15-ParCo,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Parallel Computing },
link = { http://authors.elsevier.com/sd/article/S0167819115000101 },
month = { Aug },
pages = { 3-18 },
title = { Incremental Closeness Centrality in Distributed Memory },
volume = { 47 },
year = { 2015 },
}
@inproceedings { Janies15-MEDINFO,
author = { Daniel Janies and Zachary Witter and Christian Gibson and Thomas Kraft and Izzet F. Senturk and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { MEDINFO\'15 },
month = { Aug },
title = { Syndromic Surveillance of Infectious Diseases meets Molecular Epidemiology in a Workflow and Phylogeographic Application },
year = { 2015 },
}
@inproceedings { Sariyuce15-WWW,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and C. Seshadhri and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 24th International World Wide Web Conference (WWW) },
month = { May },
optnote = { Also available as a Tech Rep on {ArXiv}. Best Paper Award Nominee. },
note = { Best Paper Award Nominee. },
title = { Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions },
year = { 2015 },
}
@inproceedings { Deveci15-IPDPS,
author = { Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 29th IEEE International Parallel and Distributed Processing Symposium },
month = { May },
title = { Fast and High Quality Topology-Aware Task Mapping },
year = { 2015 },
}
@article { Deveci15-JPDC,
author = { Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
doi = { http://dx.doi.org/10.1016/j.jpdc.2014.12.002 },
journal = { Journal of Parallel and Distributed Computing },
link = { http://www.sciencedirect.com/science/article/pii/S0743731514002275 },
month = { Mar },
pages = { 69-83 },
title = { Hypergraph partitioning for multiple communication cost metrics: Model and methods },
volume = { 77 },
year = { 2015 },
}
@article { Sariyuce15-JPDC,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Journal of Parallel and Distributed Computing },
link = { http://www.sciencedirect.com/science/article/pii/S0743731514001282 },
month = { Feb },
pages = { 106-119 },
title = { Regularizing Graph Centrality Computations },
volume = { 76 },
year = { 2015 },
}
@incollection { Saule15-HDC,
author = { Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Handbook on Data Centers },
doi = { 10.1007/978-1-4939-2092-1 },
editor = { Samee U. Khan and Albert Y. Zomoya },
link = { http://link.springer.com/book/10.1007%2F978-1-4939-2092-1 },
isbn = { ISBN 978-1-4939-2091-4 },
pages = { 647--667 },
publisher = { Springer },
title = { An Out-of-Core Task-based Middleware for Data-Intensive Scientific Computing },
year = { 2015 },
}
@article { Gerber15-IJC,
author = { Madelyn M. Gerber and Heather Hampel and Xiao-Ping Zhou and Nathan P. Schulz and Adam Suhy and Mehmet Deveci and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Amanda E. Toland },
doi = { 10.1002/ijc.29599 },
journal = { International Journal of Cancer },
link = { http://dx.doi.org/10.1002/ijc.29599 },
number = { 10 },
pages = { 2323--2331 },
title = { Allele-specific imbalance mapping at human orthologs of mouse susceptibility to colon cancer (Scc) loci },
volume = { 137 },
year = { 2015 },
}
@article { Ferhatosmanoglu15-IJDMB,
author = { Nilgun Ferhatosmanoglu and Theodore T. Allen and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { International Journal of Data Mining and Bioinformatics },
number = { 1 },
pages = { 31-49 },
title = { Mitigating Bias in Planning Two-Color Microarray Experiments },
volume = { 13 },
year = { 2015 },
}
@incollection { Deveci15-MiMB,
author = { Mehmet Deveci and Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Kemal Eren and and Doruk Bozda{\u{g}} and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Methods in Molecular Biology },
doi = { 10.1007/7651_2015_246 },
editor = { P.H. Guzzi },
link = { http://dx.doi.org/10.1007/7651_2015_246 },
publisher = { Springer },
title = { Querying Co-regulated Genes on Diverse Gene Expression Datasets Via Biclustering },
year = { 2015 },
}
@phdthesis { Hatem14-PhD,
author = { Ayat Hatem },
institution = { The Ohio State University, Electrical and Computer Engineering },
key = { Hatem14-PhD },
month = { May },
title = { Active Module Discovery: Integrated Approaches of Gene Co-Expression and PPI Networks and MicroRNA Data },
year = { 2014 },
}
@article { Kucuktunc14-ACMTIST,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { {ACM} Transactions on Intelligent Systems and Technology },
month = { Dec },
number = { 4 },
pages = { 55:1-55:21 },
title = { Diversifying Citation Recommendations },
volume = { 5 },
year = { 2014 },
link = { https://doi.org/10.1145/2668106 },
}
@techreport { Sariyuce14-ARXIV-Nucleus,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and C. Seshadhri and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1411.3312 },
month = { Nov },
number = { arXiv:1411.3312 },
title = { Finding the Hierarchy of Dense Subgraphs using Nucleus Decompositions },
year = { 2014 },
}
@techreport { Sariyuce14-ARXIV,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1407.6745 },
month = { Jul },
number = { arXiv:1407.6745 },
title = { On Distributed Graph Coloring with Iterative Recoloring },
year = { 2014 },
}
@inproceedings { Sariyuce14-NS,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Poster, SIAM Workshop on Network Science (NS14) },
month = { July },
title = { Computing the Closeness Centrality of Evolving Networks on Clusters },
year = { 2014 },
}
@inproceedings { Deveci14-CSC,
address = { Lyon, France },
author = { Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, The Sixth SIAM Workshop on Combinatorial Scientific Computing (CSC14) },
month = { July },
title = { Partitioning Hypergraphs for Multiple Communication Metrics },
year = { 2014 },
}
@inproceedings { Sariyuce14-MTAAP,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP) },
month = { May },
title = { Hardware/Software Vectorization for Closeness Centrality on Multi-/Many-Core Architectures },
year = { 2014 },
}
@inproceedings { Dufosse14-IPDPS,
author = { Fanny Dufoss\\'{e} and Kamer Kaya and Bora U{\c{c}}ar },
booktitle = { 28th IEEE International Parallel and Distributed Processing Symposium },
month = { May },
title = { Randomized matching heuristics with quality guarantees on shared memory parallel computers },
year = { 2014 },
}
@inproceedings { Deveci14-IPDPS,
author = { Mehmet Deveci and Sivasankaran Rajamanickam and Vitus Leung and Kevin T Pedretti and Stephen L Olivier and David P. Bunde and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Karen D. Devine },
booktitle = { 28th IEEE International Parallel and Distributed Processing Symposium },
month = { May },
title = { Exploiting Geometric Partitioning in Task Mapping for Parallel Computers },
year = { 2014 },
}
@inproceedings { Deveci14-PHDFORUM-IPDPS,
author = { Mehmet Deveci and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Poster, 28th IEEE International Parallel and Distributed Processing Symposium, PHD Forum },
month = { May },
note = { PhD Forum award },
title = { Load Balancing and Task Mapping for Exascale Systems },
year = { 2014 },
}
@inproceedings { AbuDoleh14-MTAAP,
author = { Anas Abu-Doleh and Kamer Kaya and Mohamed Abouelhoda and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 28th International Parallel and Distributed Processing Symposium Workshops, Workshop on Multithreaded Architectures and Applications (MTAAP) },
month = { May },
title = { Extracting Maximal Exact Matches on {GPU} },
year = { 2014 },
}
@article { Katian14-CBT,
author = { Shweta Kotian and Tapahsama Banerjee and Ainsley Lockhart and Kun Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Jeffrey D. Parvin },
doi = { 10.4161/cbt.28019 },
journal = { Cancer Biology and Therapy },
link = { https://www.landesbioscience.com/journals/cbt/article/28019/ },
month = { Feb },
number = { 5 },
pages = { 533-543 },
title = { NUSAP1 influences the DNA damage response by controlling BRCA1 protein levels },
volume = { 15 },
year = { 2014 },
}
@inproceedings { Calyam14,
author = { P. Calyam and A. Berryman and Erik Saule and H. Subramoni and P. Schopis and G. Springer and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Dhabaleswar K. Panda },
booktitle = { Computing, Networking and Communications (ICNC), 2014 International Conference on },
doi = { 10.1109/ICCNC.2014.6785344 },
month = { Feb },
pages = { 269-275 },
title = { Wide-area overlay networking to manage science DMZ accelerated flows },
year = { 2014 },
}
@incollection { Kaya14-BKDH,
author = { Kamer Kaya and Ayat Hatem and Hatice G{\"{u}}l{\c{c}}in {\"{O}}zer and Kun Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Biological Knowledge Discovery Handbook },
editor = { Mourad Elloumi and Albert Y. Zomaya },
publisher = { John Wiley \& Sons },
title = { High-Performance Computing in High-Throughput Sequencing },
year = { 2014 },
}
@article { Jung14-SP,
author = { Myoungsoo Jung and Ellis H. Wilson III and Wonil Choi and John Shalf and Hasan M. Aktulga and Chao Yang and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mahmut Kandemir },
doi = { 10.3233/SPR-140384 },
journal = { Scientific Programming },
link = { http://iospress.metapress.com/content/t5805w1557614624/ },
number = { 2 },
pages = { 125-139 },
title = { Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory },
volume = { 22 },
year = { 2014 },
}
@article { Deveci14-BMC,
author = { Mehmet Deveci and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Amanda E. Toland },
doi = { 10.1186/1471-2105-15-73 },
journal = { BMC Bioinformatics },
link = { http://www.biomedcentral.com/1471-2105/15/73 },
pages = { 73 },
title = { {mrSNP}: Software to detect {SNP} effects on {microRNA} binding },
volume = { 15 },
year = { 2014 },
}
@article { Bokhari14,
author = { Shahid H. Bokhari and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Metin N. G{\"{u}}rcan },
doi = { 10.1002/cpe.3181 },
journal = { Concurrency and Computation: Practice and Experience },
link = { http://dx.doi.org/10.1002/cpe.3181 },
note = { Also available as a {}technical report from Algopath LLC. },
number = { 18 },
pages = { 2836-2855 },
title = { Massively Multithreaded Maxflow for Image Segmentation on the Cray {XMT-2} },
volume = { 26 },
year = { 2014 },
}
@phdthesis { Kucuktunc13-PhD,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} },
institution = { The Ohio State University, Computer Science and Engineering },
key = { Kucuktunc13-PhD },
month = { May },
title = { Result Diversification on Spatial, Multidimensional, Opinion, and Bibliographic Data },
year = { 2013 },
}
@article { Dytrych13-PRL,
author = { T. Dytrych and K. D. Launey and J. P. Draayer and P. Maris and James P. Vary and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and M. Sosonkina and D. Langr and M. A. Caprio },
doi = { 10.1103/PhysRevLett.111.252501 },
journal = { Physical Review Letters },
link = { http://link.aps.org/doi/10.1103/PhysRevLett.111.252501 },
month = { Dec },
number = { 25 },
pages = { 252501 },
title = { Collective Modes in Light Nuclei from First Principles },
volume = { 111 },
year = { 2013 },
}
@article { Wang13-PloSONE,
title = { Metagenomic Insights into the Carbohydrate-Active Enzymes Carried by the Microorganisms Adhering to Solid Digesta in the Rumen of Cows },
author = { Lingling Wang and Ayat Hatem and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mark Morrison and Zhongtang Yu },
doi = { 10.1371/journal.pone.0078507 },
journal = { PLoS ONE },
link = { http://dx.doi.org/10.1371%2Fjournal.pone.0078507 },
month = { Nov },
number = { 11 },
pages = { e78507 },
publisher = { Public Library of Science },
volume = { 8 },
year = { 2013 },
}
@inproceedings { Jung13-SC,
author = { Myoungsoo Jung and Ellis H. Wilson III and Wonil Choi and John Shalf and Hasan M. Aktulga and Chao Yang and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mahmut Kandemir },
booktitle = { Proc. of Conference on High Performance Computing Networking, Storage and Analysis (SC \'13) },
month = { Nov },
title = { Exploring the Future of Out-Of-Core Computing with Compute-Local Non-Volatile Memory },
year = { 2013 },
}
@inproceedings { Sariyuce13-BigData,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc of IEEE Int\'l Conference on BigData },
month = { Oct },
title = { Incremental Algorithms for Closeness Centrality },
year = { 2013 },
}
@inproceedings { deveci13-icpp-matching,
author = { Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 42nd Int\'l. Conf. on Parallel Processing },
month = { Oct },
title = { A Push-Relabel-based Maximum Cardinality Bipartite Matching Algorithm on {GPU}s },
year = { 2013 },
}
@inproceedings { deveci13-icpp-sparsification,
author = { Mehmet Deveci and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 42nd Int\'l. Conf. on Parallel Processing },
month = { Oct },
title = { Hypergraph Sparsification and Its Application to Partitioning },
year = { 2013 },
}
@inproceedings { Saule13-PPAM,
author = { Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of the 10th Int\'l Conf. on Parallel Processing and Applied Mathematics (PPAM) },
month = { Sep },
title = { Performance Evaluation of Sparse Matrix Multiplication Kernels on {I}ntel {X}eon {P}hi },
year = { 2013 },
}
@inproceedings { Sariyuce13-Cluster,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of IEEE Cluster 2013 },
month = { Sep },
title = { {STREAMER}: a Distributed Framework for Incremental Closeness Centrality Computation },
year = { 2013 },
}
@inproceedings { Kaya13-PPAM,
author = { Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of the 10th Int\'l Conf. on Parallel Processing and Applied Mathematics (PPAM) },
month = { Sep },
title = { Analysis of Partitioning Models and Metrics in Parallel Sparse Matrix-Vector Multiplication },
year = { 2013 },
}
@inproceedings { Hatem13-BCB,
author = { Ayat Hatem and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB) },
month = { Sep },
title = { {PRASE}: PageRank-based Active Subnetwork Extraction },
year = { 2013 },
}
@inproceedings { AbuDoleh13-BCB,
author = { Anas Abu-Doleh and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of ACM Conference on Bioinformatics, Computational Biology and Biomedical Informatics (BCB) },
month = { Sep },
title = { Masher: Mapping Long(er) Reads with Hash-based Genome Indexing on {GPU}s },
year = { 2013 },
}
@inproceedings { Sariyuce13-VLDB,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Bugra Gedik and Gabriela Jacques-Silva and Kun-Lung Wu and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 39th International Conference on Very Large Data Bases (VLDB) },
month = { Aug },
title = { Streaming Algorithms for k-core Decomposition },
year = { 2013 },
}
@inproceedings { Kucuktunc13-ASONAM,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
month = { Aug },
title = { Towards a Personalized, Scalable, and Exploratory Academic Recommendation Service },
year = { 2013 },
}
@inproceedings { deveci13-europar,
author = { Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 19th Int\'l. Euro-Par Conf. on Parallel Processing },
month = { Aug },
title = { GPU accelerated maximum cardinality matching algorithms for bipartite graphs },
year = { 2013 },
}
@article { Benoit13-Workflow,
author = { Anne Benoit and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Yves Robert and Erik Saule },
journal = { ACM Computing Surveys },
link = { http://doi.acm.org/10.1145/2501654.2501664 },
month = { Aug },
number = { 4 },
pages = { 50:1-50:36 },
title = { A Survey of Pipelined Workflow Scheduling: Models and Algorithms },
volume = { 45 },
year = { 2013 },
}
@inproceedings { Kucuktunc13-JCDL,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Poster, ACM/IEEE Joint Conference on Digital Libraries (JCDL 2013) },
month = { Jul },
title = { TheAdvisor: A Webservice for Academic Recommendation },
year = { 2013 },
}
@inproceedings { Sariyuce13-SDM,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { SIAM International Conference on Data Mining (SDM) },
month = { May },
note = { An extended version is available as a Tech Rep on {}ArXiv. },
title = { Shattering and Compressing Networks for Betweenness Centrality },
year = { 2013 },
}
@inproceedings { Kucuktunc13-WWW,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 22nd International World Wide Web Conference (WWW) },
month = { May },
title = { Diversified Recommendation on Graphs: Pitfalls, Measures, and Algorithms },
year = { 2013 },
}
@techreport { Catalyurek13-INRIA,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kamer Kaya and Bora U{\c{c}}ar },
institution = { Inria, France },
link = { http://hal.inria.fr/hal-00821523 },
month = { May },
number = { RR-8301 },
title = { On analysis of partitioning models and metrics in parallel sparse matrix-vector multiplication },
year = { 2013 },
}
@inproceedings { Sariyuce13-GPGPU,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Workshop on General Purpose Processing Using GPUs (GPGPU), in conjunction with ASPLOS },
month = { Mar },
title = { Betweenness Centrality on {GPU}s and Heterogeneous Architectures },
year = { 2013 },
}
@techreport { Saule13-ARXIV,
author = { Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1302.1078 },
month = { Feb },
number = { arXiv:1302.1078 },
title = { Performance Evaluation of Sparse Matrix Multiplication Kernels on Intel Xeon Phi },
year = { 2013 },
}
@techreport { Sariyuce13-ARXIV,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1303.0422 },
month = { Feb },
number = { arXiv:1303.0422 },
title = { Incremental Algorithms for Network Management and Analysis based on Closeness Centrality },
year = { 2013 },
}
@inproceedings { Kucuktunc13-CSTA,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { iConference Workshop on Computational Scientometrics: Theory and Applications },
month = { Feb },
title = { Result Diversification in Automatic Citation Recommendation },
year = { 2013 },
}
@article { Maris13-JoP,
author = { Pieter Maris and Hasan M. Aktulga and Sven Binder and Angelo Calci and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joachim Langhammer and Esmond G. Ng and Erik Saule and Robert Roth and James P. Vary and Chao Yang },
journal = { Journal of Physics: Conference Series },
link = { http://stacks.iop.org/1742-6596/454/i=1/a=012063 },
number = { 1 },
pages = { 012063 },
title = { No Core CI calculations for light nuclei with chiral 2- and 3-body forces },
volume = { 454 },
year = { 2013 },
}
@article { Kaya13-COR,
author = { Kamer Kaya and Johannes Langguth and Fredrik Manne and Bora U{\c{c}}ar },
journal = { Computers \& Operations Research },
number = { 5 },
pages = { 1266--1275 },
title = { Push-relabel based Algorithms for the Maximum Transversal Problem },
volume = { 40 },
year = { 2013 },
}
@article { Kaya13-SIMAX,
author = { Kamer Kaya and Bora U{\c{c}}ar },
journal = { SIAM Journal on Matrix Analysis and Applications },
number = { 2 },
pages = { 345--354 },
title = { Constructing Elimination Trees for Sparse Unsymmetric Matrices },
volume = { 34 },
year = { 2013 },
}
@article { Kucuktunc13-SNAM,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Social Network Analysis and Mining (SNAM) },
link = { http://link.springer.com/article/10.1007%2Fs13278-013-0106-z },
number = { 4 },
pages = { 1097-1111 },
title = { Fast Recommendation on Bibliographic Networks with Sparse-Matrix Ordering and Partitioning },
volume = { 3 },
year = { 2013 },
}
@article { Hatem13-BMC,
author = { Ayat Hatem and Doruk Bozda{\u{g}} and Amanda E. Toland and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { BMC Bioinformatics },
link = { http://www.biomedcentral.com/1471-2105/14/184 },
number = { 1 },
title = { Benchmarking Short Sequence Mapping Tools },
volume = { 14 },
year = { 2013 },
}
@article { Eren13-BIB,
author = { Kemal Eren and Mehmet Deveci and Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Briefings in Bioinformatics },
link = { http://bib.oxfordjournals.org/content/14/3/279 },
number = { 3 },
pages = { 279-292 },
title = { A Comparative Analysis of Biclustering Algorithms for Gene Expression Data },
volume = { 14 },
year = { 2013 },
}
@article { Duff13-ETNA,
author = { Iain S. Duff and Kamer Kaya },
journal = { Electronic Transactions on Numerical Analysis },
title = { Preconditioners based on Strong Subgraphs },
year = { 2013 },
}
@inproceedings { Hatem12-BCB,
author = { Ayat Hatem and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { {ACM} Conference on Bioinformatics, Computational Biology and Biomedicine (BCB) },
month = { Oct },
title = { Microarray vs. RNA-Seq: A comparison for active subnetwork discovery },
year = { 2012 },
}
@article { Catalyurek12-ParCo,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and John Feo and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
journal = { Parallel Computing },
link = { http://dx.doi.org/10.1016/j.parco.2012.07.001 },
month = { Oct-Nov },
note = { Also available as an {}arXiv Tech Report. },
number = { 10-11 },
pages = { 576--594 },
title = { Graph Coloring Algorithms for Multi-core and Massively Multithreaded Architectures },
volume = { 38 },
year = { 2012 },
}
@inproceedings { Zhou12-Cluster,
author = { Zheng Zhou and Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and Pieter Maris and James P. Vary and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of IEEE Cluster },
month = { Sep },
title = { An Out-of-core Eigensolver on SSD-equipped Clusters },
year = { 2012 },
}
@inproceedings { Zhou12-P2S2,
author = { Zheng Zhou and Erik Saule and Hasan M. Aktulga and Chao Yang and Esmond G. Ng and Pieter Maris and James P. Vary and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 2012 International Conference on Parallel Processing (ICPP) Workshops, Fifth International Workshop on Parallel Programming Models and Systems Software for High-End Computing (P2S2) },
month = { Sep },
title = { An Out-Of-Core Dataflow Middleware to Reduce the Cost of Large Scale Iterative Solvers },
year = { 2012 },
}
@techreport { Sariyuce12-ARXIV,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1209.6007 },
month = { Sep },
number = { arXiv:1209.6007 },
title = { Shattering and Compressing Networks for Centrality Analysis },
year = { 2012 },
}
@techreport { Kucuktunc12-ARXIV2,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1209.5809 },
month = { Sep },
number = { arXiv:1209.5809 },
title = { Diversifying Citation Recommendations },
year = { 2012 },
}
@inproceedings { Catalyurek12-ICPP,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kamer Kaya and Bora U{\c{c}}ar },
booktitle = { 2012 International Conference on Parallel Processing (ICPP) },
month = { Sep },
title = { On shared-memory parallelization of a sparse matrix scaling algorithm },
year = { 2012 },
}
@inproceedings { Kucuktunc12-ASONAM,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Kamer Kaya and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM) },
month = { Aug },
title = { Fast Recommendation on Bibliographic Networks },
year = { 2012 },
}
@inproceedings { Saule12-MTAAP,
author = { Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Multithreaded Architectures and Applications (MTAAP) },
month = { May },
title = { An Early Evaluation of the Scalability of Graph Algorithms on the {I}ntel {MIC} Architecture },
year = { 2012 },
}
@inproceedings { Sariyuce12-PCO,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 26th International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO) },
month = { May },
title = { Scalable Hybrid Implementation of Graph Coloring using MPI and OpenMP },
year = { 2012 },
}
@inproceedings { Catalyurek12-IPDPS,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar },
booktitle = { 26th IEEE International Parallel and Distributed Processing Symposium },
month = { May },
title = { Multithreaded Clustering for Multi-level Hypergraph Partitioning },
year = { 2012 },
}
@article { Saule12-JPDC,
author = { Erik Saule and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Journal of Parallel and Distributed Computing },
link = { http://www.sciencedirect.com/science/article/pii/S0743731511002474 },
month = { Apr },
number = { 4 },
pages = { 489-503 },
title = { Optimizing the maximum stretch of independent tasks on a cluster : From sequential tasks to moldable tasks },
volume = { 72 },
year = { 2012 },
}
@inproceedings { Kaya12-DNASDM,
title = { Algorithms for Offline Tracking of Connected Components in Large Evolving Networks },
author = { Kamer Kaya and Erik Saule and Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Workshop on Dynamic Network Analysis (DNA-SDM) },
month = { Apr },
year = { 2012 },
}
@techreport { Kucuktunc12-ARXIV,
title = { Recommendation on Academic Networks using Direction Aware Citation Analysis },
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { ArXiv },
link = { http://arxiv.org/abs/1205.1143 },
month = { Apr },
number = { arXiv:1205.1143 },
year = { 2012 },
}
@article { Jeannot-12-JPDC,
title = { Optimizing Performance and Reliability on Heterogeneous Parallel Systems: Approximation Algorithms and Heuristics },
author = { Emmanuel Jeannot and Erik Saule and Denis Trystram },
doi = { http://dx.doi.org/10.1016/j.jpdc.2011.11.003 },
journal = { Journal of Parallel and Distributed Computing },
link = { http://dx.doi.org/10.1016/j.jpdc.2011.11.003 },
month = { Feb },
number = { 2 },
pages = { 268 -- 280 },
volume = { 72 },
year = { 2012 },
}
@inproceedings { Catalyurek13-Cluster,
title = { A divisive clustering technique for maximizing the modularity },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kamer Kaya and Johannes Langguth and Bora U{\c{c}}ar },
booktitle = { 10th DIMACS Implementation Challenge - Graph Partitioning and Graph Clustering },
month = { Feb },
note = { Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013. },
year = { 2012 },
}
@inproceedings { Catalyurek13-UMPa,
title = { UMPa: A multi-objective, multi-level partitioner for communication minimization },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mehmet Deveci and Kamer Kaya and Bora U{\c{c}}ar },
booktitle = { 10th DIMACS Implementation Challenge Workshop: Graph Partitioning and Graph Clustering },
month = { Feb },
note = { Published in Contemporary Mathematics, Vol. 588, Editors D.A. Bader, H. Meyerhenke, P. Sanders, D. Wagner, 2013. },
year = { 2012 },
}
@article { Xian12,
title = { Merging network patterns: a general framework to summarize biomedical network data },
author = { Yang Xiang and David Fuhry and Kamer Kaya and Ruoming Jin and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kun Huang },
journal = { Network Modeling and Analysis in Health Informatics and Bioinformatics },
link = { http://dx.doi.org/10.1007/s13721-012-0009-3 },
number = { 3 },
pages = { 103-116 },
publisher = { Springer },
volume = { 1 },
year = { 2012 },
}
@article { Teodoro12-CC,
author = { George Teodoro and Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Renato Ferreira },
journal = { Cluster Computing },
link = { http://dx.doi.org/10.1007/s10586-010-0151-6 },
number = { 2 },
pages = { 125-144 },
title = { Optimizing dataflow applications on heterogeneous environments },
volume = { 15 },
year = { 2012 },
}
@article { Saule12-JPDC-spart,
title = { Load-Balancing Spatially Located Computations using Rectangular Partitions },
author = { Erik Saule and Erdeniz O. Bas and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Journal of Parallel and Distributed Computing },
link = { http://dx.doi.org/10.1016/j.jpdc.2012.05.013 },
optnote = { Also available as a {}Tech Rep on arXiv. },
number = { 10 },
pages = { 1201-1214 },
volume = { 72 },
year = { 2012 },
}
@inproceedings { Sariyuce12-SIAMPP,
title = { Considerations on Parallel Graph Coloring Algorithms },
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, SIAM Conference on Parallel Processing for Scientific Computing },
year = { 2012 },
}
@inproceedings { Maris12-HITES,
title = { Large-scale ab initio configuration interaction calculations for light nuclei },
author = { Pieter Maris and Hasan M. Aktulga and Mark A Caprio and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Edmong Ng and Dossay Oryspayev and Hugh Potter and Erik Saule and Masha Sosonkina and James P. Vary and Chao Yang and Zheng Zhou },
booktitle = { Journal of Physics: Conference Series. HITES 2012: \'Horizons of Innovative Theories, Experiments, and Supercomputing in Nuclear Physics\' },
doi = { doi:10.1088/1742-6596/403/1/012019 },
link = { http://iopscience.iop.org/1742-6596/403/1/012019/ },
number = { 012019 },
volume = { 403 },
year = { 2012 },
}
@article { Kayaaslan12-SISC,
author = { Enver Kayaaslan and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
link = { http://epubs.siam.org/sisc/resource/1/sjoce3/v34/i2/pA970_s1 },
note = { A longer version is also available as a {}Tech Rep. },
number = { 2 },
pages = { A970-A992 },
title = { Partitioning Hypergraphs in Scientific Computing Applications through Vertex Separators on Graphs },
volume = { 34 },
year = { 2012 },
}
@inproceedings { Kucuktunc12-DBRank,
author = { Onur K{\"{u}}{\c{c}}{\"{u}}ktun{\c{c}} and Erik Saule and Kamer Kaya and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of the 6th International Workshop on Ranking in Databases (DBRank) },
note = { An extended version is available as a Tech Rep on {}ArXiv. },
pages = { 6 },
title = { Direction Awareness in Citation Recommendation },
year = { 2012 },
}
@article { Hartley12-PARCO,
author = { Timothy D. R. Hartley and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Parallel Computing },
link = { http://dx.doi.org/10.1016/j.parco.2012.03.005 },
number = { 6-7 },
pages = { 289-309 },
title = { Improving Performance of Adaptive Component-Based Dataflow Middleware },
volume = { 38 },
year = { 2012 },
}
@incollection { Boman12-CSC-Zoltan,
author = { Erik G. Boman, {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cedric Chevalier and Karen D. Devine },
booktitle = { Combinatorial Scientific Computing },
editor = { Uwe Naumann and Olaf Schenk },
publisher = { Chapman \& Hall / CRC Press },
series = { Computational Science },
title = { Parallel Partitioning, Coloring, and Ordering for Scientific Computing },
year = { 2012 },
}
@article { Boman12-SciProg,
author = { Erik G. Boman and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cedric Chevalier and Karen D. Devine },
journal = { Scientific Programming },
link = { http://iospress.metapress.com/content/U40KU26NRQKP1318 },
number = { 2 },
pages = { 129-150 },
title = { The Zoltan and Isorropia parallel toolkits for combinatorial scientific computing: Partitioning, ordering and coloring },
volume = { 20 },
year = { 2012 },
}
@incollection { Bisseling12-CSC-2D,
author = { Rob H. Bisseling and Bas O. Fagginger Auer and A.N. Yzelman and Tristan van Leeuwen and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Combinatorial Scientific Computing },
editor = { Uwe Naumann and Olaf Schenk },
publisher = { Chapman \& Hall / CRC Press },
series = { Computational Science },
title = { Two-dimensional approaches to sparse matrix partitioning },
year = { 2012 },
}
@inproceedings { Bas12-SIAMPP,
author = { Erdeniz O. Bas and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, SIAM Conference on Parallel Processing for Scientific Computing },
title = { Load-Balancing Spatially Located Computations using Rectangular Partitions },
year = { 2012 },
}
@phdthesis { Hartley11-PhD,
author = { Timothy D. R. Hartley },
institution = { The Ohio State University, Electrical and Computer Engineering },
key = { Hartley11-PhD },
month = { May },
title = { Accelerating Component-Based Dataflow Middleware with Adaptivity and Heterogeneity },
year = { 2011 },
}
@inproceedings { Sariyuce11-HiPC,
author = { Ahmet Erdem Sar{\i}y{\"{u}}ce and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of the 18th Annual International Conference on High Performance Computing (HiPC 2011) },
month = { Dec },
title = { Improving Graph Coloring on Distributed Memory Parallel Computers },
year = { 2011 },
}
@inproceedings { Hatem11-BIBM,
author = { Ayat Hatem and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { IEEE International Conference on Bioinformatics and Biomedicine (BIBM11) },
month = { Nov },
note = { A longer version is also available as a {}Tech Rep. },
title = { Benchmarking Short Sequence Mapping Tools },
year = { 2011 },
}
@article { Vydyanathan11-PC,
author = { Nagavijayalakshmi Vydyanathan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
journal = { Parallel Computing },
link = { http://dx.doi.org/10.1016/j.parco.2010.05.003 },
month = { Oct-Nov },
number = { 10-11 },
pages = { 694-712 },
title = { Optimizing Latency and Throughput of Application Workflows on Clusters },
volume = { 37 },
year = { 2011 },
}
@inproceedings { Cooper11-HISB,
author = { Lee Cooper and Joel H. Saltz and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kun Huang },
booktitle = { Proceedings of the IEEE Health Informatics and Systems Biology Conference },
month = { Jul },
title = { Acceleration of Point Correlation Function Calculation for Pathology Image Segmentation },
year = { 2011 },
}
@inproceedings { Catalyurek11-DIDC,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kamer Kaya and Bora U{\c{c}}ar },
booktitle = { 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) },
month = { Jun },
title = { Integrated Data Placement and Task Assignment for Scientific Workflows in Clouds },
year = { 2011 },
}
@article { Janies11-Supramap,
author = { D. A. Janies and T. Treseder and B. Alexandrov and F. Habib and J. J. Chen and R. Ferreira and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and A. Varon and W. C. Wheeler },
journal = { Cladistics },
link = { http://onlinelibrary.wiley.com/doi/10.1111/j.1096-0031.2010.00314.x/abstract },
month = { Feb },
number = { 1 },
pages = { 61-66 },
title = { The Supramap project: Linking pathogen genomes with geography to fight emergent infectious diseases },
volume = { 27 },
year = { 2011 },
}
@article { Catalyurek11-Order,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat and Enver Kayaaslan },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
link = { http://dx.doi.org/10.1137/090757575 },
month = { Feb },
number = { 4 },
pages = { 1996-2023 },
title = { Hypergraph Partitioning-Based Fill-Reducing Ordering },
volume = { 33 },
year = { 2011 },
}
@article { Vieland11-KELVIN,
author = { V.J. Vieland and Y. Huang and S.C. Seok and J. Burian and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and J. O{\'}Connell and A. Segre and W. Valentine-Cooper },
journal = { Human Heredity },
link = { http://www.ncbi.nlm.nih.gov/pubmed/22189470 },
number = { 5 },
pages = { 276-288 },
title = { KELVIN: a Software Package for Rigorous Measurement of Statistical Evidence in Human Genetics },
volume = { 72 },
year = { 2011 },
}
@inproceedings { Saule11-IPDPS,
author = { Erik Saule and Erdeniz O. Bas and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 25th IEEE International Parallel and Distributed Processing Symposium },
title = { Partitioning Spatially Located Computations using Rectangles },
year = { 2011 },
}
@article { Igual11,
author = { F. Igual and R. Mayo and Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Antonio Ruiz and M. Ujaldon },
journal = { International Journal of High Performance Computing Applications },
link = { http://hpc.sagepub.com/content/early/2010/12/21/1094342010390340 },
number = { 4 },
pages = { 404-427 },
title = { Color and Texture Analysis on Emerging Architectures Parallel Architectures },
volume = { 25 },
year = { 2011 },
}
@inproceedings { Deveci11-BCB,
author = { Mehmet Deveci and Kemal Eren and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Poster, {ACM} International Conference on Bioinformatics and Computational Biology },
note = { Runner-up of the poster award },
title = { A comparison of recent biclustering algorithms },
year = { 2011 },
}
@inproceedings { Aktulga11-HPSS,
author = { Hasan M. Aktulga and C. Yang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and P. Maris and James P. Vary and E. G. Ng },
booktitle = { Workshop on Algorithms and Programming Tools for Next-Generation High-Performance Scientific Software (HPSS 2011), in conjunction with the Euro-Par },
title = { On Reducing I/O Overheads in Large-Scale Invariant Subspace Projections },
year = { 2011 },
}
@incollection { Catalyurek11-EPC-HP,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Bora U{\c{c}}ar and Cevdet Aykanat },
booktitle = { Encyclopedia of Parallel Computing },
editor = { David Padua },
link = { http://www.springerlink.com/content/v2124348m4nkh635/ },
pages = { 871-881 },
publisher = { Springer },
title = { Hypergraph Partitioning },
year = { 2011 },
}
@incollection { Catalyurek11-EPC-PaToH,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
booktitle = { Encyclopedia of Parallel Computing },
editor = { David Padua },
link = { http://www.springerlink.com/content/g5t6638gm542837t/ },
pages = { 1479-1487 },
publisher = { Springer },
title = { {PaToH} (Partitioning Tool for Hypergraphs) },
year = { 2011 },
}
@inproceedings { Catalyurek11-PCO,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Florin Dobrian and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
booktitle = { 2011 International Parallel and Distributed Processing Symposium, Workshops and PhD Forum (IPDPSW), Workshop on Parallel Computing and Optimization (PCO\'11) },
pages = { 1966-1975 },
title = { Distributed-Memory Parallel Algorithms for Matching and Coloring },
year = { 2011 },
}
@phdthesis { Sertel10-PhD,
author = { Olcay Sertel },
institution = { The Ohio State University, Electrical and Computer Engineering },
key = { Sertel10-PhD },
month = { May },
title = { Image Analysis for Computer-Aided Histopathology },
year = { 2010 },
}
@techreport { Benoit10-Workflow,
address = { ENS Lyon, France },
author = { Anne Benoit and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Yves Robert and Erik Saule },
institution = { LIP },
link = { http://hal.archives-ouvertes.fr/hal-00521712/fr/ },
month = { Sep },
number = { RR-LIP-2010-28 },
title = { A Survey of Pipelined Workflow Scheduling: Models and Algorithms },
year = { 2010 },
}
@inproceedings { Sertel10-ICPR,
author = { Olcay Sertel and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and G. Lozanski and A. Shanaah and Metin N. G{\"{u}}rcan },
booktitle = { 20th International Conference on Pattern Recognition (ICPR) },
month = { Aug },
pages = { 273 -276 },
title = { An Image Analysis Approach for Detecting Malignant Cells in Digitized H amp;E-stained Histology Images of Follicular Lymphoma },
year = { 2010 },
}
@article { Ucar10-ParCo,
author = { Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
doi = { DOI: 10.1016/j.parco.2009.12.008 },
journal = { Parallel Computing },
number = { 5-6 },
pages = { 254 - 272 },
title = { A matrix partitioning interface to {PaToH} in {MATLAB} },
volume = { 36 },
year = { 2010 },
}
@inproceedings { Ucar10-PDP,
author = { Bora U{\c{c}}ar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of the PDP 2010: 18th Euromicro International Conference on Parallel, Distributed and Network-Based Computing },
title = { On scalability of hypergraph models for sparse matrix partitioning },
year = { 2010 },
}
@inproceedings { Teodoro10-HPDC,
author = { George Teodoro and Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Renato Ferreira },
booktitle = { Proc. of the 19th ACM International Symposium on High Performance Distributed Computing (HPDC) },
link = { http://portal.acm.org/Graph Based Citation Analysis.cfm?id=1851479 },
note = { Best Student Paper Award },
pages = { 13--24 },
title = { Run-time optimizations for replicated dataflows on heterogeneous environments },
year = { 2010 },
}
@inproceedings { Saule10-Aussois,
author = { Erik Saule and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, 3rd Scheduling in Aussois Workshop },
title = { Optimizing the maximum stretch of online tasks on a parallel system without preemption },
year = { 2010 },
}
@inproceedings { Saule10-JSSPP,
author = { Erik Saule and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Job Scheduling Strategies for Parallel Processing },
publisher = { Springer },
series = { Lecture notes in Computer Science },
title = { A Moldable Online Scheduling Algorithm and its Application to Parallel Short Sequence Mapping },
volume = { 6253 },
year = { 2010 },
}
@inproceedings { Saule10-NCST,
author = { Erik Saule and Erdeniz O. Bas and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, New Challenges on Scheduling Theory, Workshop },
title = { Partitioning Spatially Located Load with Rectangles: Algorithms and Simulations },
year = { 2010 },
}
@inproceedings { Hatem10-OCCBIO,
author = { Ayat Hatem and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, Bioinformatics, 2010 Ohio Collaborative Conference },
title = { Benchmarking Short Sequence Alignment Tools },
year = { 2010 },
}
@inproceedings { Hartley10-HiPC,
author = { Timothy D. R. Hartley and Erik Saule and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of The 17th International Conference on High Performance Computing (HiPC 2010) },
title = { Automatic Dataflow Application Tuning for Heterogeneous Systems },
year = { 2010 },
}
@inproceedings { Bozdag10-BCB,
author = { Doruk Bozda{\u{g}} and A.S. Kumar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { {ACM} International Conference on Bioinformatics and Computational Biology },
title = { Comparative Analysis of Biclustering Algorithms },
year = { 2010 },
}
@inproceedings { Bozdag10-HiCOMB,
author = { Doruk Bozda{\u{g}} and Ayat Hatem and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 9th IEEE International Workshop on High Performance Computational Biology (in conjunction with IPDPS) },
title = { Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform },
year = { 2010 },
}
@article { Bozdag10-SISC,
author = { Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and F. {\"{O}}zg{\"{u}}ner },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
link = { http://dx.doi.org/10.1137/080732158 },
number = { 4 },
pages = { 2418-2446 },
title = { Distributed-memory Parallel Algorithms for Distance-2 Coloring and Related Problems in Derivative Computation },
volume = { 32 },
year = { 2010 },
}
@article { Catalyurek10-RESS,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and B. Rutt and K. Metzroth and Aram Hakobyan and T. Aldemir and R. Denning and S. Dunagan and D. Kunsman },
journal = { Reliability Engineering and System Safety },
link = { http://dx.doi.org/10.1016/j.ress.2009.10.008 },
number = { 3 },
pages = { 278 - 294 },
title = { Development of a code-agnostic computational infrastructure for the dynamic generation of accident progression even trees },
volume = { 95 },
year = { 2010 },
}
@incollection { Catalyurek10-SCMA,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Renato Ferreira and Timothy D. R. Hartley and Rafael Sachetto and George Teodoro },
booktitle = { Scientific Computing with Multicore and Accelerators },
editor = { Jack Dongarra and David A. Bader and Jakub Kurzak },
publisher = { Chapman and Hall / CRC Press },
title = { Dataflow frameworks for emerging heterogeneous architectures and its application to biomedicine },
year = { 2010 },
}
@article { Catalyurek10-SISC,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat and Bora U{\c{c}}ar },
doi = { 10.1137/080737770 },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
link = { http://dx.doi.org/10.1137/080737770 },
number = { 2 },
pages = { 656-683 },
publisher = { SIAM },
title = { On Two-Dimensional Sparse Matrix Partitioning: Models, Methods, and a Recipe },
volume = { 32 },
year = { 2010 },
}
@article { Vydyanathan09-TPDS,
author = { Nagavijayalakshmi Vydyanathan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
journal = { IEEE Transactions on Parallel and Distributed Systems },
link = { http://dx.doi.org/10.1109/TPDS.2008.219 },
month = { Aug },
number = { 8 },
title = { An Integrated Approach to Locality Conscious Processor Allocation and Scheduling of Mixed Parallel Applications },
volume = { 20 },
year = { 2009 },
}
@article { Catalyurek09-JPDC,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Erik G. Boman and K.D. Devine and Doruk Bozda{\u{g}} and R. Heaphy and L.A. Fisk },
journal = { Journal of Parallel and Distributed Computing },
month = { Aug },
number = { 8 },
pages = { 711-724 },
title = { A Repartitioning Hypergraph Model for Dynamic Load Balancing },
volume = { 69 },
year = { 2009 },
}
@article { Ruiz09-JDMB,
author = { Antonio Ruiz and Olcay Sertel and Manuel Ujaldon and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz and Metin N. G{\"{u}}rcan },
journal = { International Journal of Data Mining and Bioinformatics },
month = { Jun },
opturl = { http://www.ingentaconnect.com/content/ind/ijdmb/2009/00000003/00000003/art00003 },
pages = { 280-298 },
title = { Stroma classification for neuroblastoma on graphics processors },
volume = { 3 },
year = { 2009 },
}
@article { Bozdag09-TPDS,
author = { Doruk Bozda{\u{g}} and F. {\"{O}}zg{\"{u}}ner and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { {IEEE} Transactions on Parallel and Distributed Systems },
link = { http://doi.ieeecomputersociety.org/10.1109/TPDS.2008.260 },
month = { Jun },
number = { 6 },
pages = { 857-871 },
title = { Compaction of Schedules and a Two-Stage Approach for Duplication-Based {DAG} Scheduling },
volume = { 20 },
year = { 2009 },
}
@inproceedings { Hartley09-HCW,
author = { Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 23rd Int\'l. Parallel and Distributed Processing Symposium, The 18th Heterogeneous Computing Workshop (HCW 2009) },
month = { May },
title = { A Component-Based Framework for the Cell Broadband Engine },
year = { 2009 },
}
@inproceedings { Bozdag09-IPDPS,
author = { Doruk Bozda{\u{g}} and C.C. Barbacioru and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 23rd Int\'l. Parallel and Distributed Processing Symposium },
month = { May },
pages = { 1-10 },
title = { Parallel Short Sequence Mapping for High Throughput Genome Sequencing },
year = { 2009 },
}
@inproceedings { Teodoro09-Cluster,
author = { George Teodoro and Rafael Sachetto and Olcay Sertel and Metin N. G{\"{u}}rcan and Wagner Meira and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Renato Ferreira },
booktitle = { Proc. of the 2009 IEEE International Conference on Cluster Computing },
title = { Coordinating the Use of {GPU} and {CPU} for Improving Performance of Compute Intensive Applications },
year = { 2009 },
}
@article { Sertel09-SPS,
author = { Olcay Sertel and Jun Kong and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Gerard Lozanski and Joel H. Saltz and Metin N. G{\"{u}}rcan },
journal = { Signal Processing Systems },
link = { http://dx.doi.org/10.1007/s11265-008-0201-y },
number = { 1-3 },
pages = { 169-183 },
title = { Histopathological Image Analysis Using Model-Based Intermediate Representations and Color Texture: Follicular Lymphoma Grading },
volume = { 55 },
year = { 2009 },
}
@article { Sertel09-PatRec,
author = { Olcay Sertel and Jun Kong and H. Shimada and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz and Metin N. G{\"{u}}rcan },
journal = { Pattern Recognition },
link = { http://dx.doi.org/10.1016/j.patcog.2008.08.027 },
number = { 6 },
pages = { 1093-1103 },
title = { Computer-aided prognosis of neuroblastoma on whole-slide images: Classification of stromal development },
volume = { 42 },
year = { 2009 },
}
@inproceedings { Parvin09-OCCBIO,
address = { Los Alamitos, CA },
author = { Jeffrey D. Parvin and Zeina Kais and Mansi Arora and Shweta Kotian and Alicia Zha and Derek Ransburgh and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Kun Huang },
booktitle = { Bioinformatics, 2009 Ohio Collaborative Conference },
link = { http://doi.ieeecomputersociety.org/10.1109/OCCBIO.2009.37 },
pages = { 71-75 },
publisher = { IEEE Computer Society },
title = { Identification of a Breast Cancer Associated Regulatory Network },
year = { 2009 },
}
@inproceedings { Ozer09-BICOB,
author = { Hatice G. Ozer and Doruk Bozda{\u{g}} and T. Camerlengo and J. Wu and Y.-W. Huang and Timothy D. R. Hartley and Jeffrey D. Parvin and T. Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and K. Huang },
booktitle = { Proc. of 1st Int\'l. Conf. on Bioinformatics and Computational Biology },
link = { http://dx.doi.org/10.1007/978-3-642-00727-9_30 },
pages = { 320-330 },
publisher = { Springer },
series = { Lecture notes in Computer Science },
title = { A Comprehensive Analysis Workflow for Genome-Wide Screening Data from ChIP-Sequencing Experiments },
volume = { 5462 },
year = { 2009 },
}
@inproceedings { igual09parco,
author = { Francisco Igual and Rafael Mayo and Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Antonio Ruiz and Manuel Ujaldon },
booktitle = { Proc. of the 2009 International Conference on Parallel Computing (ParCo2009) },
title = { Exploring the {GPU} for Enhancing Parallelism on Color and Texture Analysis },
year = { 2009 },
}
@inproceedings { Hartley09-PPAC,
author = { Timothy D. R. Hartley and Ahmed R. Fasih and Charles A. Berdanier and F{\"u}sun {\"{O}}zg{\"{u}}ner and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of the IEEE International Conference on Cluster Computing, Workshop on Parallel Programming on Accelerator Clusters (PPAC) },
title = { Investigating the Use of {GPU}-Accelerated Nodes for {SAR} Image Formation },
year = { 2009 },
}
@inproceedings { hartley09ipdps-poster,
author = { Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Poster, 23rd Int\'l. Parallel and Distributed Processing Symposium PhD Forum },
title = { High-Performance Filter-Stream Frameworks for Hierarchical, Heterogeneous, Distributed Supercomputers },
year = { 2009 },
}
@article { Erdal09-JDI,
author = { Selnur Erdal and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Philip R. O. Payne and Joel H. Saltz and Jyoti Kamal and Metin N. G{\"{u}}rcan },
journal = { J. Digital Imaging },
number = { 2 },
pages = { 166-182 },
title = { A Knowledge-Anchored Integrative Image Search and Retrieval System },
volume = { 22 },
year = { 2009 },
}
@inproceedings { Devine09-DAGSTUHL,
address = { Dagstuhl, Germany },
author = { Karen D. Devine and Erik G. Boman and Lee Ann Riesen and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cedric Chevalier },
booktitle = { Abstract, Combinatorial Scientific Computing },
editor = { Uwe Naumann and Olaf Schenk and Horst D. Simon and Sivan Toledo },
link = { http://drops.dagstuhl.de/opus/volltexte/2009/2088 },
number = { 09061 },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
series = { Dagstuhl Seminar Proceedings },
title = { Getting Started with Zoltan: A Short Tutorial },
year = { 2009 },
}
@inproceedings { Bozdag09-BICOB,
author = { Doruk Bozda{\u{g}} and Jeffrey D. Parvin and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 1st Int\'l. Conf. on Bioinformatics and Computational Biology },
link = { http://dx.doi.org/10.1007/978-3-642-00727-9_16 },
pages = { 151-163 },
publisher = { Springer },
series = { Lecture notes in Computer Science },
title = { A Biclustering Method to Discover Co-regulated Genes Using Diverse Gene Expression Datasets },
volume = { 5462 },
year = { 2009 },
}
@inproceedings { Bozdag09-CAMDA,
author = { Doruk Bozda{\u{g}} and Terry Camerlengo and Hatice G. Ozer and Joanne Trgovcich and Tea Meulia and Kun Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Extended abstract, 9th International Conference for the Critical Assesment of Massive Data Analysis },
title = { Parallel Computing Strategies for Sequence Mapping of NGS Data },
year = { 2009 },
}
@inproceedings { Bozdag09-Dagstuhl,
address = { Dagstuhl, Germany },
author = { Doruk Bozda{\u{g}} and Catalin C. Barbacioru and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, Combinatorial Scientific Computing },
link = { http://drops.dagstuhl.de/opus/volltexte/2009/2129 },
number = { 09061 },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
series = { Dagstuhl Seminar Proceedings },
title = { Parallelization of Mapping Algorithms for Next Generation Sequencing Applications },
year = { 2009 },
}
@inproceedings { Bozdag09-SC,
author = { Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and F. Dobrian and Assefaw H. Gebremedhin and Mahantesh Halappanavar and Alex Pothen },
booktitle = { Poster, 21st Supercomputing Conference },
title = { Combinatorial Algorithms Enabling Scientific Computing: Petascale Algorithms for Graph Coloring and Matching },
year = { 2009 },
}
@inproceedings { Bisseling09-DAGSTUHL,
address = { Dagstuhl, Germany },
author = { Rob Bisseling and Tristan van Leeuwen and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Abstract, Combinatorial Scientific Computing },
editor = { Uwe Naumann and Olaf Schenk and Horst D. Simon and Sivan Toledo },
link = { http://drops.dagstuhl.de/opus/volltexte/2009/2081 },
number = { 09061 },
publisher = { Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik },
series = { Dagstuhl Seminar Proceedings },
title = { Combinatorial Problems in High-Performance Computing: Partitioning },
year = { 2009 },
}
@incollection { Catalyurek09-IOS,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Timothy D. R. Hartley and Olcay Sertel and Manuel Ujaldon and Antonio Ruiz and Joel H. Saltz and Metin G{\"{u}}rcan },
booktitle = { High Performance and Large Scale Computing },
editor = { W. Gentzsch and L. Grandinetti and G. Joubert },
link = { http://www.booksonline.iospress.nl/Content/View.aspx?piid=14174 },
pages = { 341-364 },
publisher = { IOS Press },
title = { Processing of Large-Scale Biomedical Images on a Cluster of Multi-Core {CPU}s and {GPU}s },
volume = { 18 },
year = { 2009 },
}
@incollection { Catalyurek09-Wiley,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Doruk Bozda{\u{g}} and Erik G. Boman and K.D. Devine and R. Heaphy and L.A. Fisk },
booktitle = { Advanced Computational Infrastructures for Parallel and Distributed Adaptive Applications },
editor = { M. Parashar and X. Li and S. Chandra },
publisher = { Wiley Publishing },
title = { Hypergraph-based Dynamic Partitioning and Load Balancing },
year = { 2009 },
}
@phdthesis { Bozdag08-PhD,
author = { Doruk Bozda{\u{g}} },
institution = { The Ohio State University, Biomedical Informatics },
key = { Bozdag08-PhD },
month = { May },
title = { Graph Coloring and Clustering Algorithms for Science and Engineering Applications },
year = { 2008 },
}
@inproceedings { Khanna_SC08,
author = { Gaurav Khanna and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Rajkumar Kettimuthu and P. Sadayappan and Ian Foster and Joel H. Saltz },
booktitle = { Proceedings of {SC2008} High Performance Computing, Networking, and Storage Conference },
month = { Nov },
title = { Using Overlays for Efficient Data Transfer over Shared Wide-Area Networks },
year = { 2008 },
}
@article { Kumar08-TITB,
author = { V.S. Kumar and B. Rutt and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tony C. Pan and S. Chow and S. Lamont and M. Martone and Joel H. Saltz },
doi = { 10.1109/TITB.2007.908466 },
journal = { {IEEE} Transactions on Information Technology in Biomedicine },
month = { Mar },
number = { 2 },
pages = { 154-161 },
title = { Large-Scale Biomedical Image Analysis in Grid Environments },
volume = { 12 },
year = { 2008 },
}
@inproceedings { Vydyanathan08-ICPP,
author = { N. Vydyanathan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { 2008 International Conference on Parallel Processing (ICPP) },
link = { http://dx.doi.org/10.1109/ICPP.2008.68 },
pages = { 254-261 },
title = { A Duplication Based Algorithm for Optimizing Latency Under Throughput Constraints for Streaming Workflows },
year = { 2008 },
}
@article { DeSupinski:2008,
author = { Bronis R de Supinski and Martin Schulz and Vasily V Bulatov and William Cabot and Bor Chan and Andrew W Cook and Erik W Draegerl and James N Glosli and Jeffrey A Greenough and Keith Henderson and Alison Kubota and Steve Louis and Brian J Miller and Mehul V Patel and Thomas E Spelce and Frederick H Streitz and Peter L Williams and Robert K Yates and Andy Yoo and George Almasi and Gyan Bhanot and Alan Gara and John A Gunnels and Manish Gupta and Jose Moreira and James Sexton and Bob Walkup and Charles Archer and Francois Gygi and Timothy C Germann and Kai Kadau and Peter S Lomdahl and Charles Rendleman and Michael L Welcome and William McLendon and Bruce Hendrickson and Franz Franchetti and Stefan Kraig and Juergen Lorenz and Christoph W Ueberhuber and Edmond Chow and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
doi = { 10.1177/1094342007085025 },
journal = { International Journal of High Performance Computing },
month = { Jan },
number = { 1 },
pages = { 33--51 },
title = { Bluegene/L applications: Parallelism on a massive scale },
volume = { 22 },
year = { 2008 },
}
@inproceedings { Khanna_IPDPS08,
address = { Miami, Florida },
author = { Gaurav Khanna and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Rajkumar Kettimuthu and P. Sadayappan and Joel H. Saltz },
booktitle = { Proc. of 22th International Parallel and Distributed Processing Symposium (IPDPS) },
title = { A Dynamic Scheduling Approach for Coordinated Wide-Area Data Transfers using GridFTP },
year = { 2008 },
}
@inproceedings { Hartley08,
author = { Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Antonio Ruiz and F. Igual and R. Mayo and M. Ujaldon },
booktitle = { Proc. of the 22nd Annual International Conference on Supercomputing, ICS 2008 },
link = { http://doi.acm.org/10.1145/1375527.1375533 },
pages = { 15-25 },
title = { Biomedical Image Analysis on a Cooperative Cluster of {GPU}s and Multicores },
year = { 2008 },
}
@article { Hakobyan08-NED,
author = { Aram Hakobyan and Tunc Aldemir and Richard Denning and Sean Dunagan and David Kunsman and Benjamin Rutt and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
doi = { DOI: 10.1016/j.nucengdes.2008.08.005 },
journal = { Nuclear Engineering and Design },
link = { http://www.sciencedirect.com/science/article/B6V4D-4TNTNB4-1/2/221594203a453de4482f2b297907f6f4 },
number = { 12 },
pages = { 3457 - 3467 },
title = { Dynamic generation of accident progression event trees },
volume = { 238 },
year = { 2008 },
}
@inproceedings { Bozdag08-CSC,
author = { Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman },
booktitle = { Abstract, Workshop on Combinatorial Scientific Computing and Petascale Simulations },
title = { Parallel Distance-2 Coloring },
year = { 2008 },
}
@article { Bozdag08-JPDC,
author = { Doruk Bozda{\u{g}} and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { Journal of Parallel and Distributed Computing },
link = { http://dx.doi.org/10.1016/j.jpdc.2007.08.002 },
number = { 4 },
pages = { 515--535 },
title = { A framework for scalable greedy coloring on distributed-memory parallel computers },
volume = { 68 },
year = { 2008 },
}
@inproceedings { Boman08-JPCS,
author = { Erik G. Boman and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and K. D. Devine and Assefaw H. Gebremedhin and P. D. Hovland and Alex Pothen },
booktitle = { Journal of Physics: Conference Series },
title = { Combinatorial algorithms for computational science and engineering },
volume = { 125 },
year = { 2008 },
}
@inproceedings { Catalyurek07-IPDPS,
address = { Long Beach, CA },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Erik G. Boman and K.D. Devine and Doruk Bozda{\u{g}} and R. Heaphy and L.A. Fisk },
booktitle = { Proc. of 21st Int\'l. Parallel and Distributed Processing Symposium },
month = { Mar },
note = { Best Algorithms Paper Award },
pages = { 1-11 },
title = { Hypergraph-based Dynamic Load Balancing for Adaptive Scientific Computations },
year = { 2007 },
}
@techreport { ZoltanUsersGuideV3,
title = { {Zoltan 3.0}: Parallel Partitioning, Load-balancing, and Data Management Services; User\'s Guide },
author = { Erik Boman and Karen Devine and Lee Ann Fisk and Robert Heaphy and Bruce Hendrickson and Courtenay Vaughan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Doruk Bozdag and William Mitchell and James Teresco },
institution = { Sandia National Laboratories },
address = { Albuquerque, NM },
year = { 2007 },
note = { Tech. Report SAND2007-4748W \url{http://www.cs.sandia.gov/Zoltan/ug_html/ug.html} },
}
@techreport { ZoltanDevelopersGuideV3,
title = { {Zoltan 3.0}: Parallel Partitioning, Load-balancing, and Data Management Services; Developer\'s Guide },
author = { Erik Boman and Karen Devine and Lee Ann Fisk and Robert Heaphy and Bruce Hendrickson and Courtenay Vaughan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Doruk Bozdag and William Mitchell and James Teresco },
institution = { Sandia National Laboratories },
address = { Albuquerque, NM },
year = { 2007 },
note = { Tech. Report SAND2007-4749W, \url{http://www.cs.sandia.gov/Zoltan/dev_html/dev.html} },
}
@inproceedings { Weng07-Grid,
author = { L. Weng and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and G. Agrawal and Joel H. Saltz },
booktitle = { Proc. of 8th IEEE/ACM International Conference on Grid Computing (GRID 2007) },
link = { http://dx.doi.org/10.1109/GRID.2007.4354141 },
pages = { 259-266 },
title = { Optimizing multiple queries on scientific datasets with partial replicas },
year = { 2007 },
}
@inproceedings { Vydyanathan07,
author = { Nagavijayalakshmi Vydyanathan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007) },
link = { http://dx.doi.org/10.1007/978-3-540-74466-5_20 },
pages = { 173-183 },
title = { Toward Optimizing Latency Under Throughput Constraints for Application Workflows on Clusters },
year = { 2007 },
}
@inproceedings { Tavares07-CCGRID,
author = { T. Tavares and G. Teodoro and Tahsin M. Kurc and R. Ferreira and D. Neto and W. Meira and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and S. Hastings and S. Oster and S. Langella and Joel H. Saltz },
booktitle = { Prof. of Seventh IEEE International Symposium on Cluster Computing and the Grid (CCGrid 2007) },
link = { http://dx.doi.org/10.1109/CCGRID.2007.20 },
pages = { 445-452 },
title = { An Efficient and Reliable Scientific Workflow System },
year = { 2007 },
}
@inproceedings { ruiz07,
author = { Antonio Ruiz and Olcay Sertel and Manuel Ujaldon and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz and M. G{\"{u}}rcan },
booktitle = { Proc. of IEEE Int. Conf. on Bioinformatics and Biomedicine },
pages = { 78--85 },
title = { Pathological image analysis using the {GPU}: Stroma classification for neuroblastoma },
year = { 2007 },
}
@inproceedings { Kumar07-CLUSTER,
author = { V. S. Kumar and Tahsin M. Kurc and Jun Kong and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and M. N. G{\"{u}}rcan and Joel H. Saltz },
booktitle = { Proc. of the 2007 IEEE International Conference on Cluster Computing },
link = { http://dx.doi.org/10.1109/CLUSTR.2007.4629222 },
pages = { 100-109 },
title = { Performance vs. accuracy trade-offs for large-scale image analysis applications },
year = { 2007 },
}
@inproceedings { Khanna07,
author = { G. Khanna and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { Proceedings of the 13th International Euro-Par Conference (Euro-Par 2007) },
link = { http://dx.doi.org/10.1007/978-3-540-74466-5_24 },
pages = { 214-223 },
title = { Scheduling File Transfers for Data-Intensive Jobs on Heterogeneous Clusters },
year = { 2007 },
}
@inproceedings { hartley07sc,
author = { Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Andy Yoo },
booktitle = { Poster, 19th Supercomputing Conference, 2nd Place Student Poster },
title = { Storing and Searching Massive Scale-free Graphs },
year = { 2007 },
}
@inproceedings { Gurcan2007-AMIA,
author = { Metin N. G{\"{u}}rcan and Jun Kong. and Olcay Sertel and Barla B. Cambazoglu and Joel H. Saltz and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { 2007 AMIA Annual Symposium },
title = { Computerized pathological image analysis for neuroblastoma prognosis },
year = { 2007 },
}
@inproceedings { Cambazoglu07,
author = { Barla B. Cambazoglu and Olcay Sertel and Jun Kong and Joel H. Saltz and Metin N. G{\"{u}}rcan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of the International Workshop on Challenges of Large Applications in Distributed Environments (CLADE 07) },
title = { Efficient Processing of Pathological Images Using the Grid: Computer-Aided Prognosis of Neuroblastoma },
year = { 2007 },
}
@inproceedings { Boman07-JPCS,
author = { Erik G. Boman and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and K. D. Devine and Assefaw H. Gebremedhin and P. D. Hovland and Alex Pothen and M. M. Strout },
booktitle = { Journal of Physics: Conference Series },
pages = { 012058 (10pp) },
title = { Enabling high performance computational science through combinatorial algorithms },
volume = { 78 },
year = { 2007 },
}
@inproceedings { Vydyanathan06c,
author = { Nagavijayalakshmi Vydyanathan and Sriram Krishnamoorthy and Gerald Sabin and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { Proceedings of 2006 IEEE International Conference on Cluster Computing },
month = { Sep },
organization = { IEEE Computer Society },
title = { Locality Conscious Processor Allocation and Scheduling for Mixed Parallel Applications },
year = { 2006 },
}
@inproceedings { DUcar06,
address = { Berlin, Germany },
author = { D. Ucar and S. Asur and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and S. Parthasarathy },
booktitle = { In Proceedings of the European Conference on Principles and Practice of Knowledge Discovery in Databases (PKDD) },
month = { Sep },
title = { Improving Functional Modularity in Protein-Protein Interactions Graphs Using Hub-induced Subgraphs },
year = { 2006 },
}
@inproceedings { Hartley06,
author = { Timothy D. R. Hartley and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and F{\"u}sun {\"{O}}zg{\"{u}}ner and Andy Yoo and Scott Kohn and Keith Henderson },
booktitle = { Proceedings of 2006 IEEE International Conference on Cluster Computing },
month = { Sep },
organization = { IEEE Computer Society },
title = { {MSSG}: A Framework for Massive Scale Semantic Graphs },
year = { 2006 },
}
@inproceedings { Weng06,
author = { Li Weng and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Gagan Agrawal and Joel H. Saltz },
booktitle = { 2006 International Conference on Parallel Processing },
month = { Aug },
title = { Using Space and Attribute Partitioned Partial Replicas for Data Subsetting and Aggregation Queries },
year = { 2006 },
}
@inproceedings { Narayanan06,
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { 2006 International Conference on Parallel Processing },
month = { Aug },
title = { On Creating Efficient Object-relational Views of Scientific Datasets },
year = { 2006 },
}
@inproceedings { Khanna06,
address = { Paris, France },
author = { Gaurav Khanna and Nagavijayalakshmi Vydyanathan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Sriram Krishnamoorthy and P. Sadayappan and Joel H. Saltz },
booktitle = { Proceedings of the Fifteen International Symposium on High Performance Distributed Computing (HPDC-15) },
month = { Jun },
pages = { 241-252 },
title = { Task Scheduling and File Replication for Data-Intensive Jobs with Batch-shared {I/O} },
year = { 2006 },
}
@inproceedings { Khanna06b,
address = { Saint-Malo, France },
author = { Gaurav Khanna and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { Proceedings of the 12th International Workshop on Job Scheduling Strategies for Parallel Processing (JSSPP 2006), In Conjunction with SIGMETRICS 2006 },
month = { Jun },
title = { A Data Locality Aware Online Scheduling Approach for I/O-Intensive Jobs with File Sharing },
year = { 2006 },
}
@inproceedings { Bozdag06-HCW,
address = { Rhodes Island, Greece },
author = { Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and F. {\"{O}}zg{\"{u}}ner },
booktitle = { 15th International Heterogeneous Computing Workshop (in conjunction with IPDPS) },
link = { http://dx.doi.org/10.1109/IPDPS.2006.1639389 },
month = { Apr },
title = { A task duplication based bottom-up scheduling algorithm for heterogeneous environments },
year = { 2006 },
}
@article { Zhang06-IJHPCA,
author = { Xi Zhang and Benjamin Rutt and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Joel H. Saltz },
journal = { The Journal of High Performance Computing Applications },
number = { 3 },
pages = { 423--438 },
title = { Supporting Scalable and Distributed Data Subsetting and Aggregation in Large-scale Seismic Data Analysis },
volume = { 20 },
year = { 2006 },
}
@inproceedings { Vydyanathan06-HCW,
author = { Nagavijayalakshmi Vydyanathan and Gaurav Khanna and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Heterogeneous Computing Workshop (HCW 2006) },
title = { Scheduling of Tasks with Batch-shared I/O on Heterogeneous Systems },
year = { 2006 },
}
@inproceedings { Vydyanathan06b,
author = { Nagavijayalakshmi Vydyanathan and Sriram Krishnamoorthy and Gerald Sabin and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and P. Sadayappan and Joel H. Saltz },
booktitle = { 2006 International Conference on Parallel Processing },
title = { An Integrated Approach for Processor Allocation and Scheduling of Mixed-Parallel Applications },
year = { 2006 },
}
@inproceedings { Kumar06-SC,
author = { Vijay S. Kumar and Benjamin Rutt and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Sunny Chow and Stephan Lamont and Maryann Martone and Joel H. Saltz },
booktitle = { Proceedings of {SC2006} High Performance Computing, Networking, and Storage Conference },
title = { Large Image Correction and Warping in a Cluster Environment },
year = { 2006 },
}
@inproceedings { krishnamoorthy06-POHLL,
address = { Rhodes Island, Greece },
author = { Sriram Krishnamoorthy and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Jarek Nieplocha and P. Sadayappan },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS), Workshop on Performance Optimization for High-Level Languages and Libraries (POHLL 2006) },
title = { An Approach to Locality-Conscious Load Balancing and Transparent Memory Hierarchy Management with a Global-Address-Space Parallel Programming Model },
year = { 2006 },
}
@inproceedings { Krishnamoorthy06-SC,
author = { Sriram Krishnamoorthy and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Jarek Nieplocha and Atanas Rountev and P. Sadayappan },
booktitle = { Proceedings of {SC2006} High Performance Computing, Networking, and Storage Conference },
title = { Hypergraph Partitioning for Automatic Memory Hierarchy Management },
year = { 2006 },
}
@inproceedings { krishnamoorthy2006-NGS,
address = { Rhodes Island, Greece },
author = { Sriram Krishnamoorthy and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Jarek Nieplocha and Atanas Rountev and P. Sadayappan },
booktitle = { Proc. {IPDPS} Workshop on {N}ext {G}eneration {S}oftware },
title = { An Extensible Global Address Space Framework with Decoupled Task and Data Abstractions },
year = { 2006 },
}
@inproceedings { Devine06,
author = { K.D. Devine and Erik G. Boman and R.T. Heaphy and R.H. Bisseling and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of 20th International Parallel and Distributed Processing Symposium (IPDPS) },
publisher = { IEEE },
title = { Parallel Hypergraph Partitioning for Scientific Computing },
year = { 2006 },
}
@inproceedings { Rutt05,
address = { Boston, MA },
author = { Benjamin Rutt and Vijay S. Kumar and Tony C. Pan and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Yujun Wang and Joel H. Saltz },
booktitle = { The 2005 IEEE International Conference on Cluster Computing },
month = { Sep },
title = { Distributed Out-of-Core Preprocessing of Very Large Microscopy Images for Efficient Querying },
year = { 2005 },
}
@inproceedings { Narayanan05B,
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { Proceedings of {VLDB} Workshop Data Management in Grid 2005 ({VLDB DMG\'05} },
month = { Sep },
pages = { 98--109 },
title = { Servicing Seismic and Oil Reservoir Simulation Data through Grid Data Services },
year = { 2005 },
}
@article { Kurc05,
author = { Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and X. Zhang and Joel H. Saltz and R. Martino and Mary F. Wheeler and M. Peszynska and Alan Sussman and C. Hansen and M. Sen and R. Seifoullaev and P. Stoffa and C. Torres-Verdin and Manish Parashar },
journal = { Concurrency and Computation: Practice and Experience. },
month = { Sep },
number = { 11 },
pages = { 1441--1467 },
title = { A Simulation and Data Analysis System for Large Scale,Data-Driven Oil Reservoir Simulation Studies },
volume = { 17 },
year = { 2005 },
}
@inproceedings { Bozdag05-HPCC,
address = { Sorrento, Italy },
author = { Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Assefaw H. Gebremedhin and F. Manne and Erik G. Boman and F. {\"{O}}zg{\"{u}}ner },
booktitle = { Proc. of 1st Int\'l. Conf. on High Performance Computing and Communications },
link = { http://dx.doi.org/10.1007/11557654_90 },
month = { Sep },
pages = { 796--806 },
publisher = { Springer },
series = { Lecture notes in Computer Science },
title = { A Parallel Distance-2 Graph Coloring Algorithm for Distributed Memory Computers },
volume = { 3726 },
year = { 2005 },
}
@inproceedings { Boman05-EuroPar,
address = { Lisbon, Portugal },
author = { Erik G. Boman and Doruk Bozda{\u{g}} and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Assefaw H. Gebremedhin and F. Manne },
booktitle = { Proc. of 11th Int\'l. Euro-Par Conf. on Parallel Processing },
link = { http://dx.doi.org/10.1007/11549468_29 },
month = { Aug },
pages = { 241--251 },
publisher = { Springer },
series = { Lecture notes in Computer Science },
title = { A Scalable Parallel Graph Coloring Algorithm for Distributed Memory Computers },
volume = { 3648 },
year = { 2005 },
}
@inproceedings { Bozdag05-ICPP,
address = { Oslo, Norway },
author = { Doruk Bozda{\u{g}} and F. {\"{O}}zg{\"{u}}ner and E. Ekici and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proc. of 34th Int\'l. Conf. on Parallel Processing },
link = { http://dx.doi.org/10.1109/ICPP.2005.15 },
month = { Jun },
pages = { 630--637 },
title = { A Task Duplication Based Scheduling Algorithm Using Partial Schedules },
year = { 2005 },
}
@inproceedings { Weng05,
author = { Li Weng and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Gagan Agrawal and Joel H. Saltz },
booktitle = { Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005) },
month = { May },
title = { Servicing Range Queries on Multidimensional Datasets with Partial Replicas },
year = { 2005 },
}
@inproceedings { Khanna05,
author = { Gaurav Khanna and Nagavijayalakshmi Vydyanathan and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
booktitle = { Proceedings of the 5th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid 2005) },
month = { May },
title = { A Hypergraph Partitioning Based Approach for Scheduling of Tasks with Batch-shared {I/O} },
year = { 2005 },
}
@techreport { ZoltanParHypPar05tr,
address = { Albuquerque, NM },
author = { Erik G. Boman and K.D. Devine and R.T. Heaphy and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and R.H. Bisseling },
institution = { Sandia National Laboratories },
month = { Apr },
number = { SAND2005-2796C },
title = { Parallel Hypergraph Partitioning for Scientific Computing },
year = { 2005 },
}
@inproceedings { Narayanan05,
author = { Sivaramakrishnan Narayanan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Vijay S. Kumar and Joel H. Saltz },
booktitle = { High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference },
month = { Mar },
title = { A Runtime Framework for Partial Replication and Its Application for On-Demand Data Exploration },
year = { 2005 },
}
@inproceedings { Kumar05,
author = { Vijay S. Kumar and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { High Performance Computing Symposium (HPC 2005), SCS Spring Simulation Multiconference },
month = { Mar },
title = { Design and Implementation of a Data Server Using a Peer-to-Peer Storage System },
year = { 2005 },
}
@inproceedings { Yoo05,
author = { Andy Yoo and Edmond Chow and Keith Henderson and William McLendon and Bruce Hendrickson and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
booktitle = { Proceedings of {SC2005} High Performance Computing, Networking, and Storage Conference },
note = { Gordon Bell Finalist. },
title = { A Scalable Distributed Parallel Breadth-First Search Algorithm on {BlueGene/L} },
year = { 2005 },
}
@incollection { Ribeiro05,
author = { M. Ribeiro and Tahsin M. Kurc and Tony C. Pan and K. Huang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and X. Zhang and S. Langella and S. Hastings and S. Oster and R. Ferreira and Joel H. Saltz },
booktitle = { Grid Computing: The New Frontier Of High Performance Computing, 14 },
editor = { Lucio Grandinetti },
publisher = { Elsevier },
title = { Tools for Efficient Subsetting and Pipelined Processing of Large Scale, Distributed Biomedical Image Data },
year = { 2005 },
}
@inproceedings { DBLP:conf/iccS/ParasharMBKRKCSW05,
author = { Manish Parashar and Vincent Matossian and Wolfgang Bangerth and Hector Klie and Benjamin Rutt and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz and Mary F. Wheeler },
booktitle = { International Conference on Computational Science (2) },
link = { http://dx.doi.org/10.1007/11428848_85 },
pages = { 656-663 },
title = { Towards Dynamic Data-Driven Optimization of Oil Well Placement. },
year = { 2005 },
}
@article { Parashar2005-FGCS,
author = { Manish Parashar and Hector Klie and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Vincent Matossian and Joel H. Saltz and Mary F. Wheeler },
doi = { 10.1016/j.future.2004.09.028 },
journal = { Future Generation Computer Systems },
month = { Jan },
number = { 1 },
pages = { 19--26 },
title = { Application of Grid-enabled technologies for solving optimization problems in data-driven reservoir studies },
volume = { 21 },
year = { 2005 },
}
@article { Hastings05,
author = { Shannon Hastings and Matheus Ribeiro and Stephen Langella and Scott Oster and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tony C. Pan and Kun Huang and Renato Ferreira and Joel H. Saltz and Tahsin M. Kurc },
journal = { SIGMOD Record },
link = { http://doi.acm.org/10.1145/1084805.1084815 },
number = { 3 },
pages = { 50-55 },
title = { XML database support for distributed execution of data-intensive scientific workflows. },
volume = { 34 },
year = { 2005 },
}
@inproceedings { Langella04,
author = { Stephen Langella and Shannon Hastings and Scott Oster and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { Proceedings of 2004 IEEE International Conference on Cluster Computing },
month = { Sep },
title = { A Distributed Data Management Middleware for Data-Driven Application Systems },
year = { 2004 },
}
@inproceedings { Zhang04B,
address = { Honolulu, HI },
author = { Xi Zhang and Tahsin M. Kurc and Tony C. Pan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Sivaramakrishnan Narayanan and Pete Wyckoff and Joel H. Saltz },
booktitle = { Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13) },
month = { Jun },
publisher = { IEEE Press },
title = { Strategies for Using Additional Resources in Parallel Hash-based Join Algorithms },
year = { 2004 },
}
@inproceedings { Weng04,
address = { Honolulu, HI },
author = { Li Weng and Gagan Agrawal and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Sivaramakrishnan Narayanan and Joel H. Saltz },
booktitle = { Proceedings of the Thirteen International Symposium on High Performance Distributed Computing (HPDC-13) },
month = { Jun },
publisher = { IEEE Press },
title = { An Approach for Automatic Data Virtualization },
year = { 2004 },
}
@inproceedings { Parashar04,
author = { Manish Parashar and H. Klie and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and V. Matossian and Joel H. Saltz and Mary F. Wheeler },
booktitle = { Proceedings of Workshop on Dynamic Data Driven Application Systems (International Conference on Computational Science) },
month = { Jun },
pages = { 805-812 },
title = { Application of Grid-enabled Technologies for Solving Optimization Problems in Data-Driven Reservoir Studies },
year = { 2004 },
}
@inproceedings { Zhang04,
address = { Chicago, IL },
author = { Xi Zhang and Tony C. Pan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Joel H. Saltz },
booktitle = { Proceedings of 4th IEEE/ACM International Symposium on Cluster Computing and the Grid (CCGrid2004) },
month = { Apr },
title = { Serving Queries to Multi-Resolution Datasets on Disk-based Storage Clusters },
year = { 2004 },
}
@inproceedings { Weng04B,
author = { Li Weng and Gagan Agrawal and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { Proceedings of the 17th International Workshop on Languages and Compilers for Parallel Computing },
title = { Supporting SQL-3 Aggregations on Grid-based Data Repositories },
year = { 2004 },
}
@inproceedings { Vydyanathan04,
author = { Nagavijayalakshmi Vydyanathan and Gaurav Khanna and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Pete Wyckoff and Joel H. Saltz and P. Sadayappan },
booktitle = { Proceedings of the 5th IEEE/ACM International Workshop on Grid Computing (Grid 2004) },
title = { Use of PVFS for Efficient Execution of Jobs with Pipeline-Shared I/O },
year = { 2004 },
}
@article { Aykanat04,
author = { Cevdet Aykanat and Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
journal = { {SIAM} Journal on Scientific Computing (SISC) },
number = { 6 },
pages = { 1860--1879 },
title = { Permuting Sparse Rectangular Matrices into Block-Diagonal Form },
volume = { 26 },
year = { 2004 },
link = { https://doi.org/10.1137/S1064827502401953 },
}
@article { Catalyurek03B,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Michael D. Beynon and Chialin Chang and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
journal = { {IEEE} Transactions on Information Technology in BioMedicine },
month = { Dec },
number = { 4 },
pages = { 230--248 },
title = { The Virtual Microscope },
volume = { 7 },
year = { 2003 },
}
@inproceedings { Narayanan03B,
address = { Phoenix, Arizona },
author = { Sivaramakrishnan Narayanan and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Xi Zhang and Joel H. Saltz },
booktitle = { Proceedings of the Fourth International Workshop on Grid Computing (Grid 2003) },
month = { Nov },
pages = { 141--148 },
title = { Applying Database Support for Large Scale Data Driven Science in Distributed Environments },
year = { 2003 },
}
@inproceedings { Kurc03B,
address = { Phoenix, {AZ} },
author = { Tahsin M. Kurc and Feng Lee and Gagan Agrawal and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Renato Ferreira and Joel H. Saltz },
booktitle = { ACM/IEEE {SC2003} },
month = { Nov },
title = { Optimizing Reduction Computations In a Distributed Environment },
year = { 2003 },
}
@inproceedings { SALTZ03,
address = { Melbourne, Australia },
author = { Joel H. Saltz and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and M. Gray and S. Hastings and S. Langella and S. Narayanan and R. Martino and S. Bryant and M. Peszynska and Mary F. Wheeler and Alan Sussman and Michael D. Beynon and C. Hansen and D. Stredney and and D. Sessanna },
booktitle = { Dynamic Data Driven Application Systems Workshop, held jointly with ICCS 2003 },
month = { Jun },
title = { Driving Scientific Applications by Data in Distributed Environments },
year = { 2003 },
}
@inproceedings { Balaji03,
author = { Pavan Balaji and Jiesheng Wu and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Dhabaleswar K. Panda and Joel H. Saltz },
booktitle = { Proceedings of the Twelfth International Symposium on High Performance Distributed Computing (HPDC-12) },
month = { Jun },
publisher = { IEEE Press },
title = { Impact of High Performance Sockets on Data Intensive Applications },
year = { 2003 },
}
@inproceedings { Hastings03,
author = { Shannon Hastings and Tahsin M. Kurc and Steve Langella and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tony C. Pan and Joel H. Saltz },
booktitle = { CCGrid: IEEE International Symposium on Cluster Computing and the Grid },
month = { May },
publisher = { IEEE Press },
title = { Image Processing for the Grid: A Toolkit for Building Grid-enabled Image Processing Applications. },
year = { 2003 },
}
@inproceedings { Catalyurek03,
address = { Melbourne, FL },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Mike Gray and Tahsin M. Kurc and Joel H. Saltz and Eric Stahlberg and Renato Ferreira },
booktitle = { 18th ACM Symposium on Applied Computing (SAC2003) Bioinformatics Track },
month = { Mar },
title = { A Component-based Implementation of Multiple Sequence Alignment },
year = { 2003 },
}
@article { Narayanan03,
author = { Sivaramakrishnan Narayanan and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
journal = { Parallel Processing Letters },
number = { 2 },
pages = { 245--271 },
title = { Database Support for Data-driven Scientific Applications in the Grid },
volume = { 13 },
year = { 2003 },
}
@inproceedings { Kurc03,
author = { Tahsin M. Kurc and S. Hastings and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz and J. D. Fleig and B. D. Clymer and H. von Tengg-Kobligk and K. T. Baudendistel and R. Machiraju and M. V. Knopp },
booktitle = { The Society for Computer Applications in Radiology (SCAR 2003) },
title = { A Distributed Execution Environment for Analysis of {DCE-MR} Image Datasets },
year = { 2003 },
}
@inproceedings { Spencer02,
author = { Matthew Spencer and Renato Ferreira and Michael Beynon and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Alan Sussman and Joel H. Saltz },
booktitle = { Proceedings of the 2002 ACM/IEEE SC02 Conference },
month = { Nov },
publisher = { ACM Press },
title = { Executing Multiple Pipelined Data Analysis Operations in the {Grid} },
year = { 2002 },
}
@techreport { Catalyurek02C,
annote = { VM-TechRep },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Michael D. Beynon and Chialin Chang and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
institution = { University of Maryland, Department of Computer Science and UMIACS },
month = { Oct },
number = { CS-TR-xxxx and UMIACS-TR-2002-xx },
title = { The Virtual Microscope },
year = { 2002 },
}
@article { BEYNON02B,
author = { Michael Beynon and Chialin Chang and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Alan Sussman and Henrique Andrade and Renato Ferreira and Joel H. Saltz },
journal = { Parallel Computing },
month = { May },
note = { Special Issue on Data Intensive Computing },
number = { 5 },
pages = { 827--859 },
title = { Processing Large-Scale Multidimensional Data in Parallel and Distributed Environments },
volume = { 28 },
year = { 2002 },
}
@inproceedings { Beynon02C,
address = { Fort Lauderdale, Florida },
author = { Michael D. Beynon and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Alan Sussman and Joel H. Saltz },
booktitle = { Proceedings of 16th International Parallel and Distributed Processing Symposium ({IPDPS}) },
month = { Apr },
title = { Efficient Manipulation of Large Datasets on Heterogeneous Storage Systems },
year = { 2002 },
}
@inproceedings { Catalyurek02B,
address = { Fort Lauderdale, Florida },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Eric Stahlberg and Renato Ferreira and Tahsin M. Kurc and Joel H. Saltz },
booktitle = { Proceedings of 16th International Parallel and Distributed Processing Symposium ({IPDPS}), First Workshop on High Performance Computational Biology },
month = { Apr },
title = { Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments },
year = { 2002 },
}
@inproceedings { ANDRADE02D,
author = { Henrique Andrade and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Alan Sussman and Joel H. Saltz },
booktitle = { Proceedings of the Sixth Workshop on Languages, Compilers and Run-time Systems for Scalable Computers },
month = { Mar },
publisher = { Springer-Verlag },
title = { Persistent Caching in a Multiple Query Optimization Framework },
year = { 2002 },
}
@inproceedings { Catalyurek01C,
address = { Denver, {CO} },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
booktitle = { ACM/IEEE {SC2001} },
key = { CATALYUREK01C },
month = { Nov },
title = { A Hypergraph-Partitioning Approach for Coarse-Grain Decomposition },
year = { 2001 },
}
@article { Beynon01-ParCo,
author = { Michael D. Beynon and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
journal = { Parallel Computing },
link = { http://linkinghub.elsevier.com/retrieve/pii/S0167819101000990 },
month = { Oct },
number = { 11 },
pages = { 1457--1478 },
title = { Distributed Processing of Very Large Datasets with {DataCutter} },
volume = { 27 },
year = { 2001 },
}
@inproceedings { BEYNON01D,
annote = { DataCutter },
author = { Michael D. Beynon and Alan Sussman and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Joel H. Saltz },
booktitle = { Proceedings of the Third Annual International Workshop on Active Middleware Services (AMS2001) },
month = { Aug },
title = { Performance Optimization for Data Intensive Grid Applications },
year = { 2001 },
}
@article { Catalyurek01A,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Tahsin M. Kurc and Alan Sussman and Joel H. Saltz },
journal = { Archives of Pathology and Laboratory Medicine },
key = { CATALYUREK01A },
month = { Aug },
number = { 8 },
title = { Improving the Performance and Functionality of the Virtual Microscope },
volume = { 125 },
year = { 2001 },
}
@article { Kurc01B,
author = { Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
journal = { IEEE Computer Graphics and Applications },
month = { Jul/Aug },
number = { 4 },
pages = { 24--33 },
title = { Visualization of Large Datasets with the {Active Data Repository} },
volume = { 21 },
year = { 2001 },
}
@techreport { Beynon01-TR,
annote = { DataCutter },
author = { Michael D. Beynon and Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Alan Sussman and Joel H. Saltz },
institution = { University of Maryland, Department of Computer Science and UMIACS },
month = { May },
number = { CS-TR-4249 and UMIACS-TR-2001-34 },
title = { A Component-based Implementation of Iso-surface Rendering for Visualizing Large Datasets },
year = { 2001 },
}
@inproceedings { Catalyurek01B,
address = { San Francisco, {CA} },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
booktitle = { Proceedings of 15th International Parallel and Distributed Processing Symposium ({IPDPS}) },
key = { CATALYUREK01B },
month = { Apr },
title = { A Fine-Grain Hypergraph Model for {2D} Decomposition of Sparse Matrices },
year = { 2001 },
}
@inproceedings { CHANG01B,
author = { Chialin Chang and Tahsin M. Kurc and Alan Sussman and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Joel H. Saltz },
booktitle = { Proceedings of the Eleventh SIAM Conference on Parallel Processing for Scientific Computing },
month = { Mar },
organization = { SIAM },
title = { A Hypergraph-Based Workload Partitioning Strategy for Parallel Data Aggregation },
year = { 2001 },
}
@techreport { Kurc01,
author = { Tahsin M. Kurc and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Chialin Chang and Alan Sussman and Joel H. Saltz },
institution = { University of Maryland, Department of Computer Science and UMIACS },
month = { Jan },
note = { Also appears in IEEE Computer Graphics and Applications, Jul/Aug 2001 },
number = { CS-TR-4208 and UMIACS-TR-2001-04 },
title = { Exploration and Visualization of Very Large Datasets with the {Active Data Repository} },
year = { 2001 },
}
@phdthesis { Catalyurek99PhD,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { Bilkent University, Computer Engineering and Information Science },
key = { Catalyurek99PhD },
month = { Nov },
title = { Hypergraph Models for Sparse Matrix Partitioning and Reordering },
year = { 1999 },
}
@article { Catalyurek99,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
journal = { IEEE Transactions on Parallel and Distributed Systems },
key = { CATALYUREK99 },
number = { 7 },
pages = { 673--693 },
title = { Hypergraph-Partitioning Based Decomposition for Parallel Sparse-Matrix Vector Multiplication },
volume = { 10 },
year = { 1999 },
link = { https://doi.org/10.1109/71.780863 },
}
@techreport { patohmanual,
address = { Ankara, 06533 Turkey },
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
institution = { Bilkent University, Department of Computer Engineering },
link = { https://faculty.cc.gatech.edu/~umit/software.html },
title = { {PaToH}: A Multilevel Hypergraph Partitioning Tool, Version 3.0 },
year = { 1999 },
}
@article { Pinar96,
author = { Ali P{\i}nar and {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat and M. P{\i}nar },
journal = { Lecture notes in Computer Science },
pages = { 473--482 },
title = { Decomposing linear programs for parallel solution },
volume = { 1041 },
year = { 1996 },
link = { https://doi.org/10.1007/3-540-60902-4_50 },
}
@inproceedings { Catalyurek96,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
booktitle = { Proceedings of 3rd International Symposium on Solving Irregularly Structured Problems in Parallel, Irregular\'96 },
key = { CATALYUREK96 },
pages = { 75--86 },
publisher = { Springer-Verlag },
series = { Lecture notes in Computer Science },
title = { Decomposing irregularly sparse matrices for parallel matrix-vector multiplications },
volume = { 1117 },
year = { 1996 },
}
@inproceedings { Catalyurek95,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and Cevdet Aykanat },
booktitle = { Proceedings of International Conference on High Performance Computing },
month = { Dec },
title = { A Hypergraph Model for Mapping Repeated Sparse Matrix-Vector Product Computations onto Multicomputers },
year = { 1995 },
}
@mastersthesis { Catalyurek94,
author = { {\"{U}}mit V. {\c{C}}ataly{\"{u}}rek },
institution = { Bilkent University, Computer Engineering and Information Science },
month = { Sep },
title = { A Constructive Multi-way Circuit Partitioning Algorithm Based on Minimum Degree Ordering },
year = { 1994 },
}