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Oliver Ruebel

Oliver Ruebel
Data & Analytics Group
Phone: (510) 486-4064
Fax: (510) 486-5812
1 Cyclotron Rd
MS 50F1650
Berkeley, CA 94720

Journal Articles

Jiyan Yang, Oliver Ruebel, Prabhat, Michael Mahoney, Ben Bowen, "Identifying important ions and positions in mass spectroscopy imaging data using CUR matrix decompositions", Analytical Chemistry, March 31, 2015,

Oliver Rübel, Annette Greiner, Shreyas Cholia, Katherine Louie, E. Wes Bethel, Trent R. Northen, Benjamin P. Bowen, "OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging", Analytical Chemistry, 2013, 85 (21), pp 10354–10361, October 2, 2013, doi: 10.1021/ac402540a

O. Rübel, G. H. Weber, M. Y. Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. Knowles, J. Malik, H. Hagen, B. Hamann, "Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data", IEEE Transactions on Computational Biology and Bioinformatics, Jan/Mar 2010, January 2010, 7 (1):64-79,

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. Kr\ uger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. R\ ubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu., "Occam s Razor and Petascale Visual Data Analysis", Journal of Physics Conference Series, Proceedings of SciDAC 2009, 2009, 180:012084,

Conference Papers

Allen R. Sanderson, Brad Whitlock, Oliver R\ ubel, Hank Childs, Gunther H. Weber, Prabhat, Kesheng Wu, "A System for Query Based Analysis and Visualization", Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, 2012, 25--29, LBNL 5507E, doi: 10.2312/PE/EuroVAST/EuroVA12/025-029

E. Wes Bethel, Surendra Byna, Jerry Chou, Estelle Cormier-Michel, Cameron G. R. Geddes, Mark Howison, Fuyu Li, Prabhat, Ji Qiang, Oliver R\ ubel, Robert D. Ryne, Michael Wehner, Kesheng Wu, "Big Data Analysis and Visualization: What Do LINACS and Tropical Storms Have In Common?", 11th International Computational Accelerator Physics Conference, ICAP 2012, Rostock-Warnem\ unde, Germany, 2012,

Prabhat, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, E. Wes Bethel, "TECA: A Parallel Toolkit for Extreme Climate Analysis", Third Worskhop on Data Mining in Earth System Science (DMESS 2012) at the International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, 2012,

Oliver Rübel, Sean Ahern, E. Wes Bethel, Mark D. Biggin, Hank Childs, Estelle Cormier-Michel, Angela DePace, Michael B. Eisen, Charless C. Fowlkes, Cameron G. R. Geddes, Hans Hagen, Bernd Hamann, Min-Yu Huang, Soile V. E. Keränen, David W. Knowles, Cris L. Luengo Hendriks, Jitendra Malik, Jeremy Meredith, Peter Messmer, Prabhat, Daniela Ushizima, Gunther H. Weber, Kesheng Wu, "Coupling Visualization and Data Analysis for Knowledge Discovery from Multi-Dimensional Scientific Data", Proceedings of International Conference on Computational Science, ICCS 2010, May 2010,


G. H. Weber, S. Ahern, E. W. Bethel, S. Borovikov, H. R. Childs, E. Deines, C. Garth, H. Hagen, B. Hamann, K. I. Joy, D. Martin, J. Meredith, Prabhat, D. Pugmire, O. Rübel, B. Van Straalen, and K. Wu, "Recent Advances in VisIt: AMR Streamlines and Query-Driven Visualization", Numerical Modeling of Space Plasma Flows: Astronum-2009 (Astronomical Society of the Pacific Conference Series), 2010, 429:329–334,

Oliver R\ ubel, Prabhat, Kesheng Wu, Hank Childs, Jeremy Meredith, Cameron G. R. Geddes, Estelle Cormier-Michel, Sean Ahern, Gunther H. weber, Peter Messmer, Hans Hagen, Bernd Hamann, E. Wes Bethel, "High Performance Multivariate Visual Data Exploration for Extemely Large Data", SuperComputing 2008 (SC08), Austin, Texas, USA, 2008,

Book Chapters

Oliver Rübel, Soile V. E. Keränen, Mark D. Biggin, David W. Knowles, H. Weber, Hans Hagen, Bernd Hamann, E. Wes Bethel, "Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data", Mathematical Methods for Visualization in Medicine and Life Sciences II, (Springer-Verlag: 2012) Pages: 267--286, LBNL 4891E,

Oliver Rubel, Wes Bethel, Prabhat, Kesheng Wu, "Query Driven Visualization and Analysis", High Performance Visualization: Enabling Extreme-Scale Scientific Insight, (CRC Press: 2012)

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rübel, Gunther Weber, Bernard Hamann, Peter Messmer, and Hans Hagen, "Automated Detection and Analysis of Particle Beams in Laser-Plasma Accelerator Simulations", In-Tech, ( 2010) Pages: 367 - 389

Oliver R\ ubel, Cameron G. R. Geddes, Estelle Cormier-Michel Kesheng Wu, Prabhat, Gunther H. Weber, Daniela M. Ushizima, Peter Messmer, Hans Hagen, Bernd Hamann, Wes Bethel, "Automatic Beam Path Analysis of Laser Wakefield Particle Acceleration Data", IOP Computational Science \& Discovery, ( 2009)

Web Articles

"A Standard for Neuroscience Data", Oliver Ruebel, Kris Bouchard, Prabhat, NERSC Science Highlight, December 16, 2014,


E. Wes Bethel, Rob Ross, Wei-Ken Liao, Prabhat, Karen Schuchardt, Peer-Timo Bremer, Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, John Patchett, Han-Wei Shen, David Pugmire, Dean Williams, "Recent Advances in Visual Data Exploration and Analysis of Climate Data", SciDAC 3 Principal Investigator Meeting, 2012,

Oliver Ruebel, Cameron Geddes, Min Chen, Estelle Cormier, Ji Qiang, Rob Ryne, Jean-Luc Vey, David Grote, Jerry Chou, Kesheng Wu, Mark Howison, Prabhat, Brian Austin, Arie Shoshani, E. Wes Bethel, "Scalable Data Management, Analysis and Visualization of Particle Accelerator Simulation Data", SciDAC 3 Principal Investigator Meeting, 2012,

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, J\ org Meyer, Prabhat, Oliver R\ ubel, Daniela Ushizima, Gunther Weber, "Towards Exascale: High Performance Visualization and Analytics -- Project Status Report", 2012,

R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, G. R. Geddes, W. Leemans, Prabhat X. Li, J. Qiang, R\ ubel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon, N. Yampolsky, "High Performance Computing in Accelerator Science: Past Successes, Future Challenges", ASCR/BES Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, 2011,

Prabhat, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", DOE/ASCR Exascale kickoff meeting, 2011,