Publications

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Author Title [ Type(Asc)] Year
Journal
P. Cozzini, Kellogg, G., Spyrakis, F., Abraham, D., Costantino, G., Emerson, A., Fanelli, F., Gohlke, H., Kuhn, L., Morris, G., Orozco, M., Perthinhez, T., Rizzi, M., and Sotriffer, C., Target Flexibility: An Emerging Consideration in Drug Discovery and Design. J. Med. Chem., 2008, 51 (20), pp 6237?6255, 2008.
T. Cortes and Labarta, J., Taking Advantage of Heterogeneity in Disk Arrays. Journal on Parallel and Distributed Computing (JPDC), 2003.
A. Stein, Rueda, M., Panjkovich, A., Orozco, M., and Aloy, P., A systematic study of the energetics involved in structural changes upon association and connectivity in protein-protein interaction networks. In second revision, 2011.
A. Stein, Rueda, M., Panjkovich, A., Orozco, M., and Aloy, P., A systematic study of the energetics involved in structural changes upon association and connectivity in protein interaction networks., Structure (London, England : 1993), vol. 19, no. 6. pp. 881-9, 2011.
R. Lavery, Zakrzewska, K., Beveridge, D., Bishop, T. C., Case, D., Cheatham, T. E., Dixit, S., Jayaram, B., Lankas, F., Laughton, C., Maddocks, J. H., Michon, A., Osman, R., Orozco, M., Pérez, A., Spacková, N., and Sponer, J., A systematic molecular dynamics study of nearest-neighbor effects on base pair and base pair step conformations and fluctuations in B-DNA. Nucl. Acids Res. (2010) 38 (1): 299-313, 2009.
R. Bertran, Gonzalez, M., Martorell, X., Navarro, N., and Ayguadé, E., A Systematic Methodology to Generate Decomposable and Responsive Power Models for CMPs, IEEE Transactions on Computers, vol. 62. IEEE Computer Society, Los Alamitos, CA, USA, pp. 1289-1302, 2013.
R. Bertran, Gonzalez Tallada, M., Martorell, X., Navarro, N., and Ayguadé, E., A Systematic Methodology to Generate Decomposable and Responsive Power Models for CMPs, Computers, IEEE Transactions on, vol. PP. IEEE Computer Society, Los Alamitos, CA, USA, p. 1, 2012.
A. Papayannis, Amiridis, V., Mona, L., Tsaknakis, G., Balis, D., Bösenberg, J., Chaikovski, F., De Tomasi, F., Grigorov, I., Mattis, I., Mitev, V., Müller, D., Nickovic, S., Pérez, C., Pietruczuk, A., Pisani, G., Ravetta, F., Rizi, V., Sicard, M., Trickl, T., Wiegner, M., Gerding, M., Mamouri, R. E., D'Amico, G., and Pappalardo, G., Systematic lidar observations of Saharan dust over Europe in the frame of EARLINET (2000-2002), Journal of Geophysical Research, vol. 113, no. D10204. AMER GEOPHYSICAL UNION, UNITED STATES , pp. 1-17, 2008.
A. Papayannis, Mamouri, R. E., Amiridis, V., Kazadzis, S., Pérez, C., Tsaknakis, G., Kokkalis, P., and Baldasano, J. M., Systematic lidar observations of Saharan dust layers over Athens, Greece in the frame of EARLINET project (2004?2006), Annales Geophysicae, vol. 27, no. 9. COPERNICUS GESELLSCHAFT MBH , GERMANY, pp. 3611-3620, 2009.
L. Mona, Papagiannopoulos, N., Basart, S., Baldasano, J. M., Binietoglou, I., Cornacchia, C., and Pappalardo, G., Systematic comparison of dust BSC-DREAM8b modeled profiles with Potenza EARLINET lidar database, Atmospheric Chemistry and Physics Discussions, vol. 13. Copernicus Publications, Germany, pp. 31363–31407, 2013.
T. Castaño, Wang, H., Campillo, N. E., Ballester, S., González-García, C., Hernández, J., Pérez, C., Cuenca, J., Pérez-Castillo, A., Martínez, A., Huertas, O., Gelpí, J. L., Luque, F. J., Ke, H., and Gil, C., Synthesis, structural analysis, and biological evaluation of thioxoquinazoline derivatives as phosphodiesterase 7 inhibitors., ChemMedChem, vol. 4, no. 5. pp. 866-76, 2009.
P. Molina-Espeja, Cañellas, M., Plou, F. J., Hofrichter, M., Lucas, F., Guallar, V., and Alcalde, M., Synthesis of 1-Naphthol by a Natural Peroxygenase engineered by Directed Evolution, ChemBioChem, vol. 17, no. 4. pp. 341-349, 2016.
S. Martínez-Montero, Deleavey, G. F., Dierker-Viik, A., Lindovska, P., Ilina, T., Portella, G., Orozco, M., Parniak, M. A., González, C., and Damha, M. J., Synthesis and Properties of 2'-Deoxy-2',4'-difluoroarabinose-Modified Nucleic Acids, Journal of Organic Chemistry, vol. 80, no. 6. pp. 3083-3091, 2015.
M. Torchala, Moal, I. H., Chaleil, R. A. G., Fernández-Recio, J., and Bates, P. A., SwarmDock: a server for flexible protein-protein docking., Bioinformatics (Oxford, England). 2013.
J. Guitart, Torres, J., and Ayguadé, E., A Survey on Performance Management for Internet Applications, Concurrency and Computation: Practice and Experience, vol. 22, no. 1. pp. 68-106, 2010.
Í. Goiri, Julià, F., Fitó, O., Macías, M., and Guitart, J., Supporting CPU-based Guarantees in Cloud SLAs via Resource-level QoS Metrics, Future Generation Computer Systems, vol. 28, no. 8. pp. 1295-1302, 2012.
J. N. Amaral, Badia, R. M., Blanquer, I., Candela, L., Castelli, D., Giovanni, R. D., Lezzi, D., Rafanell, R., Gray, W. A., Pagano, P., Perez-Canhos, V., Quevedo, F., Rebello, V., and Torres, E., Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure, Concurrency and Computation Practice and Experience, vol. 27. pp. 376–394, 2014.
R. Amaral, Badia, R. M., Blanquer, I., Braga-Neto, R., Candela, L., Castelli, D., Flann, C., De Giovanni, R., Gray, W. A., Jones, A., Lezzi, D., Pagano, P., Perez-Canhos, V., Quevedo, F., Rafanell, R., Rebello, V., Sousa-Baena, M. S., and Torres, E., Supporting biodiversity studies with the EUBrazilOpenBio Hybrid Data Infrastructure, Concurrency and Computation: Practice and Experience, vol. 27. pp. 376–394, 2015.
C. Pérez, Sicard, M., Jorba, O., Comerón, A., and Baldasano, J. M., Summertime re-circulations of air pollutants over the north-eastern Iberian coast observed from systematic EARLINET lidar measurements in Barcelona, Atmospheric Environment, vol. 38, no. 24. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND, pp. 3983-4000, 2004.
A. Hernández-Ortega, Borrelli, K., Ferreira, P., Medina, M., Martínez, A. T., and Guallar, V., Substrate diffusion and oxidation in GMC oxidoreductases: an experimental and computational study on fungal aryl-alcohol oxidase., The Biochemical journal, vol. 436, no. 2. pp. 341-50, 2011.
M. Yubero-Gómez, Rubio-Campillo, X., and López-Cachero, J., The study of spatiotemporal patterns integrating temporal uncertainty in late prehistoric settlements in northeastern Spain, Archaeological and Anthropological Sciences. Springer Berlin Heidelberg, pp. 1–14, 2015.
I. Soteras, Lozano, O., Escolano, C., Orozco, M., Amat, M., Bosch, J., and Luque, F. J., Structure-directed reversion in the pi-facial stereoselective alkylation of chiral bicyclic lactams. J. Org. Chem., 2008, 73 (19), pp 7756?7763, 2008.
T. Dršata, Pérez, A., Orozco, M., Morozov, A. V., Sponer, J., and Lankaš, F., Structure, Stiffness and Substates of the Dickerson-Drew Dodecamer., Journal of chemical theory and computation, vol. 9, no. 1. pp. 707-721, 2013.
A. Arcella, Portella, G., Ruiz, M. L., Eritja, R., Vilaseca, M., Gabelica, V., and Orozco, M., Structure of triplex DNA in the gas phase., Journal of the American Chemical Society, vol. 134, no. 15. pp. 6596-606, 2012.
J. Fort, de la Ballina, L. R., Burghardt, H. E., Ferrer-Costa, C., Turnay, J., Ferrer-Orta, C., Usón, I., Zorzano, A., Fernández-Recio, J., Fernández, P. L., Orozco, M., Lizarbe, M. A., Fita, I., and Palacín, M., Structure of human 4F2hc ectodomain: crystallographic and in vivo evidence for homodimerization. J.Biol.Chem, 43, 31444-31452, 2007.
A. Arcella, Portella, G., Collepardo-Guevara, R., Chakraborty, D., Wales, D. J., and Orozco, M., Structure and properties of DNA in apolar solvents., J Phys Chem B, vol. 118, no. 29. pp. 8540-8, 2014.
A. Arcella, Dreyer, J., Ippoliti, E., Ivani, I., Portella, G., Gabelica, V., Carloni, P., and Orozco, M., Structure and dynamics of oligonucleotides in the gas phase., Angewandte Chemie International Edition, vol. 54, no. 2. pp. 467-471, 2015.
A. Aviñó, Cubero, E., Gargallo, R., González, C., Orozco, M., and Eritja, R., Structural Properties of G.T-parallel duplexes carrying 8-aminopurine residues. J.Nucleic Acids. (2010). Article ID 7636658, 1-11., 2009.
E. Fernández-Fueyo, Acebes, S., Ruiz-Dueñas, F. J., Martínez, M. Jesús, Romero, A., Medrano, F. Javier, Guallar, V., and Martínez, A. T., Structural implications of the C-terminal tail in the catalytic and stability properties of manganese peroxidases from ligninolytic fungi, Acta Crystallographica Section D: Biological Crystallography, vol. 70. International Union of Crystallography, pp. 0–0, 2014.
G. Rossetti, Dans, P. D., Gomez-Pinto, I., Ivani, I., González, C., and Orozco, M., The structural impact of DNA mismatches, Nucleic Acids Research, vol. 43, no. 8. pp. 4309-4321, 2015.
J. R. Blas, Huertas, O., Tabares, C., Sumpter, B. G., Fuentes-Cabrera, M., Orozco, M., Ordejón, P., and Luque, F. J., Structural, dynamical, and electronic transport properties of modified DNA duplexes containing size-expanded nucleobases., The journal of physical chemistry. A, vol. 115, no. 41. pp. 11344-54, 2011.
C. Pons, D'Abramo, M., Svergun, D. I., Orozco, M., Bernadó, P., and Fernández-Recio, J., Structural characterization of protein-protein complexes by integrating computational docking with small-angle scattering data. J.Mol.Biol (2010). 403, 217-230, 2010.
M. Lucas, Gaspar, A. H., Pallara, C., Rojas, A. Lucely, Fernandez-Recio, J., Machner, M. P., and Hierro, A., Structural basis for the recruitment and activation of the Legionella phospholipase VipD by the host GTPase Rab5., Proc Natl Acad Sci U S A, vol. 111, no. 34. pp. E3514-23, 2014.
Y. Chen, Tascón, I., Neunuebel, R. M., Pallara, C., Brady, J., Kinch, L. N., Fernández-Recio, J., Rojas, A. L., Machner, M. P., and Hierro, A., Structural basis for Rab1 de-AMPylation by the Legionella pneumophila effector SidD., PLoS pathogens, vol. 9, no. 5. p. e1003382, 2013.
A. Rosell, Meury, M., Alvarez-Marimon, E., Costa, M., Pérez-Cano, L., Zorzano, A., Fernández-Recio, J., Palacín, M., and Fotiadis, D., Structural bases for the interaction and stabilization of the human amino acid transporter LAT2 with its ancillary protein 4F2hc., Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 8. pp. 2966-71, 2014.
S. Ayuso-Tejedor, García-Fandiño, R., Orozco, M., Sancho, J., and Bernadó, P., Structural analysis of an equilibrium folding intermediate in the apoflavodoxin native ensemble by small-angle X-ray scattering., Journal of molecular biology, vol. 406, no. 4. pp. 604-19, 2011.
A. Ramirez, Larriba-Pey, J. L., and Valero, M., A Stream Processor Front-end, IEEE Technical Committee on Computer Architecture Newsletter. pp. 10-13, 2000.
J. Oliver, Guitart, J., Ayguadé, E., Navarro, N., and Torres, J., Strategies for Efficient Exploitation of Loop-Level Parallelism in Java Concurrency and Computation, Concurrency and Computation: Practice and Experience, vol. 13, no. 8-9. pp. 663-680, 2001.
E. D. Babot, José, C., Cañellas, M., Sancho, F., Lucas, F., Guallar, V., Kalum, L., Lund, H., Gröbe, G., Scheibner, K., and , Steroid hydroxylation by basidiomycete peroxygenases: A combined experimental and computational study, Applied and environmental microbiology, vol. 81. American Society for Microbiology, pp. 4130–4142, 2015.
A. Hernández-Ortega, Ferreira, P., Merino, P., Medina, M., Guallar, V., and Martínez, A. T., Stereoselective Hydride Transfer by Aryl-Alcohol Oxidase, a Member of the GMC Superfamily., Chembiochem : a European journal of chemical biology. 2012.
J. L. Lérida, Solsona, F., Hernández, P., Giné, F., Hanzich, M., and Conde, J., State-based predictions with self-correction on Enterprise Desktop Grid environments, Journal of Parallel and Distributed Computing, vol. 73, no. 6. Elsevier, pp. 777-789, 2013.
J. - B. Girardo, Sharapov, S., Boom, J., Dumont, R., Eriksson, J., Fitzgerald, M., Garbet, X., Hawkes, N., Kiptily, V., Lupelli, I., Mantsinen, M., Sarazin, Y., Schneider, M., and , Stabilization of sawteeth with third harmonic deuterium ICRF-accelerated beam in JET plasmas, Physics of Plasmas, vol. 23. AIP Publishing, p. 012505, 2016.
M. Perucho, Martí, J. M., Cela, J. M., Hanasz, M., de la Cruz, R., and Rubio, F., Stability of three-dimensional relativistic jets: implications for the FRI/FRII dichotomy, Astronomy & Astrophysics. 2009.
P. Villar, Spin bath interaction effects on the geometric phase, Physics Letters A, vol. 373. pp. 206 - 209, 2009.
A. Pajuelo, González, A., and Valero, M., Speculative Execution for Hiding Memory Latency. Computer Architecture News, 2005.
A. Queralt and Teniente, E., Specifying the Semantics of Operation Contracts in Conceptual Modeling, J. Data Semantics VII. pp. 33-56, 2006.
A. Aviñó, Portella, G., Ferreira, R., Gargallo, R., Mazzini, S., Gabelica, V., Orozco, M., and Eritja, R., Specific loop modifications of the thrombin-binding aptamer trigger the formation of parallel structures., The FEBS journal. 2013.
R. M. Badia, Gannon, D., and Lee, C., Special section: Selected papers from the 7th IEEE/ACM international conference on grid computing (Grid2006). Future Generation Computer Systems, 2008.
M. T. Pay, Jiménez-Guerrero, P., Jorba, O., Basart, S., Querol, X., Pandolfi, M., and Baldasano, J. M., Spatio-temporal variability of concentrations and speciation of particulate matter across spain in the caliope modeling system, Atmospheric Environment, vol. 46, no. January 2012. PERGAMON-ELSEVIER SCIENCE LTD, ENGLAND, pp. 376-396, 2012.
X. Rubio-Campillo, Cardona, F. X. H., and Gómez, M. Yubero, The Spatiotemporal Model of an 18th-Century City Siege, Social Science Computer Review. 2014.

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