Publications

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M. Vázquez, Codina, R., and Zienkiewicz, O. C., A fractional step method for the solution of the Navier - Stokes equations, CIMNE, UPC, Barcelona, 1996.
H. Servat, Llort, G., Huck, K., Giménez, J., and Labarta, J., Framework for a Productive Performance Optimization, Parallel Computing Systems and Applications, vol. 39, no. 8. Elsevier, pp. 336-353, 2013.
A. - S. J, R, A., Houzeaux, G., and Vázquez, M., A framework for anti-arrhythmic drugs testing using a multi-scale computational heart employing Alya Red, UT Austin - Portugal Workshop on Modeling and Simulation of physiological systems. 2012.
R. Tolosana-Delgado, Soret, A., Jorba, O., Sánchez-Arcilla, A., and Baldasano, J. M., A framework for assessing the impact of atmospheric coupling and altimeter assimilation on wave predictions at the Catalan-Balearic Sea (NW Mediterranean), WISE 2012-19th International Conference (Waves in Shallow Environments). LIM/UPC - Laboratorio de Ingeniería Marítima , 16-18 April, 2012. Barcelona, Spain, 2012.
S. Chen, Bronevetsky, G., Li, B., Casas, M., and Peng, L., A framework for evaluating comprehensive fault resilience mechanisms in numerical programs, The Journal of Supercomputing. Springer US, pp. 1-22, 2015.
D. Georgiev, Atanassov, E., and Alexandrov, V., A Framework for Parallel Genetic Algorithms for Distributed Memory Architectures, ACM Digital Library. pp. pp. 47-53, 2014.
A. Snavely, Carrington, L., Wolter, N., Labarta, J., Badia, R. M., and Purkayastha, A., A Framework for Performance Modeling and Prediction. SuperComputing ' 02, 2002.
A. Snavely, Carrington, L., Wolter, N., and Labarta, J., A Framework for Practical Applications Performance Modeling. Parallel Computing 2003 (ParCo'2003), 2003.
F. Javier Doblas-Reyes, Framing climate services research. CLIVAR-ES, Tortosa, Spain, 2015.
H. Owen and Codina, R., A free surface finite element model for low Froude number mould filling problems on fixed meshes, International Journal for Numerical Methods in Fluids, vol. 66. John Wiley & Sons, Ltd., pp. 833–851, 2011.
N. Sönmez, Arcas, O., Sayilar, G., Cristal, A., Hur, I., Unsal, O., Singh, S., and Valero, M., From Plasma to BeeFarm: Design Experience of an FPGA-based Multicore Prototype, The 7th International Symposium on Applied Reconfigurable Computing (ARC 2011). Belfast, United Kingdom, pp. 1–10, 2011.
N. Sonmez, Arcas, O., Sayilar, G., Unsal, O., Cristal, A., Hur, I., Singh, S., and Valero, M., From Plasma to BeeFarm: Design Experience of an FPGA-based Multicore Prototype, ARC'11. 2011.
N. Sonmez, Arcas, O., Sayilar, G., Unsal, O., Cristal, A., Hur, I., Singh, S., and Valero, M., From plasma to beefarm: Design experience of an FPGA-based multicore prototype, Reconfigurable Computing: Architectures, Tools and Applications. Springer, pp. 350–362, 2011.
A. Pérez, Luque, F. J., and Orozco, M., Frontiers in Molecular Dynamics Simulations of DNA., Accounts of chemical research. 2012.
M. T. Pay, Piot, M., Jorba, O., Gassó, S., Gonçalves, M., Basart, S., Dabdub, D., Jiménez-Guerrero, P., and Baldasano, J. M., A full year evaluation of the CALIOPE-EU air quality modeling system over Europe for 2004, Atmospheric Environment, vol. 44, no. 27. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND , pp. 3322-3342, 2010.
J. M. Baldasano, Funciones y Requerimientos de un Sistema de Pronóstico de la Calidad del Aire. Universidad La Salle, Bogotá, Colombia, 16 Octubre, 2014.
J. Mykkanen, Torrents, D., Pineda, M., Camps, M., ME, Y., Horelli-Kuitunen, N., Huoponen, K., Heinonen, M., Oksanen, J., Simell, O., ML, S., Zorzano, A., Palacín, M., and Aula, P., Functional analysis of novel mutations in y(+)LAT-1 amino acid transporter gene causing lysinuric protein intolerance (LPI).. Hum Mol Genet., 2000.
N. Reig, del Rio, C., Casagrande, F., Ratera, M., Gelpí, J. L., Torrents, D., Henderson, P. J. F., Xie, H., Baldwin, S. A., Zorzano, A., Fotiadis, D., and Palacín, M., Functional and structural characterization of the first prokaryotic member of the L-amino acid transporter (LAT) family: a model for APC transporters., The Journal of biological chemistry, vol. 282, no. 18. pp. 13270-81, 2007.
J. Fernández-Recio, Functional characterization and modeling of protein-protein interfaces: lessons from docking, Protein-Protein Interactions on the Genomic Scale. Paris (France). 2014.
M. Terrazas, Alagia, A., Faustino, I., Orozco, M., and Eritja, R., Functionalization of the 3'-ends of DNA and RNA strands with N-ethyl-N-coupled nucleosides: a promising approach to avoid 3'-exonuclease-catalyzed hydrolysis of therapeutic oligonucleotides., Chembiochem : a European journal of chemical biology, vol. 14, no. 4. pp. 510-20, 2013.
M. - C. Marinescu and Sánchez, C., Fusing statecharts and java, ACM Trans. Embed. Comput. Syst., vol. 12. ACM, New York, NY, USA, pp. 45:1–45:21, 2013.
A. Queralt, Cortes, T., Baars, H., Brinkmann, A., and Martí, J., Fusing Storage and Computing for the Domain of Business Intelligence and Analytics – Research Opportunities, 48th Annual Hawaii International Conference on System Sciences. 2015.
S. Sharapov, Hellsten, T., Kiptily, V. G., Craciunescu, T., Eriksson, J., Fitzgerald, M., Girardo, J. - B., Goloborod’ko, V., Hellesen, C., Hjalmarsson, A., Johnson, T., Kazakov, Y., Koskela, T., Mantsinen, M. J., Monakhov, I., and , Fusion product studies via fast ion D-D and D-3He fusion on JET, Nuclear Fusion. 2016.
J. M. Baldasano, Soret, A., López, E., Jiménez-Guerrero, P., and Gonçalves, M., Future Air Quality (year 2015) by managing the vehicular mobility in the city of Barcelona (Spain). 17th Transport and Air Pollution Symposium - 3rd Environment and Transport Symposium (ETTAP09), Toulouse (France), 2009.
C. Bonadonna, Folch, A., Loughlin, S., and Puempel, H., Future Developments in Modeling and Monitoring of Volcanic Ash Clouds, EOS. 2011.
A. Cristal, Llosa, J., Valero, M., and Ortega, D., Future ILP processors, International Journal of High Performance Computing and Networking, vol. 2, pp. 1–10, 2004.
O. Flores, Deniz, O., Soler-López, M., and Orozco, M., Fuzziness and noise in nucleosomal architecture., Nucleic Acids Res, vol. 42, no. 8. pp. 4934-46, 2014.
C. Álvarez, Corbal, J., and Valero, M., Fuzzy Memoization for Floating Point Multimedia Applications. IEEE Transactions on Computers, 2005.
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A. Folch, Costa, A., and Macedonio, G., G. APOLLO: An automatic procedure to forecast transport and deposition of tephra. EGU General Assembly, Vienna, 2008.
A. Badia and Jorba, O., Gas-phase evaluation of the online NMMB/BSC-CTM model over Europe for 2010 in the framework of the AQMEII-Phase2 project, Atmospheric Environment. Elsevier, 2014.
M. Rueda, Luque, F. J., and Orozco, M., G-DNA can maintain its structure in the gas phase. J. Am. Chem. Soc., 2006.
X. Sáez and Soba, A., GENE. Installation guide and performance analysis, in Technical Report. CASE-08 - 3, Barcelona Supercomputing Center, 2008.
O. C. Zienkiewicz, Morgan, K., Satya Sai, B. V. K., Codina, R., and Vázquez, M., A General Algorithm for Compressible and Incompressible Flow. Part II: Tests on the Explicit Form. Int. J. Num. Meth. Fluids, 1995.
R. Codina, Vázquez, M., and Zienkiewicz, O. C., A General Algorithm for Compressible and Incompressible Flow. Part III: The Semi - Implicit form. Int. J. Num. Meth. Fluids, 1998.
R. Codina, Vázquez, M., and Zienkiewicz, O. C., A General Algorithm for Compressible and Incompressible Flows. The Semi - Implicit form, CIMNE, UPC, Barcelona, 1997.
P. González-Férez, Piernas, J., and Cortes, T., A general framework for dynamic and automatic I/O scheduling in hard and solid-state drives, Journal of Parallel and Distributed Computing, vol. 74. pp. 2380–2391, 2014.
J. Díaz, Reyes, S., Badia, R. M., Niño, A., and Muñoz-Caro, C., A General Model for the Generation and Scheduling of Parameter Sweep Experiments in Computational Grid Environments. proceedings of the International Conference on Computational Science 2010, ICCS2010, 2010.
F. Rubio, Hanzich, M., Farrès, A., de la Puente, J., Ferrer, M., and Cela, J. M., Generalized Elastic Staggered Grids on Multi-GPU Platforms, SEG Technical Program Expanded Abstracts. pp. 1-5, 2012.
M. King, Khan, A., Agarwal, A., Arcas, O., and Arvind, Generating Infrastructure for FPGA-Accelerated Applications, 23rd International Conference on Field Programmable Logic and Applications. IEEE, Porto, Portugal, pp. 1–6, 2013.
L. W. Hillier, Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature, 2005.
G. Rodríguez, Badia, R. M., and Labarta, J., Generation of Simple Analytical Models for Message Passing Applications. 10th International Euro-Par Conference, 2004.
J. Martí, Geyer, A., and Folch, A., A genetic classification of collapse calderas based on field studies, analogue and theoretical modelling, THORDARSON, T., SELF, S., LARSEN, G., ROWLAND, S. K. & HOSKULDSSON, A. (eds) Studies in Volcanology: The Legacy of George Walker. Special Publications of IAVCEI, 2, 249?266. Geological Society, London, 2009.
M. Macías and Guitart, J., A Genetic Model for Pricing in Cloud Computing Markets, 26th ACM Symposium On Applied Computing (SAC'11). Taichung, Taiwan, pp. 113-118, 2011.
M. Orozco, Genome scale protein simulation. CASP7.5 Meeting, 2008.
R. G. S. P. Consortium and Torrents, D., Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature, 2004.
A. Julià, Domènech, E., Chaparro, M., García-Sánchez, V., Gomollón, F., Panés, J., Mañosa, M., Barreiro-de Acosta, M., Gutiérrez, A., García-Planella, E., Aguas, M., Muñoz, F., Esteve, M., Mendoza, J. L., Vera, M., Márquez, L., Tortosa, R., López-Lasanta, M., Alonso, A., Gelpí, J. L., García-Montero, A. C., Bertranpetit, J., Absher, D., Myers, R. M., Gisbert, J. P., and Marsal, S., A genome-wide association study identifies a novel locus at 6q22.1 associated with ulcerative colitis., Hum Mol Genet, vol. 23, no. 25. pp. 6927-34, 2014.
A. Julià, González, I., Fernández-Nebro, A., Blanco, F., Rodriguez, L., González, A., Cañete, J. D., Maymó, J., Alperi-López, M., Olivé, A., Corominas, H., Martínez-Taboada, V., Erra, A., Sánchez-Fernández, S., Alonso, A., López-Lasanta, M., Tortosa, R., Codó, L., Gelpí, J. L., García-Montero, A. C., Bertranpetit, J., Absher, D., S Bridges, L., Myers, R. M., Tornero, J., and Marsal, S., A genome-wide association study identifies SLC8A3 as a susceptibility locus for ACPA-positive rheumatoid arthritis., Rheumatology . 2016.
A. Julià, Domènech, E., Ricart, E., Tortosa, R., García-Sánchez, V., Gisbert, J. P., Nos Mateu, P., Gutiérrez, A., Gomollón, F., Mendoza, J. L., García-Planella, E., Barreiro-de Acosta, M., Muñoz, F., Vera, M., Saro, C., Esteve, M., Andreu, M., Alonso, A., López-Lasanta, M., Codó, L., Gelpí, J. L., García-Montero, A. C., Bertranpetit, J., Absher, D., Panés, J., and Marsal, S., A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300., Gut. 2013.
D. Torrents, Suyama, M., Zdobnov, E. M., and Bork, P., A genome-wide survey of human pseudogenes. Genome Res., 2003.
E. M. Novoa, Castro, M., Orozco, M., and de Pouplana., L. R., A genomics method to identify pathogenicity-related proteins. Application to aminoacyl-tRNA synthetase-like proteins. FEBS Lett., (2010), 584, 460-466., 2009.

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