Publications | Comp Immuno

top of page

Lab's main publications

2025

Usset J, de Ligt J, Roerink S, Roepman P, Cuppen E, Martínez-Jiménez F. Systematic identification of genomic non-response biomarkers to cancer therapies. bioRxiv preprint. 2025. doi: https://doi.org/10.1101/2025.10.06.680777

Gumpert N, Sagie S, Arnedo-Pac C, Babu T, Weller C, Gonzalez-Perez A, Wang Y, Michel Todó L, Levy R, Chen X, Greenberg P, Dayan-Rubinov M, Yakubovich E, Wasserman-Bartov T, Zerbib M, Gong J, Rebernick RJ, Oliveira Tercero A, Agundez Muriel L, Benedek G, Kedmi M, Oren R, Ben-Dor S, Levin Y, Troyanskaya OG, Munzur AD, Wyatt AW, Cieslik MP, Quigley DA, Van Allen EM, Anandasabapathy N, Mateo J, Yang X, Martínez-Jiménez F, Lopez-Bigas N, Samuels Y. Recurrent immunogenic neoantigens and their cognate T-cell receptors in treatment-resistant metastatic prostate cancer. Cancer Discov. 2025 Oct 8. doi: 10.1158/2159-8290.CD-24-1213. Epub ahead of print. PMID: 41056506.

2024

Martínez-Jiménez F*, Chowell D*. Genetic immune escape in cancer: timing and implications for treatment. Trends in Cancer. 2024. doi: 10.1016/j.trecan.2024.11.002

Usset J, Rosendahl Huber A, Andrianova MA, Batlle E, Carles J, Cuppen E, Elez E, Felip E, Gómez-Rey M, Lo Giacco D, Martinez-Jimenez F, Muñoz-Couselo E, Siu LL, Tabernero J, Vivancos A, Muiños F, Gonzalez-Perez A, Lopez-Bigas N. Five latent factors underlie response to immunotherapy. Nat Genet. 2024 Sep 12. doi: 10.1038/s41588-024-01899-0. Epub ahead of print. PMID: 39266764.

Marcos-Villar L, Perdiguero B, Anthiya S, Borrajo ML, Lou G, Franceschini L, Esteban I, Sánchez-Cordón PJ, Zamora C, Sorzano CÓS, Jordá L, Codó L, Gelpí JL, Sisteré-Oró M, Meyerhans A, Thielemans K, Martínez-Jiménez F, López-Bigas N, García F, Alonso MJ, Plana M, Esteban M, Gómez CE. Modulating the immune response to SARS-CoV-2 by different nanocarriers delivering an mRNA expressing trimeric RBD of the spike protein: COVARNA Consortium. NPJ Vaccines. 2024 Mar 6;9(1):53. doi: 10.1038/s41541-024-00838-8. Erratum in: NPJ Vaccines. 2024 May 18;9(1):84. doi: 10.1038/s41541-024-00882-4. PMID: 38448450; PMCID: PMC10918104.

Krishna, C., Tervi, A., Saffern, M., Wilson, E. A., Yoo, S. K., Mars, N., Roudko, V., Cho, B. A., Jones, S. E., Vaninov, N., Selvan, M. E., Gümüş, Z. H., FinnGen§, Lenz, T. L., Merad, M., Boffetta, P., Martínez-Jiménez, F., Ollila, H. M., Samstein, R. M., & Chowell, D. (2024). An immunogenetic basis for lung cancer risk. Science (New York, N.Y.), 383(6685), eadi3808. https://doi.org/10.1126/science.adi3808

2023

Martínez-Jiménez F*, Movasati A, Brunner SR, et al. Pan-cancer whole-genome comparison of primary and metastatic solid tumours. Nature. 2023;618(7964):333-341. doi:10.1038/s41586-023-06054-z

Martínez-Jiménez F*^, Priestley P*, Shale C, Baber J, Rozemuller E, Cuppen E. Genetic immune escape landscape in primary and metastatic cancer. Nature Genetics. 2023;55(5):820-831. doi:10.1038/s41588-023-01367-1

2022

Garcia-Prieto CA, Martínez-Jiménez F, Valencia A, Porta-Pardo E. Detection of oncogenic and clinically actionable mutations in cancer genomes critically depends on variant calling tools. Bioinformatics. 2022;38(12):3181-3191. doi:10.1093/bioinformatics/btac306

2021

Muiños F*, Martínez-Jiménez F*, Pich O, Gonzalez-Perez A, Lopez-Bigas N. In silico saturation mutagenesis of cancer genes. Nature. 2021;596(7872):428-432. doi:10.1038/s41586-021-03771-1

2020

Martínez-Jiménez F*, Muiños F, Sentís I,..., Lopez-Bigas N. A compendium of mutational cancer driver genes. Nature Rev Cancer. 2020 Oct;20(10):555-572. doi: 10.1038/s41568-020-0290-x

Martínez-Jiménez F*, Muiños F, López-Arribillaga E, Lopez-Bigas N, Gonzalez-Perez A. Systematic analysis of alterations in the ubiquitin proteolysis system reveals its contribution to driver mutations in cancer. Nature Cancer. 2020 Jan;1(1):122-135. doi: 10.1038/s43018-019-0001-2

<2020

Martínez-Jiménez F*, Overington JP, Al-Lazikani B, Marti-Renom MA^. Rational design of non-resistant targeted cancer therapies. Sci Rep. 2017 Apr 24;7:46632. doi: 10.1038/srep46632.

Martínez-Jiménez F*, Marti-Renom MA^. Ligand-target prediction by structural network biology using nAnnoLyze. PLoS Comput Biol. 2015 Mar 27;11(3):e1004157. doi: 10.1371/journal.pcbi.1004157

Martínez-Jiménez F*, Papadatos G*, Yang L*, ..., Brown JR^, Overington JP^, Marti-Renom MA^ (1/10). Target prediction for an open access set of compounds active against Mycobacterium tuberculosis. PLoS Comput Biol. 2013;9(10):e1003253. doi: 10.1371/journal.pcbi.1003253.

bottom of page