Peer reviewed

2017

Journals

  1. M. Pérez-Abril, C. Lucas-Abellán, J. Castillo-Sánchez, H. Pérez-Sánchez, J.P. Cerón-Carrasco, I. Fortea, J.A. Gabaldón, E. Núñez-Delicado, (2017), “Systematic investigation and molecular modelling of complexation between several groups of flavonoids and HP-β-cyclodextrins ”, Journal of Functional Foods, DOI:10.1016/j.jff.2017.06.052.
  2. S. Yuan, J.F. Chan*, H. den-Haan, K.K. Chik, A.J. Zhang, C.C. Chan, V.k. POON, C.C. Yip, W. Mak, Z. Zhu, Z. Zou, K. Tee, J. Cai, K. Chan, J. Peña-García, H. Pérez-Sánchez*, J.P. Cerón-Carrasco*, K. Yuen*, (2017), “Structure-based discovery of clinically approved drugs as Zika virus NS2B-NS3 protease inhibitors that potently inhibit Zika virus infection in vitro and in vivo”, Antiviral Research, DOI:10.1016/j.antiviral.2017.07.007.
  3. R. Choudharya, P.M., J. Vecstaudzac, M.J. Yáñez-Gascón, H. Pérez Sánchez, R.N., J. Locs, S. Swamiappana, (2017), “Preparation of Nanocrystalline Forsterite by Combustion of Different Fuels and their Comparative In-vitro Bioactivity, Dissolution behaviour and Antibacterial studies”, Materials Science & Engineering C-Materials for Biological Applications, DOI:10.1016/j.msec.2017.03.308.
  4. T. Suzuki*, J.P. Cerón-Carrasco, H. Tamaoki, Y. Ishigaki, R. Katoono, T. Fukushima, H. Pérez-Sánchez*, (2017), “Stereoselective encapsulation for a Triarylmethylium o,o-dimer by natural g-cyclodextrin: Origin of chiral recognition for the axially chiral dicationic guest”, Heterocycles, DOI:10.3987/COM-17-13674.
  5. A. Pérez-Garrido, F. Girón-Rodŕıguez, A. Bueno-Crespo, J. Soto, H. Pérez-Sánchez, A. Morales-Helguera, (2017), “Fuzzy clustering as rational partition method for QSAR”, Chemometrics and Intelligent Laboratory Systems, DOI:10.1016/j.chemolab.2017.04.006.
  6. O. Brovarets, I. Voiteshenko, H. Pérez-Sánchez, D.M. Hovorun, (2017), “A QM/QTAIM research under the magnifying glass of the DPT tautomerisation of the wobble mispairs involving 2-aminopurine”, New Journal of Chemistry, DOI:10.1039/C7NJ00717E.
  7. O. Brovarets, I. Voiteshenko, H. Pérez-Sánchez, D.M. Hovorun, (2017), “A QM/QTAIM detailed look at the Watson-Crick↔wobble tautomeric transformations of the 2-aminopurine·pyrimidine mispairs”, Journal of Biomolecular Structure & Dynamics, DOI:10.1080/07391102.2017.1331864.
  8. B. Imbernón, J.M. Cecilia, H. Pérez-Sánchez, D. Giménez, (2017), “METADOCK: A Parallel Metaheuristic schema for Virtual Screening methods” , International Journal of High Performance Computing Applications, DOI: 10.1177/1094342017697471.
  9. M. Yar, L. Shahzadi, A. Farooq, S.J. Imran, J.P. Cerón-Carrasco, H. den-Haan, S. Kumar, J. Peña-García, H. Pérez-Sánchez, A. Grycova, Z. Dvorak, R. Vrzal, (2017), “In vitro modulatory effects of functionalized pyrimidines and piperidine derivatives on aryl hydrocarbon receptor (AhR) and glucocorticoid receptor (GR) activities”, Bioorganic Chemistry, DOI:10.1016/j.bioorg.2017.02.013.
  10. R. Choudharya, P.M., J. Vecstaudzac, M.J. Yáñez-Gascón, H. Pérez Sánchez, R.N., J. Locs, S. Swamiappana, (2017), “Preparation of Nanocrystalline Forsterite by Combustion of Different Fuels and their Comparative In-vitro Bioactivity, Dissolution behaviour and Antibacterial studies”, Materials Science & Engineering C-Materials for Biological Applications, DOI:10.1016/j.msec.2017.03.308.
  11. D. Vashisht, A. Pandey, A. Hermenean, M.J. Yáñez-Gascón, H. Pérez-Sánchez, K.J. Kumar*, (2016), “Effect of dry heating and ionic gum on the physicochemical and release properties of starch from Dioscorea”, International Journal of Biological Macromolecules, 10.1016/j.ijbiomac.2016.11.064.
  12. G. Cano, J García-Rodríguez, A. García-García, H. Pérez-Sánchez, J. A. Benediktsson, A. Thapa, A. Barre., (2016), “Automatic Selection of Molecular Descriptors using Random Forest: Application to Drug Discovery”, Expert Systems With Applications, DOI: 10.1016/j.eswa.2016.12.008.
  13. M. Collado-González, M. G. Montalbán, J. Peña-García, H. Pérez-Sánchez, G. Víllora, F.G. Díaz Baños, (2017), “Chitosan as stabilizing agent for negatively charged nanoparticles”, Carbohydrate Polymers, DOI:10.1016/j.carbpol.2016.12.043.
  14. A. Rauf, T.B. Hadda, J.P. Cerón-Carrasco, J. Peña-García, H. Pérez-Sánchez, H. Khan, S. Bawazeer, S. Patel, M. Mubarak, Y.N. Mabkhot, (2017), “Sedative-hypnotic-like effect and molecular docking of di-naphthodiospyrol from Diospyros lotus in an animal model”. Biomedicine & Pharmacotherapy, DOI:10.1016/j.biopha.2017.01.043.

 

2016

Journals

  1. H. Pérez-Sánchez*, V. Rezaei, V. Mezhuyev, D. Man, J. Peña-García, H. den-Haan, S. Gesing, (2016), “Developing Science Gateways for Drug Discovery in a Grid Environment”, SpringerPlus, DOI: 10.1186/s40064-016-2914-x.
  2. D.K. Yadav, R. Rai, N. Kumar, S. Singh, S. Misra, P. Sharma, P. Shaw, H. Pérez-Sánchez, R.L. Mancera, E.H. Choi, M. Kim, R. Pratap, (2016), “New arylated benzo[h]quinolines induces anti-cancer activity by Oxidative stress-mediated DNA damage”, Nature Scientific Reports, DOI:10.1038/srep38128.
  3. S. Shityakov, R. Salmas, S. Durdagi, E. Salvador, K. Pápai, M. Yañez-Gascón, H. Pérez-Sánchez, I. Puskás, N. Roewer, C. Förster, J. Broscheit, (2016), “Characterization, In Vivo Evaluation and Molecular Modeling of Different Propofol-Cyclodextrin Complexes to Assess Their Drug Delivery Potential at The Blood-Brain Barrier Level”, Journal of Chemical Information and Modeling, DOI: 10.1021/acs.jcim.6b00215.
  4. O. Brovarets*, H. Pérez-Sánchez*, D.M. Hovorun, (2016), “Structural grounds for the 2-aminopurine mutagenicity: A novel insight into the old problem of the replication errors”, RSC Advances, DOI: 10.1039/C6RA17787E.
  5. V. Citro, J. Peña-García, H. den-Haan, H. Pérez-Sánchez*, R. Prete, L. Liguori, C. Cimmaruta, M.V. Cubellis*, G. Andreotti, (2016), “Identification of an allosteric binding site on human lysosomal alpha-galactosidase opens the way to new pharmacological chaperones for Fabry disease”, PLOS ONE, DOI:10.1371/journal.pone.0165463.
  6. I.E. Orhan*, N. Kucukboyaci, I. Calis, J.P. Cerón-Carrasco, H den-Haan, J. Peña-García, H. Pérez-Sánchez*, (2016), “Acetylcholinesterase inhibitory assessment of isolated constituents from Salsola grandis Freitag, Vural & Adıgüzel and molecular modeling studies on N-acetyltryptophan”, Phytochemistry Letters, (in press).
  7. O. Brovarets, H. Pérez-Sánchez, (2016), “Whether 2-aminopurine induces incorporation errors at the DNA replication? A quantum-mechanical answer on the actual biological issue”, Journal of Biomolecular Structure & Dynamics, (in press).
  8. F. Ghasemi, A. Fassihi, H. Pérez-Sánchez, A. Mehridehnavi, (2016), “The role of Different Sampling Methods in Improving Biological Activity Prediction Using Deep Belief Network”, Journal of Computational Chemistry, (in press).
  9. D.K. Yadav, R. Rai, N. Kumar, S. Singh, S. Misra, P. Sharma, P. Shaw, H. Pérez-Sánchez, R.L. Mancera, E.H. Choi, M. Kim, R. Pratap, (2016), “New arylated benzo[h]quinolines induces anti-cancer activity by Oxidative stress-mediated DNA damage”, Nature Scientific Reports, (in press).
  10. F.S. Senola, S. Ślusarczy, A. Matkowskib, A. Pérez-Garrido, F. Girón-Rodríguez, J.P. Cerón-Carrasco, H. den-Haan, J. Peña-García, H. Pérez-Sánchez*, K. Domaradzki, I.E. Orhan*, (2016), “Selective in vitro and in silico butyrylcholinesterase inhibitory activity of diterpenes and rosmarinic acid isolated from Perovskia atriplicifolia Benth. and Salvia glutinosa L.”, Phytochemistry, (in press).
  11. O. Brovarets, H. Pérez-Sánchez, (2016), “Whether the amino-imino tautomerism of 2-aminopurine is involved into its mutagenicity? Results of a thorough QM investigation”, RSC Advances, (in press).
  12. M.C. Ballesta, D. Moreno-Fernández, H. Pérez-Sánchez, M. Carvajal, (2016), “Plant plasma membrane aquaporins in natural vesicles as potential stabilizers and carriers of glucosinolates”, Colloids and Surfaces B: Biointerfaces, DOI:10.1016/j.colsurfb.2016.03.056.
  13. I. Terekhova*, R. Kumeev, G. Alper, S. Chakraborty, H. Pérez-Sánchez, E. Núñez-Delicado, (2016), “Molecular recognition of aromatic carboxylic acids by hydroxypropyl-γ-cyclodextrin: experimental and theoretical evidence”, RSC Advances, DOI: 10.1039/c6ra06340c.
  14. M. Goodarzi, H. Pérez-Sánchez, (2016), “Octanol-Water Partition Coefficient of Armchair Polyhex BN Nanotubes with Molecular Descriptors”, Russian Journal of Physical Chemistry A, (in press).
  15. V.K. Sharma, P.P. Nandekar, A. Sangamwar, H. Pérez-Sánchez, S.M. Agarwal, (2016), “Structure guided design and binding analysis of EGFR inhibiting analogues of erlotinib and AEE788 using ensemble docking, molecular dynamics and MM-GBSA”, RSC Advances, (in press).
  16. A. Hermenean*, C. Balta, A. Ardlean, C. Cotoraci, I. Navarro-González, J.M. Vegara-Meseguer, S. Chakraborty, H. Pérez-Sánchez*, (2016), “Hepatoprotective Activity of Chrysin is Mediated by Inhibition of TNF-α in Chemically Induced Acute Liver Injury: In Vivo Study and Molecular Modelling”, Experimental and Therapeutic Medicine, (in press).
  17. P. Rajathi Queen, R. Sivaraj, P. Mosae Selvakumar, F.G Díaz Baños, G. Villora, José P. Cerón-Carrasco, H. Pérez-Sánchez, Israel M.V. Enoch, (2016), “Enhanced Zn2+ Ion–Sensing By a Benzothiazole Derivative On Encapsulation in β-Cyclodextrin”, RSC Advances, DOI: 10.1039/c6ra01202g.
  18. A. Llanes, José M. Cecilia, A. Sánchez, J. M. García, M. Amos, M. Ujaldón, (2016), “Dynamic Load Balancing on Heterogeneous Clusters for Parallel Ant Colony Optimization”, Cluster Computing, DOI:10.1007/s10586-016-0534-4
  19. G. Cano, J. García-Rodríguez, S. Orts, J. Peña-García, A. Pérez-Garrido, H. Pérez-Sánchez, (2016), “Drug solubility Prediction with Support Vector Machines on Graphic Processor Units”, Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, DOI: 10.1016/j.rimni.2015.12.001.
  20. X. Zhang, H. Pérez-Sánchez, F. Lightstone, (2016), “A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin”, Current Topics in Medicinal Chemistry, (in press).
  21. A. Llanes, A. Muñóz, A. Bueno-Crespo, T. García-Valverde, A. Sánchez, F. Arcas-Túnez, H. Pérez-Sánchez, J.M. Cecilia, (2016), “Soft Computing Techiniques for the Protein Folding Problem on High Performance Computing Architectures”, Current Drug Targets, DOI:10.2174/1389450117666160201114028.
  22. S. López-Miranda, A. Serrano-Martínez, P. Hernández-Sánchez, L. Guardiola, H. Pérez-Sánchez, I. Fortea, J.A. Gabaldón, E. Núñez-Delicado, (2016), “Use of cyclodextrins to recover catechin and epicatechin from red grape pomace”, Food Chemistry, (in press).
  23. J. L. Abellán, A. Coskun, A. Gu, W. Jin, A. Joshi, A. Kahng, J. Klamkin, C. Morales, J. Recchio, V. Srinivas and T. Zhang (2016), “Adaptive Tuning of Photonic Devices in a Photonic NoC Through Dynamic Workload Allocation” IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems. DOI:10.1109/TCAD.2016.2600238

Conference proceedings

  1. J. Peña-García, A. Pérez-Garrido, A. Muñoz, H. den-Haan, B. Imbernón, J.P. Cerón-Carrasco, D. Mrozek, A. Thapa, J. Soto, A. Banegas-Luna and H. Pérez-Sánchez, (2016) “ZincFetcher: a tool for easy compound filtering from ZINC database” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  2. H. Pérez-Sánchez, J. Peña-García, H. den-Haan, R. Rodríguez-Schmidt, A.N. Raposo, M. Bouarkat, S.A. Sabeur and F.G. Pérez-Sánchez, (2016) “HYDROWEB, an online tool for the calculation of hydrodynamic properties of macromolecules” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  3. F. Girón-Rodríguez, A. Pérez-Garrido, H. Pérez-Sánchez and J. Soto, (2016), “Fuzzy vs Kmeans clustering in QSAR data partition. A comparative study” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  4. J. Pedro Cerón-Carrasco, J. Peña and H. Pérez-Sánchez, (2016), “Non-steroidal anti-inflammatory drugs as inhibitors of cyclooxygenases: what we have learned and what is next” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  5. D. Kumar-Yadav, S. Misra, P. Sharma, H. Pérez-Sánchez, H. Singh and S. Kumar, (2016), “Molecular modeling studies of thieno[3,2-c]pyran analogues as inhibitor against the anti-inflammatory target COX-2” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  6. A. Llanes, C. Velez, A. M. Sánchez, H. Pérez-Sánchez and José M. Cecilia, (2016), “Parallel Ant Colony Optimization for the HP Protein Folding Problem” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  7. J. Pérez-Sianes, H. Pérez-Sánchez and F. Díaz, (2016) “Virtual Screening: A Challenge for Deep Learning”, In PACBB16, 10th International Conference on Practical Applications of Computational Biology & Bioinformatics (accepted).
  8. S.P. Martín, J.L. Redondo, H. den-Haan, H. Pérez-Sánchez and P.M. Ortigosa, (2016) “Multiobjective based scoring function for ligand based Virtual Screening”, In: XIII Global Optimization Workshop (GOW’16) (accepted).
  9. S. Puertas Martín, H. den-Haan, J. López Redondo, H. Pérez-Sánchez and P. Martínez Ortigosa, (2016) “Multiobjective based scoring function for ligand based virtual screening” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  10. J. Peña-García, H. den-Haan, A. Caballero, B. Imbernón, J.P. Cerón-Carrasco, A. Vicente-Contreras, H. Pérez-Sánchez*, (2016) “GrantFinder, a web based tool for the search of research grant calls” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).
  11. R. Rodríguez-Schmidt, J. Peña-García, A. Pérez-Garrido, H. den-Haan, A. Bueno-Crespo, J.P. Cerón-Carrasco, A. Thapa, J. Atli-Benediktsson, J. Soto and H. Pérez-Sánchez*, (2016) “A hybrid machine learning and molecular modeling methodology for the prediction of novel blood anticolagulants” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2016 (accepted).

2015

Journals

  1. I. Timón, J. Soto, H. Pérez-Sánchez, J.M. Cecilia, (2015), “Parallel Implementation of Fuzzy Minimals Clustering Algorithm”, Expert Systems with Applications (ESWA), DOI:10.1016/j.eswa.2015.11.011.
  2. J.P. Cerón-Carrasco*, H. den-Haan, J. Peña-García, J. Contreras-García, H. Pérez-Sánchez*, (2015), “Exploiting the cyclodextrins ability for antioxidants encapsulation: a computational approach to carnosol and carnosic acid embedding”, Computational and Theoretical Chemistry,DOI:10.1016/j.comptc.2015.10.028.
  3. G. Budryn, D. Zaczyńska, B. Pałecz, D. Rachwał-Rosiak, J. Oracz, S. Belica, H. den-Haan, J. Peña-García, H. Pérez-Sánchez, (2015) “ Interactions of free and encapsulated hydroxycinnamic acids and their esters from green coffee with egg ovalbumin, whey and soy protein hydrolysates”, LWT – Food Science and Technology. DOI:10.1016/j.lwt.2015.09.001.
  4. José P. Cerón-Carrasco and D. Jacquemin. Photoactivatable platinum(II) compounds: in search of novel anticancer drugs. Theor. Chem. Acc. (2015) 134:146
  5. José P. Cerón-Carrasco, D. Jacquemin and A. D. Laurent. First computational step towards the understanding of the antioxidant activity of the Phycocyanobilin: Ferredoxin Oxidoreductase in complex with biliverdin IXα. Comput. There. Chem. (2015) doi:10.1016/j.comptc.2015.10.018
  6. J. Carretero, J. Garcia-Blas, D. E. Singh, F. Isaila, A. Lastovetsky, T. Fahringer, R. Prodan, C. Symeonidou, G. Bosilca, A. Fassihi, H. Pérez-Sánchez, (2015), “Acceleration of MPI mechanisms for sustainable HPC applications”, Supercomputing Frontiers and Innovations, DOI: 10.14529/jsfi150202.
  7. Z. Alamiddine, B. Selvam, J. P. Cerón-Carrasco, M. Mathé-Allainmat, J. Lebreton, S. H. Thany, A. D. Laurent, J. Graton and J.-Y. Le Questel, (2015), “Molecular recognition of thiaclopride by Aplysia californica AChBP: new insights from a computational investigation”, J. Comput. Aided. Mol. Des., DOI:10.1007/s10822-015-9884-x
  8. Martinez-Mas, J., Bueno-Crespo, A., Garcia-Laencina, P. J., Martinez-Cendan, J. P., Isaac-Montero, A., Garcia-Nicolas, A. B., & Remezal-Solano, M. (2015). A Benign Ovarian Tumour developing an Endometrial Cancer? Sertoliform Ovarian Cystoadenoma getting together with an Endometrioid Adenocarcinoma. International Archives of Medicine8.
  9. Bueno-Crespo, A., Menchón-Lara, R. M., & Sancho-Gómez, J. L. (2015). Related Tasks Selection to Multitask Learning Schemes. In Bioinspired Computation in Artificial Systems (pp. 213-221). Springer International Publishing.
  10. Menchón-Lara, R. M., Bueno-Crespo, A., & Sancho-Gómez, J. L. (2015). Estimation of the Arterial Diameter in Ultrasound Images of the Common Carotid Artery. In Artificial Computation in Biology and Medicine (pp. 358-367). Springer International Publishing.
  11. A. Pérez-Garrido, V. Rivero-Buceta, G. Cano, S. Kumar, H. Pérez-Sánchez, M. Tejeira-Bautista, (2015), “QSAR study of adenosine A2B receptor affinity of Xanthines and deazaxanthines”, Molecular Diversity, DOI:10.1007/s11030-015-9608-0.
  12. M. Hernández, B. Imbernón, J.M. Navarro, J.M. García, J.M. Cebrián, J.M. Cecilia (2015). Evaluation of the 3-D Finite Difference Implementation of the Acoustic Diffusion Equation Model on Massively Parallel Architectures. doi:10.1016/j.compeleceng.2015.07.001
  13. D. Morshedi, F. Aliakbari, A.T. Marvian, A. Fassihi, F. Pan-Montojo, H. Pérez-Sánchez, (2015), “Cuminaldehyde as the major component of Cuminum cyminum, a natural aldehyde with inhibitory effect on alpha-synuclein fibrillation and cytotoxicity”, Journal of Food Science, DOI:10.1111/1750-3841.1301.
  14. D. Kalarickal Vijayan, R. Chandran, J. Cerezo, A. Fassihi, H. Pérez-Sánchez, C. Sadasivan, (2015), “A comparative studies on the inhibitory activities of selected benzoic acid derivatives against secretory phospholipase A2, a key enzyme involved in the inflammatory pathway”, Molecular Biosystems, DOI: 10.1039/C5MB00073D
  15. S. Sepehri, H. Pérez-Sánchez, A. Fassihi, (2015) “Hantzsch-Type Dihydropyridines and Biginelli-Type Tetrahydropyrimidines: a Review on the Chemotherapeutic Activities”, Journal of Pharmacy and Pharmaceutical Sciences, 18(1), 1-52.
  16. J.M. Vegara-Meseguer, H. Pérez-Sánchez, R. Araujo, F. Martín, B. Soria, (2015), “L-type Ca2+ channels and SK channels in mouse embryonic stem cells and their contribution to cell proliferation”, Journal of Membrane Biology, DOI:10.1007/s00232-015-9779-8.
  17. H. den Haan, A. Fassihi, A. Bueno-Crespo, J. Soto, J. Vegara-Meseguer, S. Montoro, H. Pérez-Sánchez, (2015) “Application of Modern Drug Discovery Techniques in the Context of Diabetes Mellitus and Atherosclerosis”, Drug Designing, 4, e125, doi:10.4172/2169-0138.1000e125
  18. Chao Chen, José L. Abellán, Ajay Joshi. Managing Laser Power in Silicon-Photonic NoC Through Cache and NoC Reconfiguration. IEEE Trans. on CAD of Integrated Circuits and Systems 34(6): 972-985 (2015)
  19. Epifano Gaona, José L. Abellán, Manuel E. Acacio. Fast and efficient commits for Lazy-Lazy hardware transactional memory. The Journal of Supercomputing. DOI 10.1007/s11227-015-1523-8
  20. Amir Kavyan Ziabari, José L. Abellán, Rafael Ubal, Chao Chen, Ajay Joshi, David R. Kaeli: Leveraging Silicon-Photonic NoC for Designing Scalable GPUs. ICS 2015: 273-282
  21. Amir Kavyan Ziabari, José L. Abellán, Yenai Ma, Ajay Joshi, David R. Kaeli: Asymmetric NoC Architectures for GPU Systems. NOCS 2015: 25:1-25:8
  22. A.M. Hernández-Díaz, J.M. Cecilia, M.D. García-Román (2015), “Ajuste de modelos de cortante en hormigón estructural mediante algoritmos evolutivos” Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, doi:10.1016/j.rimni.2015.10.001.
  23. M. Hernández, B. Imbernón, J.M. Navarro, J.M. García, J.M. Cebrián, J.M. Cecilia.
    (2015). “Evaluation of the 3-D finite difference implementation of the acoustic diffusion equation model on massively parallel architectures”, Computers & Electrical Engineering 46, 190-201.

Conference proceedings

  1. J.M. García-Martínez, E.M. Garzón, J.M. Cecilia, H. Pérez-Sánchez, P.M. Ortigosa, (2015) “A GPU solution of the HP Protein Folding Problem based on UEGO” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015 (accepted).
  2. X. Zhang, H. Pérez-Sánchez, F. Lightstone, (2015) “Molecular Dynamics Simulations of Ligand Recognition upon Binding Antithrombin: A MM/GBSA Approach” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 584-593.
  3. F. Ghasemi, A. Mehri, J. Peña-García, H. den-Haan, A. Pérez-Garrido, A. Fassihi , H. Pérez-Sánchez, (2015) “Improving activity prediction of Adenosine A2B receptor antagonists by machine learning methods” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 635-644.
  4. G. Cano, J. García-Rodríguez, S. Orts-Escolano, D. Kumar-Yadav, A. Pérez-Garrido , H. Pérez-Sánchez, (2015) “Support Vector Machines Prediction of drug solubility on GPUs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 645-654.
  5. A. Sánchez-Pérez, A. Muñóz, J. Peña-García, H. den-Haan, N. Bekas, A. Katsikoudi, A. G. Tzakos, H. Pérez-Sánchez, (2015) “DIA-DB: a web-accessible database for the prediction of diabetes drugs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 655-663.
  6. R. Pratap, D. Kumar-Yadav, S. Singh, R. Rai, N. Kumar, H. Uhm, H. Singh, H. Pérez-Sánchez, (2015) “Molecular docking and Biological evaluation of functionalized benzo[h]quinolines as Colon cancer agents” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 664-673.
  7. H. Pérez-Sánchez, A. Fassihi, J. M. Cecilia, H. H. Ali, M. Cannataro, (2015) “Applications of High Performance Computing in Bioinformatics, Computational Biology and Computational Chemistry” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 527-541.
  8. B. Imbernón, A. Llanes, J. Peña-García, J.L. Abellán, H. Pérez-Sánchez, J. M. Cecilia, (2015) “Enhancing the parallelization of Non-Bonded Interactions Kernel for Virtual Screening on GPUs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2015, 620-626.
  9. B. Imbernón, J. M. Cecilia, D. Giménez, (2015), “Enhancing Metaheuristic-based Virtual Screening Methods on Massively Parallel and Heterogeneous Systems”. Accepted for publication in International Workshop on Programming Models and Applications for Multicores and Manycores. ACM.
  10. M. Hernández, J. M. Cebrian, J. M. Cecilia y J. M. García (2015), “Evaluating 3-D Stencil codes on Intel Xeon Phi: Limitations and Trade-offs”, XXVI Jornadas de Paralelismo, Córdoba (Spain), pp. 568-573.
  11. M. Hernández, J. M. García, J. M. Cebrián, J. M. Cecilia (2015), “Guidelines to Enhance 3-D Stencil Codes on the Intel Xeon Phi Coprocessor” PARCO Conference, Edimburgh, UK.
  12. J.M. Navarro, B. Imbernón, J.J. López, J.M. Cecilia (2015)
  13. “Comparison of Parallel Computing Approaches of a Finite-Difference Implementation of the Acoustic Diffusion Equation Model”, Audio Engineering Society Convention 139

2014

Journals

  1. A. Pérez-Garrido, F. Girón-Rodríguez, A.M. Helguera, F. Borges, R.D. Combes, (2014), “Topological structural alerts modulations of mammalian cell mutagenicity for halogenated derivatives”. SAR and QSAR in Environmental Research, 25, pp. 17 – 33. ISSN 1062-936X
  2. I. Merelli, H. Pérez-Sánchez, S. Gesing, D. D’Agostino, (2014) “High-Performance Computing and Big Data in Omics-Based Medicine”, Biomed Research International, Article ID 825649.
  3. I. Merelli, D. D’Agostino, H. Pérez-Sánchez, S. Gesing, (2014) “Managing, Analysing and Integrating Big Data in medical bioinformatics: open problems and future perspectives”, Biomed Research International, DOI:10.1155/2014/134023.
  4. J.M. García-Martínez, E.M. Garzón, J.M. Cecilia, H. Pérez-Sánchez, P.M. Ortigosa, (2014) “An efficient approach for solving the HP Protein Folding Problem based on UEGO”, Journal of Mathematical Chemistry, (in press).
  5. G. Budryn, B. Palecz, D. Rachwal-Rosiak, J. Oracz, D. Zaczynska, S. Belica, I. Navarro-González, J. Vegara-Meseguer, H. Pérez-Sánchez, (2014), “Effect of inclusion of hydroxycinnamic and chlorogenic acids from green coffee bean in β-cyclodextrin on their interactions with whey, egg white and soy protein isolates ”, Food Chemistry (in press).
  6. J.P. Cerón-Carrasco, J. Cerezo, A. Requena, J. Zúñiga, J. Contreras-García, S. Chavan, M. Manrubia-Cobo, H. Pérez-Sánchez, (2014), “Labelling Herceptin with a novel oxaliplatin derivative: A computational approach towards the selective drug delivery”, Journal of Molecular Modeling, (in press).
  7. H. Pérez-Sánchez, G. Cano, J. García-Rodríguez, (2014), “Descubrimiento de Fármacos basado en Cribado Virtual Refinado con Enfoques Neuronales Paralelos”, Revista Internacional de Métodos Numéricos para Cálculo y Diseño en Ingeniería, (in press).
  8. Teresa García-Valverde, Andrés Muñoz, Francisco Arcas, Andrés Bueno-Crespo, and Alberto Caballero, “Heart Health Risk Assessment System: A non-intrusive proposal using ontologies and expert rules”, BioMed Research International, (in press).
  9. Alberto Caballero Martínez, Andrés Muñoz Ortega, Jesús Soto Espinosa, Juan Botía Blaya.“Resource assignment in intelligent environments based on similarity, trust and reputation”. Journal of Ambient Intelligence and Smart Environments. 7, pp. 0 – 0. IOS Press, 2014. ISSN 1876-1364
  10. Q. Bai, H. Pérez-Sánchez, Y. Zhang, Y. Shao, D. Shi, H. Liu, X. Yao, (2014) “Ligand Induced Change of β2 Adrenergic Receptor from Active to Inactive Conformation and Its Implication with Close and Open of Water Channel: Insight from Molecular Dynamics Simulation, Free Energy Calculation and Markov State Model Analysis”, Physical Chemistry Chemical Physics, (in press).
  11. G.D. Guerrero, B. Imbernón, H. Pérez-Sánchez, F. Sanz, J.M. García, J.M. Cecilia, (2014) “A Performance/Cost Evaluation for a GPU-Based Drug Discovery Application on Volunteer Computing”, BioMed Research International, (in press).
  12. Cecilia, J. M., García, J. M., Guerrero, G. D., & Ujaldón, M. (2014). Evaluating the SAT problem on P systems for different high-performance architectures.The Journal of Supercomputing, 1-25.
  13. Guerrero, G. D., Cecilia, J. M., Llanes, A., García, J. M., Amos, M., & Ujaldón, M. (2014). Comparative evaluation of platforms for parallel Ant Colony Optimization. The Journal of Supercomputing, 1-12.
  14. I. Navarro-González, H. Pérez-Sánchez, G. Martin-Pozuelo, J. García-Alonso, M.J. Periago, (2013) “The inhibitor effects of bioactive compounds of tomato juice binding to hepatic HMGCR: in vivo study and molecular modelling”. PLOS ONE, DOI: 10.1371/journal.pone.0083968.
  15. V. Rezaei, H. Pezeshk, H. Pérez-Sánchez, (2013) “Generalized Baum-Welch Algorithm Based on The Similarity Between Sequences”, PLOS ONE, DOI: 10.1371/journal.pone.0080565.
  16. G. Cano, J. García, H. Pérez-Sánchez, (2014) “Improvement of Virtual Screening predictions using Computational Intelligence methods”, Letters in Drug Design & Discovery, 11(1), 33-39.
  17. H. Pérez-Sánchez, J.M. Cecilia, B. Imbernón Tudela, A. Pérez-Garrido, J. Soto, I. Timón-Pérez, J. García-Rodríguez, G. Cano, A. Bueno-Crespo, J. Vegara-Meseguer, (2014) “The Need for an Integrated Computational/Experimental Approach in the Discovery and Design of New Drugs”, Drug Designing, 3, e121, doi:10.4172/2169-0138.1000e121.

Conference proceedings

  1. J. Fang, A. Lucia Varbanescu, B. Imbernón, J. M. Cecilia, H. Peréz-Sánchez, (2014) “Parallel Computation of Non-Bonded Interactions in Drug Discovery: Nvidia GPUs vs. Intel Xeon Phi” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  2. J. P. Cerón-Carrasco, J. Cerezo, J. Zúñiga, A. Requena, J. Contreras-García, S. Chavan, M. Manrubia-Cobo, B. Imbernón, J. M. Cecilia, H. Pérez-Sánchez, (2014) “Application of parallel blind docking with BINDSURF for the study of platinum derived compounds as anticancer drugs” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  3. D. Bonetti, H. Pérez-Sánchez, A. Delbem, (2014) “An Efficient Solvent Accessible Surface Area calculation applied in Ab Initio Protein Structure Prediction” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).
  4. D. Man, I. Timón-Pérez, J. Soto, A. Flores-Sintas, J. M. Cecilia, H. Pérez-Sánchez, (2014) “An improved Fuzzy Clustering methodology applied to the study of Protein Conformational Ensembles” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014 (accepted).

2013

Journals

  1. J.M. López-Nicolas, M. Escorial-Camps, H. Pérez-Sánchez, F. García-Carmona, (2013) “Physicochemical and thermodynamic characterization of the encapsulation of methyl jasmonate by natural and modified cyclodextrins using reserved phase high pressure liquid chromatography”. Journal of Agriculural and Food Chemistry,  61(47), 11347-11354.
  2. H. Pérez-Sánchez, G. Cano, J. García, (2013) “Improving Drug Discovery using Hybrid Softcomputing Methods”. Applied Soft Computing, http://dx.doi.org/10.1016/j.asoc.2013.10.033.
  3. G.D. Guerreo, J.M. Cebrián, H. Pérez-Sánchez, J.M. García, M. Ujaldón, J.M. Cecilia, (2013) “Towards an energy efficient heterogenous processors: Findings on Virtual Screening methods”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3119.
  4. Andrés Bueno-Crespo, Pedro J. García-Laencina, José-Luis Sancho-Gómez, Neural architecture design based on extreme learning machine, Neural Networks, Volume 48, December 2013, Pages 19-24, ISSN 0893-6080, http://dx.doi.org/10.1016/j.neunet.2013.06.010.
  5. G.D. Guerrero, R.M. Wallace, J.L. Vazquez-Poletti, J.M. Cecilia, J.M. García, D. Mozos, H. Pérez-Sánchez, (2013) “A Performance/Cost Model for a CUDA Drug Discovery Application on Physical and Public Cloud Infrastructures”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3117.
  6. Q. Zhang, G.D. Guerrero, J.M. Cecilia, J.M. García, J. Wang, H. Pérez-Sánchez, T. Hou, (2013) “Accelerated Conformational Entropy Calculations using Graphic Processing Units”, Journal of Chemical Information and Modeling, 53, 2057-2064.
  7. I. Merelli, H. Pérez-Sánchez, S. Gesing, D. D’Agostino, (2013) “Latest Advances in Distributed, Parallel, and GPU-accelerated Approaches to Computational Biology”, Concurrency and Computation: Practice and Experience, doi: 10.1002/cpe.3111.
  8. H. Pérez-Sánchez, (2013) “Exploitation of Massively Parallel Architectures for Drug Discovery”, Drug Designing, 2, e108.
  9. M. Hernández, G. Guerrero, J. M. Cecilia, José M. García, A. Inuggi, et al. Accelerating Fibre Orientation Estimation from Diffusion Weighted Magnetic Resonance Imaging Using GPUs.. (2013) PLoS ONE 8(4): e61892. doi:10.1371/journal.pone.0061892
  10. Guillermo Vigueras,  Juan Manuel Orduña,  Miguel Lozano,  Jose María Cecilia, José Manuel García. International Journal of High Performance Computing Applications, doi:10.1177/1094342013476119, first published on February 19, 2013.
  11. José M. Cecilia, Andy Nisbet, Martyn Amos, José M. García, Manuel Ujaldón. Enhancing GPU Parallelism in Nature-inspired Algorithms. Journal of Supercomputing, 63(3), 773-789, 2013.
  12. José M. Cecilia, Andy Nisbet, Martyn Amos, José M. García, Manuel Ujaldón. Enhancing Data Parallelism for Ant Colony Optimizations on GPU. Journal Parallel and Distributed Computing. Special Issue on Metaheuristics on GPUs , 73(1), 42–51, 2013.
  13. Morales Helguera, Aliuska, Alfonso Pérez-Garrido, Alexandra Gaspar, Joana Reis, Fernando Cagide, Dolores Vina, M. Cordeiro, and Fernanda Borges. “Combining QSAR classification models for predictive modeling of human monoamine oxidase inhibitors.” European Journal of Medicinal Chemistry 59, (2013): 75-90.

Conference proceedings

  1. H. Pérez-Sánchez, G. D. Guerrero, J. M. Garcia, J. Peña, J. M. Cecilia, G. Cano, S. Orts-Escolano. J. Garcia-Rodriguez, (2012), “Improving Drug Discovery using a neural networks based parallel scoring function” In: International Joint Conference on Neural Networks, IJCNN 2013, 1436-1440..
  2. G. Cano, M. Manrubia-Cobo, H. den-Haan, J. García-Rodríguez, H. Pérez-Sánchez, (2013) “Improvement of Virtual Screening predictions using Support Vector Machines” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  3. H. Pérez-Sánchez, G.D. Guerrero, F. Sanz, J.M. Cecilia, (2013) “A GPU based Volunteer Computing Platform for the discovery of bioactive compounds” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  4. J. Peña, J. M. Cecilia, H. Pérez-Sánchez, (2013) “Application of Ant Colony Optimization in an hybrid coarse-grained and all-atom based Protein Structure prediction strategy” In: 13th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2013), (accepted).
  5. G.D. Guerrero, J.M. Cecilia, J.M. García, H. Pérez-Sánchez, (2013) “Impact of implicit solvation models on database enrichment in GPU based blind Virtual Screening” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2013, 731-734.
  6. Q. Zhang, J.M. García, J. Wang, T. Hou, H. Pérez-Sánchez, (2013) “A GPU based Conformational Entropy Calculation Method” In: International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2013, 735-744.

2012

Journals

  1. J. Navarro-Fernández, H. Pérez-Sánchez, I. Martínez-Martínez, I. Meliciani, J.A. Guerrero, V. Vicente, J. Corral, W. Wenzel, (2012) “In-silico discovery of a compound with nanomolar affinity to antithrombin causing partial activation and increased heparin affinity”, Journal of Medicinal Chemistry, 55(14), 6403-6412.
  2. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2012) “High-Throughput parallel blind Virtual Screening using BINDSURF”, BMC Bioinformatics, 13(Suppl 14):S13 (Highly accessed).
  3. Javier Palarea-Albaladejo, Josep Antoni Martín-Fernández, Jesús A. Soto. Dealing with Distances and Transformations for Fuzzy C-Means Clustering of Compositional Data, Journal of Classification. Volume 29, Issue 2, pp 144-169. July 2012.
  4. José M. Cecilia, José L. Abellán, Juan Fernández, Manuel E. Acacio, José M. García, Manuel Ujaldón. Stencil computations on Heterogeneous Platforms for the Jacobi Method: GPU Vs CellBE. Journal of Supercomputing, 62(2), 787-803, 2012.
  5. Irene Sánchez-Linares, Horacio Pérez-Sánchez, José M. Cecilia and José M. García. High-Throughput parallel blind Virtual Screening using BINDSURF. BMC Bioinformatics 2012, 13 (Suppl 14):S13 (7 September 2012).
  6. José M. Cecilia, José M. García, Ginés D. Guerrero, Miguel A. Martínez-del-Amor, Mario J. Pérez-Jiménez, Manuel Ujaldón: The GPU on the simulation of cellular computing models. Soft Comput. 16(2): 231-246 (2012).
  7. Ruiz, G.; De Vicente, E.; Vegara, J. (2012) “Sedentary behavior and physical activity levels in university students and workers”. Journal of Sport and Health research, 4(1): 83-92
  8. Andrés Bueno-Crespo, Antonio Sánchez-García, José-Luis Sancho-Gómez, (2012) “Improving learning by using artificial hints”. Neurocomputing 79: 18-25
  9. H. Pérez-Sánchez, E. J. Cepas Quiñonero, J.M. Cecilia, and J. M. García, (2012) “Parallel blind Virtual Screening with implicit solvation models” In: Applied Computing 2012 (IADIS), 421-423.
  10. Alfonso Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Juana M. Morillas Ruiz, Pilar Zafrilla Rentero. “Topological sub-structural molecular design approach: Radical scavenging activity”. European Journal of Medicinal Chemistry 49, (2012): 86-94
  11. F. Almeida, J. Cuenca, D. Giménez, A. Llanes-Castro, J.P. Martínez-Gallar, (2012), “A framework for the application of methaheuristics to task-to-processors assingation problems”. The Journal of Supercomputing, 62, pp 698-723. DOI 10.1007/s11227-009-0309-2.

Conference proceedings

  1. G.D. Guerrero, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2012) “Parallelization of Virtual Screening in Drug Discovery on Massively Parallel Architectures” In: 20th Euromicro International Conference on Parallel, Distributed, and Network-Based Processing PDP 2012, 588-595.
  2. E. J. Cepas Quiñonero, P. Koehl, H. Pérez-Sánchez, and J. M. García, (2012) “Analytical solvent accessible surface area calculation on GPUs” In: 12th International Conference on Computational and Mathematical Methods in Science and Engineering (CMMSE 2012), 307-309.
  3. Moisés Hernández, Ginés D. Guerrero, José M. Cecilia, José M. García, Alberto Inuggi and Stamatios 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.

2011

Journals

  1. H. Pérez-Sánchez, W. Wenzel, (2011) “Optimization methods for virtual screening on novel computational architectures”, Current Computer Aided Drug Design, 7, 44-52.
  2. Pedro J. García-Laencina, Andrés Bueno-Crespo y José-Luis Sancho-Gómez, “Design and Training of Neural Architectures using Extreme Learning Machine”, Neurocomputing: Learning, Architectures and Modeling, ISBN: 978-1-61324-699-3, Nova Science Publishers, 2011.
  3. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Fernanda Borges, M. Natália DS Cordeiro, Virginia Rivero, and Amalio Garrido Escudero. “Two new parameters based on distances in a receiver operating characteristic chart for the selection of classification models.” Journal of Chemical Information and Modeling 51, no. 10 (2011): 2746-2759.

Conference proceedings

  1. G.D. Guerrero, H. Pérez-Sánchez, W. Wenzel, J.M. Cecilia, J.M. García, (2011) “Effective Non-Bonded Interactions Kernel for Virtual Screening on emergent parallel architectures”, In PACBB11, 5th International Conference on Practical Applications of Computational Biology & Bioinformatics. Advances in Intelligent and Soft Computing, 93, 63-69.
  2. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. García, (2012) “Accelerating Grid Kernels for Virtual Screening on Graphics Processing Units” In: Proceedings of the 2011 International Conference on Parallel Computing (ParCo 2011), Advances in Parallel Computing (22), 413-420.
  3. H. Pérez-Sánchez, I. Kondov, J.M. García, K. Klenin, W. Wenzel, (2011) “A Pipeline Pilot based SOAP implementation of FlexScreen for High-Throughput Virtual Screening” In: IWSG-Life 2011 (3rd International Workshop on Science Gateways for Life Sciences).
  4. I. Sánchez-Linares, H. Pérez-Sánchez, G.D. Guerrero, J.M. Cecilia, J.M. García, (2011) “Accelerating multiple target drug screening on GPUs” In: CMSB 2011 (9th International Conference on Computational Methods in Systems Biology).
  5. I. Sánchez-Linares, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2011) “BINDSURF: a fast blind Virtual Screening methodology on GPUs” In: NETTAB 2011 workshop focused on Clinical Bioinformatics, 95-97.
  6. E. J. Cepas Quiñonero, H. Pérez-Sánchez, J.M. Cecilia, J.M. García, (2011) “MURCIA: Fast parallel solvent accessible surface area calculation on GPUs and application to drug discovery and molecular visualization” In: NETTAB 2011 workshop focused on Clinical Bioinformatics, 52-55.
  7. José M. Cecilia, José M. García, Manuel Ujaldón, Andy Nisbet and Martyn Amos. Parallelization Strategies for Ant Colony Optimisation on GPUs. In 14th Int. Workshop on Nature Inspired Distributed Computing -NIDISC11- (in conjunction with IPDPS 2011), Anchorage (Alaska), May 2011.

2010

Journals

  1. J. García de la Torre, F.G. Díaz Baños, H.E. Pérez Sánchez, (2010) “Kerr constant of multi-subunit particles and semiflexible, wormlike chains”, Journal of Physics : Condensed Matter, 22,
  2. José M. Cecilia, José M. Garcia, Ginés D. Guerrero, Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado and Mario J. Pérez-Jimenez. 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.
  3. José M. Cecilia, José M. Garcia, Ginés D. Guerrero, Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado and Mario J. Pérez-Jiménez. Simulation of P systems with active membranes on CUDA. Briefings in Bioinformatics, Vol. 11, Number 3, pp. 313-322, May 2010.
  4. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Gabriel Caravaca López, M.Natália D.S. Cordeiro, and Amalio Garrido Escudero. “A topological substructural molecular design approach for predicting mutagenesis end-points of α, β-unsaturated carbonyl compounds”. Toxicology 268, no 1-2 (2010): 64–77.
  5. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Francisco Girón Rodríguez, and M. N. D. S. Cordeiro. “QSAR models to predict mutagenicity of acrylates, methacrylates and, α, β-unsaturated carbonyl compounds.” Dental Materials 26, no. 5 (2010): 397-415.

Conference proceedings

  1. José M. Cecilia, José M. García, Manuel Ujaldón. The GPU on the Matrix-Matrix Multiply: Performance Study and Contributions. Advances in Parallel Computing, Vol. 19, pp. 331-340, IOS Press. Enero 2010 ISBN: 978-1-60750-529-7.
  2. Guillermo Vigueras, Juan M. Orduña, Miguel Lozano, José M. Cecilia and José M. García. Improving the GPU-Based Collision Check Procedure for Distributed Crowd Simulations. In 2010 International Workshop on GPUs and Scientific Applications (in conjuntion with the Nineteenth International Conference on Parallel Architectures and Compilations Techniques – PACT’ 10), Vienna (Austria), September 2010.
  3. A Novel Mapping Policy for Distributed Shared Caches. Alberto Ros, Manuel E. Acacio, José M. García and Marcelo Cintra. In XXI Jornadas de Paralelismo, Valencia (Spain), September 2010.
  4. José M. Cecilia, José M. García, Ginés D. Guerrero, Miguel A. Martínez-del-amor, Mario J. Pérez-Jiménez and Manuel Ujaldón. P systems simulations on massively parallel architectures. In Third International Workshop on Parallel Architectures and Bioinspired Algorithms (WPABA’ 10), in conjuntion with the Nineteenth International Conference on Parallel Architectures and Compilations Techniques (PACT’ 10), Vienna (Austria), September 2010.
  5. José María Cecilia, José Manuel García and Manuel Ujaldón. CUDA 2D Stencil Computations for the Jacobi Method. Proc. of the Para 2010: State of the Art in Scientific and Parallel Computing, Reykjavík (Iceland), June 2010.

2009

Journals

  1. J. García de la Torre, J.G. Hernández Cifre, A. Ortega, R. Rodríguez Schmidt, M.X. Fernandes, H.E. Pérez Sánchez, R. Pamies, (2009) “SIMUFLEX: Algorithms and tools for simulation of the conformation and dynamics of flexible molecules and nanoparticles in dilute solution”. Journal of Chemical Theory and Computation, 5, 2606-2618.
  2. Antonio Sánchez-García, Andrés Bueno-Crespo, José-Luis Sancho-Gómez, (2009) “An efficient statistics-based method for the automated detection of sperm whale clicks”, Applied Acoustics 71, 451-459. ISSN: 0003-682X.
  3. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, M.Natália D.S. Cordeiro, and Amalio Garrido Escudero. “QSPR Modelling With the Topological Substructural Molecular Design Approach: β-Cyclodextrin Complexation”. Journal of Pharmaceutical Sciences, 98, no. 12 (2009): 4557-4576.
  4. Pérez-Garrido, Alfonso, Aliuska Morales Helguera, Adela Abellán Guillén, M. N. D. S. Cordeiro, and Amalio Garrido Escudero. “Convenient QSAR model for predicting the complexation of structurally diverse compounds with β-cyclodextrins.” Bioorganic & Medicinal Chemistry 17, no. 2 (2009): 896-904.

Conference proceedings

  1. H.E. Pérez Sánchez and W. Wenzel. “Implementation of an effective non-bonded interactions kernel for biomolecular simulations on the Cell processor”. In Proceedings of Massively Parallel Computational Biology on GPUs, Jahrestagung der Gesellschaft für Informatik e.V., Lübeck, Germany, September 29, 2009. Volume 154 of Lecture Notes in Informatics, 721-729.
  2. José M. Cecilia, Francisco J. Moreno and José M. García. Acelerando algoritmos de deconvolución para imágenes de microscopía usando GPUs. Proc. of the II Workshop en Aplicaciones de Nuevas Arquitecturas de Consumo y Altas Prestaciones(ANACAP09). Madrid (Spain), November 2009.
  3. Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Mario J. Pérez-Jiménez, José M. Cecilia, Ginés D. Guerrero and José M. García.Simulation of P Systems with Active Membranes on CUDA. Proc. of the international Workshop on High Performance Computational Systems Biology. Trento (Italy), October 2009.
  4. Ginés D. Guerrero, José M. Cecilia, José M. García, Miguel A. Martínez–del–Amor, Ignacio Pérez–Hurtado, Mario J. Pérez–Jiménez. Analysis of P systems simulation on CUDA. Proc. of the XX Jornadas de Paralelismo. A Coruña (Spain), September 2009.
  5. Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Mario J. Pérez-Jiménez, José M. Cecilia, Ginés D. Guerrero and José M. García.Simulating active membranes systems using GPUs. Proc. of the 10th Workshop on Membrane Computing. Curtea de Arges (Romania), August 2009.
  6. Miguel A. Martínez-del-Amor, Ignacio Pérez-Hurtado, Mario J. Pérez-Jiménez, José M. Cecilia, Ginés D. Guerrero and José M. García.Simulation of Recognizer P Systems by Using Manycore GPUs. Proc. of the Seventh Brainstorming Week on Membrane Computing. Sevilla (Spain), February 2009.

2008

Journals

  1. Jesús Soto, Antonio Flores-Sintas, Javier Palarea. Improving Probabilities in a Fuzzy Clustering Partition. Fuzzy Sets and Systems 159 (2008) 406 – 421.ISSN: 0165-0114
  2. Pérez-Garrido, Alfonso, Maykel Pérez-González, and Amalio Garrido Escudero. “Halogenated derivatives QSAR model using spectral moments to predict haloacetic acids (HAA) mutagenicity”. Bioorganic & Medicinal Chemistry 16, no. 10 (2008): 5720–5732.

Conference proceedings

  1. “High Throughput in-silico Screening against flexible protein receptors”, H.E. Pérez Sánchez, B. Fischer, H. Merlitz and W. Wenzel. NIC Workshop 2008, From Computational Biophysics to Systems Biology, Jan Meinke, Ulrich H.E. Hansmann (Editors) John von Neumann Institute for Computing, Jülich, NIC Series, 40, 133-136.

2007

Journals

  1. Jesús Soto, M. Isabel Vigo Aguiar,  Antonio Flores-Sintas. Afuzzy clustering application to precise orbit determination. Journal of Computational and Applied Mathematics 204 (2007) 137-143. ISBN/ISSN: 0377-0427

Conference proceedings

  1. Jesús Soto, M. Isabel Vigo Aguiar,  Antonio Flores-Sintas. Afuzzy clustering application to precise orbit determination. Journal of Computational and Applied Mathematics 204 (2007) 137-143. ISBN/ISSN: 0377-0427

2006

Journals

  1. H.E. Pérez Sánchez, K. Tatarenko, M. Nigen, A. Imberty, Hs. Lortat-Jacob, J. García de la Torre, C. Ebel, (2006) “Organization of human interferon gamma heparin complexes from solution properties and hydrodynamics”. Biochemistry, 45, 13227-13238.
  2. *P. Vaca, *F. Martín, J.M. Vegara-Meseguer, J.M. Rovira, G. Berná, B. Soria (2006) “Induction of differentiation of ES cells into islet cells by Fetal Soluble Factors”. Stem Cells, 24: 258-265.

2005

Journals

  1. J. García de la Torre, A. Ortega, H.E. Pérez Sánchez, J.G. Hernandez Cifre, (2005) “MULTYHYDRO and MONTEHYDRO: Conformational search and Monte Carlo calculation of solution properties of rigid or flexible bead models”. Biophysical Chemistry, 116, 121-128.
  2. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2005) “Transient electric birefringence of wormlike macromolecules in electric fields of arbitrary strength: A computer simulation study”. Journal of Chemical Physics, 122, 124902-1, 12.
  3. J.M. Vegara-Meseguer, B. Soria, (2005) “Ion channels in the plasma membrane of mouse embryonic stem cells and their physiological role”. Journal of Physiology and Biochemistry, 61, 1.
  4. Andrés Bueno-Crespo, José Luis Sancho-Gómez, Rafaél Verdú, (2005) “Artificial Construction of Task for Multitask Learning.”, IADAT JOURNAL of Advanced Technology on Imaging and Graphics; 1, 50-52. ISSN: 1885-6411

2004

Conference proceedings

  1. Jesús Soto,  Antonio Flores-Sintas, M. Isabel Vigo Aguiar. Marco formal para una nueva función objetivo en agrupación difusa. Inteligencia Artificial, Revista Iberoamericana de I.A. 23 (2004) 35-42.  ISBN/ISSN: 1137-3601

2003

Journals

  1. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2003) “Birefringence, deformation and scattering of wormlike macromolecules under an external agent. Steady-state properties in an electric field”. Journal of Physical Chemistry, B. , 107, 13192-13200.
  2. J. García de la Torre, H.E. Pérez Sánchez, A. Ortega, J.G. Hernández, M.X. Fernandes, F.G. Díaz, M.C. López Martínez, (2003) “Calculation of the solution properties of flexible macromolecules: methods and application”. European Biophysics Journal, 32, 477-486.

2002

Journals

  1. H.E. Pérez Sánchez, J. García de la Torre, F.G. Díaz Baños, (2002) “Influence of field strength and flexibility on the transient electric birefringence of segmentally flexible macromolecules”. Journal of Physical Chemistry, B., 106, 6754-6761.
  2. B. Soria, T. León-Quinto, J. Jones, P. Sepulcre, J.M. Vegara-Meseguer, P. Vaca, G. Berná, E. Roche, J.A. Reig, F. Martín, (2002) “Estrategias para la obtención de células productoras de insulina a partir de células madre”, Fundación Valenciana de Estudios Avanzados. Generalitat Valenciana. Conselleria de Sanitat.