32. Alvarez I, Tirado-Herranz A, Alvarez-Palomo B, Requena Osete J, Edel M. Proteomic analysis of human iPSC derived neural stem cells and motor neurons identifies proteasome structural alterations. (2023) Cells 12:2800. https://doi.org/10.3390/cells12242800.
31. Tirado-Herranz A, Guasp P, Pastor-Moreno A, Area-Navarro M, Alvarez I. Analysis of the different subpeptidomes presented by the HLA class I molecules of the B7 supertype. (2023) Cell. Immunol. 387: 104707. doi:10.1016/j.cellimm.2023.104707.
30. Alvarez I. Purification of HLA immunopeptidomes from human thymus. (2022) Methods in Molecular Biology, Chapter 10. Fernando J. Corrales, Alberto Paradela and Miguel Marcilla (eds.) Clinical Proteomics: Methods and Protocols, Methods in Molecular Biology, vol. 2420, https://doi.org/10.1007/978-1-0716-1936-0_10. eBook ISBN: 978-1-0716-1936-0. Hardcover ISBN: 978-1-0716-1935-3. Series ISSN: 1064-3745.
29. Requena J, Alvarez-Palomo AB, Codina-Pascual M, Delgado-Morales R, Moran S, Esteller M, Sal M, Juan-Otero M, Boronat Barado A, Consiglio A, Addeleccia Bogle O, Wolvertang E, Ovchinnikov D, Alvarez I, Jaraquemada D, Mezquita-Pla J, Oliva R, Edel MJ. Global proteomic and methylome analysis in human induced pluripotent stem cells reveals overexpression of a human TLR3 affecting proper innate immune response signaling. (2019) Stem Cells. doi: 10.1002/stem.2966.
28. Mestre-Ferrer A, Scholz E, Humet-Alsius J, Alvarez I. PRBAM: a new tool to analyze the MHC class I and HLA-DR anchor motifs. (2019) Immunology 156, 187–198.
27. Scholz EM, Marcilla M, Daura X, Arribas-Layton D, James EA, Alvarez I. Human Leukocyte Antigen (HLA)-DRB1*15:01 and HLA-DRB5*01:01 present complementary peptide repertoires. (2017) Front Immunol. 8:984.
26. Scholz E, Mestre-Ferrer A, Daura X, García-Medel N, Carrascal M, James EA, Kwok WW, Canals F, Alvarez I. A comparative analysis of the peptide repertoires of HLA-DR molecules differentially associated to rheumatoid arthritis. (2016) Arthritis Rheum. 68:2412-21.
25. Marcilla M, Alvarez I, Ramos-Fernández A, Lombardía M, Paradela A, Albar JP. Comparative analysis of the endogenous peptidomes displayed by HLA*B27 and Mamu-B*08: two MHC class I alleles associated with elite control of HIV/SIV infection. (2016) J Proteome Res. 15:1059-69.
24. Alvarez I, Collado JA, Colobran R, Carrascal M, Ciudad MT, Canals F, James EA, Kwok WW, Gärtner M, Kyewski B, Pujol-Borrell R, Jaraquemada D. Central T cell tolerance: Identification of tissue-restricted autoantigens in the thymus HLA-DR peptidome. (2015) J. Autoimmun. 60:12.
23. Alvarez-Palomo AB, Lucas M, McLenachan S, Requena J, Sal M, Dilley R, Lucas A, Chen F, Da Cruz L, Alvarez I, Jaraquemada D, Edel MJ. The power and the promise of cell reprogramming: Personalized autologous body organ and cell transplant. (2014) J. Clin. Med. 3:373.
22. Collado JA, Guitart C, Ciudad MT, Alvarez I, Jaraquemada D. The repertoires of peptides presented by MHC-II in the thymus and in peripheral tissue: a clue for autoimmunity? (2013) Front Immunol. 4:442. 21. Espinosa G, Collado JA, Scholz E, Mestre-Ferrer A, Kuse N, Takiguchi M, Carrascal M, Canals F, Pujol-Borrell R, Jaraquemada D, Alvarez I. Peptides presented by HLA class I molecules in the human thymus. (2013) J Proteomics. 94:23-36. 20. Collado JA, Alvarez I, Ciudad MT, Espinosa G, Canals F, Pujol-Borrell R, Carrascal M, Abian J, Jaraquemada D. Composition of the HLA-DR-associated human thymus peptidome. (2013) Eur J Immunol. 43:2273-82. 19. Muixí L, Gay M, Muñoz-Torres PM, Guitart C, Cedano J, Abian J, Alvarez I, Jaraquemada D. The peptide-binding motif of HLA-DR8 shares important structural features with other type 1 diabetes-associated alleles. (2011) Genes Immun. 12:504-12. 18. Colomé N, Collado J, Bech-Serra JJ, Liiv I, Antón LC, Peterson P, Canals F, Jaraquemada D, Alvarez I. Increased apoptosis after autoimmune regulator expression in epithelial cells revealed by a combined quantitative proteomics approach. (2010) J Proteome Res. 9:2600-9. 17. Muixí L, Alvarez I, Jaraquemada D. Peptides presented in vivo by HLA-DR in thyroid autoimmunity. (2008) Adv Immunol. 99:165-209. 16. Muixí L, Carrascal M, Alvarez I, Daura X, Martí M, Armengol MP, Pinilla C, Abian J, Pujol-Borrell R, Jaraquemada D. Thyroglobulin peptides associate in vivo to HLA-DR in autoimmune thyroid glands. (2008) J Immunol. 181:795-807. 15. Alvarez I, Collado J, Daura X, Colomé N, Rodríguez-García M, Gallart T, Canals F, Jaraquemada D. The rheumatoid arthritis-associated allele HLA-DR10 (DRB1*1001) shares part of its repertoire with HLA-DR1 (DRB1*0101) and HLA-DR4 (DRB*0401). (2008) Arthritis Rheum. 58:1630-9. 14. Marcilla M, de Castro JA, Castaño JG, Alvarez I. Infection with Salmonella typhimurium has no effect on the composition and cleavage specificity of the 20S proteasome in human lymphoid cells. (2007) Immunology. 122:131-9. 13. Alvarez I, Carrascal M, Canals F, Muixí L, Abián J, Jaraquemada D. Analysis of the HLA class I associated peptide repertoire in a hepatocellular carcinoma cell line reveals tumor-specific peptides as putative targets for immunotherapy. (2007) Proteomics Clin Appl. 1:286-98. 12. Muntasell A, Carrascal M, Alvarez I, Serradell L, van Veelen P, Verreck FA, Koning F, Abian J, Jaraquemada D. Dissection of the HLA-DR4 peptide repertoire in endocrine epithelial cells: strong influence of invariant chain and HLA-DM expression on the nature of ligands. (2004) J Immunol. 173:1085-93. 11. Lopez de Castro JA, Alvarez I, Marcilla M, Paradela A, Ramos M, Sesma L, Vázquez M. HLA-B27: a registry of constitutive peptide ligands. (2004) Tissue Antigens. 63:424-45. 10. Sesma L, Alvarez I, Marcilla M, Paradela A, López de Castro JA. Species-specific differences in proteasomal processing and tapasin-mediated loading influence peptide presentation by HLA-B27 in murine cells. (2003) J Biol Chem. 278:46461-72. 9. Ramos M, Alvarez I, Sesma L, Logean A, Rognan D, López de Castro JA. Molecular mimicry of an HLA-B27-derived ligand of arthritis-linked subtypes with chlamydial proteins. (2002) J Biol Chem. 277:37573-81. 8. Martí M, Alvarez I, Montserrat V, López de Castro JA. Large sharing of T-cell epitopes and natural ligands between HLA-B27 subtypes (B*2702 and B*2705) associated with spondyloarthritis. (2001) Tissue Antigens. 58:351-62. 7. Alvarez I, Martí M, Vázquez J, Camafeita E, Ogueta S, López de Castro JA. The Cys-67 residue of HLA-B27 influences cell surface stability, peptide specificity, and T-cell antigen presentation. (2001) J Biol Chem. 276:48740-7. 6. Ramos M, Alvarez I, García-del-Portillo F, López de Castro JA. Minimal alterations in the HLA-B27-bound peptide repertoire induced upon infection of lymphoid cells with Salmonella typhimurium. (2001) Arthritis Rheum. 44:1677-88. 5. Alvarez I, Sesma L, Marcilla M, Ramos M, Marti M, Camafeita E, de Castro JA. Identification of novel HLA-B27 ligands derived from polymorphic regions of its own or other class I molecules based on direct generation by 20 S proteasome. (2001) J Biol Chem. 276:32729-37. 4. Alvarez I, López de Castro JA. HLA-B27 and immunogenetics of spondyloarthropathies. (2000) Curr Opin Rheumatol. 12:248-53. 3. Yagüe J, Alvarez I, Rognan D, Ramos M, Vázquez J, de Castro JA. An N-acetylated natural ligand of human histocompatibility leukocyte antigen (HLA)-B39. Classical major histocompatibility complex class I proteins bind peptides with a blocked NH(2) terminus in vivo. (2000) J Exp Med. 191:2083-92. 2. Paradela A, Alvarez I, García-Peydró M, Sesma L, Ramos M, Vázquez J, López De Castro JA. Limited diversity of peptides related to an alloreactive T cell epitope in the HLA-B27-bound peptide repertoire results from restrictions at multiple steps along the processing-loading pathway. (2000) J Immunol. 164:329-37. 1. Martí M, Alvarez I, López de Castro JA. A molecular insight on the association of HLA-B27 with spondyloarthropathies. (1999) Curr Rheumatol Rep. 1:78-85.
