CARAM

Publications

  1. Gasser, H. C., OyarzĂşn, D. A., Alfaro, J. A., & Rajan, A. (2024). Integrating MHC Class I visibility targets into the ProteinMPNN protein design process. bioRxiv, 2024-06.
  2. Faria, D., Eugénio, P., Contreiras Silva, M., Balbi, L., Bedran, G., Kallor, A. A., Javier A Alfaro & Pesquita, C. (2024). The Immunopeptidomics Ontology (ImPO). Database, 2024, baae014.
  3. Gasser, H. C., Oyarzún, D. A., Rajan, A., & Alfaro, J. A. (2024). Guiding a language-model based protein design method towards MHC Class-I immune-visibility targets in vaccines and therapeutics. ImmunoInformatics, 14, 100035.
  4. O’Neill, J. R., Mayordomo, M. Y., Mitulović, G., Al Shboul, S., Bedran, G., Faktor, J., … & Alfaro, J. (2024). Multi-omic analysis of Esophageal Adenocarcinoma uncovers candidate therapeutic targets and cancer-selective post-transcriptional regulation. Molecular & Cellular Proteomics, 100764. In Press.  https://www.mcponline.org/article/S1535-9476(24)00054-9/fulltext
  5. Kocikowski, M.*, Dziubek, K., Wegrzyn, K. E., Hrabal, V., Zavadil-Kokas, F., Vojtesek, B., Alfaro, J., Hupp, T., Parys, M.* (2024). Comparative Characterization of Two Monoclonal Antibodies Targeting Canine PD-1. Frontiers in Immunology – Comparative Immunology, in press. DOI: 10.3389/fimmu.2024.1382576.
  6. Treherne, J. M., Kuś, K., Krzykawski, M. P., Earnshaw, D. L., Krzykawska, R., Biesaga, B., … & Alfaro, J. A,  (2024). 3D culture of pancreatic cancer cells in vitro recapitulates an aberrant mitochondrial oxidative phosphorylation genotype observed in vivo. bioRxiv, 2024-03.
  7. Sng, C. C., Kallor, A. A., Simpson, B. S., Bedran, G., Alfaro, J., & Litchfield, K. (2024). Untranslated regions (UTRs) are a potential novel source of neoantigens for personalised immunotherapy. Frontiers in Immunology, 15, 1347542.
  8. Hans-Christof Gasser, Diego Oyarzun, Ajitha Rajan, Javier Alfaro. Utility of language model and physics-based approaches in modifying MHC Class-I immune-visibility for the design of vaccines and therapeutics bioRxiv 2023.07.10.548300; doi: https://doi.org/10.1101/2023.07.10.548300 In Press. Immunoinformatics.
  9. Gema, Aryo Pradipta, et al. and Javier Antonio Alfaro  “Vaxformer: Antigenicity-controlled Transformer for Vaccine Design Against SARS-CoV-2.” arXiv preprint arXiv:2305.11194 (2023). First round review.
  1. Canel, M., Sławińska, A. D., Lonergan, D. W., Kallor, A. A., Upstill-Goddard, R., Davidson, C., … & Serrels, A. (2024). FAK suppresses antigen processing and presentation to promote immune evasion in pancreatic cancer. Gut, 73(1), 131-155. IF 30
  2. Bedran, G., Polasky, D. A., Hsiao, Y., Yu, F., da Veiga Leprevost, F., Alfaro, J. A., … & Nesvizhskii, A. I. (2023). Unraveling the glycosylated immunopeptidome with HLA-Glyco. Nature Communications, 14(1), 3461.
  3. MacCoss, M. J.*, Alfaro, J. A*., Faivre, D. A., Wu, C. C., Wanunu, M., & Slavov, N*. (2023). Sampling the proteome by emerging single-molecule and mass spectrometry methods. nature methods, 20(3), 339-346.
  4. Dominic Phillips, Hans-Christof Gasser, Sebesyén Kamp, Aleksander Pałkowski, Lukasz Rabalski, Diego A. Oyarzún, Ajitha Rajan, Javier Antonio Alfaro. Generating Immune-aware SARS-CoV-2 Spike Proteins for Universal Vaccine Design. Proceedings of the 1st Workshop on Healthcare AI and COVID-19, ICML 2022, PMLR 184:100-116, 2022.
  5. Mayordomo MY., Shboul S.A., Gómez-Herranz M., Azfer A., Meynert A, Salter D., Hayward L., Patton J., Hupp T., Arends M.J.. Alfaro J.A*. Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease. BMC Med Genomics 15, 128 (2022).
  6. Bedran, G., Gasser, H. C., Weke, K., Wang, T., Bedran, D., Laird, A., … & Alfaro, J. A. (2023). The Immunopeptidome from a Genomic Perspective: Establishing the Noncanonical Landscape of MHC Class I–Associated Peptides. Cancer immunology research, 11(6), 747-762.  https://doi.org/10.1158/2326-6066.cir-22-0621
  7. Gasser H., Bedran G., Bo R., Goodlett D. , Alfaro JA* , Rajan A.* Interpreting BERT architecture predictions for peptide presentation by MHC class I proteins In NeurIPS Workshop 2021, eXplainable AI approaches for debugging and diagnosis.
  8. Padariya, M., Sznarkowska, A., Kote, S., Gómez-Herranz, M.; Mikac, S.; Pilch, M.; Alfaro, J.; Fahraeus, R.; Hupp, T.; Kalathiya, U. Functional Interfaces, Biological Pathways, and Regulations of Interferon-Related DNA Damage Resistance Signature (IRDS) Genes. Biomolecules 2021, 11, 622.
  9. Kalathiya, U., Padariya, M., Faktor, J., Coyaud, E., Alfaro, J. A., Fahraeus, R., … & Goodlett, D. R. (2021). Interfaces with structure dynamics of the workhorses from cells revealed through cross-linking mass spectrometry (CLMS). Biomolecules, 11(3), 382.
  10. Alfaro, J.A., Bohländer, P., Dai, M. et al. The emerging landscape of single-molecule protein sequencing technologies. Nat Methods 18, 604–617 (2021). https://doi.org/10.1038/s41592-021-01143-1   (5-year impact: 34.975)
  11. Weke, K., Singh, A., Uwugiaren, N., Alfaro, J. A., Wang, T., Hupp, T. R., … & Dapic, I. (2021). MicroPOTS Analysis of Barrett’s Esophageal Cell Line Models Identifies Proteomic Changes after Physiologic and Radiation Stress. Journal of Proteome Research.​​​​​​​
  12. Kalathiya U., Padariya M., Mayordomo M., Lisowska M.,Nicholson J, Singh A.,Baginski M.,Fahraeus R.,Carragher N., Ball K., Haas J., Daniels A.,Hupp T.R., Alfaro JA. (2020). Highly Conserved Homotrimer Cavity Formed by the SARS-CoV-2 Spike Glycoprotein: A Novel Binding Site. Journal of Clinical Medicine, 9(5), 1473.
  13. Very quickly at the beginning of the pandemic (Late-January 2020), I initiated a project into understanding how currently available drugs could be re-purposed to treat the disease. The result was the discovery of a novel binding site against the Spike protein alongside a panel of inhibitors that we are currently testing in the laboratory. 
  14. Padariya M., Kalathiya U., Houston D., & Alfaro JA. (2020) Recognition dynamics of cancer mutations on the ERp57-tapasin interface.
  15. Pawlicka, K., Kalathiya, U., Alfaro, JA (2020) Nonsense-mediated mRNA decay: pathologies and the potential for novel therapeutics. Cancers.12(3), 765.
  16. Kalathiya U, Padariya M, Pawlicka K, Hupp T,  Verma C , Houston D , Alfaro JA. (2019) Structural consequences of cancer mutations at the UPF2 and ATP-binding site of NMD factor UPF1. (2019) Scientific Reports. 20: 5644.
  17. Sinha A, Huang V, Livingstone J, Wang J, Fox NS, Kurganovs N, Ignatchenko V, Fritsch K, Donmez N, Heisler LE, Shiah YJ, Yao CQ, Alfaro JA, Volik S, Lapuk A, Fraser M, Kron K, Murison A, Lupien M, Sahinalp C, Collins CC, Tetu B, Masoomian M, Berman DM, van der Kwast T, Bristow RG, Kislinger T, Boutros PC. (2019) Cancer Cell.; 35(3):414-427.e6.
  18. Sinha, A., Principe, S., Alfaro, JA, Ignatchenko, A., Ignatchenko, V., & Kislinger, T. (2018) Proteomic profiling of secreted proteins, exosomes, and microvesicles in cell culture conditioned media. In The Surfaceome (pp. 91-102). Humana Press, New York, NY.
  19. Alfaro JA, Ignatchenko A, Ignatchenko V, Sinha A, Boutros PC and Kislinger T. (2017) Detecting protein variants by mass-spectrometry: A comprehensive study in cancer cell-lines. Genome Medicine. 9:62. (DOI: 10.1186/s13073-017-0454-9) Cancers.12(3), 737.
  20. Sinha A, Alfaro JA, and Kislinger T. (2017) Characterization of protein content present in exosomes isolated from conditioned media and urine. Current Protocols in Protein Science. 87:24.9.1-24.9.12..
  21. Alfaro JA, Sinha A, Kislinger T and Boutros PC. (2014) Onco-proteogenomics: cancer proteomics joins forces with genomics.  Nature Methods. 11(11):1107-13.
  22. A perspective on variant calling within  mass-spectrometry datasets highlighting the potential for the field of proteogenomics.
  23. Weinreb I, Piscuoglio S, Martelotto LG, Waggott D, Ng CK, Perez-Ordonez B, Harding NJ, Alfaro JA, et al. (2014) Hotspot activating PRKD1 somatic mutations in polymorphous low-grade adenocarcinomas of the salivary glands. Nature Genetics. 46(11):1166-9.
  24. Planello AC, Ji J, Sharma V, Singhania R, Mbabaali F, Müller F, Alfaro JA, Bock C, De Carvalho DD and Batada NN. (2014) Aberrant DNA methylation reprogramming during induced pluripotent stem cell generation is dependent on the choice of reprogramming factors. Cell Regeneration. 3(1):1.
  25. Johal AR, Blackler RJ, Alfaro JA, Schuman B, Borisova S and Evans SV. (2014) pH-induced conformational changes in human ABO(H) blood group glycosyltransferases confirm the importance of electrostatic interactions in the formation of the semi-closed state. Glycobiology. 24(3):237-46.
  26. Johal AR, Schuman B, Alfaro JA, Borisova S, Seto NOL and Evans SV. (2012) Sequence-dependent effects of cryoprotectants on the active sites of the human ABO(H) blood group A and B glycosyltransferases. Acta Cryst. D68, 268–276.
  27. Alfaro JA, Zheng RB, Persson M, Letts JA, Polakowski R, Bai Y, Borisova SN, Seto NO, Lowary TL, Palcic MM and Evans SV. (2008) ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes.  J Biol Chem. 283(15):10097-10108.
  28. Schuman, B., Alfaro, J.A., Evans, S.V. (2006). Glycosyltransferase Structure and Function. In: Peters, T. (eds) Bioactive Conformation I. Topics in Current Chemistry, vol 272. Springer, Berlin, Heidelberg .