Lawrence Berkeley National Lab

DST Recent Publications List

2019

Araujo, Silva, Resende, Ushizima, Medeiros, Carneiro & Bianchi, "Deep Learning for Cell Image Segmentation and Ranking", Computerized Medical Imaging and Graphics, (2019)
MacNeil, Ushizima, Panerai, Mansour, Barnard & Parkinson, "Interactive Volumetric Segmentation for Textile Microtomography Data using Wavelets and Non-local means", Journal of Statistical Analysis and Mining, (2019)
C. Nan-Chen Chen, "Harnessing Complexity in High Performance Computing Ecosystems: A Complex Adaptive Systems Framework", 2019 52nd Hawaii International Conference on System Sciences (HICSS), (2019)

2018

P. Enfedaque, H. Chang, H. Krishnan & S. Marchesini, "GPU-Based Implementation of Ptycho-ADMM for High Performance X-Ray Imaging", Computational Science -- ICCS 2018, 540-553 (2018)
A. Arkin, R. Cottingham, C. Henry, N. Harris, R. Stevens, S. Maslov, P. Dehal, D. Ware, F. Perez, S. Canon, M. Sneddon, M. Henderson, W. Riehl, D. Murphy-Olson, S. Chan, R. Kamimura, S. Kumari, M. Drake, T. Brettin, E. Glass, D. Chivian, D. Gunter, D. Weston, B. Allen, J. Baumohl, A. Best, B. Bowen, S. Brenner, C. Bun, J. Chandonia, J. Chia, R. Colasanti, N. Conrad, J. Davis, B. Davison, M. Dejongh, S. Devoid, E. Dietrich, I. Dubchak, J. Edirisinghe, G. Fang, J. Faria, P. Frybarger, W. Gerlach, M. Gerstein, A. Greiner, J. Gurtowski, H. Haun, F. He, R. Jain, M. Joachimiak, K. Keegan, S. Kondo, V. Kumar, M. Land, F. Meyer, M. Mills, P. Novichkov, T. Oh, G. Olsen, R. Olson, B. Parrello, S. Pasternak, E. Pearson, S. Poon, G. Price, S. Ramakrishnan, P. Ranjan, P. Ronald, M. Schatz, S. Seaver, M. Shukla, R. Sutormin, M. Syed, J. Thomason, N. Tintle, D. Wang, F. Xia, H. Yoo, S. Yoo & D. Yu, "KBase: The United States department of energy systems biology knowledgebase", Nature Biotechnology, 36, 566-569 (2018)
K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber & B. Hamann, "Measuring the Error in Approximating the Sub-level Set Topology of Sampled Scalar Data", International Journal of Computational Geometry & Applications (IJCGA), 28, 57-77 (2018)
K. E. Bouchard, J. B. Aimone, M. Chun, T. Dean, M. Denker, M. Diesmann, D. D. Donofrio, L. M. Frank, N. Kasthuri, C. Koch, O. Ruebel, H. D. Simon, F. T. Sommer & Prabhat, "International Neuroscience Initiatives through the Lens of High-Performance Computing", Computer, 51, 50-59 (2018)
Y.-W. Cheah, D. Paine, D. Ghoshal & L. Ramakrishnan, "Bringing Data Science to Qualitative Analysis", 2018 IEEE 14th International Conference on e-Science, 325-326 (2018)
E. Deelman, T. Peterka, I. Altintas, C. Carothers, K. van Dam, K. Moreland, M. Parashar, L. Ramakrishnan, M. Taufer & J. Vetter, "The future of scientific workflows", International Journal of High Performance Computing Applications, 32, 159-175 (2018)
D. Ghoshal, L. Ramakrishnan & D. Agarwal, "Dac-Man: Data Change Management for Scientific Datasets on HPC Systems", Proceedings of the International Conference for High Performance Computing, Networking, Storage, and Analysis, 72:1-72:13 (2018) PDF
Araujo, Silva, Medeiros, Farias, Calaes, Bianchi, Carneiro & Ushizima, "Active contours for overlapping cell segmentation", Int. Journal of Biomedical Engineering and Technology, (2018)
T.-W. Ke, A. S. Brewster, S. X. Yu, D. Ushizima, C. Yang & N. K. Sauter, "A Convolutional Neural Network-based Screening Tool for X-ray Serial Crystallography", Journal of Synchrotron Radiation, 25, 655-670 (2018)
B. Lessley, T. Perciano, C. Heinemann, D. Camp, H. Childs & E. W. Bethel, "DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives", 8th IEEE Symposium on Large Data Analysis and Visualization (LDAV), (2018)
T. Liebmann, G. H. Weber & G. Scheuermann, "Hierarchical Correlation Clustering in Multiple 2D Scalar Fields", Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), 37, (2018)
V. de Melo, D. Ushizima, S. Baracho & R. Coelho, "Gradient Boosting Decision Trees for Echocardiogram Images", 2018 International Joint Conference on Neural Networks (IJCNN), (2018)
E. Lohrmann, Z. Luki, D. Morozov & J. Muller, "Programmable In Situ System for Iterative Workflows", Job Scheduling Strategies for Parallel Processing, 122-131 (2018)
D. Miller, J. Siirola, D. Agarwal, A. Burgard, A. Lee, J. Eslick, B. Nicholson, C. Laird, L. Biegler, D. Bhattacharyya, N. Sahinidis, I. Grossmann, C. Gounaris & D. Gunter, "Next Generation Multi-Scale Process Systems Engineering Framework", Computer Aided Chemical Engineering, 44, 2209-2214 (2018)
R. J. Pandolfi, D. B. Allan, E. Arenholz, L. Barroso-Luque, S. I. Campbell, T. A. Caswell, A. Blair, F. De Carlo, S. Fackler, A. P. Fournier, G. Freychet, M. Fukuto, D. Gursoy, Z. Jiang, H. Krishnan, D. Kumar, R. J. Kline, R. Li, C. Liman, S. Marchesini, A. Mehta, A. T. N'Diaye, D. Y. Parkinson, H. Parks, L. A. Pellouchoud, T. Perciano, F. Ren, S. Sahoo, J. Strzalka, D. Sunday, C. J. Tassone, D. Ushizima, S. Venkatakrishnan, K. G. Yager, P. Zwart, J. A. Sethian & A. Hexemer, "Xi-cam: A Versatile Interface for Data Visualization and Analysis", Journal of Synchrotron Radiation, 25, (2018)
C. Roberts, A. Scaglione & S. Peisert, "A Holistic Approach to Distribution Grid Intrusion Detection Systems", EnergyCentral, (2018)
T. Benzel & S. Peisert, "Selected Papers from the 2017 IEEE Symposium on Security and Privacy [Guest editors' introduction]", IEEE Security & Privacy, 16, 10-11 (2018)
S. Peisert, E. Dart, W. K. Barnett, J. Cuff, R. L. Grossman, E. Balas, A. Berman, A. Shankar & B. Tierney, "The Medical Science DMZ: A Network Design Pattern for Data-Intensive Medical Science", Journal of the American Medical Informatics Association (JAMIA), 26, 267-274 (2018)
M. Jamei, A. Scaglione & S. Peisert, "Cyber-Physical Relaying Reliability Enhancement through Hybrid Network Intrusion Detection Systems", Proceedings of the 2018 IEEE International Conference on Communications, Control, and Computing Technologies for Smart Grids (SmartGridComm),, (2018)
G. Rodrigo, M. Henderson, G. Weber, C. Ophus, K. Antypas & L. Ramakrishnan, "ScienceSearch: Enabling Search through Automatic Metadata Generation", Proceedings IEEE 14th International Conference on e-Science (e-Science) 2018, 93-104 (2018)
G. Rodrigo, E. Elmroth, P.-O. Ostberg & L. Ramakrishnan, "ScSF: A Scheduling Simulation Framework", Job Scheduling Strategies for Parallel Processing, 152-173 (2018)
G. Rodrigo, P. Östberg, E. Elmroth, K. Antypas, R. Gerber & L. Ramakrishnan, "Towards understanding HPC users and systems: A NERSC case study", Journal of Parallel and Distributed Computing, 111, 206-221 (2018)
O. Ruebel & B. P. Bowen, "BASTet: Shareable and Reproducible Analysis and Visualization of Mass Spectrometry Imaging Data via OpenMSI", IEEE Transactions on Visualization and Computer Graphics, 24, 1025-1035 (2018)
E. Stewart, P. Top, M. Chertkov, D. Deka, S. Backhaus, A. Lokhov, C. Roberts, V. Hendrix, S. Peisert, A. Florita, T. King & M. Reno, "Integrated multi-scale data analytics and machine learning for the distribution grid", 2017 IEEE International Conference on Smart Grid Communications, SmartGridComm 2017, 2018-January, 423-429 (2018)
D. Stone, M. Risser, O. Angelil, M. Wehner, S. Cholia, N. Keen, H. Krishnan, T. O'Brien & W. Collins, "A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5.1-1degree", Weather and Climate Extremes, 19, 20-28 (2018)
S. Swaid, M. Maat, H. Krishnan, D. Ghoshal & L. Ramakrishnan, "Usability heuristic evaluation of scientific data analysis and visualization tools", Advances in Intelligent Systems and Computing, 607, 471-482 (2018)

2017

C. Heinemann, T. Perciano, D. Ushizima & E. W. Bethel, "Distributed Memory Parallel Markov Random Fields Using Graph Partitioning", 2017 IEEE International Conference on Big Data (Big Data), 3332-3341 (2017)
D. Agarwal, C. Varadharajan, S. Cholia, C. Snavely, V. Hendrix, D. Gunter, W. Riley, M. jones, A. budden & D. Vieglas, "Environmental System Science Data Infrastructure for a Virtual Ecosystem (ESS-DIVE)-A New US DOE Data Archive", (2017)
M. Alegro, P. Theofilas, A. Nguy, P. A. Castruita, W. Seeley, H. Heinsen, D. M. Ushizima & L. T. Grinberg, "Automating cell detection and classification in human brain fluorescent microscopy images using dictionary learning and sparse coding", Journal of Neuroscience Methods, 282, 20 - 33 (2017) PDF
E. W. Bethel, "Towards a Data-Centric Research and Development Roadmap for Large-scale Science User Facilities", 13th IEEE International Conference on eScience, (2017)
T. E. Williams, D. Ushizima, C. Zhu, A. Anders, D. J. Milliron & B. A. Helms, "Nearest-neighbour nanocrystal bonding dictates framework stability or collapse in colloidal nanocrystal frameworks", Chemical Communications, 53, 4853-4856 (2017) PDF
Y. Cheah, J. Boverhof, A. Elbashandy, D. Agarwal, J. Leek, T. Epperly, J. Eslick & D. Miller, "Data management and simulation support accelerating carbon capture through computing", Proceedings of the 2016 IEEE 12th International Conference on e-Science, e-Science 2016, 389-398 (2017)
D. S. Christianson, C. Varadharajan, B. Christoffersen, M. Detto, B. Faybishenko, B. O. Gimenez, V. Hendrix, K. J. Jardine, R. Negron-Juarez, G. Z. Pastorello & others, "A metadata reporting framework (FRAMES) for synthesis of ecohydrological observations", Ecological Informatics, 42, 148-158 (2017)
M. Farmand, R. Celestre, P. Denes, A. L. D. Kilcoyne, S. Marchesini, H. Padmore, T. Tyliszczak, T. Warwick, X. Shi, J. Lee, Y.-S. Yu, J. Cabana, J. Joseph, H. Krishnan, T. Perciano, F. R. N. C. Maia & D. A. Shapiro, "Near-edge X-ray refraction fine structure microscopy", Applied Physics Letters, 110, 063101 (2017) PDF
W. Fox, D. Ghoshal, A. Souza, G. Rodrigo & L. Ramakrishnan, "E-HPC: A library for elastic resource management in HPC environments", Proceedings of WORKS 2017: 12th Workshop on Workflows in Support of Large-Scale Science - Held in conjunction with SC 2017: The International Conference for High Performance Computing, Networking, Storage and Analysis, (2017)
D. Ghoshal, V. Hendrix, W. Fox, S. Balasubhramanian & L. Ramakrishnan, "FRIEDA: Flexible Robust Intelligent Elastic Data Management Framework", The Journal of Open Source Software, 2, 164-164 (2017)
D. Ghoshal & L. Ramakrishnan, "MaDaTS: Managing data on tiered storage for scientific workflows", HPDC 2017 - Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing, 41-52 (2017)
B. Lessley, T. Perciano, M. Mathai, H. Childs & E. W. Bethel, "Maximal Clique Enumeration with Data Parallel Primitives", 7th IEEE Symposium on Large Data Analysis and Visualization (LDAV), (2017)
J. Lukasczyk, R. Maciejewski, G. H. Weber, C. Garth & H. Leitte, "Nested Tracking Graphs", Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), 36, 12-22 (2017)
S. Murugesan, K. Bouchard, J. A. Brown, B. Hamann, W. W. Seeley, A. Trujillo & G. H. Weber, "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity", IEEE Transactions on Computational Biology and Bioinformatics, 14, 805-818 (2017)
S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann & G. H. Weber, "Multi-scale Visual Analysis of Time-varying Electrocorticography Data via Clustering of Brain Regions", BMC Bioinformatics, 18, 236 (2017)
P. Oesterling, C. Heine, G. H. Weber, D. Morozov & G. Scheuermann, "Computing and Visualizing Time-Varying Merge Trees for High-Dimensional Data", Topological Methods in Data Analysis and Visualization IV: Theory, Algorithms, and Applications, 87-101 (2017)
G. Pastorello, D. Gunter, H. Chu, D. Christianson, C. Trotta, E. Canfora, B. Faybishenko, Y. Cheah, N. Beekwilder, S. Chan, S. Dengel, T. Keenan, F. O'brien, A. Elbashandy, C. Poindexter, M. Humphrey, D. Papale & D. Agarwal, "Hunting data rogues at scale: Data quality control for observational data in research infrastructures", Proceedings - 13th IEEE International Conference on eScience, eScience 2017, 446-447 (2017)
S. Peisert, "Security in High-Performance Computing Environments", Communications of the ACM (CACM), 60, 72-80 (2017)
M. Jamei, A. Scaglione, C. Roberts, E. Stewart, S. Peisert, C. McParland & A. McEachern, "Automated Anomaly Detection in Distribution Grids Using μPMU Measurements", Proceedings of the 50th Hawaii International Conference on System Sciences (HICSS), Electric Energy Systems Track, Resilient Networks Minitrack, (2017)
S. Peisert & V. Welch, "The Open Science Cyber Risk Profile: The Rosetta Stone for Open Science and Cybersecurity", IEEE Security & Privacy, 15, 94-95 (2017)
S. Peisert, R. Gentz, J. Boverhof, C. McParland, S. Engle, A. Elbashandy & D. Gunter, "LBNL Open Power Data", (2017)
S. Peisert, M. Bishop & E. Talbot, "A Model of Owner Controlled, Full-Provenance, Non-Persistent, High-Availability Information Sharing", Proceedings of the 2017 New Security Paradigms Workshop (NSPW), 80-89 (2017)
S. Peisert, V. Welch, A. Adams, R. Bevier, M. Dopheide, R. LeDuc, P. Meunier, S. Schwab & K. Stocks, "Open Science Cyber Risk Profile (OSCRP)", (2017)
M. Jamei, A. Scaglione, C. Roberts, A. McEachern, E. Stewart, S. Peisert & C. McParland, "Online Thevenin Parameter Tracking Using Synchrophasor Data", Proceedings of the 2017 IEEE Power Engineering Society (PES) General Meeting (GM), (2017)
J. Ganz & S. Peisert, "ASLR: How Robust is the Randomness?", Proceedings of the 2017 IEEE Secure Development Conference (SecDev), (2017)
L. J. Osterweil, M. Bishop, H. M. Conboy, H. Phan, B. I. Simidchieva, G. S. Avrunin, L. A. Clarke & S. Peisert, "A Comprehensive Framework for Using Iterative Analysis to Improve Human-Intensive Process Security: An Election Example", ACM Transactions on Privacy and Security (TOPS), 20, (2017)
M. Jamei, A. Scaglione, C. Roberts, A. McEachern, E. Stewart, S. Peisert & C. McParland, "Anomaly Detection Using μPMU Measurements in Distribution Grids", IEEE Transactions on Power Systems, 33, (2017)
T. Perciano, D. Ushizima, H. Krishnan, D. Parkinson, N. Larson, D. M. Pelt, W. Bethel, F. Zok & J. Sethian, "Insight into 3D micro-CT data: exploring segmentation algorithms through performance metrics", Journal of Synchrotron Radiation, 24, 1065-1077 (2017) PDF
H. Edelsbrunner & D. Morozov, "Persistent Homology", Handbook of Discrete and Computational Geometry, 3rd ed., (2017)
L. Ramakrishnan & D. Gunter, "Ten principles for creating usable software for science", Proceedings - 13th IEEE International Conference on eScience, eScience 2017, 210-218 (2017)
G. Rodrigo, E. Elmroth, P.-O. Östberg & L. Ramakrishnan, "Enabling Workflow-Aware Scheduling on HPC Systems", Proceedings of the 26th International Symposium on High-Performance Parallel and Distributed Computing, 3-14 (2017) PDF
E. Stewart, V. Hendrix, M. Chertkov & D. Deka, "Integrated Multi-Scale Data Analytics and Machine Learning for the Distribution Grid and Building-to-Grid Interface", (2017)
B. J. Daurer, H. Krishnan, T. Perciano, F. R. N. C. Maia, D. A. Shapiro, J. A. Sethian & S. Marchesini, "Nanosurveyor: a framework for real-time data processing", Advanced Structural and Chemical Imaging, 3, 7 (2017) PDF
G. H. Weber, S. Carpendale, D. Ebert, B. Fisher, H. Hagen, B. Shneiderman & A. Ynnerman, "Apply or Die: On the Role and Assessment of Application Papers in Visualization", IEEE Computer Graphics & Applications, 37, 96-104 (2017)
G. Weber, M. Bandstra, D. Chivers, H. Elgammal, V. Hendrix, J. Kua, J. Maltz, K. Muriki, Y. Ong, K. Song, M. Quinlan, L. Ramakrishnan & B. Quiter, "Web-based visual data exploration for improved radiological source detection", Concurrency Computation, 29, e4203 (2017)

2016

U. Ayachit, B. Whitlock, M. Wolf, B. Loring, B. Geveci, D. Lonie & E. W. Bethel, "The SENSEI Generic In Situ Interface", Proceedings of In Situ Infrastructures for Enabling Extreme-scale Analysis and Visualization (ISAV 2016), (2016)
U. Ayachit, A. Bauer, E. P. N. Duque, G. Eisenhauer, N. Ferrier, J. Gu, K. Jansen, B. Loring, Z. Lukić, S. Menon, D. Morozov, P. O'Leary, M. Rasquin, C. P. Stone, V. Vishwanath, G. H. Weber, B. Whitlock, M. Wolf, K. J. Wu & E. W. Bethel, "Performance Analysis, Design Considerations, and Applications of Extreme-scale In Situ Infrastructures", ACM/IEEE International Conference for High Performance Computing, Networking, Storage and Analysis (SC16), (2016) PDF
A. C. Bauer, H. Abbasi, J. Ahrens, H. Childs, B. Geveci, S. Klasky, K. Moreland, P. O'Leary, V. Vishwanath, B. Whitlock & E. W. Bethel, "In Situ Methods, Infrastructures, and Applications on High Performance Computing Platforms, a State-of-the-art (STAR) Report", Computer Graphics Forum, Proceedings of Eurovis 2016, 35, (2016)
E. W. Bethel, M. Greenwald, K. K. van Dam, M. Parashar, S. M. Wild & H. S. Wiley, "Management, Analysis, and Visualization of Experimental and Observational Data -- The Convergence of Data and Computing", Proceedings of the 2016 IEEE 12th International Conference on eScience, (2016)
W. Bhimji, D. Bard, M. Romanus, D. Paul, A. Ovsyannikov, B. Friesen, M. Bryson, J. Correa, G. K. Lockwood, V. Tsulaia, S. Byna, S. Farrell, D. Gursoy, C. Daley, V. Beckner, B. Van Straalen, D. Trebotich, C. Tull, G. H. Weber, N. J. Wright, K. Antypas & Prabhat, "Accelerating Science with the NERSC Burst Buffer Early User Program", CUG2016 Proceedings, (2016)
A. Bhowmick, D. Brookes, S. Yost, H. Dyson, J. Forman-Kay, D. Gunter, M. Head-Gordon, G. Hura, V. Pande, D. Wemmer, P. Wright & T. Head-Gordon, "Finding Our Way in the Dark Proteome", Journal of the American Chemical Society, 138, 9730-9742 (2016)
K. E. Bouchard, J. B. Aimone, M. Chun, T. Dean, M. Denker, M. Diesmann, D. D. Donofrio, L. M. Frank, N. Kasthuri, C. Koch, O. Ruebel, H. D. Simon, F. T. Sommer & Prabhat, "High-Performance Computing in Neuroscience for Data-Driven Discovery, Integration, and Dissemination", Neuron, 92, 628 - 631 (2016) PDF
H. A. Carr, G. H. Weber, C. M. Sewell & J. P. Ahrens, "Parallel Peak Pruning for Scalable SMP Contour Tree Computation", Proceedings of the 6th IEEE Symposium on Large Data Analysis and Visualization (LDAV), 75-84 (2016)
D. C. Miller, D. A. Agarwal, D. Bhattacharyya, J. Boverhof, Y.-W. Cheah, Y. Chen, J. C. Eslick, J. Leek, J. Ma, P. Mahapatra, B. Ng, N. Sahinidis, C. Tong & Z. SEo, "Innovative computational tools and models for the design, optimization and control of carbon capture processes", 26th European Symposium on Computer Aided Process Engineering – ESCAPE 26, 2391-2396 (2016)
N. Chen, S. Poon, L. Ramakrishnan & C. Aragon, "Considering time in designing Large-Scale systems for scientific computing", Proceedings of the ACM Conference on Computer Supported Cooperative Work, CSCW, 27, 1535-1547 (2016)
D. S. Christianson & C. G. Kaufman, "Effects of sample design and landscape features on a measure of environmental heterogeneity", Methods in Ecology and Evolution, 7, 770-782 (2016)
C. Daley, D. Ghoshal, G. Lockwood, S. Dosanjh, L. Ramakrishnan & N. Wright, "Performance characterization of scientific workflows for the optimal use of Burst Buffers", CEUR Workshop Proceedings, 1800, 69-73 (2016)
D. Morozov & T. Peterka, "Block-Parallel Data Analysis with DIY2", Proceedings of the IEEE Symposium on Large Data Analysis and Visualization (LDAV), (2016)
C. R. Fischer, O. Ruebel & B. P. Bowen, "An accessible, scalable ecosystem for enabling and sharing diverse mass spectrometry imaging analyses ", Archives of Biochemistry and Biophysics , 589, 18 - 26 (2016) PDF
B. Friesen, A. Almgren, Z. Lukić, G. H. Weber, D. Morozov, V. Beckner & M. Day, "In Situ and In-transit Analysis of Cosmological Simulations", Computational Astrophysics and Cosmology, 3, 1-18 (2016)
J. Ganz, M. Bishop & S. Peisert, "Security Analysis of Scantegrity, an Electronic Voting System", (2016)
A. Greiner, E. Racah, R. Canon, J. Liu, Y. Liu, D. Bard, L. Gerhardt, R. Thomas, S. Cholia, J. Porter, W. Bhimji, Q. Koziol & Prabhat, "Data-Intensive Supercomputing for Science", (2016)
V. Hendrix, J. Fox, D. Ghoshal & L. Ramakrishnan, "Tigres Workflow Library: Supporting Scientific Pipelines on HPC Systems", Proceedings - 2016 16th IEEE/ACM International Symposium on Cluster, Cloud, and Grid Computing, CCGrid 2016, 146-155 (2016)
D. Morozov & Z. Lukić, "Master of Puppets: Cooperative Multitasking for In Situ Processing", Proceedings of the Symposium on High-Performance Parallel and Distributed Computing (HPDC), 285-288 (2016)
P. Huck, D. Gunter, S. Cholia, D. Winston, A. N'Diaye & K. Persson, "User applications driven by the community contribution framework MPContribs in the Materials Project", Concurrency Computation, 28, 1982-1993 (2016)
M. Kerber, D. Morozov & A. Nigmetov, "Geometry Helps to Compare Persistence Diagrams", Proceedings of the Workshop on Algorithm Engineering and Experiments (ALENEX), (2016)
D. Miller, D. Agarwal, D. Bhattacharyya, J. Boverhof, Y. Cheah, Y. Chen, J. Eslick, J. Leek, J. Ma, P. Mahapatra, B. Ng, N. Sahinidis, C. Tong & S. Zitney, "Innovative computational tools and models for the design, optimization and control of carbon capture processes", Computer Aided Chemical Engineering, 38, 2391-2396 (2016)
S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann & G. H. Weber, "Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data", Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, 630-639 (2016)
H. Nguyen, D. Stone & E. W. Bethel, "Statistical Projections for Multi-dimensional Visual Data Exploration", 6th IEEE Symposium on Large Data Analysis and Visualization, (2016)
H. T. Nguyen, D. Stone & E. W. Bethel, "Statistical Projections for Multi-resolution, Multi-dimensional Visual Data Exploration and Analysis", (2016)
A. Ovsyannikov, M. Romanus, B. Van Straalen, G. H. Weber & D. Trebotich, "Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science using NERSC's Burst Buffer", Proceedings of the 1st Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems, 1-6 (2016)
M. Jamei, E. Stewart, S. Peisert, A. Scaglione, C. McParland, C. Roberts & A. McEachern, "Micro Synchrophasor-Based Intrusion Detection in Automated Distribution Systems: Towards Critical Infrastructure Security", IEEE Internet Computing, 20, (2016) PDF
A. Gonzalez, J. Leigh, S. Peisert, B. Tierney, A. Lee & Jennifer M.. Schopf, "NetSage: Open Privacy-Aware Network Measurement, Analysis, And Visualization Service", Proceedings of TNC16 Networking Conference, (2016)
S. Peisert, W. K. Barnett, E. Dart, J. Cuff, R. L. Grossman, E. Balas, A. Berman, A. Shankar & B. Tierney, "The Medical Science DMZ", Journal of the American Medical Informatics Association (JAMIA), (2016) PDF
G. Rodrigo, P.-O. Ostberg, E. Elmroth, K. Antypas, R. Gerber, L. Ramakrishnan & IEEE, "Towards Understanding Job Heterogeneity in HPC: A NERSC Case Study", 2016 16TH IEEE/ACM INTERNATIONAL SYMPOSIUM ON CLUSTER, CLOUD AND GRID COMPUTING (CCGRID), 521-526 (2016) PDF
S. V. Venkatakrishnan, K. A. Mohan, K. Beattie, J. Correa, E. Dart, J. R. Deslippe, A. Hexemer, H. Krishnan, A. A. MacDowell, S. Marchesini, S. J. Patton, T. Perciano, J. A. Sethian, R. Stromsness, B. L. Tierney, C. E. Tull, D. Ushizima & D. Y. Parkinson, "Making Advanced Scientific Algorithms and Big Scientific Data Management More Accessible", Electronic Imaging, 2016, 1-7 (2016) PDF
M. Verma, J. Fisher, K. Mallick, Y. Ryu, H. Kobayashi, A. Guillaume, G. Moore, L. Ramakrishnan, V. Hendrix, S. Wolf, M. Sikka, G. Kiely, G. Wohlfahrt, B. Gielen, O. Roupsard, P. Toscano, A. Arain & A. Cescatti, "Global surface net-radiation at 5 km from MODIS Terra", Remote Sensing, 8, (2016)
O. Rübel, B. Loring, J. L. Vay, D. P. Grote, R. Lehe, S. Bulanov, H. Vincenti & E. W. Bethel, "WarpIV: In Situ Visualization and Analysis of Ion Accelerator Simulations", IEEE Computer Graphics and Applications, 36, 22-35 (2016)

2015

A. W. Wills, D. J. Michalak, P. Ercius, E. R. Rosenberg, T. Perciano, D. Ushizima, R. Runser & B. A. Helms, "Block Copolymer Packing Limits and Interfacial Reconfigurability in the Assembly of Periodic Mesoporous Organosilicas", Advanced Functional Materials, n/a-n/a (2015) PDF
D. A. Agarwal, B. Faybishenko, V. L. Freedman, H. Krishnan, C. L. Gary Kushner, E. Porter, A. Romosan, A. Shoshani, H. Wainwright, A. Weidmer & K. Wu, "A Science Data Gateway for Environmental Management", Concurrency and Computation: Practice and Experience, To appear (2015)
D. A. Agarwal, B. Faybishenko, V. L. Freedman, H. Krishnan, G. Kushner, C. Lansing, E. Porter, A. Romosan, A. Shoshani, H. Wainwright & others, "A science data gateway for environmental management", Concurrency and Computation: Practice and Experience, (2015)
C. Varadharajan, D. Agarwal, B. Faybishenko & R. Versteeg, "Agile data management for curation of genomes to watershed datasets", American Geophysical Union, Fall Meeting 2015, abstract #IN13A-1824, (2015)
E. W. Bethel, D. Camp, D. Donofrio & M. Howison, "Improving Performance of Structured-memory, Data-Intensive Applications on Multi-core Platforms via a Space-Filling Curve Memory Layout", International Workshop on High Performance Data Intensive Computing, an IEEE International Parallel and Distributed Processing Symposium (IPDPS) workshop, (2015)
R. Chard, S. Sehrish, A. Rodriguez, R. Madduri, T. Uram, M. Paterno, K. Heitmann, S. Cholia, J. Kowalkowski & S. Habib, "PDACS-A portal for data analysis services for cosmological simulations", Proceedings of GCE 2014: 9th Gateway Computing Environments Workshop, held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis, 30-33 (2015)
S. Cholia & T. Sun, "The NEWT platform: An extensible plugin framework for creating ReSTful HPC APIs", Concurrency Computation, 27, 4304-4317 (2015)
D. Chung, M. Bishop & S. Peisert, "Distributed Helios - Mitigating Denial of Service Attacks in Online Voting", (2015) PDF
C. Daley, L. Ramakrishnan, S. Dosanjh & N. Wright, "Analyses of Scientific Workflows for Effective Use of Future Architectures", The 6th International Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC-15), 2015 at SC, (2015)
E. Dede, B. Sendir, P. Kuzlu, J. Weachock, M. Govindaraju & L. Ramakrishnan, "Processing Cassandra Datasets with Hadoop-Streaming Based Approaches", Services Computing, IEEE Transactions on, PP, 1-1 (2015)
J. Yang, O. Ruebel, Prabhat, M. W. Mahoney & B. P. Bowen, "Identifying Important Ions and Positions in Mass Spectrometry Imaging Data Using CUR Matrix Decompositions", Analytical Chemistry, 87, 4658-4666 (2015) PDF
D. S. Dalisay, K. W. Kim, C. Lee, H. Yang, O. Ruebel, B. P. Bowen, L. B. Davin & N. G. Lewis, "Dirigent Protein-Mediated Lignan and Cyanogenic Glucoside Formation in Flax Seed: Integrated Omics and MALDI Mass Spectrometry Imaging", Journal of Natural Products, 78, 1231-1242 (2015) PDF
A. Agranovsky, D. Camp, K. I. Joy & H. Childs, "Subsampling-based compression and flow visualization", Proc. SPIE, 9397, 93970J-93970J-14 (2015)
J. Donatelli, M. Haranczyk, A. Hexemer, H. Krishnan, X. Li, L. Lin, F. Maia, S. Marchesini, D. Parkinson, T. Perciano, D. Shapiro, D. Ushizima, C. Yang & J. Sethian, "CAMERA: The Center for Advanced Mathematics for Energy Research Applications", Synchrotron Radiation News, 28, 4-9 (2015) PDF
B. Dong, S. Byna & K. Wu, "Heavy-tailed Distribution of Parallel I/O System Response Time", Proceedings of the 10th Parallel Data Storage Workshop, 37-42 (2015) PDF
B. Dong, S. Byna & K. Wu, "Spatially clustered join on heterogeneous scientific data sets", Big Data (Big Data), 2015 IEEE International Conference on, 371-380 (2015)
S. Duan, S. Peisert & K. Levitt, "hBFT: Fast Byzantine Fault Tolerance With Optimal Resilience", IEEE Transactions on Dependable and Secure Computing, 12, 58-70 (2015)
C. A. Emmerton, V. L. St. Louis, E. R. Humphreys, J. A. Gamon, J. D. Barker & G. Z. Pastorello, "Net ecosystem exchange of CO2 with rapidly changing high Arctic landscapes", Global Change Biology, (2015) PDF
E. Feller, L. Ramakrishnan & C. Morin, "Performance and energy efficiency of big data applications in cloud environments: A Hadoop case study", Journal of Parallel and Distributed Computing, 79-80, 80-89 (2015)
C. Simon, J. Kim, D. Gomez-Gualdron, J. Camp, Y. G. Chung, R. L. Martin, R. Mercado, M. W. Deem, D. Gunter, M. Haranczyk, D. Sholl, R. Q. Snurr & B. Smit, "The Materials Genome in Action: Identifying the Performance Limits for Methane Storage", Energy Environ. Sci., (2015) PDF
A. Jain, S. P. Ong, W. Chen, B. Medasani, X. Qu, M. Kocher, M. Brafman, G. Petretto, G.-M. Rignanese, G. Hautier, D. Gunter & K. A. Persson, "FireWorks: a dynamic workflow system designed for high-throughput applications", Concurrency and Computation: Practice and Experience, (2015) PDF
C. Simon, J. Kim, Y. G. Chung, R. L. Martin, R. Mercado, M. W. Deem, D. Gunter, M. Haranczyk, R. Q. Snurr & B. Smit, "Computer-aided search for materials to store natural gas for vehicles", New Discovery, Front. Young Minds - Understanding the Earth and its Resources, (2015)
P. Huck, A. Jain, D. Gunter, D. Winston & K. Persson, "A Community Contribution Framework for Sharing Materials Data with Materials Project", 2015 IEEE 11th International Conference on eScience, 535-541 (2015) PDF
T. Hey, D. Agarwal, C. Borgman, C. Cartaro, S. Crivelli, K. K. Van Dam, R. Luce, S. Arjun, A. Trefethen, A. Wade & others, "DOE Advanced Scientific Computing Advisory Committee (ASCAC) Subcommittee Report on Scientific and Technical Information", (2015)
P. Huck, D. Gunter, S. Cholia, D. Winston, A. N'Diaye & K. Persson, "User applications driven by the community contribution framework MPContribs in the Materials Project", Concurrency and Computation: Practice and Experience, (2015)
P. Huck, D. Gunter, S. Cholia, D. Winston, A. N'Diaye & K. Persson, "User Applications Driven by the Community Contribution Framework MPContribs in the Materials Project.", CoRR, abs/1510.05727, (2015)
J. Kim, B. Dong, S. Byna & K. Wu, "Security for the scientific data services framework", Big Data (Big Data), 2015 IEEE International Conference on, 1871-1875 (2015)
R. Madduri, A. Rodriguez, T. Uram, K. Heitmann, T. Malik, S. Sehrish, R. Chard, S. Cholia, M. Paterno, J. Kowalkowski & others, "PDACS: A Portal for Data Analysis Services for Cosmological Simulations", Computing in Science & Engineering, 17, 18-26 (2015)
R. Madduri, A. Rodriguez, T. Uram, K. Heitmann, T. Malik, S. Sehrish, R. Chard, S. Cholia, M. Paterno, J. Kowalkowski & S. Habib, "PDACS: A Portal for Data Analysis Services for Cosmological Simulations", Computing in Science and Engineering, 17, 18-26 (2015)
Y. Yao, T. Sun, T. Wang, O. Ruebel, T. Northen & B. P. Bowen, "Analysis of Metabolomics Datasets with High-Performance Computing and Metabolite Atlases", Metabolites, 5, 431 (2015) PDF
S. Ong, S. Cholia, A. Jain, M. Brafman, D. Gunter, G. Ceder & K. Persson, "The Materials Application Programming Interface (API): A simple, flexible and efficient API for materials data based on REpresentational State Transfer (REST) principles", Computational Materials Science, 97, 209-215 (2015) PDF
S. Peisert & et al., "ASCR Cybersecurity for Scientific Computing Integrity --- Research Pathways and Ideas Workshop", (2015)
A. Chavez, W. M. Stout & S. Peisert, "Techniques for the Dynamic Randomization of Network Attributes", Proceedings of the 49th Annual International Carnahan Conference on Security Technology, (2015)
G. Koutsandria, R. Gentzand, M. J. A. Scaglione, S. Peisert & C. McParland, "A Real-Time Testbed Environment for Cyber-Physical Security on the Power Grid", Proceedings of the First ACM Workshop on Cyber-Physical Systems Security & Privacy (CPS-SPC), (2015)
S. Duan, J. Sun & S. Peisert, "Towards a Self-Adaptive Middleware for Building Reliable Publish/Subscribe Systems", Proceedings of the 8th International Conference on Internet and Distributed Computing Systems (IDCS), (2015)
G. Rodrigo Álvarez, P.-O. Östberg, E. Elmroth & L. Ramakrishnan, "A2L2: An Application Aware Flexible HPC Scheduling Model for Low-Latency Allocation", Proceedings of the 8th International Workshop on Virtualization Technologies in Distributed Computing, 11-19 (2015) PDF
G. Rodrigo Álvarez, P.-O. Östberg, E. Elmroth, K. Antypas, R. Gerber & L. Ramakrishnan, "HPC System Lifetime Story: Workload Characterization and Evolutionary Analyses on NERSC Systems", Proceedings of the 24th International Symposium on High-Performance Parallel and Distributed Computing, 57-60 (2015)
G. Rosenberg, P. Haghnegahdar, P. Goddard, P. Carr, K. Wu & M. L. de Prado, "Solving the optimal trading trajectory problem using a quantum annealer", Proceedings of the 8th Workshop on High Performance Computational Finance, 7 (2015)
O. Ruebel, M. Prabhat, P. Denes, D. Conant, E. Chang & K. Bouchard, "BRAINformat: A Data Standardization Framework for Neuroscience Data", bioRxiv, (2015)
H. Sim, Y. Kim, S. Vazhkudai, D. Tiwari, A. Anwar, A. Butt, L. Ramakrishnan & ACM, "AnalyzeThis: An Analysis Workflow-Aware Storage System", PROCEEDINGS OF SC15: THE INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS, (2015) PDF
J. H. Song, M. Lopez de Prado, H. D. Simon & K. Wu, "Understanding Natural Gas Futures Trading Through Data Analysis", Available at SSRN 2657224, (2015)
N. Wright, S. Dosanjh, A. Andrews, K. Antypas, B. Draney, R. Canon, S. Cholia, C. Daley, K. Fagnan, R. Gerber, L. Gerhardt, L. Pezzaglia, A. Prabhat, K. Schafer & J. Srinivasan, "Cori: A pre-exascale supercomputer for big data and HPC applications", Advances in Parallel Computing, 26, 82-100 (2015)
L. Wu, K. Wu, A. Sim, M. Churchill, J. Y. Choi, A. Stathopoulos, CS. Chang & S. Klasky, "Towards Real-Time Detection and Tracking of Blob-Filaments in Fusion Plasma Big Data", (2015)
X. Zou, K. Wu, I. I. D. Boyuka, D. Martin, S. Byna, H. Tang, K. Bansal, T. Ligocki, H. Johansen & N. Samatova, "Parallel In Situ Detection of Connected Components in Adaptive Mesh Refinement Data", IEEE/ACM CCGrid, (2015) PDF

2014

A. Agranovsky, D. Camp, C. Garth, E. W. Bethel, K. I. Joy & H. Childs, "Improved Post Hoc Flow Analysis Via Lagrangian Representations", Proceedings of the IEEE Symposium on Large Data Visualization and Analysis (LDAV), 67-75 (2014)
D. H. Bailey, S. Ger, M. L. de Prado, A. Sim & K. Wu, "Statistical Overfitting and Backtest Performance", (2014)
J. Balderrama, M. Simonin, L. Ramakrishnan, V. Hendrix, C. Morin, D. Agarwal & C. Tedeschi, "Combining workflow templates with a shared space-based execution model", Proceedings of WORKS 2014: The 9th Workshop on Workflows in Support of Large-Scale Science - held in conjunction with SC 2014: The International Conference for High Performance Computing, Networking, Storage and Analysis, 50-58 (2014)
D. Baldocchi, D. Agarwal, D. Papale & M. Torn, "Update on Fluxnet and the Role of Flux Networks in Biogeosciences", AGU Fall Meeting Abstracts, 1, 05 (2014)
K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber & B. Hamann, "Measuring the Distance Between Merge Trees", Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, 151-166 (2014)
S. Blanas, K. Wu, S. Byna, B. Dong & A. Shoshani, "Parallel Data Analysis Directly on Scientific File Formats", SIGMOD'14, 385-396 (2014)
E. Dede, B. Sendir, P. Kuzlu, M. Govindaraju & L. Ramakrishnan, "A Processing Pipeline for Cassandra Datasets Based on Hadoop Streaming", IEEE International Congress on Big Data, (2014)
T. Chang, S. Duan, H. Meling & S. Peisert, "P2S: A Fault-Tolerant Publish/Subscribe Infrastructure", Proceedings of the 8th ACM International Conference on Distributed Event Based Systems (DEBS), 189-197 (2014)
R. Chard, S. Sehrish, A. Rodriguez, R. Madduri, T. D. Uram, M. Paterno, K. Heitmann, S. Cholia, J. Kowalkowski & S. Habib, "PDACS: a portal for data analysis services for cosmological simulations", Proceedings of the 9th Gateway Computing Environments Workshop, 30-33 (2014)
H.-T. Chiu, J. Chou, V. Vishwanath, S. Byna & K. Wu, "Simplifying Index File Structure to Improve I/O Performance of Parallel Indexing", The 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2014), (2014)
R. Cowles, C. Jackson, V. Welch & S. Cholia, "A model for identity management in future scientific collaboratories", Proceedings of Science, 23-28-March-2014, (2014)
R. Cowles, C. Jackson, V. Welch & S. Cholia, "A Model for Identity Management in Future Scientific Collaboratories", International Symposium on Grids and Clouds (ISGC), (2014)
B. Dong, S. Byna & K. Wu, "Parallel query evaluation as a Scientific Data Service", Cluster Computing (CLUSTER), 2014 IEEE International Conference on, 194-202 (2014)
S. Duan, H. Meling, S. Peisert & H. Zhang, "BChain: Byzantine Replication with High Throughput and Embedded Reconfiguration", Proceedings of the 18th International Conference on Principles of Distributed Systems (OPODIS), (2014)
S. Duan, K. Levitt, H. Meling, S. Peisert & H. Zhang, "Byzantine Fault Tolerance from Intrusion Detection", Proceedings of the 33rd IEEE International Symposium on Reliable Distributed Systems (SRDS), 253-264 (2014)
V. Freedman, D. Agarwal, K. Bensema, S. Finsterle, C. Gable, E. Keating, H. Krishnan, C. Lansing, W. Moeglein, G. Pau & others, "Akuna: An Open Source User Environment for Managing Subsurface Simulation Workflows", AGU Fall Meeting Abstracts, 1, 04 (2014)
T. Hawk, I. Raicu & L. Ramakrishnan, "Scalable State Management for Scientific Applications in the Cloud", IEEE International Congress on Big Data, (2014)
R. Gerber, W. Allcock, C. Beggio, S. Campbell, A. Cherry, S. Cholia, E. Dart, C. England, T. Fahey, F. Foertter & others, "DOE High Performance Computing Operational Review (HPCOR): Enabling Data-Driven Scientific Discovery at HPC Facilities", (2014)
E. Dede, Z. Fadika, M. Govindaraju & L. Ramakrishnan, "Benchmarking MapReduce Implementations Under Different Application Scenarios", Future Generation Computer Systems , (2014)
H. Childs, S. Biersdorff, D. Poliakoff, D. Camp & A. D. Malony, "Particle Advection Performance Over Varied Architectures and Workloads", 21th Annual International Conference on High Performance Computing, HiPC 2014, (2014)
A. Harris, J. Gamon, G. Pastorello & C. Wong, "Retrieval of the photochemical reflectance index for assessing xanthophyll cycle activity: a comparison of near-surface optical sensors", Biogeosciences Discussions, 11, 11903-11942 (2014) PDF
W. Harvey, I.-H. Park, O. Ruebel, V. Pascucci, P.-T. Bremer, C. Li & Y. Wang, "A collaborative visual analytics suite for protein folding research", Journal of Molecular Graphics and Modelling, 53, 59-71 (2014)
V. Hendrix, L. Ramakrishnan, Y. Ryu, C. Van Ingen, K. Jackson & D. Agarwal, "CAMP: Community access MODIS pipeline", Future Generation Computer Systems, 36, 418-429 (2014)
H. Öhman, S. Panitkin & V. Hendrix, "Using Puppet to contextualize computing resources for ATLAS analysis on Google compute engine", Journal of Physics: Conference Series, 513, (2014)
M. Howison & E. Bethel, "GPU-Accelerated Denoising of 3D Magnetic Resonance Images", Journal of Real-Time Image Processing, 1-12 (2014) PDF
S. Hubbard, D. Agarwal, J. Banfield, H. Beller, E. Brodie, P. Long, P. Nico, C. Steefel, T. Tokunaga & K. Williams, "Genome-to-Watershed Predictive Understanding of Terrestrial Environments", AGU Fall Meeting Abstracts, 1, 0020 (2014)
D. Ushizima, T. Perciano, H. Krishnan, B. Loring, H. Bale, D. Parkinson & J. Sethian, "Structure Recognition from High Resolution Images of Ceramic Composites", IEEE International Conference on Big Data, (2014)
G. Koutsandria, V. Muthukumar, M. Parvania, S. Peisert, C. McParland & A. Scaglione, "A Hybrid Network IDS for Protective Digital Relays in the Power Transmission Grid", Proceedings of the 5th IEEE International Conference on Smart Grid Communications (SmartGridComm), 908-913 (2014)
Q. Liu, J. Logan, Y. Tian, H. Abbasi, N. Podhorszki, J. Y. Choi, S. Klasky, R. Tchoua, J. Lofstead, R. Oldfield, M. Parashar, N. Samatova, K. Schwan, A. Shoshani, M. Wolf, K. Wu & W. Yu, "Hello ADIOS: the challenges and lessons of developing leadership class I/O frameworks", Concurrency and Computation: Practice and Experience, 26, 1453-1473 (2014)
J. Liu, S. Byna, B. Dong, K. Wu & Y. Chen, "Model-Driven Data Layout Selection for Improving Read Performance", Parallel Distributed Processing Symposium Workshops (IPDPSW), 2014 IEEE International, 1708-1716 (2014)
P. E. Long, S. S. Hubbard, J. F. Banfield, H. R. Beller, E. L. Brodie, P. S. Nico, C. I. Steefel, T. K. Tokunaga, K. H. Williams & D. A. Agarwal, "Predictive Understanding of Subsurface Biogeochemical Functioning: Using Genomes to Inform Watershed-Scale Models", 2014 GSA Annual Meeting in Vancouver, British Columbia, (2014)
E. Dede, Z. Fadika, M. Govindaraju & L. Ramakrishnan, "MARIANE: Using MApReduce In HPC Environments", Future Generation Computer Systems , (2014)
C. McParland, S. Peisert & A. Scaglione, "Monitoring Security of Networked Control Systems: It's the Physics", IEEE Security & Privacy, 12, 32-39 (2014)
O. Menzer, G. Pastorello, S. Metzger, C. Poindexter, D. Agarwal & D. Papale, "Mapping AmeriFlux footprints: Towards knowing the flux source area across a network of towers", AGU Fall Meeting Abstracts, 1, 0155 (2014)
D. C. Miller, M. Syamlal, D. Mebane, C. Storlie, D. Bhattacharyya, N. V. Sahinidis, D. Agarwal, C. Tong, S. E. Zitney, A. Sarkar, X. Sun, S. Sundaresan, E. Ryan, D. Engel & C. Dale, "Carbon Capture Simulation Initiative: A Case Study in Multiscale Modeling and New Challenges", Annual Review of Chemical and Biomolecular Engineering, 5, (2014)
S. Panitkin, F. Megino, J. Bejar, D. Benjamin, A. Girolamo, I. Gable, V. Hendrix, J. Hover, K. Kucharczyk, R. Llamas, P. Love, H. Ohman, M. Paterson, R. Sobie, R. Taylor, R. Walker & A. Zaytsev, "ATLAS cloud R&D", Journal of Physics: Conference Series, 513, (2014)
M. Parvania, G. Koutsandria, V. Muthukumar, S. Peisert, C. McParland & A. Scaglione, "Hybrid Control Network Intrusion Detection Systems for Automated Power Distribution Systems", Proceedings of the 1st International Workshop on Trustworthiness of Smart Grids (ToSG), (2014)
G. Pastorello, D. Agarwal, T. Samak, D. Papale, C. Trotta, A. Ribeca, C. Poindexter, B. Faybishenko, D. Gunter, R. Hollowgrass & E. Canfora, "Observational data patterns for time series data quality assessment", Proceedings of the 10th IEEE International Conference on e-Science, (2014)
G. Pastorello, B. Faybishenko, C. Poindexter, O. Menzer, D. Agarwal, D. Papale & D. Baldocchi, "Evaluation of Growing Season Milestones, Using Eddy Covariance Time-Series of Net Ecosystem Exchange", AGU Fall Meeting Abstracts, 1, 0207 (2014)
G. Pastorello, C. Poindexter, C. van Ingen, D. Papale & D. Agarwal, "The many facets of integrating data and metadata for research networks: experience from the AmeriFlux Network", AGU Fall Meeting Abstracts, 1, 05 (2014)
G. Pastorello, C. Poindexter, D. Agarwal, D. Papale, C. van Ingen & M. Torn, "An overview of AmeriFlux data products and methods for data acquisition, processing, and publication", AGU Fall Meeting Abstracts, 1, 0158 (2014)
S. Peisert & J. Margulies, "Closing the Gap on Securing Energy Sector Control Systems [Guest editors' introduction]", Security & Privacy, IEEE, 12, 13-14 (2014)
S. Peisert, J. Margulies, E. Byres, P. Dorey, D. Peterson & Z. Tudor, "Control Systems Security from the Front Lines", Security & Privacy, IEEE, 12, 55-58 (2014)
S. Peisert, J. Margulies, D. M. Nicol, H. Khurana & C. Sawall, "Designed-in Security for Cyber-Physical Systems", Security & Privacy, IEEE, 12, 9-12 (2014)
L. Ramakrishnan, S. Poon, V. Hendrix, D. Gunter, G. Pastorello & D. Agarwal, "Experiences with user-centered design for the tigres workflow API", Proceedings - 2014 IEEE 10th International Conference on eScience, eScience 2014, 1, 290-297 (2014)
L. Ramakrishnan, D. Ghoshal, V. Hendrix, E. Feller, P. Mantha & C. Morin, "Storage and Data Life Cycle Management in Cloud Environments with FRIEDA.", Cloud Computing for Data-Intensive Applications, 357-378 (2014) PDF
O. Rubel, C. G. Geddes, M. Chen, E. Cormier-Michel & E. W. Bethel, "Feature-Based Analysis of Plasma-Based Particle Acceleration Data", IEEE Transactions on Visualization and Computer Graphics, 20, 196-210 (2014)
F. Rusu, P. Nugent & K. Wu, "Implementing the Palomar Transient Factory Real-Time Detection Pipeline in GLADE: Results and Observations", Databases in Networked Information Systems, 8381, 53-66 (2014)
J. H. Song, M. L. de Prado, H. D. Simon & K. Wu, "Exploring Irregular Time Series Through Non-uniform Fast Fourier Transform", Proceedings of the 7th Workshop on High Performance Computational Finance, 37-44 (2014) PDF
J. H. Song, K. Wu & H. D. Simon, "Parameter Analysis of the VPIN (Volume synchronized Probability of Informed Trading) Metric", Quantitative Financial Risk Management: Theory and Practice, (2014)
G. H. Weber & H. Hauser, "Interactive Visual Exploration and Analysis", Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization, 161-174 (2014)
G. H. Weber, H. Johansen, D. T. Graves & T. J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), (2014)
L. Wu, K. Wu, A. Sim, M. Churchill, J. Y. Choi, A. Stathopoulos, C. Chang & S. Klasky, "High-Performance Outlier Detection Algorithm for Finding Blob-Filaments in Plasma", 5th International Workshop on Big Data Analytics: Challenges, and Opportunities (BDAC'14), (2014)

2013

D. Agarwal, S. Pullman, J. Voytek, G. Z. Pastorello, D. Papale, S. Biraud, W.-y. S. Chan, S. S. Hubbard & M. S. Torn, "Enabling Mobile Data and Metadata Collection and Submission in Support of AmeriFlux and NGEE Data Collection and Access", Eos Trans. American Geophysical Union, (2013)
E. W. Bethel, P. Prabhat, S. Byna, O. Rübel, K. J. Wu & M. Wehner, "Why high performance visual data analytics is both relevant and difficult", IS&T/SPIE Electronic Imaging, 86540B-86540B-10 (2013) PDF
J. Y. Choi, K. Wu, J. C. Wu, A. Sim, Q. G. Liu, M. Wolf, C. Chang & S. Klasky, "ICEE: Wide-area In Transit Data Processing Framework For Near Real-Time Scientific Applications", PDAC workshop, SC13, (2013)
E. Masanet, A. Shehabi, L. Ramakrishnan, J. Liang, X. Ma, B. Walker, V. Hendrix & P. Mantha, "The Energy Efficiency Potential of Cloud-Based Software: A U.S.Case Study", (2013)
M. Di Pierro, J. Hetrick, S. Cholia, J. Simone & C. DeTar, "The new “Gauge Connection” at NERSC", (2013)
M. Di Pierro, J. Hetrick, S. Cholia, J. Simone & C. Deta, "The new "Gauge Connection" at NERSC", Proceedings of Science, 29-July-2013, (2013)
B. Dong, S. Byna & K. Wu, "Expediting scientific data analysis with reorganization of data", Cluster Computing (CLUSTER), 2013 IEEE International Conference on, 1-8 (2013)
B. Dong, S. Byna & K. Wu, "SDS: a framework for scientific data services", Proceedings of the 8th Parallel Data Storage Workshop, (2013)
B. Faybishenko, D. Agarwal, D. Baldocchi, C. van Ingen, S. Biraud, G. Pastorello & D. Papale, "Intercomparison of the AmeriFlux In Situ Measurements Across Multiple Biomes as an Alternative to Climatic Classification", American Geophysical Union, Fall Meeting 2013, (2013)
E. Feller, L. Ramakrishnan & C. Morin, "On the Performance and Energy Efficiency of Hadoop Deployment Models", The IEEE International Conference on Big Data 2013 (IEEE BigData 2013), (2013)
J. Gamon, F. Huemmrich, C. Emmerton, E. Humphreys, P. Lafleur, G. Pastorello, A. Rocha, G. Shaver, V. St.Louis, M. Tenuta, D. Thayer & S. Williamson, "Observing dynamic Arctic surface optical properties with an optical sensor network", American Geophysical Union, Fall Meeting 2013, (2013)
W. Gu, J. Choi, M. Gu, H. D. Simon & K. Wu, "Fast Change Point Detection for electricity market analysis", 2013 IEEE International Conference on Big Data, 50-57 (2013)
D. Gunter, L. Ramakrishnan, S. Poon, G. Pastorello, V. Hendrix & D. Agarwal, "Experiences with User-Centered Design for the Tigres Workflow API (poster)", Proceedings of the 9th IEEE International Conference on e-Science, (2013)
A. Jain, S. Ong, G. Hautier, W. Chen, W. Richards, S. Dacek, S. Cholia, D. Gunter, D. Skinner, G. Ceder & K. Persson, "Commentary: The materials project: A materials genome approach to accelerating materials innovation", APL Materials, 1, 011002 (2013)
K.-W. Lin, S. Byna, J. Chou & K. Wu, "Optimizing FastQuery performance on Lustre file system", Proceedings of the 25th International Conference on Scientific and Statistical Database Management, 29 (2013)
Y.-W. Cheah, R. Canon, B. Plale & L. Ramakrishnan, "Milieu: Provenance Collection and Query Framework for High Performance Computing Systems", IEEE Big Data Congress [Acceptance rate:30\%], (2013)
E. Dede, M. Govindaraju, D. Gunter, R. Canon & L. Ramakrishnan, "Semi-Structured Data Analysis using MongoDB and MapReduce: A Performance Evaluation", Proceedings of the 4th international workshop on Scientific cloud computing, (2013)
S. Ong, W. Richards, A. Jain, G. Hautier, M. Kocher, S. Cholia, D. Gunter, V. Chevrier, K. Persson & G. Ceder, "Python Materials Genomics (pymatgen): A robust, open-source python library for materials analysis", Computational Materials Science, 68, 314-319 (2013)
G. Pastorello, J. Gamon & D. Agarwal, "Comparison of Broadband Optical Sensor Responses for Proxy NDVI Measurements", American Geophysical Union, Fall Meeting 2013, (2013)
S. Peisert & M. Bishop, "Dynamic, Flexible, and Optimistic Access Control", (2013)
S. Peisert, E. Talbot & T. Kroeger, "Principles of Authentication", Proceedings of the 2013 New Security Paradigms Workshop (NSPW) (to appear), (2013)
L. Ramakrishnan, A. Scovel, I. Sakrejda, S. Coghlan, S. Canon, A. Liu, D. Ghoshal, K. Muriki & N. J. Wright, "On the Road to Exascale Computing: Contemporary Architectures in High Performance Computing ", (2013)
O. Rübel, A. Greiner, S. Cholia, K. Louie, E. Bethel, T. Northen & B. Bowen, "OpenMSI: A high-performance web-based platform for mass spectrometry imaging", Analytical Chemistry, 85, 10354-10361 (2013)
A. Romosan, A. Shoshani, K. Wu, V. Markowitz & K. Mavrommatis, "Accelerating gene context analysis using bitmaps", Proceedings of the 25th International Conference on Scientific and Statistical Database Management, 26 (2013)
S. Whalen, S. Peisert & M. Bishop, "Multiclass Classification of Distributed Memory Parallel Computations", Pattern Recognition Letters (PRL), 34, 322-329 (2013)
K. Wu, W. Bethel, M. Gu, D. Leinweber & O. Rübel, "A Big Data Approach to Analyzing Market Volatility", Algorithmic Finance, 2, 241-267 (2013)
K. Wu, W. Bethel, M. Gu, D. Leinweber & O. Rübel, "Testing VPIN on Big Data", (2013)

2012

D. Agarwal, A. Wiedmer, B. Faybishenko, T. Whiteside, J. Hunt, G. Kushner, A. Romosan & S. Arie, "A Methodology for Management of Heterogeneous Site Characterization and Modeling Data", Proceedings XIX International Conference on Water Resources (CMWR), (2012)
E. Bethel, S. Byna, J. Chou, E. Cormier-Michel, C. Geddes, M. Howison, F. Li, J. Q. Prabhat, O. Rübel, R. Ryne & others, "Big Data Analaysis and Visualization: What Do LINACS and Tropical Storms Have In Common?", 11th International Computational Accelerator Physics Conference, ICAP 2012, (2012)
E. W. Bethel, D. Leinweber, O. Rübel & K. Wu, "Federal Market Information Technology in the Post-Flash Crash Era: Roles for Supercomputing", The Journal of Trading, 7, 9-25 (2012)
E. W. Bethel, S. Byna, J. Chou, E. Cormier-Michel, C. G. R. Geddes, M. Howison, F. Li, Prabhat, J. Qiang, O. Rübel, R. D. Ryne, M. Wehner & K. Wu, "Big Data Analysis and Visualization: What Do LINACS and Tropical Storms Have In Common?", 11th International Computational Accelerator Physics Conference, ICAP 2012, Germany, (2012)
S. Byna, J. Chou, O. Rübel, Prabhat, H. Karimabadi, W. S. Daughton, V. Roytershteyn, E. W. Bethel, M. Howison, K.-J. Hsu, K.-W. Lin, A. Shoshani, A. Uselton & K. Wu, "Parallel I/O, Analysis, and Visualization of a Trillion Particle Simulation", Proceedings of SuperComputing 2012, (2012) PDF
L. Coles-Kemp, C. Gates, D. Gollmann, S. Peisert, C. W. Probst, L. Coles-Kemp, C. Gates, D. Gollmann, S. Peisert & C. Probst, "Organizational Processes for Supporting Sustainable Security (Dagstuhl Seminar 12501).", Dagstuhl Reports, 2, 37-48 (2012)
A. El-Atawy & T. Samak, "End-to-end verification of QoS policies", 2012 IEEE Network Operations and Management Symposium, Maui, HI, USA, April 16-20, 2012, 426-434 (2012)
D. Ghoshal & L. Ramakrishnan, "FRIEDA: Flexible Robust Intelligent Elastic Data Management in Cloud Environments", The Third International Workshop on Data Intensive Computing in the Clouds (DataCloud 2012) Best Paper Award, (2012)
D. Gunter, S. Cholia, A. Jain, M. Kocher, K. Persson, L. Ramakrishnan, S. Ong & G. Ceder, "Community accessible datastore of high-throughput calculations: Experiences from the materials project", Proceedings - 2012 SC Companion: High Performance Computing, Networking Storage and Analysis, SCC 2012, 1244-1251 (2012)
F. Harald Barreiro Megino, D. Benjamin, K. De, I. Gable, V. Hendrix, S. Panitkin, M. Paterson, A. De Silva, D. Van Der Ster, R. Taylor, R. Vitillo & R. Walker, "Exploiting virtualization and cloud computing in ATLAS", Journal of Physics: Conference Series, Journal of Physics: Conference Series, 396, (2012) PDF
V. Hendrix, D. Benjamin & Y. Yao, "Scientific cluster deployment and recovery - Using puppet to simplify cluster management", Journal of Physics: Conference Series, 396, (2012) PDF
A. Jain, G. Hautier, S. Ong, C. Moore, B. Kang, H. Chen, X. Ma, J. Kim, M. Kocher, D. Gunter, S. Cholia, A. Greiner, D. Bailey, D. Skinner, K. Persson & G. Ceder, "Materials Project: A public materials database and its application to lithium ion battery cathode design", ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY, 243, (2012) PDF
E. Kissel, A. El-Hassany, G. Fernandes, M. Swany, D. Gunter, T. Samak & J. Schopf, "Scalable Integrated Performance Analysis of Multi-Gigabit Networks", 5th Workshop on Distributed Autonomous Network Management System (DANMS), co-located with NOMS 2012, (2012)
G. F. Lofstead, Q. Liu, J. Logan, Y. Tian, H. Abbasi, N. Podhorszki, J. Y. Choi, S. Klasky, R. Tchoua, R. A. Oldfield & others, "Hello ADIOS: The Challenges and Lessons of Developing Leadership Class I/O Frameworks", (2012)
B. Ma, A. Shoshani, A. Sim, K. Wu, Y.-I. Byun, J. Hahm & M.-S. Shin, "Efficient Attribute-Based Data Access in Astronomy Analysis", The 2nd International Workshop on Network-Aware Data Management Workshop (NDM2012), 562-571 (2012)
E. Dede, Z. Fadika, J. Hartog, M. Govindaraju, L. Ramakrishnan, D. Gunter & R. S. Canon, "MARISSA: MApReduce Implementation for Streaming Science Applications", eScience, (2012)
D. Papale, D. Agarwal, D. Baldocchi, R. Cook, J. B. Fisher & C. van_Ingen, "Database Maintenance, Data Sharing Policy, Collaboration", Eddy Covariance, 399-424 (2012)
X. Li, Z. Wang, V. Muthukumar, A. Scaglione, C. McParland & S. Peisert, "Networked Loads in the Distribution Grid", Proceedings of the 2012 APSIPA Annual Summit and Conference, (2012)
S. Peisert, E. Talbot & M. Bishop, "Turtles All The Way Down: A Clean-Slate, Ground-Up, First-Principles Approach to Secure Systems", Proceedings of the 2012 New Security Paradigms Workshop (NSPW), 15-26 (2012)
E. Pourabbas, A. Shoshani & K. Wu, "Minimizing index size by reordering rows and columns", SSDBM, 467-484 (2012)
Prabhat, O. Rübel, S. Byna, K. Wu, F. Li, M. Wehner & E. W. Bethel, "TECA: A Parallel Toolkit for Extreme Climate Analysis", Third Workshop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, (2012)
L. Ramakrishnan, R. S. Canon, K. Muriki, I. Sakrejda & N. J. Wright, "Evaluating Interconnect and Virtualization Performance for High Performance Computing", Special Issue of ACM Performance Evaluation Review, 40(2), (2012)
T. Samak, D. Gunter, M. Goode, E. Deelman, G. Juve, F. Silva & K. Vahi, "Failure Analysis of Distributed Scientific Workflows Executing in the Cloud", 8th International Conference on Network and Service Management, CNSM 2012, Las Vegas, USA, October 22-26, 2012, (2012)
T. Samak, D. Gunter & Z. Wang, "Prediction of Protein Solubility in E. Coli", eScience, (2012)
T. Samak, D. Gunter & V. Hendrix, "Scalable analysis of network measurements with Hadoop and Pig", Proceedings of the 2012 IEEE Network Operations and Management Symposium, NOMS 2012, 1254-1259 (2012)
A. R. Sanderson, B. Whitlock, O. Rübel, H. Childs, G. H. Weber, Prabhat & K. Wu, "A System for Query Based Analysis and Visualization", Third International Eurovis Workshop on Visual Analytics EuroVA 2012, (2012)
K. Schuchardt, D. Agarwal, S. Finsterle, C. Gable, I. Gorto, L. Gosink & etal., "Akuna - Integrated Toolsets Supporting Advanced Subsurface Flow and Transport Simulations for Environmental Management", to appear in XIX International Conference on Water Resources (CMWR), (2012)
K. Vahi, I. Harvey, T. Samak, D. Gunter, K. Evans, D. Rogers, I. Taylor, M. Goode, F. Silva, E. Al-Shakarchi, G. Mehta, A. Jones & E. Deelman, "A General Approach to Real-time Workflow Monitoring", The Seventh Workshop on Workflows in Support of Large-Scale Science (WORKS12), in conjunction with SC 2012, Salt Lake City, November 10-16 2012, (2012)
S. Whalen, S. Engle, S. Peisert & M. Bishop, "Network-Theoretic Classification of Parallel Computation Patterns", International Journal of High Performance Computing Applications (IJHPCA), 26, 159-169 (2012)
I. Yamazaki & K. Wu, "A Communication-Avoiding Thick-Restart Lanczos Method on a Distributed-Memory System", Euro-Par 2011: Parallel Processing Workshops, 7155, 345-354 (2012)
Z. Fadika, M. Govindaraju, S. Canon & L. Ramakrishnan, "Evaluating Hadoop for Data-Intensive Scientific Operations", IEEE Cloud Computing, (2012 )

2011

D. Agarwal, Y.-W. Cheah, D. Fay, J. Fay, D. Guo, T. Hey, M. Humphrey, K. Jackson, J. Li, C. Poulain, Y. Ryu & C. van_Ingen, "Data-intensive science: The Terapixel and MODISAzure projects", International Journal of High Performance Computing Applications, 25, 304-316 (2011) PDF
E. W. Bethel, D. Leinweber, O. Rübel & K. Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles for Supercomputing", WHPCF, 23-30 (2011)
S. Byna, Prabhat, M. F. Wehner & K. Wu, "Detecting Atmospheric Rivers in Large Climate Datasets", PDAC-11, (2011)
D. C. Miller, M. Syamlal, J. C. Meza, D. L. Brown, M. M. Fox, M. Khaleel, R. K. Cottrell, J. D. Kress, X. Sun, S. Sundaresan, N. Sahinidis, S. E. Zitney, D. A. Agarwal, C. Tong, G. Lin, B. C. Letellier, D. Engel, P. Calafiura, G. A. Richards & J. H. Shinn, "The US Department of Energys Carbon Capture Simulation Initiative", 10th Annual Conference on Carbon Capture & Sequestration, (2011)
D. C. Miller, M. Syamlal, J. C. Meza, D. L. Brown, M. M. Fox, M. Khaleel, R. K. Cottrell, J. D. Kress, X. Sun, S. Sundaresan, N. Sahinidis, S. E. Zitney, D. A. Agarwal, C. Tong, G. Lin, B. C. Letellier, D. Engel, P. Calafiura, G. A. Richards & J. H. Shinn, "Overview of the US DOEs Carbon Capture Simulation Initiative for Accelerating the Commercialization of CCS Technology", 36th International Technical Conference on Clean Coal & Fuel Systems, (2011)
J. Chou, K. Wu & Prabhat, "FastQuery: A General Indexing and Querying System for Scientific Data", SSDBM, 573-574 (2011)
J. Chou, K. Wu & Prabhat, "FastQuery: A Parallel Indexing System for Scientific Data", IASDS, (2011)
J. Chou, K. Wu, O. Rübel, M. Howison, J. Qiang, Prabhat, B. Austin, E. W. Bethel, R. D. Ryne & A. Shoshani, "Parallel Index and Query for Large Scale Data Analysis", SC11, (2011)
M. Di Pierro, J. Hetrick, S. Cholia & D. Skinner, "Making QCD Lattice Data Accessible and Organized through Advanced Web Interfaces", arXiv preprint arXiv:1112.2193, (2011)
D. Gunter, E. Deelman, T. Samak, C. X. Brooks, M. Goode, G. Juve, G. Mehta, P. Moraes, F. Silva, D. M. Swany & K. Vahi, "Online workflow management and performance analysis with Stampede", 7th International Conference on Network and Service Management, CNSM 2011, Paris, France, October 24-28, 2011, 1-10 (2011)
E. Dede, L. Ramakrishnan, D. Gunter & M. Govindaraju, "Riding the Elephant: Managing Ensembles with Hadoop", The 4th Workshop on Many-Task Computing on Grids and Supercomputers (MTAGS), (2011)
D. Gunter, T. Samak, E. Deelman, C. H. Brooks, M. Goode, G. Juve, G. Mehta, P. Moraes, F. Silva, M. Swany & K. Vahi, "Online Workflow Management and Performance Analysis with STAMPEDE", 7th International Conference on Network and Service Management (CNSM 2011), (2011)
T. Samak, D. Gunter, M. Goode, E. Deelman, G. Juve & F. Silva, "Using Machine Learning Techniques for Online Failure Prediction in Large Scientific Workflows", (2011)
D. Ghoshal, R. S. Canon & L. Ramakrishnan, "I/O Performance of Virtualized Cloud Environments", The Second International Workshop on Data Intensive Computing in the Clouds (DataCloud-SC11), (2011)
J. Kim, H. Abbasi, L. Chacón, C. Docan, S. Klasky, Q. Liu, N. Podhorszki, A. Shoshani & K. Wu, "Parallel In Situ Indexing for Data-intensive Computing", LDAV, 65-72 (2011)
E. Kissel, D. Gunter, T. Samak, A. El-Hassany, G. Fernandes & M. Swany, "An Instrumentation and Measurement Framework for End-to-End Performance Analysis", (2011)
K. Madduri & K. Wu, "Massive-Scale RDF Processing Using Compressed Bitmap Indexes", SSDBM, 470-479 (2011)
D. C. Miller, D. A. Agarwal, X. Sun & C. Tong, "iCCSI and the role of advanced computing in accelerating the commercial deployment of carbon capture systems", Proceedings of the SciDAC 2011 Conference, (2011)
Z. Fadika, E. Dede, M. Govindaraju & L. Ramakrishnan, "Benchmarking MapReduce Implementations for Application Usage Scenarios", Grid 2011: 12th IEEE/ACM International Conference on Grid Computing, 0, 1-8 (2011)
M. Pala, S. Cholia, S. A. Rea & S. W. Smith, "Federated PKI authentication in computing grids: Past, present, and future", Cloud, Grid and High Performance Computing: Emerging Applications, 165-179 (2011)
M. Pierro, J. Hetrick, S. Cholia & D. Skinner, "Making QCD lattice data accessible and organized through advanced web interfaces", Proceedings of Science, 139, (2011)
Prabhat, Q. Koziol, K. Schuchardt, E. W. Bethel, J. Chuo, M. Howison, M. McGreevy, B. Palmer, O. Ruebel & K. Wu, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", SciDAC 2011, (2011)
Prabhat, S. Byna, C. Paciorek, G. Weber, K. Wu, T. Yopes, M. F. Wehner, G. Ostrouchov, D. Pugmire, R. Strelitz, W. Collins & E. W. Bethel, "Pattern Detection and Extreme Value Analysis on Large Climate Data", (2011)
Prabhat, S. Byna, C. Paciorek, G. Weber, K. Wu, T. Yopes, M. Wehner, W. Collins, G. Ostrouchov, R. Strelitz & E. W. Bethel, "Pattern Detection and Extreme Value Analysis on Large Climate Data", (2011)
L. Ramakrishnan, J. Chase, D. Gannon, D. Nurmi & R. Wolski, "Deadline-Sensitive Workflow Orchestration Without Explicit Rescource Control", J. Parallel Distributed Computing, 71, 343-353 (2011) PDF
L. Ramakrishnan, P. T. Zbiegel, S. Campbell, R. Bradshaw, R. Canon, S. Coghlan, I. Sakrejda, N. Desai, T. Declerck & A. Liu, "Magellan: Experiences from a science cloud", proceedings of the 2nd international workshop on Scientific cloud computing,ScienceCloud'11, 49-58 (2011)
R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, C. G. R. Geddes, W. Leemans, X. Li, Prabhat, J. Qiang, O. Rübel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon & N. Yampolsky, "High Performance Computing in Accelerator Science: Past Successes, Future Challenges", (2011)
T. Samak, D. Gunter, E. Deelman, G. Juve, G. Mehta, F. Silva & K. Vahi, "Online Fault and Anomaly Detection for Large-Scale Scientific Workflows", 13th IEEE International Conference on High Performance Computing and Communications (HPCC-2011), (2011)
T. Samak, D. Gunter, M. Goode, E. Deelman, G. Mehta, F. Silva & K. Vahi, "Failure Prediction and Localization in Large Scientific Workflows", The Sixth Workshop on Workflows in Support of Large-Scale Science (WORKS11), (2011)
K. R. Jackson, K. Muriki, L. Ramakrishnan, K. J. Runge & R. C. Thomas, "Performance and cost analysis of the Supernova factory on the Amazon AWS cloud", Sci. Program., 19, 107-119 (2011) PDF
S. Whalen, S. Peisert & M. Bishop, "Network-Theoretic Classification of Parallel Computation Patterns", Proceedings of the First International Workshop on Characterizing Applications for Heterogeneous Exascale Systems (CACHES), (2011)
K. Wu, R. R. Sinha, C. Jones, S. Ethier, S. Klasky, K.-L. Ma, A. Shoshani & M. Winslett, "Finding regions of interest on toroidal meshes", Computational Science & Discovery, 4, 015003 (2011)
K. Wu, S. Byna, D. Rotem & A. Shoshani, "Scientific Data Services -- A High-Performance I/O System with Array Semantics", HPCDB, (2011)
W. Yu, K. Wu, W.-S. Ku, C. Xu & J. Gao, "BMF: Bitmapped Mass Fingerprinting for Fast Protein Identification", CLUSTER, (2011)

2010

D. Agarwal, M. Humphrey, N. Beekwilder, K. Jackson, M. Goode & C. van Ingen, "A Data Centered Collaboration Portal to Support Global Carbon-Flux Analysis", Concurrency and Computation: Practice and Experience - Successes in Furthering Scientific Discovery, (2010)
M. Altunay, D. Olson & M. Helm, "OSG-ESnet Joint Identity Management Workshop report", OSG Doc 931, (2010)
S. J. Bailey, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bongard, C. Buton, M. Chidress, N. Chotard, Y. Copin, H. Fakhouri, E. Gangler, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Runge, R. Scalzo, G. S. C. Tao, R. C. Thomas & C. Wu, "Using Spectra to Make Cosmology's Best Standard Candles Even Better", Bulletin of the American Astronomical Society, 42, 313 (2010)
S. Binet, P. Calafiura, S. Snyder, W. Wiedenmann & F. Winklmeier, "Harnessing Multicores:Strategies and Implementations in Atlas", J. Phys. Conf, (2010)
M. Bishop, J. Cummins, S. Peisert, A. Singh, B. Bhumiratana, D. Agarwal, D. Frincke & M. Hogarth, "Relationships and data sanitization: a study in scarlet", Proceedings of the 2010 workshop on New security paradigms, 151-164 (2010)
Y. Simmhan, E. Soroush, C. van Ingen, D. Agarwal & L. Ramakrishnan, "Brew: Blackbox Resource Selection for e-science Workflows", Fifth Workshop on Workflows in Support of Large-SCale Science(WORKS10), 1-10 (2010)
E. Carvalho, D. Ushizima, F. Medeiros, C. Martins, R. Marques & I. Oliveira, "SAR\ imagery segmentation by statistical region growing and hierarchical merging ", Digital Signal Processing , 20, 1365 - 1378 (2010) PDF
S. Cholia, "Integrating Grid Services into the Cray XT4 Environment", Lawrence Berkeley National Laboratory, (2010)
S. Cholia, D. Skinner & J. Boverhof, "NEWT: A RESTful service for building High: Performance Computing web applications", 2010 Gateway Computing Environments Workshop, GCE 2010, 1-11 (2010)
S. Callaghan, E. Deelman, D. Gunter, G. Juve, P. Maechling, C. Brooks, K. Vahi, K. Milner, R. Graves, E. Field, D. Okaya & T. Jordan, "Scaling up Workflow-based Applications", Journal of Computer and System Sciences, 76, 428-446 (2010)
L. Hajdu, L. Dideno, J. Lauret & D. Olson, "Comparison of Cloud Approaches: Overview and Perspectives from STAR", International Symposium on Grid Computing, (2010)
D. Hasenkamp, A. sim, M. Wehner & K. Wu, "Finding Tropical Cyclones on a Cloud Computing Cluster: Using Parallel Virtualization for Large-Scale Climate Simulation Analysis", CloudCom, 201-208 (2010)
K. Jackson, L. Ramakrishnan, R. Thomas & K. Runge, "Seeking Supernovae in the Clouds: A performance Study", High Perfomrance Distributed Computing, (2010)
K. Jackson, L. Ramakrishnan, K. Muriki, S. Canon, S. Cholia, J. Shalf, H. Wasserman & N. Wright, "Performance analysis of high performance computing applications on the Amazon Web Services cloud", Proceedings - 2nd IEEE International Conference on Cloud Computing Technology and Science, CloudCom 2010, 159-168 (2010)
R. Kettimuthu, A. Sim, D. Gunter, B. Allcock, P. T. Bremer, J. Bresnahan, A. Cherry, L. Childers, E. Dart, I. Foster, K. Harms, J. Hick, J. Lee, M. Link, J. Long, K. Miller, V. Natarajan, V. Pascucci, K. Raffenetti, D. Ressman, D. Williams, L. Wilson & L. Winkler, "Lessons learned from moving earth system grid data sets over a 20 Gbps wide-area network", Proceedings of the 19th ACM International Symposium on High Performance Distributed Computing, 316-319 (2010) PDF
O. Komogortsev, S. Jayarathna, C. Aragon & M. Mahmoud, "Biometric Identification via an Oculomotor Plant Mathematical Model", Eye Tracking Research and Applications, ETRA, (2010)
J. Li, D. Agarwal, M. Humphrey, C. van Ingen, K. Jackson & Y. Ryu, "eScience in the Cloud: A MODIS Satellite Data Reprojection and Reduction Pipeline in the Windows Azure Platform", 24th IEEE International Parallel and Distributed Precessing Symposium, IPDPS, (2010)
J. Li, M. Humphrey, Y. Cheah, Y. Ryu, D. Agarwal, K. Jackson & C. van Ingen, "Fault Tolerance and Scaling in e-Science Cloud Applications: Observations from the Continuing Development of MODISAzure", 2010 IEEE Sixth International Conference on eScience, 246-253 (2010)
A. Meier, C. Aragon, B. Hurwitz, D. Mujumdar, T. Peffer, D. Perry & M. Pritoni, "How People Actually use Thermostats", The American Council for an Energy-Efficient Economy inproceedings, ACEEE 2010, (2010)
P. G. Neumann, M. Bishop, S. Peisert & M. Schaefer, "Reflections on the 30th Anniversary of the IEEE Symposium on Security and Privacy", Proceedings of the 31st IEEE Symposium on Security & Privacy, 3-13 (2010)
E. Otoo & K. Wu, "Accelerating Queries on Very Large Datasets", Scientific Data Management: Challenges, Existing Technology, and Deployment, 183-234 (2010)
M. Pala, "Interoperable PKI Data Distribution in Computational Grids", Lawrence Berkeley National Laboratory, (2010)
B. I. Simidchieva, S. J. Engle, M. Clifford, A. C. Jones, S. Peisert, M. Bishop, L. A. Clarke & L. J. Osterweil, "Modeling Faults to Improve Election Process Robustness", Proceedings of the 2010 Electronic Voting Technology Workshop/Workshop on Trustworthy Computing (EVT/WOTE '10), (2010)
S. Peisert, "Fingerprinting Communication and Computation on HPC Machines", (2010)
S. Peisert, M. Bishop & K. Marzullo, "What Do Firewalls Protect? An Empirical Study of Vulnerabilities and Attacks", (2010)
M. Bishop, S. Engle, D. A. Frincke, C. Gates, F. L. Greitzer, S. Peisert & S. Whalen, "A Risk Management Approach to the ``Insider Threat''", Insider Threats in Cybersecurity, (2010)
L. Ramakrishnan, D. Gannon & B. Plale, "WORKEM: Representing and Emulating Disturbed Scientific Workflow Execution State", 10th IEEE/ACM International Symposium on Cluster, Cloud and Grip Computing, CCGid, (2010)
L. Ramakrishnan & B. Plale, "A multidimensional classification model for scientific workflow characteristics", 1st Int'l Workshop on Workflow Approaches for New Data-Centric Science, (2010)
L. Ramakrishnan, C. Guok, K. Jackson, E. Kissel, D. M. Swany & D. Agarwal, "On-demand Overlay Networks for Large Scientific Data Transfer", 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing, CCGrid, (2010)
L. Ramakrishnan, K. Jackson, S. Canon, S. Cholia & J. Shalf, "Defining future platform requirements for e-Science clouds", Proceedings of the 1st ACM Symposium on Cloud Computing, SoCC '10, 101-106 (2010)
R. Roberts, T.Trucano, P. Pope, C. Aragon, M. Jiang, T. Wei, L. Chilton & A. Bakel, "On the Verification and Validation of Geospatial Image Analysis Algorithms", IEEE International Geoscience and Remote Sensing Sympsium, IGARSS, (2010)
O. Rübel, S. Ahern, E. W. Bethel, M. D. Biggin, H. Childs, E. Cormier-Michel, A. DePace, M. B. Eisen, C. C. Fowlkes, C. G. R. Geddes, H. Hagen, B. Hamann, M.-Y. Huang, S. V. E. Keränen, D. W. Knowles, C. L. L. Hendriks, J. Malik, J. Meredith, P. Messmer, Prabhat, D. Ushizima, G. H. Weber & K. Wu, "Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data", Procedia Computer Science, 1, 1751-1758 (2010)
R. Scalzo, C. Akerlof, G. Aldering, P. Antilogus, C. Aragon, S. Bailey, C. Baltay, A. Bauer, D. Birchall, S. Bongard, C. Buton, M. Childress, Y. Copin, A. Gal-Yam, E. Gangler, J. Holtzman, S. Hoyer, M. Kasliwal, S. Loken, J. Miller, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, C. Peters, G. Smadja, C. Tao, R. Thomas, J. Thorstensen, B. Weaver, C. Wu & F. Yuan, "Nearby Supernova Factory Observations of SN 2007if: Evidence for Shell Structure in the Explosion of a Super-Chandrasekhar-Mass White Dwarf,", American Astronomical Society,, 42, 450 (2010)
R. Scalzo, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bailey, S. Bongard, C. Buton, M. Childress, N. Chotard, Y. Copin, E. Gangler, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Runge, G. Smadja, H. Swift, C. Tao, R. Rabinowitz, G. Rigaudier, K. Runge, G. Smadja, H. Swift, C. Tao, R. Thomas & C. Wu, "Nearby Supernova Factory Observations of SN 2007if: First Total Mass Measurement of a Super -Chandrasekhar-Mass Progenitor", Astrophysical Journal, 713, 1073-1094 (2010)
A. Sim, D. Gunter, V. Natarajan, A. Shoshani, D. Williams, J. Long, J. Hick, J. Lee & E. Dart, "Efficient bulk data:replication for the earthy systems grid", International Symposium on Grid Computing.National Science Council, (2010)
A. Sim, D. Gunter, V. Natarajan, A. Shoshani, D. Williams, J. Long, J. Hick, J. Lee & E. Dart, "Efficient Bulk Data Replication for the Earth System Grid", Data Driven E-science: Use Cases and Successful Applications of Distributed Computing Infrastructures (Isgc 2010), 435 (2010)
Y. Simmhan & L. Ranakrishnan, "Comparison of resource platform selection approaches for scientific workflows", 1st Workshop on Scientific Cloud Computing, Colocated with ACM and High Performance Distributed Computing, (2010)
G. H. Weber, S. Ahern, E. W. Bethel, S. Borovikov, H. R. C. E. Deines, C. Garth, H. Hagen, B. Hamann, K. I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. V. Strallen & K. Wu, "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization", Numerical Modeling of Space Plasma Flows: Astronum-2009, ASP Conference Series, 429, 329-334 (2010)
K. Wu, K. Madduri & S. Cannon, "Multi-level bitmap indexes for flash memory storage", IDEAS, (2010)
I. Yamazaki, Z. Bai, H. D. Simon, L.-W. Wang & K. Wu, "Adaptive Projection Subspace Dimension for the Thick-Restart Lanczos Method", ACM Transactions on Mathematical Software, 37, (2010)
Y. Yao, P. Calafirua, J. Poffet, A. Cavalli, C. Leggett & B. Frederic, "Virtual Machine Logbook:EnablingVirtualization for Atlas", J. Phys. Conference Series, (2010)

2009

L. Ramakrishnan & D. A. Reed, "“Predictable quality of service atop degradable distributed systems, ", Cluster Computing , (2009)
S. Bailey, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bongard, C. Buton, M. Childress, N. Chotard, E. G. Copin, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Runge, R. Scalzo, G. Smadja, H. Swift, C., Tao, R. C. Thomas & C. Wu, "Using Spectral Flux Ratios to Standardize SN Ia Luminosities,", Astronomy & Astrophysics Letters, (2009)
L. Ramakrishnan, D. Nurmi, A. Mandal, C. Koelbel, D. Gannon, T. M. Huang, Y.-S. Kee, G. Oberteli, K. Thyagaraja, R. Wolski, A. Yarkhan & D. Zagorodnov, "Automated Analysis for Detecting Beams in Laser Wakefield Simulations,", ACM/IEEE SC inproceedings, (2009)
S. Callaghan, E. Deelman & others (in submission), "Scaling up Workflow-based Applications", Journal of Computer and System Sciences, (2009)
F. Gey, "Dynamic Change in Classification Systems: A Preliminary Model for Instance-based Matching, ", (2009)
K. Chard, J. Boverhof, W. Tan, R. Madduri & I. Foster, "Wrap Scientific Applications as WSRF Grid Services using gRAVI,", The International Conference on Web Services, (2009)
C. R. Aragon, "Collaborative analytics for astrophysics explorations, ", Springer Handbook of Automation, (2009)
K. Keck, B. Bargmeyer & others, "Committee Draft 1 of ISO/IEC 11179 Information Technology -- Metadata registries (MDR) Part 3 Edition 3", (2009)
S. S. Poon, R. C. Thomas, C. R. Aragon & B. Lee, "Context-Linked Intelligent User Interfaces, ", Workshop on Human Interaction with Intelligent and Networked Systems at the IUI International Conference on Intelligent User Interfaces, (2009)
B. Bargmeyer, "Emerging Semantic Technology Standards - Making Life Easier in the Information World", Proceedings of the 12th Open Forum on Metadata Registries, (2009)
B. Bargmeyer & S. Chance, "Environmental Data: Edge Issues and the Path Forward", Environmental Data Exchange Network For Inland Water, (2009)
B. Bargmeyer, "Metadata Registries: Research, Standards Development and Practice", International Journal of Metadata, Special Edition of Semantics and Ontologies (IJMSO), , (2009)
M. Piette, G. Ghatikar, S. Kiliccote, E. Koch, D. Hennage, P. Palensky & C. McParland, "Open Automated Demand Response Communications Specification (Version 1.0)", Journal of Cluster Computing, (2009)
C.R.Aragon & K. J. Runge, "Workflow Management for High Volume Supernova Search,", ACM Symposium on Applied Computing SAC '09, (2009)
C. Aragon, S. Poon, A. Monroy-Hernandez & D. Aragon, "A Tale of Two Online Communities: Fostering Collaboration and Creativity in Scientists and Children", ACM Conference on Creativity and Cognition, (2009)
C. Aragon, S. Poon, G. Aldering, R. C. Thomas & R. Quimby, "Using Visual Analytics to Develop Situation Awareness in Astrophysics,", Journal of Information Visualization, (2009)
S. Bailey, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bongard, C. Buton, M. Childress, N. Chotard, Y. Copin, E. Gangler, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, P. Ripoche, K. Runge, R. Scalzo, G. Smadja, C. Tao, R. Thomas & C. Wu, "Generalized Spectral Correlations of Type Ia Supernovae from the Nearby Supernova Factory", Bulletin of the American Astronomical Society, 41, (2009)
S. Bailey, G. Aldering, P. Antilogus, C. Aragon, C. Baltay, S. Bongard, C. Buton, M. Childress, N. Chotard, Y. Copin, E. Gangler, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinowitz, G. Rigaudier, K. Runge, R. Scalzo, G. Smadja, H. Swift, C. Tao, R. C. Thomas & C. Wu, "Using Spectral Flux Ratios to Standardize SN Ia Luminosities", Astronomy & Astrophysics Letters, (2009)
B. Bargmeyer, "Metadata Registries: Research, Standards Development and Practice", International Journal of Metadata, Semantics and Ontologies,Special Edition of Semantics and Ontologits, 4, (2009)
B.Bargmeyer, "Metadata Registries and Cloud Computing-Standards Challenges", 13th Open Forum on Metadata Registries, (2009)
E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Kruger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock & K. Wu, "Occam's Razor and Petascale Visual Data Analysis", SciDAC 2009, (2009) PDF
S. Canon, S. Cholia, J. Shalf, K. Jackson, L. Ramakrishnan & V. Markowitz, "A performance comparison of massively parallel sequence matching computations on cloud computing platforms and hpc clusters using hadoop", Using Clouds for Parallel Computations in Systems Biology Workshop, Held at SC09, (2009)
S. Cholia & R. Porter, "Publication and Protection of Sensitive Site Information in a Grid Infrastructure", International Journal of Grid and High Performance Computing, 1, 45-55 (2009)
Y. Copin, G. Aldering, P. Antilogus, C. Aragon, S. Bailey, C. Baltay, S. Bongard, C. Buton, M. Childress, E. Gangler, J. Jerke, S. Loken, P. Nugent, R. Pain, E. Pecontal, R. Pereira, S. Perlmutter, D. Rabinovitz, G. Rigaudier, P. Ripoche, K. Runge, R. Scalzo, G. Smadja, H. Swift, C. Tao, R. C. Thomas & C. Wu, "The Nearby Supernova Factory: First Results", EAS Publications Series, 36, 11-15 (2009)
L. J. Gosink, K. Wu, E. W. Bethel, J. D. Owens & K. I. Joy, "Data Parallel Bin-Based Indexing for Answering Queries on Multi-core Architectures", SSDBM, 5566, 110-129 (2009)
B. R. Supinski, S. Alam, D. H. Bailey, L. Carrington, C. Daley, A. Dubey, T. Gamblin, D. Gunter, P. D. Hovland, H. Jagode, K. Karavanic, G. Marin, J. Mellor-Crummey, S. Moore, B. Norris, L. Oliker, C. Olschanowsky, P. C. Roth, M. Schulz, S. Shende, A. Snavely, W. Spear, M. Tikir, J. Vetter, P. Worley & N. Wright, "Modeling the Office of Science ten year facilities plan: The PERI Architecture Tiger Team", Journal of Physics: Conference Series, 180, 012039+ (2009) PDF
L. He, Y. Chao, K. Suzuki & K. Wu, "Fast Connected-Component Labeling", Pattern Recognition, 42, 1977-1987 (2009)
M. Humphrey, D. Agarwal & C. van Ingen, "Fluxdata.org: Publication and Curation of Shared Scientific Climate and Earth Sciences Data", 2009 Fifth IEEE International Conference on e-Science, 118-125 (2009)
O. Komogortsev, S. Jayarathna, C. Aragon & M. Mahmoud, "Biometric Identificaton Via an Oculomotor Plant Mathematical Model", (2009)
J. Li, Y.Ryu, K. Jackson, D. Agarwal, M. Humphrey & C. van Ingen, "A Cloud Computing Service for Remote Sensing Data Reprojection and Science Reduction", EOS Trans. Amercian Geophysical Union, (2009)
J. Li, Y. Ryu, K. Jackson, D. Agarwal, M. Humphrey & C. van Ingen, "Process-based estimates of terrestrial CO2 assimilation and evEovs", Trans. American Geophysical Union, (2009)
K. Madduri & K. Wu, "Efficient joins with compressed bitmap indexes", CIKM, 1017-1026 (2009)
C. McParland, "The Evolution of the Internet Community and the 'Yet-to-evolve'Smart Grid Community:Parallels and Lessons-to-be-learned", Grid-Interop Forum, (2009)
M. Nagappan, K. Wu & M. A. Vouk, "Efficiently Extracting Operational Profiles from Execution Logs Using Suffix Arrays", ISSRE, 41-50 (2009)
M. Pala, S. Cholia, S. Rea & S. Smith, "Interoperable PKI data distribution in computational grids", International Journal of Grid and High Performance Computing, 1, 56-73 (2009)
M. Bishop, S. Peisert, C. Hoke, M. Graff & D. Jefferson, "E-Voting and Forensics: Prying Open the Black Box", Proceedings of the 2009 Electronic Voting Technology Workshop/Workshop on Trustworthy Computing (EVT/WOTE), (2009)
S. Peisert, M. Bishop, L. Corriss & S. Greenwald, "Quis Custodiet ipsos Custodes? A New Paradigm for Analyzing Security Paradigms", Proceedings of the 2009 New Security Paradigms Workshop (NSPW), 133-144 (2009)
L.Ramkrishnan, D. Nurmi, A. Mandal, C. Koelbel, D. Gannon, T. Huang, Y. S. Kee, G. Oberteli, K. Thyagaraja, R. Wolski, A. Yarhan & D. Zagorodnov, "VGrADS: Enabling eScience Workflows on Grids and Clouds with Fault Tolerance", ACM/IEEE SC2009 Conference on High Performance Computing, Networking, Storage and Analysis, (2009)
O. Rübel, C. G. R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G. H. Weber, D. M. Ushizima, P. Messmer, H. Hagen, B. Hamann & W. Bethel, "Automatic beam path analysis of laser wakefield particle acceleration data", Computational Science & Discovery, 2, 015005 (2009)
R. R. Sinha, M. Winslett & K. Wu, "Finding Regions of Interest in Large Scientific Datasets", SSDBM, 5566, 130-147 (2009)
K. Wu, S. Ahern, E. W. Bethel, J. Chen, H. Childs, E. Cormier-Michel, C. Geddes, J. Gu, H. Hagen, B. Hamann, W. Koegler, J. Lauret, J. Meredith, P. Messmer, E. Otoo, V. Perevoztchikov, A. Poskanzer, Prabhat, O. Rübel, A. Shoshani, A. Sim, K. Stockinger, G. Weber & W.-M. Zhang, "FastBit: Interactively Searching Massive Data", SciDAC 2009, (2009)
K. Wu, E. Otoo & K. Suzuki, "Optimizing two-pass connected-component labeling algorithms", Pattern Analysis & Applications, 12, 117-135 (2009)

2008

D. Ushizima, O. Ruebel, Prabhat, G. Weber, E. W. Bethel, C. Aragon, C. Geddes, E. Cormier-Michel, B. Hamann, P. Messmer & H. Hagen, "Automated Analysis for Detecting Beams in Laser Wakefield Simulations", Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA, (2008)
D. Agarwal, D. Baldocchi, M. Goode, M. Humphreys, C. van Ingen, D. Papale, M. Reichstein, M. Rodriguez, Y. Ryu & R. Vargas, "An Evolving La Thuile Fluxnet Dataset and Support Infrastructure", European Geosciences Union General Assembly, (2008)
C. van Ingen, "Environmental Science as a data intensive Science", BWC and Innovation Center, (2008)
S. Callaghan, P. Maechling & others, "Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows?Experiences from SCEC CyberShake", Fourth IEEE International Conference on eScience , (2008)
C. Guok, D. W. Robertson, E. Chaniotakis, M. R. Thompson, W. E. Johnston & B. L. Tierney, "A User Driven Dynamic Circuit Network Implementation.", Distributed Autonomous Network Management Systems, (2008)
S. S. Poon, R. C. Thomas, C. R. Aragon & B. Lee, "Context-Linked Virtual Assistants for Distributed Teams: An Astrophysics Case Study ", CSCW: ACM Conference on Computer Supported Cooperative Work, (2008)
M. Humphrey, N. Beekwilder, D. Agarwal, D. Baldocchi, M. Goode, J. Gupchup, C. van Ingen, D. Papale, M. Reichstein, M. Rodriguez, Y. Ryu, R. Vargas & N. Li, "Creating and Accessing the Global Fluxnet Data Set", Microsoft eScience All Hands Meeting, (2008)
F. Olken & L. Gruenwald, "Data Stream Management: Aggregation, Classification, Modeling, and Operator Placement", IEEE Internet Computing , 12, 9-12 (2008) PDF
C. van Ingen, D. Agarwal, M. Humphrey & J. Li, "Deriving Daytime Variables From the AmeriFlux Standard Eddy Covariance Data Set", Eos Trans. American Geophysical Union, Fall Meet. Suppl., (2008) PDF
C. R. Aragon & S. S. Poon, "Designing Scientific Workflow Management Systems for Data-Intensive Astrophysics Projects", Designing Cyberinfrastructure to Support Science Workshop, CSCW 2008: ACM Conference on Computer Supported Cooperative Work, (2008)
W. Johnston, B. Tierney, C. Tull, A. Hanushevsky & others, "Data-Intensive Computing in Widely Distributed Environments", (2008)
A. Baranovski, K. Beattie, S. Bharathi, J. Boverhof, J. Bresnahan, A. Chervenak, I. Foster, T. Freeman, D. Gunter, K. Keahey, C. Kesselman, R. Kettimuthu, N. Leroy, M. Link, M. Livny, R. Madduri, G. Oleynik, L. Pearlman, R. Schuler, B. Tierney & F. N. A. Laboratory, "Enabling petascale science: data management, troubleshooting, and scalable science services", Journal of Physics: Conference Series, 125, 012068+ (2008) PDF
D. Agarwal, M. Humphrey, C. van Ingen, N.Beekwilder, M. Goode, K. Jackson, M. Rodriguez & R. Weber, "Fluxnet Synthesis Dataset Collaboration Infrastructure", 1, (2008)
D. Agarwal, M. Humphrey, N. Beekwilder, M. Goode, K. Jackson, R. Weber, C. van Ingen & D. Baldocchi, "Interaction Support for the Global FLUXNET Data Set,", Eos Trans. American Geophysical Union, (2008)
S. Bailey, C. Aragon, R. Romano, R. C. Thomas, B. A. Weaver & D.Wong, "Object classification at the Nearby Supernova Factory ", Astronomische Nachrichten , 329, 292-294 (2008)
M. Humphrey, D. Agarwal & C. van Ingen, "Publication and Curation of Large-Scale Shared Environmental Scientific Data", (2008)
C. R. Aragon, S. J. Bailey, S. Poon, K. Runge & R. C. Thomas, "Sunfall: A Collaborative Visual Analytics System for Astrophysics ", J. Phys.: Conf. Ser, 125, (2008)
S. S. Poon & C. R. Aragon, "Towards Virtual Radical Collocation in Science Projects,", Distributed Team Work Workshop, CSCW ACM Conference on Computer Supported Cooperative Work, (2008)
C. Aragon, S. Poon, G. Aldering, R. Thomas & R. Quimby, "Using Visual Analytics to Maintain Situational Awareness in Astrophysics ", IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST), (2008)
E. W. Bethel, O. Rübel, Prabhat, K. Wu, G. H. Weber, V. Pascucci, H. Childs, A. Mascarenhas, J. Meredith & S. Ahern, "Modern Scientific Visualization is More than Just Pretty Pictures", Numerical Modeling of Space Plasma Flows: Astronum-2008 (Astronomical Society of the Pacific Conference Series), 301-317 (2008)
S. Cholia & R. Porter, "Publication and protection of sensitive site information in a grid infrastructure", Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid, 639-644 (2008)
L. J. Gosink, K. Wu, E. W. Bethel, J. D. Owens & K. I. Joy, "Bin-Hash Indexing: A Parallel Method For Fast Query Processing", (2008)
S. Callaghan, P. Maechling, E. Deelman, K. Vahi, G. Mehta, G. Juve, K. Milner, R. Graves, E. Field, D. Okaya, D. Gunter, K. Beattie & T. Jordan, "Reducing Time-to-Solution Using Distributed High-Throughput Mega-Workflows - Experiences from SCEC CyberShake", Proceedings of the 2008 Fourth IEEE International Conference on eScience, 151-158 (2008) PDF
M. Nagappan, M. A. Vouk, K. Wu, A. Sim & A. Shoshani, "Efficient Operational Profiling of Systems Using Suffix Arrays on Execution Logs", ISSRE, 313-314 (2008)
M. Pala, S. Cholia, S. Rea & S. Smith, "Extending PKI interoperability in computational grids", Proceedings CCGRID 2008 - 8th IEEE International Symposium on Cluster Computing and the Grid, 645-650 (2008)
O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C. G. R. Geddes, E. Cormier-Michel, S. Ahern, G. H. Weber, P. Messmer, H. Hagen, B. Hamann & E. W. Bethel, "Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data", IEEE Visualization 2008, (2008)
O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C. G. R. Geddes, E. Cormier-Michel, S. Ahern, G. H. weber, P. Messmer, H. Hagen, B. Hamann & E. W. Bethel, "High Performance Multivariate Visual Data Exploration for Extemely Large Data", SuperComputing 2008 (SC08), 51 (2008)
R. R. Sinha, M. Winslett, K. Wu, K. Stockinger & A. Shoshani, "Adaptive Bitmap Indexes for Space-Constrained Systems", ICDE 2008, 1418-1420 (2008)
K. Stockinger, J. Cieslewicz, K. Wu, D. Rotem & A. Shoshani, "Using Bitmap Indexing Technology for Combined Numerical and Text Queries", New Trends in Data Warehousing and Data Analysis, 3, 1-23 (2008)
K. Wu, K. Stockinger & A. Shosani, "Breaking the Curse of Cardinality on Bitmap Indexes", SSDBM'08, 348-365 (2008)
I. Yamazaki, K. Wu & H. Simon, "nu-TRLan User Guide version 1.0", (2008)

2007

J. M. Schopf, A. Chervenak, I. Foster, D. Fraser, D. Gunter, N. LeRoy & B. Tierney, "End-to-End Data Solutions for Distributed Petascale Science", CTWatch Quarterly, (2007)
I. Zaslavsky, M. Rodriguez, B. Beran, D. Valentine & C. van Ingen, "OLAP Cube Visualization of Hydrologic Data Catalogs", Eos Trans., 88, (2007)
J. Jung, R. Milito & V. Paxson, "On the Adaptive Real-Time Detection of Fast-Propagating Network Worms", Fourth GI International Conference on Detection of Intrusions & Malware, and Vulnerability Assessment, (2007)
M. Allman, V. Paxson & J. Terrell, "A Brief History of Scanning", ACM Internet Measurement inproceedings, (2007)
J. M. Gonzalez, V. Paxson & N. Weaver, "A Hardware/Software Architecture for Flexible, High-Performance Network Intrusion Prevention ", Proc. ACM CCS , (2007)
D. Agarwal, C. van Ingen, S. Holladay & M. Krassovski, "AmeriFlux Data Server User Tutorial,", AmeriFlux Annual Meeting, (2007)
V. Paxson, R. Sommer & N. Weaver, "An Architecture for Exploiting Multi-Core Processors to Parallelize Network Intrusion Prevention", IEEE Sarnoff Symposium, (2007)
D. Agarwal, D. Baldocchi, T. Boden, B. Cook, D. Frank, M. Goode, J. Gupchup, S. Holladay, M. Humphreys, C. van Ingen, B. Jackson, D. Papale, M. Reichstein, M. Rodriguez, Y. Ryu, R. Vargas, B. Wilson & N. Li, "Creating and Accessing the Global Fluxnet Data Set", Eos Trans. American Geophysical Union, 88, (2007)
J. McCarthy & B. Bargmeyer, "Ecoinformatics Project: Semantics Management and Semantics Services, Committee Draft 1 of Part 3, Edition 3 of the ISO/IEC 11179 Metadata Registries Standard", (2007)
I. Foster, D. Gunter, K. Jackson, J. M. Schopf & e. A. B. Tierney, "Enabling Distributed Petascale Science", SciDAC, (2007)
B. Tierney & e. a. Dan Gunter, "Grid Logging: Best Practices Guide", (2007)
M. Allman & V. Paxson, "Issues and Etiquette Concerning Use of Shared Measurement Data ", ACM Internet Measurement Conference , (2007)
C. Guok, J. R. Lee & K. Berket, "Improving the Bulk Data Transfer Experience", Special issue of the journal on Management of IP Networks and Services , (2007)
D. Gunter, B. L. Tierney, A. Brown, M. Swany, J. Bresnahan & J. M. Schopf, "Log Summarization and Anomaly Detection for Troubleshooting Distributed Systems", Grid Computing, 2007 8th IEEE/ACM International Conference on, IEEE/ACM International Conference on Grid Computing, 226-234 (2007) PDF
W. Lavrijsen & S. Binet, "Optimizations in Python-based HEP Analysis", CHEP inproceedings, (2007)
D. H. Bailey, R. Lucas, P. Hovland, B. Norris, K. Yelick, D. Gunter, B. de Supinski, D. Quinlan, P. Worley, J. Vetter, P. Roth, J. Mellor-Crummey, A. Snavely, J. Hollingsworth, D. Reed, R. Fowler, Y. Zhang, M. Hall, J. Chame, J. Dongarra & S. Moore, "Performance Engineering: Understanding and Improving the Performance of Large-Scale Codes", CT Watch Quarterely, 3, 18-23 (2007) PDF
E. Bresson, O. Chevassut & D. Pointcheval, "Provably-Secure Authenticated Group Diffie-Hellman Key Exchange", ACM Transactions on Information and System Security Journal , (2007) PDF
L. Ramakrishnan, Y. Simmhan & B. Plale, "Realization of Dynamically Adaptive Weather Analysis and Forecasting in LEAD,", In Dynamic Data Driven Applications Systems Workshop (DDDAS) in conjunction with ICCS, (2007)
S. Kamil, A. Pinar, D. Gunter, M. Lijewski, L. Oliker & J. Shalf, "Reconfigurable hybrid interconnection for static and dynamic scientific applications", Conference on Computing Frontiers , (2007)
M. Humphrey, M. R. Thompson & K. R. Jackson, "Security for grids", Proceedings of IEEE, 93, 644-652 (2007) PDF
J. M. Gonzalez, V. Paxson & N. Weaver, "Shunting: A Hardware/Software Architecture for Flexible, High-Performance Network Intrusion Prevention ", ACM CCS , (2007)
M. Abdalla, E. Bresson, O. Chevassut, B. Moller & D. Pointcheval, "Strong Password-Based Authentication in TLS Using the Three-Party Group Diffie-Hellman Protocol", International Journal of Security and Networks, 2, (2007) PDF
B. L. Tierney, D. Gunter & J. M. Schopf, "“The CEDPS Troubleshooting Architecture and Deployment on the Open Science Grid", SciDAC, (2007)
K. S. Beattie, C. T. Day, D. Glowacki, K. D. Hanson, J. E. Jacobsen, C. P. McParland & S. J. Patton, "The IceCube Data Acquisition Software: Lessons Learned during Distributed, Collaborative, Multi-Disciplined Software Development. ", CHEP , (2007)
M. Vallentin, R. Sommer, J. Lee, C. Leres, V. Paxson & B. Tierney, "The NIDS Cluster: Scalable, Stateful Network Intrusion Detection on Commodity Hardware", Symposium on Recent Advances in Intrusion Detection, (2007)
N. Weaver, V. Paxson & N. Weaver, "The Shunt: An FPGA-Based Accelerator for Network Intrusion Prevention", FPGA , (2007)
D. Agarwal, M. Goode, J. Gupchup, J. Hunt, C. van Ingen, R. Leonardson, M. Rodriguez & N. Li, "Unifying Diverse Watershed Data to Enable Analysis ,", EOS Trans. American Geophysical Union Fall Meet. Suppl., (2007)
D. Agarwal, M. Goode, J. Gupchup, J. Hunt, C. van Ingen, R. Leonardson, M. Rodriguez & N. Li, "Using the database to rapidly assess FLUXNET data,", Eos Trans. American Geophysical Union Fall Meet. Suppl., (2007)
B. L. Tierney, D. Gunter & J. M. Schopf, "The CEDPS troubleshooting architecture and deployment on the open science grid", Journal of Physics: Conference Series, 78, 012075+ (2007) PDF
J. M. Schopf, A. Chervenak, I. Foster, D. Fraser, D. Gunter, N. LeRoy & B. Tierney, "End-to-End Data Solutions for Distributed Petascale Science", CTWatch Quarterly, 3, 1+ (2007) PDF
E. O'Neil, P. O'Neil & K. Wu, "Bitmap Index Design Choices and Their Performance Implications", IDEAS 2007, 72-84 (2007)
F. Reiss, K. Stockinger, K. Wu, A. Shoshani & J. M. Hellerstein, "Enabling Real-Time Querying of Live and Historical Stream Data", SSDBM 2007, (2007)
K. Wu, "FastBit Reference Manual", (2007)
K. Wu, K. Stockinger & A. Shoshani, "Performance of Multi-Level and Multi-Component Compressed Bitmap Indexes", ACM Transactions on Database Systems, 35, 1-52 (2007)

2006

C. Guok, D. Robertson, M. Thompson, J. Lee, B. Tierney & W. Johnston, "Intra and Interdomain Circuit Provisioning Using the OSCARS Reservation System ", GridNets Third International Workshop on Networks for Grid Applications, , (2006)
M. Abdalla, E. Bresson, O. Chevassut & D. Pointcheval, "Password-Based Group Key Exchange in a Constant Number of Rounds", Workshop on Practice and Theory in Public Key Cryptography PKC , (2006)
W. Liebig, D. Rousseau, P. Calafiura, W. Lavrijsen, P. Loch & A. Salzburger, "Physics-level Job Configuration", Computing in High Energy and Nuclear Physics,, (2006)
M. Abdalla, E. Bresson, O. Chevassut, B. Moeller & D. Pointcheval, "Provably Secure Password-Based Authentication in TLS", ACM Symposium on InformAtion, Computer and Communications Security (ASIACCS'06), (2006)
K. Berket, A. Essiari & D. Agarwal, "A New Approach to Asymmetric Group Communication Membership", (2006)
J. Zurawski, M. Swany & D. Gunter, "A Scalable Framework for Representation and Exchange of Network Measurments", 2nd International IEEE/Create-Net Conference on Testbeds and Research Infrastructures for the Development of Networks and Communities (Tridentcom) , (2006)
E. Bresson, O.Chevassut & D. Pointcheval, "A Security Solution for IEEE 802.11 Ad-hoc Mode: Password-Authentication and Group Diffie-Hellman Key Exchange", Wireless and International Journal of Mobile Computing (IJWMC)--Special Issue on Security of Computer Network and Mobile Systems, (2006)
R. Pang, V. Paxson, R. Sommer & L. Peterson, "binpac: A yacc for Writing Application Protocol Parsers", ACM Internet Measurement Conference , (2006)
B. E. Bargmeyer, "Common Sense, Common Logic", ISO Focus Journal , (2006)
E. Hjort, D. Olson, J. Lauret, A. Sim & A. Shoshani, "Data and Computational Grid decoupling in STAR An Analysis Scenario using SRM Technology", Computing in High Energy and Nuclear Physics Conference (CHEP), (2006)
W. Lavrijsen & S. Binet, "Eclipse-Based Physicist Work Environment", Computing in High Energy and Nuclear Physics, (2006)
H. Palle & B. Bargmeyer, "Chapter Title: Environmental Data: Edge Issues and the Path Forward Doc_Format ", (2006)
S. Floyd, V. Paxson & A. Falk, "IAB Thoughts on the Role of the Internet Research Task Force (IRTF) ", (2006)
K. Berket, C. Guok & J. R. Lee, "Improving the Bulk Data Transfer Experience ", The special issue of the IJIPT journal on Management of IP Networks and Services, (2006)
D. Agarwal & D. Ramsey, "Protecting DOE Office of Science Resources while Maintaining an Effective Open Collaborative Science Environment", (2006)
W. Cui, V. Paxson, N. Weaver & R. Katz, "Protocol-Independent Adaptive Replay of Application Dialog", NDSS, (2006)
V. Paxson, K. Asanovic, S. Dharmapurikar, J. Lockwood, R. Pang, R.Sommer & N. Weaver, "Rethinking Hardware Support for Network Analysis and Intrusion Prevention", USENIX Hot Security , (2006)
J. R. Burruss, T. W. Fredian & M. R. Thompson, "Security on the US Fusion Grid: Simplifying FusionGrid Security, Security Challenges of Large", Applications in Distributed Environments (CLADE) workshop at HPDC14, (2006)
J. Kannan, J. Jung, V. Paxson & C. Koksal, "Semi-Automated Discovery of Application Session Structure", ACM Internet Measurement Conference , (2006)
R. Pang, M. Allman, V. Paxson & J. Lee, "The Devil and Packet Trace Anonymization", Computer Communication Review, 36, (2006) PDF
E. Bresson, O.Chevassut & D. Pointcheval, "The Group Diffie-Hellman Protocol,Password-based Group key Exchange in a Constant Number of Rounds", ACM Transactions on Information and System Security , (2006)
O. Chevasut, P. A. Fouque, P. Gaudry & D. Pointcheval, "The Twist-Augmented Technique for Key Exchange", International Workshop on Practice and Theory in Public Key Cryptography (PKC), (2006)
E. W. Bethel, S. Campbell, E. Dart, K. Stockinger & K. Wu, "Accelerating Network Traffic Analysis Using Query-Driven Visualization", Symposium on Visual Analytics Science and Technology (VAST), Baltimore, Maryland, USA, October 31 - November 2, 2006, 115-122 (2006)
E. Bethel, S. Campbell, E. Dart, J. Shalf, K. Stockinger & K. Wu, "High Performance Visualization using Query-Driven Visualization and Analytics", (2006)
L. Gosink, J. Shalf, K. Stockinger, K. Wu & W. Bethel, "HDF5-FastQuery: Accelerating Complex Queries on HDF Datasets using Fast Bitmap Indices", SSDBM 2006, Vienna, Austria, July 2006, 149-158 (2006)
F. Reiss, K. Stockinger, K. Wu, A. Shoshani & J. M. Hellerstein, "Efficient analysis of live and historical streaming data and its application to cybersecurity", (2006)
D. Rotem, K. Stockinger & K. Wu, "Minimizing I/O Costs of Multi-Dimensional Queries with Bitmap Indices", SSDBM 2006, Vienna, Austria, July 2006, (2006)
K. Stockinger, K. Wu, R. Brun & P. Canal, "Bitmap indices for fast end-user physics analysis in ROOT", Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment, 559, 99-102 (2006)
K. Stockinger, D. Rotem, A. Shoshani & K. Wu, "Analyzing Enron Data: Bitmap Indexing Outperforms MySQL Queries by Several Orders of Magnitude", (2006)
K. Stockinger & K. Wu, "Bitmap Indices for Data Warehouses", Data Warehouses and OLAP: Concepts, Architectures and Solutions, 179-202 (2006)
K. Stockinger, E. W. Bethel, S. Campbell, E. Dart & K. Wu, "Detecting distributed scans using high-performance query-driven visualization", SC '06, 82 (2006)
K. Stockinger, D. Rotem, A. Shoshani & K. Wu, "Enron Data Revisited - Neighborhood Queries with FastBit Win over Popular Commercial Database System", (2006)
K. Wu, K. Stockinger, A. Shoshani & W. Bethel, "FastBit--Helps Finding the Proverbial Needle in a Haystack", (2006)
K. Wu, E. Otoo & A. Shoshani, "Optimizing bitmap indices with efficient compression", ACM Transactions on Database Systems, 31, 1-38 (2006)

2005

J. Hellerstein, V. Paxson, L. Peterson, T. Roscoe, S. Shenker & D. Wetherall, "The Network Oracle", Data Engineering, 28, (2005)
R. Pang, M. Allman, M. Bennett, J. Lee, V. Paxson & B. Tierney, "A First Look at Modern Enterprise Traffic", ACM Internet Measurement inproceedings, (2005)
M. Allman, E. Blanton & V. Paxson, "An Architecture for Developing Behavioral History", Steps to Reducing Unwanted Traffic on the Internet (SRUTI) , (2005)
A. Antony, J. Blom, C. de Laat & J. Lee, " Exploring practical limitations of TCP over TransAtlantic networks", High-Speed Networks and Services for Data-Intensive Grids: the DataTAG Project, special issue, Future Generation Computer Systems, 21, (2005)
M. Humphrey, G. Wasson, K. Jackson, J. Boverhof, M. Rodriguez, J. Gawor, S. Lang, J. Bester, I. Foster, S. Meder, S. Pickles & M. McKeown, " State and Events for Web Services: A Comparison of Five WS-Resource Framework and WS-Notification Implementations", 14th IEEE International Symposium on High Performance Distributed Computing (HPDC-14), Research Triangle , (2005)
J. R. Burruss, T. Fredian & M. Thompson, "Data Security on the National Fusion Grid", Fifth International Atomic Energy Agency (IAEA) Technical Meeting on Control, Data Acquisition, and Remote Participation for Fusion Research, , (2005)
H. Dreger, C. Kreibich, V. Paxson & R. Sommer, "Enhancing the accuracy of network-based intrusion detection with host-based context", Conference on Detection of Intrusions and Malware and Vulnerability Assessment (DIMVA), (2005)
W. Bethel, S. Campbell, J. L. E. Dart, S. A. Smith, K. Stockinger, B. Tierney & K. Wu, "Interactive Analysis of Large Network Data Collections Using Query-Driven Visualization", (2005)
J. Ahrens, C. McParland & others, "NEW RESULTS FROM THE ANTARCTIC MUON AND NEUTRINO DETECTOR ARRAY", Nucl.Phys. B Suppl., 143, 343-350 (2005)
M. Humphrey, G. Wasson, K. Jackson, J. Boverhof, M. Rodriguez & et al, "State and Events for Web Services: A Comparison of Five WS-Resource Framework and WS-Notification Implementations", High Performance Distributed Computing, (2005)
I. C. (A. Achterberg & others), "The icecube collaboration:", 29th International Cosmic Ray Conference (ICRC) , (2005)
V. Yegneswaran, P. Barford & V. Paxson, "Using Honeynets for Internet Situational Awareness", ACM SIGCOMM HotNets, (2005)
M. Abdalla, O.Chevassut, P. A. .. Fouque & D. Pointcheval, " A Simple Threshold Authenticated Key Exchange from Short Secrets ", Asiacrypt inproceedings, (2005)
M. Thompson, V. Welch, M. Lorch, R. Lepro, D. Chadwick & V. Ciaschini, "Attributes Used in OGSI Authorization", Global Grid Forum, (2005)
D. K. Gunter, K. R. Jackson, D. E. Konerding, J. R. Lee & B. L. Tierney, "Essential Grid Workflow Monitoring Elements", International Conference on Grid Computing and Applications (GCA'05) , (2005)
R. Sommer & V. Paxson, "Exploiting independent state for network intrusion detection", Annual Computer Security Applications Conference , (2005)
A. Kumar, V. Paxson & N. Weaver, "Exploiting Underlying Structure for Detailed Reconstruction of an Internet Scale Event", ACM IMC, (2005)
M. Ackermann, C. McParland & others, "FLUX LIMITS ON ULTRA HIGH ENERGY NEUTRINOS WITH AMANDA-B10First measurements of inclusive W and Z cross sections from run II of the Tevatron collider.", Astropart.Phys, 22, 339-353 (2005)
M. Thomas, J. Burruss, L. cinquini, G. Fox, D. Gannon, I. Gilbert, G. von Laszewski, K. Jackson, D. Middleton, R. Moore, M. Pierce, B. Plale, A. Rajasekar, R. Regno, E. Roberts, D. Schissel, A. Seth & W. Schroeder, "Grid Portal Architectures for Scientific Applications", Journal of Physics, 16, 596-600. (2005)
M. Abdalla, O.Chevassut & D. Pointcheval, "One-time Verifier-based Encrypted Key Exchange", International Workshop on Practice and Theory in Public Key Cryptography (PKC), (2005)
S. Dharmapurikar & V. Paxson, "Robust TCP Stream Reassembly in the Presence of Adversaries ", USENIX Security Symposium , (2005)
D. K. Gunter, B. L. Tierney & S. J. Bailey, "Scalable Analysis of Distributed Workflow Traces ", International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA) , (2005)
K. Berket, A. Essiari & M. R. Thompson, "Securing Resources in Collaborative Environments: A Peer-to-Peer Approach", The 17th IASTED International Conference on Parallel and Distributed Computing and Systems (PDCS), (2005)
E. W. Bethel, S. Campbell, E. Dart, J. Lee, S. A. Smith, K. Stockinger, B. Tierney & K. Wu, "Interactive Analysis of Large Network Data Collections Using Query-Driven Visualization", (2005)
S. J. Bailey, B. Tierney & D. K. Gunter, "Scalable Analysis of Distributed Workflow Traces", PDPTA, 849-855 (2005) PDF
D. Rotem, K. Stockinger & K. Wu, "Optimizing Candidate Check Costs for Bitmap Indices", CIKM, 648-655 (2005)
D. Rotem, K. Stockinger & K. Wu, "Optimizing I/O Costs of Multi-Dimensional Queries using Bitmap Indices", DEXA, Copenhagen, Denmark, August 2005, 220-229 (2005)
D. Rotem, K. Stockinger & K. Wu, "Towards Optimal Multi-Dimensional Query Processing with Bitmap Indices", (2005)
K. Stockinger, J. Shalf, W. Bethel & K. Wu, "DEX: Increasing the Capability of Scientific Data Analysis Pipelines by Using Efficient Bitmap Indices to Accelerate Scientific Visualization", SSDBM, 35-44 (2005)
K. Stockinger, K. Wu, S. Campbell, S. Lau, M. Fisk, E. Gavrilov, A. Kent, C. E. Davis, R. Olinger, R. Young, J. Prewett, P. Weber, T. P. Caudell, E. W. Bethel & S. Smith, "Network Traffic Analysis With Query Driven Visualization", SC 2005, (2005)
K. Stockinger, J. Shalf, W. Bethel & K. Wu, "Query-Driven Visualization of Large Data Sets", IEEE Visualization 2005, Minneapolis, MN, October 23-28, 2005, 22 (2005)
K. Wu, "FastBit: an efficient indexing technology for accelerating data-intensive science", Journal of Physics: Conference Series, 16, 556-560 (2005)
K. Wu, J. Gu, J. Lauret, A. M. Poskanzer, A. Shoshani, A. Sim & W.-M. Zhang, "Grid Collector: Facilitating Efficient Selective Access from Data Grids", (2005)
K. Wu, E. Otoo & A. Shoshani, "Optimizing Connected Component Labeling Algorithms", Proceedings of SPIE Medical Imaging Conference 2005, San Diego, CA, (2005)
K. Wu & E. Otoo, "A simpler proof of the average case complexity of union-find with path compression", (2005)
K. Wu, E. Otoo & K. Suzuki, "Two Strategies to Speed up Connected Component Labeling Algorithms", (2005)

2004

N. Weaver & V. Paxson, "A Worst-Case Worm", Third Annual Workshop on Economics and Information Security (WEIS04), (2004)
R. Pang, V. Yegneswaran, P. Barford, V. Paxson & L. Peterson, "Characteristics of Internet Background Radiation", ACM IMC, (2004)
R. Sommer & V. Paxson, "Exploiting Independent State For Network Intrusion Detection", (2004)
J. Jung, V. Paxson, A. Berger & H. Balakrishnan, "Fast Portscan Detection Using Sequential Hypothesis Testing ", IEEE Symposium on Security and Privacy, (2004)
E. Bresson, O.Chevassut, A. Essiari & D. Pointcheval, "Mutual Authentication and Group Key Agreement for Low-Power Mobile Devices", Journal of Computer Communications - Special Issue on Security and Performance in Wireless and Mobile Networks, (2004)
G. Jin, "Packet Drop Avoidance for High-speed network transmission protocol", International Conference on Information Technology: Research and Education, (2004)
K. Berket, D. G. A. Essiari & W. Hoschek, "Peer-to-Peer I/O (P2PIO) Protocol Specification", I/O (P2PIO) Protocol Specification Version 0.6 , (2004)
W. Lavrijsen, "PYBUS: A Python software bus", Computing in High-Energy Physics (CHEP), (2004)
J. Generowicz, W. Lavrijsen & M. Marino, "Reflection-Based Python-C++ Bindings", Computing in High Energy and Nuclear Physics, (2004)
D. Konerding, "Review of An Essential Guide to the Basic Local Alignment Search Tool", Bioinformatics, 5, 93-96 (2004)
M. Ackermann, C. McParland & others, "Search for Extraterrestrial Point Sources of High Energy Neutrinos With AMANDA-II ", Phys.Rev.D, 71, (2004)
J. Schopf & K. Jackson, "“So You Want to Set Up a Grid", ClusterWorld, 2:2., (2004)
C. Leggett, P. Calafiura, W. Lavrijsen, M. Marino & D. Quarrie, "The Athena Control Framework in Production, New Developments and Lessons Learned", Computing in High Energy and Nuclear Physics, (2004)
K. Jackson, D. Konerding, J. Lee, D. Olson & B. Tierney, "The Grid2003 Production Grid: Principles and Practice", 13th IEEE Intl. Symposium on High Performance Distributed Computing (HPDC-13) , (2004)
V. Paxson, "Strategies for Sound Internet Measurement", ACM IMC, (2004)
W. Kramer, A. Shoshani, D. Agarwal, B. Draney, G. Jin, G. Butler & J. Hules, "Deep scientific computing requires deep data", IBM Research and Development, 48, 209-232 (2004)
S.Tueke, V. Welch, D.Engert, L.Pearlman & M.Thompson, "Internet X.509 Public Key Infrastructure Proxy Certificate Profile", (2004)
F. Liang, S. Meder, O. Chevassut & F. Siebenlist, "Secure password-based authenticated key exchange for web services", ACM Computer and Communications Security (ACM CCS), Workshop on Secure Web Services , (2004)
W. Sjouw, A. Antony, J. Blom, C. de Laat & J. Lee, "TCP Behaviour On Transatlantic Lambda's", Grid Computing: First European Across Grids inproceedings, Santiago de , (2004)
E. Bresson, O.Chevassut & D. Pointcheval, "The Group Diffie-Hellman Protocol", International Workshop on Practice and Theory in Public Key Cryptography (PKC), , (2004)
P. Schissel, K. Keahey, T. Araki, J. Burruss, E. Feibush, S. Flanagan, I. Foster, T. Fredian, M. Greenwald, S. Klasky, T. Leggett, K. Li, D. McCune, P. Lane, M. Papka, Q. Peng, L. Randerson, A. Sanderson, J. Stillerman, M. Thompson & G. Wallace, "The National Fusion Collaboratory Project ", Applying Grid Technology For Magnetic Fusion Research, Workshop on Case Studies on Grid Applications, (2004)
S. Staniford, D. Moore, V. Paxson & N. Weaver, "The Top Speed of Flash Worms", ACM CCS WORM, (2004)
N. Weaver, S. Staniford & V. Paxson, "Very Fast Containment of Scanning Worms", USENIX Security Symposium, (2004)
S. S. N. Weaver, D. Ellis & V. Paxson, "Worms vs. Perimeters: The Case for Hard-LANs", Hot Interconnects, (2004)
J. R. Chelikowsky, Y. Saad, N. Troullier, A. Stathopoulos, K. Wu, S. Ogut, H. Kim, M. Jain, I. Vasiliev, L. Kronik & M. Alemany, "Pseudopotential Algorithms for Real Space Energy Calculations (PARSEC)", (2004)
D. Rotem, K. Stockinger & K. Wu, "Efficient binning for bitmap indices on high-cardinality attributes", (2004)
K. Stockinger, K. Wu & A. Shoshani, "Evaluation Strategies for Bitmap Indices with Binning", International Conference on Database and Expert Systems Applications (DEXA 2004), Zaragoza, Spain, (2004)
K. Stockinger & K. Wu, "Improved searching for spatial features in spatio-temporal data", (2004)
K. Wu, W.-M. Zhang, V. Perevoztchikov, J. Lauret & A. Shoshani, "The Grid Collector: Using an Event Catalog to Speed up User Analysis in Distributed Environment", Proceedings of Computing in High Energy and Nuclear Physics (CHEP) 2004, (2004)
K. Wu, E. Otoo & A. Shoshani, "On the performance of bitmap indices for high cardinality attributes", VLDB, 24-35 (2004)
K. Wu, A. Shoshani & E. J. Otoo, "Word aligned bitmap compression method, data structure, and apparatus", (2004)

2003

R. Pang & V. Paxson, " A High-level Programming Environment for Packet Trace Anonymization and Transformation", ACM SIGCOMM , (2003)
D. Agarwal, M.Lorch, M.Thompson & M. Perry, "A New Security Model for Collaborative Environments", Workshop on Advanced Collaborative Environments,, (2003)
J. Gonzalez & p. V. Paxson, "A Packet Capture and Injection Daemon, Proc. Passive & Active Measurement", PAM, (2003)
N. Weaver, V. Paxson, S. Staniford & R. Cunningham, "A Taxonomy of Computer Worms", ACM CCS , (2003)
U. Shankar & V. Paxson, "Active Mapping: Resisting NIDS Evasion Without Altering Traffic ", IEEE Symposium on Security and Privacy, (2003)
D. Agarwal, J. M. Gonzalez, J. Guojun & B. Tierney, "An infrastructure for passive network monitoring of application data streams", ACM Internet Measurement inproceedings, (2003)
G. Jin, "Available bandwidth measurement and sampling", ISMA Bandwidth Estimation Workshop Best, SDSC Auditorium , (2003)
M.Thompson, A. Essiari & S. Mudumbai, "Certificate-based Authorization Policy in a PKI Environment", ACM Transactions on Infomation and System Security , 566-588 (2003)
M. Perry & D. Agarwal, "Collaborative editing within the pervasive collaborative computing environment", European Computer Support for Cooperative Work inproceedings(ECSCW2003), , (2003)
S. Patton, "Concrete uses of XML in software development and data analysis", Computing in High-Energy and Nuclear Physics (CHEP) , (2003)
D. A. Agarwal, K. Berket & O. Chevassut, "Enabling Efficient Group Communication in a Collaborative Enviroment", Workshop on Advanced Collaborative Environments, (2003)
B. Lowekamp, B. Tierney, L. Cottrell, R. Hughes-Jones, T. Kielmann & M. Swany, "Enabling Network Measurement Portability Through a Hierarchy of Characteristics", 4th International Workshop on Grid Computing, , (2003)
K. Berket & D. Agarwal, "Enabling secure Ad-hoc collaboration", Proceedings of the Workshop on Advanced Collaborative Environments, (2003)
R. Sommer & V. Paxson, " Enhancing Byte-Level Network Intrusion Detection Signatures with Context", ACM CCS , (2003)
S. Patton, "FAYE: A Java implement of the Frame / Stream / Stop analysis model", Conference for Computing in High-Energy and Nuclear Physics (CHEP), , (2003)
M. Thompson, A. Essiari, V. W. K. Keahey, S.Lang & B.Lui, "Fine-grained Authorization for Job and Resource Management using Akenti and Globus", Computing in High Energy and Nuclear Physics (CHEP), (2003)
K. Harrison, W. Lavrijsen, C. Tull, P. Mato, A. Soroko, C. Tan, N. Brook & R. Jones, "GANGA: a user-Grid interface for Atlas and LHCb", Computing in High Energy and Nuclear Physics, (2003)
D. Gunter, W. Lavrijsen, D. Quarrie, B. Tierney & C. Tull, "GMA Instrumentation of the Athena Framework using NetLogger", Computing in High Energy and Nuclear Physics, (2003)
B. Tierney & J. Hollingsworth, "The Grid: Blueprint for a New Computing Infrastructure, 2nd Edition", (2003)
S. Patton & D. Glowacki, "IceCube's development environment", Computing in High Energy and Nuclear Physics, (2003)
D. Moore, V. Paxson, S. Savage, C. Shannon, S. Staniford & N. Weaver, "Inside the Slammer Worm", Security and Privacy, (2003)
B. Tierney & J. Hollingsworth, "Instrumentation and Monitoring", The Grid 2: Blueprint for a New Computing Infrastructure, (2003)
E. Bresson, O.Chevassut, A. Essiari & D. Pointcheval, "Mutual Authentication and Group Key Agreement for Low-Power Mobile Devices", 5th IFIP-TC6 International Conference on Mobile and Wireless Communications Networks, (2003)
G. Jin & B. Tierney, "Netest: A Tool to Measure Maximum Burst Size, Available Bandwidth and Achievable Throughput", Proceedings of the International Conference on Information Technology, (2003)
D. Gunter & B. Tierney, "NetLogger: A Toolkit for Distributed System Tuning and Debugging ", Proceedings of The 8th IFIP/IEEE International Symposium on Integrated Network Management, (2003)
E. Bresson, O. Chevassut & D. Pointcheval, "New Security Results on Encrypted Key Exchange", International Workshop on Practice and Theory in Public Key Cryptographyc (PKC), (2003)
D. Gunter, B. Tierney, C. E. Tull & V. Virmani, "On-Demand Grid Application Tuning and Debugging with the NetLogger Activation Service ", 4th International Workshop on Grid Computing (Grid), (2003)
S. Peggs, T. Satogata, D. Agarwal & D. Rice, "Remote operations in a global accelerator network", Particle Accelerator inproceedings, (2003)
M. Thompson & K. Jackson, "Resource Management for Grid Computing.", (2003)
E. Bresson, O. Chevassut & D. Pointcheval, "Security Proofs for an efficient password-based key exchange", 10th ACM Conference on Computer and Communications Security (ACM CCS'03), (2003)
D. Agarwal & K. Berket, "Supporting Dynamic Ad hoc Collaboration Capabilities ", Conference for Computing in High Energy and Nuclear Physics, (2003)
G. Jin & B. Tierney, "System Capability Effects on Algorithms for Network Bandwidth Measurement", Proceedings of the Internet Measurement inproceedings, (2003)
W. Lavrijsen, "The Athena startup kit", Conference for Computing in High-Energy and Nuclear Physics (CHEP 03), (2003)
P. Calafiura, C. Leggett, D. Quarrie, H. Ma & S.Rajagopalan, "The StoreGate: A Data model for the Atlas software architecture", Conference for Computing in High-Energy and Nuclear Physics (CHEP 03)24-28 Mar . In the Proceedings of Conference for Computing in High-Energy and Nuclear Physics (CHEP), , (2003)
S. Cannon, D. O. S. Chan, C. E. Tull, V. Welch & L. Pearlman, "Using CAS to manage role based VO subgroups", Computing in High-Energy and Nuclear Physics (CHEP 03), 5 (2003)
B. Tierney, "Using NetLogger and Web100 for TCP analysis", First International Workshop on Protocols for Fast Long-Distance Networks, (2003)
G. von Laszweski, J. Gawor, S. Krishnan & K. Jackson, "Commodity Grid Kits: Middleware for Building Grid Computing Environments", Grid Computing: Making The Global Infrastructure a Reality, (2003)
G. von Laszewski, J. Gawor, S. Krishnan & K. Jackson, "Creating and Managing Grid Services in Grid Computing, A Practical Guide to Technology and Applications", (2003)
J. Burress, S. Flanagan, K. Keahey, C. Ludescher, D. McCune, Q. Peng, L. Randerson, D. Schissel & M. Thompson, "Remote Computing Using the National Fusion Grid", 4th IAEA Technical Meeting on Control, Data Acquisition, and Remote Participation for Fusion Research, (2003)
X. Bai, T. Gaisser, S. T. (B. R. Ins), J. Becker, k.-H. Becker, P. Ekstrom, H. Geenen, A. Gross, K. Goldmann, T.Messarius & e. A. W. Rhode, "Search for diffuse fluxes of extraterrestrial muon-neutrinos with the Amanda detector", 28th International Cosmic Ray inproceedingss (ICRC) , (2003)
J. Adams, D. Olson & others, "STAR Collaboration Transverse momentum and collision energy dependence of high pT hadron suppression in Au+Au collisions at ultrarelativistic energies . ", Phys. Rev. Lett, 91, (2003)
R. Chytracek, J. Generowicz, W. Lavrijsen, M. Marino, P. Mato, L. Moneta, S. Roiser, L. Tuura & M. Winkler, "Status of the SEAL Project", 9th International Workshop on Advanced Computing and Analysis Techniques in Physics Research (ACAT 03), (2003)
W. Sjouw, A. Antony, J. Blom, C. de Laat & J. Lee, "TCP behaviour on transatlantic Lambda's", Springer Verlag LNCS, (2003)
A. Bazan, T. Bouedo, P. Ghez, M. Marino & C. Tull, "The Athena data dictionary and description language", Conference for Computing in High-Energy and Nuclear Physics (CHEP), 4 (2003)
K. Wu, W.-M. Zhang, A. Sim, J. Gu & A. Shoshani, "Grid Collector: An Event Catalog With Automated File Management", Proceedings of IEEE Nuclear Science Symposium 2003, (2003)
K. Wu, W. Koegler, J. Chen & A. Shoshani, "Using Bitmap Index for Interactive Exploration of Large Datasets", Proceedings of SSDBM 2003, 65-74 (2003)

2002

K. Berket, D. A. Agarwal & O. Chevassut, "Practical Approach to the InterGroup Protocols", Future Generation Computer Systems, 18, 709-719 (2002)
O. Chevassut, "Authenticated Group Diffie-Hellman Key Exchange : Theory and Practice", (2002)
D. Agarwal, G. Olson & J. Olson, "Collaboration Tools for the Global Accelerator Network Workshop Report", (2002)
E. Bresson, O.Chevassut & D. Pointcheval, "Group Diffie-Hellman Key Exchange Secure Against Dictionary Attacks", Asiacrypt, (2002)
E. Bresson, O.Chevassut & D. Pointcheval, "Group Diffie-Hellman Key Exchange under Standard Assumptions", Eurocrypt , 6, 566-88 (2002)
J. Lee, D. Gunter, M. Stoufer & B. Tierney, "Monitoring Data Archives for Grid Environments", Supercomputing, ACM/IEEE 2002 inproceedings, 66 (2002)
K. R. Jackson, "PyGlobus: A python interface to the globus toolkit", Concurrency and Computation: Practice and Experience , 14, (13-15) (2002)
T. Dunigan, M. Mathis & B. Tierney, "A TCP tuning daemon", IEEE Supercomputing, , (2002)
A. Antony, J. Blom, C. de Laat, J. Lee & W. Sjouw, "Microscopic Examination of TCP Flows Over Transatlantic Links, ", (2002)
D. Agarwal, C. McParland & M. Perry, "Supporting collaborative computing and interaction", Grace Hopper Celebration of Women in Computing , (2002)
A. Stathopoulos & K. Wu, "A Block Orthogonalization Procedure with Constant Synchronization Rquirements", SIAM Journal on Scientific Computing, 23, 2165-2182 (2002)
K. Stockinger, K. Wu & A. Shoshani, "Strategies for processing ad hoc queries on large data warehouses", Proceedings of DOLAP'02, 72-79 (2002)
K. Wu, E. Otoo & A. Shoshani, "Compressing Bitmap Indexes for Faster Search Operations", Proceedings of SSDBM'02, 99-108 (2002)
K. Wu, E. Otoo & A. Shoshani, "An Efficient Compression Scheme For Bitmap Indices", (2002)

2001

D. Agarwal, "Discussion of Reliable Multicast Deployment Progress for the Continuous Data Protocol", 23rd Annual DoD/DOE Seismic Research Review: Worldwide Monitoring of Nuclear Explosions , (2001)
D. Agarwal, O. Chevassut & G. Tsudik, "Integrating access control with secure group communication for wide-area networks", Network and Distributed System Security Symposium, (2001)
D. Agarwal, B. Tierney, D. Gunter, J. Lee & W. Johnston, "Network Aware High-Performance Distributed Applications", Proceedings of the Workshop on New Visions for Large-Scale Networks: Research and Applications , (2001)
J. Becla & I. Gaponenko, "Optimizing parallel access to the BABAR database system using CORBA servers", CHEP: Computing in High-Energy Physics and Nuclear, (2001)
K. Berket, D. A. Agarwal, P. M. Melliar-Smith & L. E. Moser, "Overview of the InterGroup Protocols", LNCS, 316-25 (2001)
O. Chevassut, E. Bresson & D. Pointcheval, "Provably Authenticated Group Diffie-Hellman Key Exchange - The Dynamic Case", Asiacrypt'01, (2001)
S. Patton & A. Mohktarani, "Support in the BaBar objectivity database for multiple federations", CHEP'01: Computing in, High-EnergyPhysics and Nuclear, (2001)
I. Gaponenko, A. Mokhtarani, S. Patton, D. Quarrie, A. Adesanya, A. H. J. Becla, A. Hasan & A. Trunov, "The BABAR database: Challenges, trends and projections", CHEP'01: Computing in High-Energy Physics and Nuclear, (2001)
W. Bethel, B. Tierney, J. Lee, D. Gunter & S. Lau, "Using High-Speed WANs and Network Data Caches to Enable Remote and Distributed Visualization", 10th IEEE Symposium on High Performance Distributed Computing, (2001)
S. Loken & C. McParland, "Workflow Management for a Cosmology Collaboratory", CHEP, (2001)
G. Jin, G. Yang, B. Crowley & D. Agarwal, "Network Characterization Service (NCS)", 10th IEEE Symposium on High Performance Distributed Computing , (2001)
L. Bernardo, H. Nordberg, D. Olson, A. Shoshani, A. Sim, A. Vaniachine, D. Zimmerman, B. Gibbard, R. Porter, T. Wenaus & D. Malon, "New capabilities in the HENP Grand Challenge Storage Access System and its application at RHIC", Computer Physics Communications, 140, 179-188 (2001)
K. Wu, E. Otoo & A. Shoshani, "Compressed bitmap indices for efficient query processing", (2001)
K. Wu, E. Otoo, A. Shoshani & H. Nordberg, "Notes on Design and Implementation of Compressed Bit Vectors", (2001)
K. Wu, E. Otoo & A. Shoshani, "A Performance Comparison of bitmap indexes", CIKM, 559-561 (2001)

2000

K. Wu & B. Milne, "A survey of packages for large linear systems", (2000)
K. Wu & H. Simon, "Thick-restart Lanczos method for large symmetric eigenvalue problems", SIAM J. Matrix Anal. Appl., 22, 602-616 (2000)

1999

K. Wu & H. Simon, "A Parallel Lanczos method for symmetric generalized eigenvalue problems", Computing and Visualization in Science, 2, 37-46 (1999)
K. Wu & H. D. Simon, "Dynamic Restarting Schemes For Eigenvalue Problems", (1999)
K. Wu & H. Simon, "An Evaluation of Parallel Shift-and-Invert Lanczos Method", Proceedings of The 1999 International Conference on Parallel and Distributed Processing Techniques and Applications, Las Vegas, Nevada, June 28 - July 1, 1999, 2913-19 (1999)
K. Wu & H. Simon, "Parallel Efficiency of the Lanczos method for eigenvalue problems", (1999)
K. Wu, A. Canning, H. D. Simon & L.-W. Wang, "Thick-Restart Lanczos method for electronic structure calculations", Journal of Computational Physics, 154, 156-173 (1999)
K. Wu & H. Simon, "TRLAN user guide", (1999)

1998

A. Stathopoulos, Y. Saad & K. Wu, "Dynamic thick restarting of the Davidson and the implicitly restarted Arnoldi methods", SIAM Journal on Scientific Computing, 19, 227-245 (1998)
K. Wu, Y. Saad & A. Stathopoulos, "Inexact Newton Preconditioning Techniques for Eigenvalue Problems", Electronic Transactions on Numerical Analysis, 7, 202-214 (1998)
K. Wu, A. Canning & H. D. Simon, "A new Lanczos method for electronic structure calculations", Proceedings of ACM/IEEE SC98 Conference, November 7-13, 1998, in Orlando, FL, (1998)
K. Wu & H. Simon, "Thick-restart Lanczos method for symmetric eigenvalue problems", (1998)
K. Wu & H. D. Simon, "Thick-restart Lanczos method for symmetric eigenvlaue problems", IRREGULAR'98, 1457, 43-55 (1998)

1997

K. Wu, "Preconditioned Techniques for Large Eigenvalue Problems", (1997)
K. Wu, "Restarted variants of DQGMRES", Proceedings of 1997 International Workshop on Computational Science and Engineering, 59-63 (1997)

1996

J. R. Chelikowsky, X. Jing, K. Wu & Y. Saad, "Molecular dynamics with quantum forces: Vibrational spectra of localized systems", Physical Review B, 53, 12071 (1996)
Y. Saad & K. Wu, "DQGMRES: a quasi-minimal residual algorithm based on incomplete orthogonalization", Numerical Linear Algebra with Applications, 3, 329-343 (1996)
Y. Saad, A. Stathopoulos, J. Chelikowsky, K. Wu & S. ÖgüT, "Solution of large eigenvalue problems in electronic structure calculations", BIT, 36, 563-578 (1996)
A. Stathopoulos, Y. Saad & K. Wu, "Thick restarting of the Davidson method: an extension to implicit restarting", Copper Mountain Conference on Iterative Methods, (1996)
K. Wu, "An experimental study of Krylov subspace accelerators", (1996)
K. Wu, Y. Saad & A. Stathopoulos, "Preconditioned Krylov subspace methods for eigenvalue problems", Copper Mountain Conference on Iterative Methods, (1996)

1995

J. R. Chelikowsky, S. Ö˘ güt, X. Jing, K. Wu, A. Stathopoulos & Y. Saad, "Atomic and Electronic Structure of Germanium Clusters at Finite Temperature Using Finite Difference Methods", Mat. Res. Soc., 408, (1995)
J. R. Chelikowsky, N. R. Troullier, X. Jing, D. Dean, N. Binggeli, K. Wu & Y. Saad, "Algorithms for the structural properties of clusters", Computer Physics Communications, 85, 325-335 (1995)
X. Jing, N. R. Troullier, J. R. Chelikowsky, K. Wu & Y. Saad, "Vibrational modes of silicon nanostructures", Solid State Communication, 96, 231-235 (1995)
Y. Saad & K. Wu, "Design of an iterative solution module for a parallel matrix library (PSPARSLIB)", Applied Numerical Mathematics, 19, 343-357 (1995)
Y. Saad, A. Stathopoulos, J. R. Chelikowsky, K. Wu & S. Ögüt, "Solution of large eigenvalue problems in electronic structure calculations", (1995)

1994

S. Carney, M. Heroux, G. Li & K. Wu, "A revised proposal for a sparse BLAS toolkit: SPARKER working note 3", (1994)
J. R. Chelikowsky, N. Troullier, K. Wu & Y. Saad, "Algorithms for predicting properties of real materials on high performance computers", Proceedings of the Toward Teraflop Computing Conference, (1994)
J. R. Chelikowsky, N. Troullier, K. Wu & Y. Saad, "Combining a higher-order finite-difference method with ab Initio pseudopotentials: application to diatomic molecules", (1994)
J. R. Chelikowsky, N. Troullier, K. Wu & Y. Saad, "Higher order finite difference pseudopotential method: an application to diatomic molecules", Phys. Rev. B, 50, 11355-11364 (1994) PDF
X. Jing, N. R. Troullier, D. Dean, N. Binggeli, J. R. Chelikowsky, K. Wu & Y. Saad, "Ab Initio molecular dynamics simulations of Si clusters using the higher-order finite-difference-pseudopotential method", Physical Review B, 50, 12234-12237 (1994)
Y. Saad & K. Wu, "Parallel SPARSe matrix LIBrary (PSPARSLIB): the iterative solvers module", (1994)

1993

J. R. Chelikowsky, N. Troullier, K. Wu & Y. Saad, "Algorithms for predicting properties of real materials on high-performance computers", (1993)
W. Ferng, S. Petiton & K. Wu, "Basic sparse computations on data parallel computers", Proceedings of Sixth SIAM Conference on Parallel Processing for Scientific Computing, 462-266 (1993)
S. Petiton, Y. Saad, K. Wu & W. Ferng, "Basic sparse matrix computations on the CM-5", International Journal of Modern Physics C, 4, (1993)
Y. Saad, K. Wu & S. Petiton, "Sparse matrix computations on the CM-5", Proceedings of Sixth SIAM Conference on Parallel Processing for Scientific Computing, 414-420 (1993)
K. Wu & Y. Saad, "Performance of the CM-5 message passing primitives", Proceedings of Sixth SIAM Conference on Parallel Processing for Scientific Computing, 937-942 (1993)
K. Wu, R. Savit & W. Brock, "Statistical tests for deterministic effects in broad band time series", Physica D, 69, 172-188 (1993)

1992

W. Ferng, K. Wu, S. Petiton & Y. Saad, "Basic sparse matrix computations on massively parallel computers", (1992)
K. Wu, "Stability of midpoint methods on second order ODEs", (1992)