Publications

Systems Biology, Structural Biology and Bioinformatics Publons PubMed

  1. Castellanos, E., Rosas, I., Negro, A., Gel, B., Alibés, A., Baena, N., Pineda, M., Pi, G., Pintos, G., Salvador, H., Lazaro, C., Blanco, I., Vilageliu, L., Brems, H., Grinberg, D., Legius, E., Serra, E. "Mutational spectrum by phenotype: panel-based NGS testing of patients with clinical suspicion of RASopathy and children with multiple café-au-lait macules" (2020) Clinical Genetics, 97, 264-275 link

  2. González, B. , Fece de la Cruz, F. , Samuelsson, J.K., Alibés, A., Alonso, S. "Epigenetic and transcriptional dysregulation of VWA2 associated with a MYC-driven oncogenic program in colorectal cancer" (2018) Scientific Reports, 8, Article num: 11097 link

  3. Alonso, S., González, B., Alibés, A., Perucho, M. "Analysis of Somatic DNA Methylation Alterations of Genes Encoding Cell Surface Metallopeptidases in Colorectal Cancer" Proteases and Cancer in the series Methods in Molecular Biology, Vol. 1731, Humana Press. Eds. Santiago Cal and Álvaro Obaya (2018), 1731:271-294 link

  4. Samuelsson J.K., Dumbovic G., Polo C., Moreta C., Alibés A., Ruiz-Larroya T., Giménez-Bonafé P., Alonso S., Forcales S.V, Perucho M. "Helicase Lymphoid-Specific Enzyme Contributes to the Maintenance of Methylation of SST1 Pericentromeric Repeats That Are Frequently Demethylated in Colon Cancer and Associate with Genomic Damage" (2017) Epigenomes, 1, 2 link

  5. Kato F., Fiorentino F.P., Alibés A., Perucho M., Sánchez-Céspedes M., Kohno T., Yokota J. "MYCL is a Target of a BET Bromodomain Inhibitor, JQ1, on Growth Suppression Efficacy in Small Cell Lung Cancer Cells" (2016) Oncotarget, 7, 77378-77388 link

  6. Hosseini A., Alibés A., Noguera-Julian M., Gil V., Paredes R., Soliva R., Orozco M., Guallar V., "Computational Prediction of HIV-1 Resistance to Protease Inhibitors" (2016) Journal of Chemical Information and Modeling, 56, 915-923 link (Cited in El País)

  7. Alonso S., Alibés A., Perucho M., "Tècniques de diagnòstic molecular aplicades a l’estudi del càncer" (2015) Treballs de la Societat Catalana de Biologia , 66, 53-61 link

  8. Chen W.H., van Noort V., Lluch-Senar M., Hennrich M.L., H Wodke J.A.H., Yus E., Alibés A., Roma G., Mende D.R., Pesavento C., Typas A., Gavin A.C., Serrano L., Bork P. "Integration of multi-omics data of a genome-reduced bacterium: Prevalence of post-transcriptional regulation and its correlation with protein abundances" (2016) Nucleic Acids Research, 44, 1192-1202 link

  9. Wodke, J.A.H.*, Alibés, A.*, Hermoso, A., Cozzuto, L., Yus, E., Lluch-Senar, M., Serrano, L., Roma, G. "MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae" (2015) Nucleic Acids Research, 43 (Database issue), D618-D623link

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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)

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

Astrophysics:

  1. 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

  2. Alibés, A., Labay, J., and Canal, R. "Chemical evolution and abundance gradients in the Milky Way" (2001) arXiv:astro-ph/0107016 link

  3. 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

  4. 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

  5. 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

  6. 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