Publications



    Systems Biology, Structural Biology and Bioinformatics PubMed :

  1. Mancuso, F.M., Montfort, M., Carreras, A., Alibés, A., Roma, G. "HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data" (2011) BMC Research Notes, 4, 546 link
  2. De Masi, F.*, Grove, C.A.*, Vedenko, A., Alibés, A., Gisselbrecht, S.S., Serrano, L., Bulyk, M.L., Walhout, A.J.M. "Using a structural and logics systems approach to infer bHLH–DNA binding specificity determinants" (2011) Nucleic Acids Research, 39, 4553-4563 link
  3. Nadra, A.D., Serrano, L., Alibés, A. "DNA-binding specificity prediction with FoldX" (2011) Methods in Enzymology: Synthetic Biology, Part B - Computer Aided Design and DNA Assembly, 498, 3-18  link
  4. Muñoz, I.G., Prieto, J., Subramanian, S., Coloma, J., Redondo, P., Villate, M., Merino, N., Marenchino, M., D'Abramo, M., Gervasio, F.L., Grizot, S., Daboussi, F., Smith, J., Chion-Sotinel, I., Pâques, F., Duchateau, P., Alibés, A., Stricher, F., Serrano, L., Blanco, F.J., Montoya, G. "Molecular basis of engineered meganuclease targeting of the endogenous human RAG1 locus" (2011) Nucleic Acids Research, 39, 729-743 link
  5. Alibés, A.*, Nadra, A.D.*, De Masi, F., Bulyk, M.L., Serrano, L., Stricher, F. "Using protein design algorithms to understand the molecular basis of disease caused by protein-DNA interactions: the Pax6 example" (2010) Nucleic Acids Research, 38, 7422-7431 link
  6. Alibés, A., Serrano, L., Nadra, A.D. "Structure-based DNA binding prediction and design" Engineered Zinc Finger Proteins in the series Methods in Molecular Biology, Vol. 649,  Humana Press. Eds. Joel Mackay and David Segal (2010), 77-88. abstract book link help page
  7. Redondo, P., Prieto, J., Muñoz, I.G., Alibés, A., Stricher, F., Serrano, L., Cabaniols, J-P., Daboussi, F., Arnould, S., Perez, C., Duchateau, P., Pâques, F., Blanco, F.J., Montoya, G. "Molecular basis of xeroderma pigmentosum group C DNA recognition by engineered meganucleases" (2008) Nature, 456, 107-11: link (Rated 'Exceptional' by F1000 Biology, cited in ElPais)
  8. Marcaida, M.J., Prieto, J., Redondo, P., Nadra, A.D., Alibés, A., Serrano, L., Grizot, S., Duchateau, P., Pâques, F., Blanco, F.J., Montoya, G. "Crystal structure of I-DmoI in complex with its target DNA provides new insights into meganuclease engineering" (2008) Proc. Natl Acad. Sci USA, 105, 16888-16893: link
  9. Alibés, A.*, Cañada, A.*, Díaz-Uriarte, R. "PaLS: filtering common literature, biological terms and pathway information" (2008) Nucleic Acids Research 36 (Web Server Issue) W364-W367: link
  10. Díaz-Uriarte, R., Alibés, A., Morrissey, E.R., Cañada, A., Rueda, O.M., Neves, M.L., "Asterias: integrated analysis of expression and aCGH data using an open-source, web-based, parallelized software suite" (2007) Nucleic Acids Resarch 35 (Web Server issue) W75-W80: link
  11. Alibés, A., Yankilevich, P., Cañada, A., Díaz-Uriarte, R. "IDconverter and IDClight: Conversion and annotation of gene and protein IDs" (2007) BMC Bioinformatics, 8:9 link
  12. Alibés, A., Morrissey, E.R., Cañada, A., Rueda, O., Casado, D., Yankilevich, P., Díaz-Uriarte, R. "Asterias: a parallelized web-based suite for the analysis of expression and aCGH data" (2007) Cancer Informatics, 2, 1 link
  13. Robinson-Rechavi, M., Alibés, A., Godzik, A. "Contributions of electrostatic interactions, compactness and quaternary structure to protein thermostability: lessons from structural genomics of Thermotoga maritima" (2006) Journal of Molecular Biology, 356, 547-557 link

    14. Astrophysics:

  14. Alibés, A., Labay, J.,  and Canal, R. "Galactic Cosmic Rays from Superbubbles and the Abundances of Lithium, Beryllium, and Boron" (2002) The Astrophysical Journal, 571, 326. link
  15. Alibés, A., Labay, J.,  and Canal, R. "Chemical evolution and abundance gradients in the Milky Way" (2001) arXiv:astro-ph/0107016 link
  16. Alibés, A., Labay, J.,  and Canal, R. "Galactic chemical abundance evolution in the solar neighborhood up to the iron peak" (2001) Astronomy and Astrophysics, 370, 1103. link
  17. Alibés, A., Labay, J.,  and Canal, R."Galactic chemical evolution and the abundances of lithium, beryllium and boron" (2001) Cosmic evolution, World Scientific, 129  link
  18. Alibés, A., Labay, J.,  and Canal, R."Light element evolution at the Solar Neighborhood" (2000) Light Elements and Their Evolution. IAU Symposia, 198, 563 link
  19. Alibés, A., and Canal, R. "Light Element Evolution in the Galactic Halo" (1999) LiBeB Cosmic Rays, and Related X- and Gamma-Rays, ASP Conference Series, Vol. 171., Astronomical Society of the Pacific, 131 link

* Joint first authors

Contact -- Last Update: Dec 2nd, 2011