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WP1: LIBRARY AND APPLICATION OPTIMIZATION

“Non-Rigid Registration for Large Set of Microscopic Images on Graphics Processors”
Ruiz, M. Ujaldon, L. Cooper and K. Huang
J. of Signal Processing Systems for Signal, Image and Video Technology, Springer ,  2008
“Improving Quantum Gate Simulation using a GPU”
E. Gutierrez, S. Romero, M.A. Trenas and E.L. Zapata
Int’l. Electronic Conf. on Computer Science, AIP Conf. Proc., Vol. 1060, pp. 293-297 ,  2008
“On the Computation of the Circle Hough Transform by a GPU Rasterizer”
M. Ujaldon, A. Ruiz and N. Guil
Pattern Recognition Letters, Vol. 29, Iss. 3, pp. 309-318 ,  2008
“Optimizing Co-occurrence Matrices on Graphics Processors Using Sparse Representations”
F. Igual, R. Mayo, T. Hartley, U. Catalyurek, A. Ruiz and M. Ujaldon
9th Int’l. Workshop on State-of-the-Art in Scientific and Parallel Computing, Trondheim, Norway ,  2008
“Pathological Image Segmentation for Neuroblastoma Using the GPU”
Ruiz, J. Kong, M. Ujaldon, K. Boyer, J. Saltz and M. Gurcan
5th Int’l. Symp. on Biomedical Imaging: From Nano to Macro, Paris, France, pp. 296-299 ,  2008
“Memory Locality Exploitation Strategies for FFT on the CUDA Architecture”
E. Gutierrez, S. Romero, M.A. Trenas and E.L. Zapata
8th Int’l. Meeting on High Performance Computing for Computational Science (VECPAR’08), Toulouse, France, (Springer LNCS 5336, pp. 430-443 ). ,  2008
“Biomedical Image Analysis on a Cooperative Cluster of GPUs and Multicores”
T. Hartley, U. Catalyurek, A. Ruiz, F. Igual, R. Mayo and M. Ujaldon
22nd ACM Int’l. Conf. on Supercomputing, Isla de Kos, Greece ,  2008
“Parallel Quantum Computer Simulation on the CUDA Architecture”
E. Gutierrez, S. Romero, M.A. Trenas and E.L. Zapata
8th Int’l. Conf. on Computational Science (ICCS’08), Krakow, Poland (Springer LNCS 5101, pp. 700-709). ,  2008
"GPUs for Parallel On-Board Hyperspectral Image Processing"
J. Setoain, M. Prieto, C. Tenllado, F. Tirado
International Journal of High Performance Computing Applications, Vol. 22, No. 4, pp, 424-437 ,  2008
“Recognition of Circular Patterns on GPUs: Performance Analysis and Contributions”
Ruiz, N. Guil and M. Ujaldon
J. of Parallel and Distributed Computing, Vol. 62, Iss. 10, pp. 1329-1338 ,  2008
"Parallel implementation of the 2D Discrete Wavelet Transform on Graphics Processing Units: Filter-Bank versus Lifting"
C. Tenllado, J. Setoain, M. Prieto, L. Piñuel, F. Tirado
IEEE Transactions on Parallel and Distributed Computing, Vol. 19, No. 3, pp, 299-310, ,  2008
High resolution modelling results of the wind flow over Canary Islands during the meteorological situation of the extratropical storm Delta
Jorba O., C. Marrero, E. Cuevas and J.M. Baldasano
Advances in Science and Research, 2: 81-87, ISSN: 1992-0628, ,  2008
BioNMF: A web-based tool for Non-negative Matrix Factorization in biology
E. Mejía-Roa, P. Carmona-Saez, R. Nogales, C. Vicente, M. Vázquez, XY. Yang, C. García, F. Tirado, A. Pascual-Montano
Nucleic Acid Research Nucleic Acids Research; doi: 10.1093/nar/gkn335 ,  2008
"GPUs for Parallel On-Board Hyperspectral Image Processing"
J. Setoain, M. Prieto, C. Tenllado, F. Tirado
International Journal of High Performance Computing Applications, Vol. 22, No. 4. Pp 424-437 ,  2008
“Stroma Classification for Neuroblastoma on Graphics Processors"
A. Ruiz, O. Sertel, M. Ujaldon, U. Catalyurek, J. Saltz and M. Gurcan
Int’l. J. of Data Mining and Bioinformatics, 29 (3), pp. 280-298 ,  2009
“Non-Rigid Registration for Large Set of Microscopic Images on Graphics Processors”
A. Ruiz, M. Ujaldon, L. Cooper and K. Huang
J. of Signal Processing Systems for Signal, Image and Video Technology, 55 (1), pp. 229-250 ,  2009
“Strategies for Exploiting the GPU Memory Hierarchy for FFT”
E. Gutierrez, S. Romero, M.A. Trenas, O. Plata and E.L. Zapata
14th Int’l. Workshop on Compilers for Parallel Computers (CPC 2009), (Zurich, Switzerland) ,  2009
“Acceleration of Zernike Moments for Large-Scale Images”
M. Ujaldon
IEEE Int’l. Parallel and Distributed Processing Symposium (IPDPS’09), (Rome, Italy) ,  2009
“High Performance Circle Detection Through a GPU Rasterization Approach”
M. Ujaldon and N. Guil
Int’l. Conf. on Pattern Recognition and Image Analysis (IbPRIA’09), (Povoa do Varzim, Portugal) ,  2009
“Experiences with Mapping Non-Linear Memory Access Patterns into GPUs”
E. Gutierrez, S. Romero, M.A. Trenas and O. Plata
Int’l. Conf. on Computational Science (ICCS’2009), (Baton Rouge, LA, USA) ,  2009
“High-Performance Signal Processing on Emerging Many-Core Architectures Using CUDA”
M. Ujaldon and U. Catalyurek
IEEE Int’l. Conf. on Multimedia and Expo, (New York, NY, USA) ,  2009
“Exploring the GPU for Enhancing Parallelism on Color and Texture Analysis”
F. Igual, R. Mayo, T. Hartley, U. Catalyurek, A. Ruiz and M. Ujaldon
Int’l. Conf. on Parallel Computing (ParCo’09), (Lyon, France) ,  2009
“Parallelization of a Video Segmentation Algorithm on CUDA-Enabled Graphics Processing Units”
J. Gómez, J.M. González-Linares, I. Benavides and N. Guil
Int’l. European Conf. on Parallel and Distributed Computing (Euro-Par 2009), (Delft, The Netherlands) ,  2009
The GPU on the Matrix-Matrix Multiply: Performance Study and Contributions”
J.M. Cecilia, J.M. Garcıa-Carrasco and M. Ujaldon
Int’l. Conf. on Parallel Computing (ParCo’09), (Lyon, France) ,  2009
“Concurrent Calculations on Reconfigurable Logic Devices Applied to the Analysis of Video Images”
S.R. Geninatti, M.H. Calviño, I. Benavides and N. Guil
Southern Conf. on Programable Logic, (Sao Paulo, Brasil) ,  2009
“Fast Texture Analysis via Zernike Moments on Graphics Processors”
M.J. Martın-Requena and M. Ujaldon
II ECCOMAS Thematic Conf. on Computational Vision and Medical Image Processing (VIPIMAGE 2009), (Porto, Portugal) ,  2009
“Efficient Image Alignment Using Linear Appearence Models”
J. González-Mora, F. de la Torre, N. Guil and E.L. Zapata
IEEE Conf. on Computer Vision and Pattern Recognition (CVPR 2009), (Miami, FL, USA) ,  2009
The histone variant macroH2A is an epigenetic regulator of key developmental genes
Buschbeck, M, Uribesalgo I, Wibowo I, Rué P, Martin D, Gutierrez A, Morey L, Guigó R, López-Schier H, Di Croce L
Nat. Struct. Mol. Biol. 16:1074–1079. ,  2009
Implementation of an online chemical mechanism within a global-regional atmospheric model: design and initial steps
Jorba O.; C. Pérez; J.M. Baldasano
Geophysical Research Abstracts, Vol. 11, EGU2009-7943-2. EGU General Assembly 2009, Viena, eISSN: 1607-7962. 20-24 ,  2009
“Evaluating the Consistency of the 1982-1999 NDVI Trends in the Iberian Peninsula across Four Time-Series Derived from the AVHRR Sensor: LTDR, GIMMS, FASIR, and PAL-II”
D. Alcaraz-Segura, E. Liras, S. Tabik, J. Paruelo and J. Cabello
Sensors, 10 (2), pp. 1291-1314 ,  2010
“Using GPUs for Accelerating Electromagnetic Simulations”
M. Ujaldón
Journal of Applied Computational Electromagnetics Society, special issue on Hardware Accelerated Computational Techniques for Electromagnetic Simulations of Complex Problems, 25 (4), pp. 294-302 ,  2010
“Parallel 3D Wavelet Transform on Multicore CPUs and Manycore GPUs”
J. Franco, G. Bernabé, J. Fernández and M. Ujaldón
2nd Workshop on Emerging Parallel Architectures (co-located with 10th Int’l. Conf. on Computational Science (ICCS’10)) (Amsterdam, The Netherlands) ,  2010
“CUDA 2D Stencil Computations for the Jacobi Method”
J.M. Cecilia, J.M. García-Carrasco and M. Ujaldón
10th Para 2010: State of the Art in Scientific and Parallel Computing (Reykjavik, Iceland) ,  2010
“Acceleration of the 2D Wavelet Transform for CUDA-enabled Devices”
J. Franco, G. Bernabé, J. Fernández, M.E. Acacio and M. Ujaldón
10th Para 2010: State of the Art in Scientific and Parallel Computing, Minisymposium on GPU Computing (Reykjavik, Iceland) ,  2010
"Enhanced Scaling-Free CORDIC"
F.J. Jaime, M.A. Sánchez, J. Hormigo, J. Villalba and E.L. Zapata
IEEE Transactions on Circuits and Systems I: Regular Papers, 57 (7), pp. 1654-1662 ,  2010

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