Research Publications

Journals

 

  • M. Hernández, G. D. Guerrero, J. M. Cecilia, J. M. García, A. Inuggi, S. Jbabdi, T. E. J. Behrens and S. N. Sotiropoulos. Accelerating Fibre Orientation Estimation from Difusion Weighted Magnetic Resonance Imaging using GPUs PLoS ONE 8(4): e61892. doi:10.1371/journal.pone.0061892.
  • G. Vigueras, J. M. Orduña, M. Lozano, J. M. Cecilia and J. M. García. Accelerating Large-scale Crowd Simulations on Multi-core and Manu-core Architectures. International Journal of High Performance Computing. SAGE Publications (in press).
  • J. M. Cecilia, J. M. García, A. Nisbet, M. Amos and M. Ujaldón. Enhancing GPU parallelism in nature-inspired algorithms. The Journal of Supercomputing, vol. 63, no. 3, pp. 773-789, March 2013.
  • J. M. Cecilia, J. M. García, A. Nisbet, M. Amos and M. Ujaldón. Enhancing Data Parallelism for Ant Colony Optimisation on GPUs. Journal of Parallel and Distributed Computing, vol. 73, no. 1, pp. 42-51, January 2013.
  • J. M. Cecilia, J. L. Abellán, J. Fernández, M. E. Acacio, J. M. García and M. Ujaldón. Stencil computations on heterogeneous platforms for the Jacobi method: GPUs versus Cell BE. The Journal of Supercomputing, Volume 62, Number 2, pp. 787-803, 2012.
  • I. Sánchez-Linares, H. Pérez-Sánchez, J. M. Cecilia and J. M. García. High-Throughput parallel blind Virtual Screening using BINDSURF. BMC Bioinformatics 2012, 13(Suppl 14):S13 (7 September 2012).
  • J. M. Cecilia, G. D. Guerrero, J. M. García, Miguel A. Martínez-del-Amor, Mario J. Pérez-Jiménez and Manuel Ujaldón. The GPU on the simulation of cellular computing models. Soft Computing – A Fusion of Foundations, Methodologies and Applications. Vol 16, N. 2, pp. 231-246, February 2012.
  • J. M. Cecilia, G. D. Guerrero, J. M. García, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. Simulating a P system based efficient solution to SAT by using GPUs. Journal of Logic and Algebraic Programming, Vol 79, pp. 317-325, August 2010.
  • J. M. Cecilia, G. D. Guerrero, J. M. García, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. Simulation of P systems with Active Membranes. Briefings in Bioinformatics, Vol. 11, Number 3, pp. 313-322, May 2010.

 

Book Chapters

 

  • J. M. Cecilia, J. M. García and M. Ujaldón. The GPU on the Matrix-Matrix Multiply: Performance Study and Contributions. Advances in Parallel Computing, Parallel Computing: From multicore and GPU’s to Petascale. IOS Press, Vol 19, pp 331- 340, ISBN: 978-1-60750-529-7, 2010.
  • Horacio Pérez-Sanchéz, J. M. Cecilia, J. M. García. Recent Advances and Future Trends on the Emerging Role of GPUs as Platforms for Virtual Screening-Based Drug Discovery. Virtual Screening. Intech, pp 19-52, ISBN: 978-953-51-0308-0, 2012.

 

Peer-Reviewed Conferences

 

  • H. Pérez, G. D. Guerrero, J. M. García, J. Peña, J. M. Cecilia, G. Cano, S. Ortos-Escolano, J. García-Rodríguez. Improving Drug Discovery using a neural networks based parallel scoring functions. Accept for publication in the International Joint Conference on Neural Networks (IJCNN 2012), Dallas (USA), August 2013.
  • G. D. Guerrero, J. M. Cecilia, J. M. García and H. Pérez-Sánchez. Impact of implicit solvation models on database enrichment in GPU based blind Virtual Screening. International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBIO 2013), Granada (Spain), March 2013.
  • M. Hernández, G. D. Guerrero, J. M. Cecilia, J. M. García, A. Inuggi and S. N. Sotiropoulos. Accelerating Fibre Orientation Estimation from Diffusion Weighted Magnetic Resonance Imaging using GPUs. 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP 2012), Munich (Germany), February 2012.
  • G. D. Guerrero, H. Pérez-Sánchez, J. M. Cecilia and J. M. García. Parallelization of Virtual Screening in Drug Discovery on Massively Parallel Architectures. 20th Euromicro International Conference on Parallel, Distributed and Network-Based Processing (PDP 2012), Munich (Germany), February 2012.
  • E. J. Cepas, H. Pérez-Sánchez, J. M. Cecilia and J. M. García. MURCIA: Fast parallel solvent accessible surface area calculation on GPUs and application to drug discovery and molecular visualization. Network Tools and Applications in Biology (NETTAB 2011), Pavia (Italy), October 2011.
  • I. Sánchez-Linares, H. Pérez-Sánchez, J. M. Cecilia and J. M. García. BINDSURF: a fast blind Virtual Screening methodology on GPUs. Network Tools and Applications in Biology (NETTAB 2011), Pavia (Italy), October 2011.
  • I. Sánchez-Linares, H. Pérez-Sánchez, G. D. Guerrero, J. M. Cecilia and J. M. García. Accelerating multiple target drug screening on GPUs. In Proceedings of the 9th International Conference on Computational Methods in Systems Biology in cooperation with the ACM SIG Bioinformatics.
  • G. D. Guerrero, H. Pérez-Sánchez, W. Wenzel, J. M. Cecilia and J. M. García. Effective Parallelization of Non-bonded Interactions Kernel for Virtual Screening on GPUs. In Proceedings of International Conference on Practical Applications of Computational Biology & Bioinformatics (Salamanca, Spain, 2011), Springer, pp. 63-69.
  • J. M. Cecilia, J. M. García, M. Ujaldón, A. Nisbet and M. Amos. Parallelization Strategies for Ant Colony Optimisation on GPUs. In Proceedings of International Workshop on Nature Inspired Distributed Computing, in conjunction with the 25th International Parallel and Distributed Processing Symposium (Anchorage, Alaska, 2011), NIDISC11 in conjunction with IPDPS 2011, IEEE, CD-ROM.
  • J. M. Cecilia, J. M. García and M. Ujaldón. CUDA 2D Stencil Computation for the Jacobi Method. In Proceedings of 10th Intl. Workshop on State-of-the-Art in Scientific and Parallel Computing (Reykjavik, Iceland, 2010), PARA10, ACM, pp. 173-197.
  • J. M. Cecilia, J. M. García, G. D. Guerrero, M. A. Martínez-del-Amor, M. J. Pérez-Jiménez and M. Ujaldón. P Systems Simulations on Massively Parallel Architectures. In Proceedings of the third International Workshop on Parallel Architectures and Bioinspired Algorithms, in conjunction with the Nineteenth International Conference on Parallel Architectures and Compilation Techniques (Vienna, Austria, 2010), WPABA10-PACT10, UCM, pp. 17-26.
  • J. M. Cecilia, G. D. Guerrero, J. M. García, M. A. Martínez-del-Amor, M. J. Pérez-Jiménez and Manuel Ujaldón. Enhancing the simulation of P systems for the sat problem on GPUs. Poster presentation in Symposium on Application Accelerators in High Performance Computing (Knoxville, Tennessee, USA, 2010), SAAHPC’10.
  • J. M. Cecilia, G. D. Guerrero, J. M. García, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. Simulation of P Systems with Active Membranes on CUDA. In Proceedings of International Workshop in High Performance Computational Systems Biology (Trento, Italy, 2009), HiBi 2009, SERSC, pp. 61-70.
  • J. M. Cecilia, J. M. García, G. D. Guerrero, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. Implementing P systems parallelism by means of GPUs. In Proceedings of International Workshop on Membrane Computing (Curtea deArges, Romanie, 2009), WMC 2009, LNCS(Springer-Verlag), vol. 5957, pp. 227-241.
  • J. M. Cecilia, G. D. Guerrero, J. M. García, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. A massively parallel framework using p systems and GPUs. Poster presentation in Symposium on Application Accelerators in High Performance Computing (Urbana-Champaign, Illinois, USA, 2009), SAAHPC’09.
  • M. A. Martínez-del-Amor, I. Pérez-Hurtado, M. J. Pérez-Jiménez, J. M. Cecilia, G. D. Guerrero and J. M. García. Simulation of recognizer p systems by using manycore GPUs. In Proceedings of the 7th Brainstorming Week on Membrane Computing (Seville, Spain, 2009), Fénix Editora, pp. 45-58.

 

 

Non Peer-Reviewed Conferences

 

  • E. J. Cepas, G. D. Guerrero, J. M. Cecilia, J. M. García and J. T. Fernández. Estrategias de Paralelización de Algoritmos de Razonamiento para Ontologías Biomédicas. In Proceedings of the XXII Jornadas de Paralelismo (La Laguna, Spain, 2011).
  • M. Hernández, G. D. Guerrero, J. M. Cecilia, J. M. García and A. Inuggi. Paralelización del Análisis de Imágenes con Tensor de Difusión en Resonancia Magnética usando GPUs. In Proceedings of the XXII Jornadas de Paralelismo (La Laguna, Spain, 2011).
  • J. M. Cecilia, F. J. Moreno and J. M. García. Acelerando algoritmos de deconvolución para imágenes de microscopía usando GPUs. In Proceedings of the II Workshop en Aplicaciones de Nuevas Arquitecturas de Consumo y altas prestaciones (Madrid, Spain, 2009), ANACAP09, URJC1, CD-ROM.
  • G. D. Guerrero, J. M. Cecilia, J. M. García, M. A. Martínez-del-Amor, I. Pérez-Hurtado and M. J. Pérez-Jiménez. Analysis of P systems simulation on CUDA. In Proceedings of the XX Jornadas de Paralelismo (A Coruña, Spain, 2009), pp. 195-200.