Arnedo-Pac, C., Lopez-Bigas, N., & Muiños, F. (2021). Predicting disease variants using biodiversity and machine learning. Nature Biotechnology. https://doi.org/10.1038/s41587-021-01187-w

Peri, A., Greenstein, E., Alon, M., Pai, J. A., Dingjan, T., Reich-Zeliger, S., Barnea, E., Barbolin, C., Levy, R., Arnedo-Pac, C., Kalaora, S., Dassa, B., Feldmesser, E., Shang, P., Greenberg, P., Levin, Y., Benedek, G., Levesque, M. P., Adams, D. J., … Samuels, Y. (2021). Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma. The Journal of Clinical Investigation, 131(20), e129466. https://doi.org/10.1172/JCI129466

Bonet, J., Chen, M., Dabad, M., Heath, S., Gonzalez-Perez, A., Lopez-Bigas, N., & Lagergren, J. (2021). DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinformatics (Oxford, England), btab745. https://doi.org/10.1093/bioinformatics/btab745

Zhang, T., Joubert, P., Ansari-Pour, N., Zhao, W., Hoang, P. H., Lokanga, R., Moye, A. L., Rosenbaum, J., Gonzalez-Perez, A., Martínez-Jiménez, F., Castro, A., Muscarella, L. A., Hofman, P., Consonni, D., Pesatori, A. C., Kebede, M., Li, M., Gould Rothberg, B. E., Peneva, I., … Landi, M. T. (2021). Genomic and evolutionary classification of lung cancer in never smokers. Nature Genetics, 53(9), 1348–1359. https://doi.org/10.1038/s41588-021-00920-0

González-Gil, C., Morgades, M., Lopes, T., Fuster-Tormo, F., García-Chica, J., Zhao, R., Montesinos, P., Torrent, A., Diaz-Beya, M., Coll, R., Hermosín, L., Mercadal, S., González-Campos, J., Zamora, L., Artola, T., Vall-Llovera, F., Tormo, M., Gil-Cortés, C., Barba, P., … Genescà, E. (2023). Genomics improves risk stratification of adults with T-cell acute lymphoblastic leukemia enrolled in measurable residual disease-oriented trials. Haematologica, 108(4), 969. https://doi.org/10.3324/haematol.2022.281196 Cite

Gonzalez, S., Lopez-Bigas, N., & Gonzalez-Perez, A. (2023). Copy number footprints of platinum-based anticancer therapies. PLoS Genetics, 19(2), e1010634. https://doi.org/10.1371/journal.pgen.1010634 Cite

Mangiante, L., Alcala, N., Sexton-Oates, A., Di Genova, A., Gonzalez-Perez, A., Khandekar, A., Bergstrom, E. N., Kim, J., Liu, X., Blazquez-Encinas, R., Giacobi, C., Le Stang, N., Boyault, S., Cuenin, C., Tabone-Eglinger, S., Damiola, F., Voegele, C., Ardin, M., Michallet, M.-C., … Fernandez-Cuesta, L. (2023). Multiomic analysis of malignant pleural mesothelioma identifies molecular axes and specialized tumor profiles driving intertumor heterogeneity. Nature Genetics, 55(4), 607. https://doi.org/10.1038/s41588-023-01321-1 Cite

Bonet, J., Chen, M., Dabad, M., Heath, S., Gonzalez-Perez, A., Lopez-Bigas, N., & Lagergren, J. (2022). DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data. Bioinformatics (Oxford, England), 38(5), 1235. https://doi.org/10.1093/bioinformatics/btab745 Cite

Arnedo-Pac, C., Lopez-Bigas, N., & Muiños, F. (2022). Predicting disease variants using biodiversity and machine learning. Nature Biotechnology, 40(1), 27. https://doi.org/10.1038/s41587-021-01187-w Cite

Pich, O., Reyes-Salazar, I., Gonzalez-Perez, A., & Lopez-Bigas, N. (2022). Discovering the drivers of clonal hematopoiesis. Nature Communications, 13(1), 4267. https://doi.org/10.1038/s41467-022-31878-0 Cite

Nadeu, F., Royo, R., Massoni-Badosa, R., Playa-Albinyana, H., Garcia-Torre, B., Duran-Ferrer, M., Dawson, K. J., Kulis, M., Diaz-Navarro, A., Villamor, N., Melero, J. L., Chapaprieta, V., Dueso-Barroso, A., Delgado, J., Moia, R., Ruiz-Gil, S., Marchese, D., Giró, A., Verdaguer-Dot, N., … Campo, E. (2022). Detection of early seeding of Richter transformation in chronic lymphocytic leukemia. Nature Medicine, 28(8), 1662. https://doi.org/10.1038/s41591-022-01927-8 Cite

Palafox, M., Monserrat, L., Bellet, M., Villacampa, G., Gonzalez-Perez, A., Oliveira, M., Brasó-Maristany, F., Ibrahimi, N., Kannan, S., Mina, L., Herrera-Abreu, M. T., Òdena, A., Sánchez-Guixé, M., Capelán, M., Azaro, A., Bruna, A., Rodríguez, O., Guzmán, M., Grueso, J., … Serra, V. (2022). High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER. Nature Communications, 13(1), 5258. https://doi.org/10.1038/s41467-022-32828-6 Cite

Stobbe, M. D., Gonzalez-Perez, A., Lopez-Bigas, N., & Gut, I. G. (2022). Ten simple rules for a successful international consortium in big data omics. PLoS Computational Biology, 18(10), e1010546. https://doi.org/10.1371/journal.pcbi.1010546 Cite

Frigola, J., Sabarinathan, R., Gonzalez-Perez, A., & Lopez-Bigas, N. (2021). Variable interplay of UV-induced DNA damage and repair at transcription factor binding sites. Nucleic Acids Research, 49(2), 891. https://doi.org/10.1093/nar/gkaa1219 Cite

Aissa, A. F., Islam, A. B. M. M. K., Ariss, M. M., Go, C. C., Rader, A. E., Conrardy, R. D., Gajda, A. M., Rubio-Perez, C., Valyi-Nagy, K., Pasquinelli, M., Feldman, L. E., Green, S. J., Lopez-Bigas, N., Frolov, M. V., & Benevolenskaya, E. V. (2021). Single-cell transcriptional changes associated with drug tolerance and response to combination therapies in cancer. Nature Communications, 12(1), 1628. https://doi.org/10.1038/s41467-021-21884-z Cite

Woolston, A., Barber, L. J., Griffiths, B., Pich, O., Lopez-Bigas, N., Matthews, N., Rao, S., Watkins, D., Chau, I., Starling, N., Cunningham, D., & Gerlinger, M. (2021). Mutational signatures impact the evolution of anti-EGFR antibody resistance in colorectal cancer. Nature Ecology & Evolution, 5(7), 1024. https://doi.org/10.1038/s41559-021-01470-8 Cite

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

Pich, O., Cortes-Bullich, A., Muiños, F., Pratcorona, M., Gonzalez-Perez, A., & Lopez-Bigas, N. (2021). The evolution of hematopoietic cells under cancer therapy. Nature Communications, 12(1), 4803. https://doi.org/10.1038/s41467-021-24858-3 Cite

Zhang, T., Joubert, P., Ansari-Pour, N., Zhao, W., Hoang, P. H., Lokanga, R., Moye, A. L., Rosenbaum, J., Gonzalez-Perez, A., Martínez-Jiménez, F., Castro, A., Muscarella, L. A., Hofman, P., Consonni, D., Pesatori, A. C., Kebede, M., Li, M., Gould Rothberg, B. E., Peneva, I., … Landi, M. T. (2021). Genomic and evolutionary classification of lung cancer in never smokers. Nature Genetics, 53(9), 1348. https://doi.org/10.1038/s41588-021-00920-0 Cite

Peri, A., Greenstein, E., Alon, M., Pai, J. A., Dingjan, T., Reich-Zeliger, S., Barnea, E., Barbolin, C., Levy, R., Arnedo-Pac, C., Kalaora, S., Dassa, B., Feldmesser, E., Shang, P., Greenberg, P., Levin, Y., Benedek, G., Levesque, M. P., Adams, D. J., … Samuels, Y. (2021). Combined presentation and immunogenicity analysis reveals a recurrent RAS.Q61K neoantigen in melanoma. The Journal of Clinical Investigation, 131(20). https://doi.org/10.1172/JCI129466 Cite

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

Borgsmüller, N., Bonet, J., Marass, F., Gonzalez-Perez, A., Lopez-Bigas, N., & Beerenwinkel, N. (2020). BnpC: Bayesian non-parametric clustering of single-cell mutation profiles. Bioinformatics (Oxford, England), 36(19), 4854. https://doi.org/10.1093/bioinformatics/btaa599 Cite

Boni, J., Rubio-Perez, C., López-Bigas, N., Fillat, C., & de la Luna, S. (2020). The DYRK Family of Kinases in Cancer: Molecular Functions and Therapeutic Opportunities. Cancers, 12(8). https://doi.org/10.3390/cancers12082106 Cite

Martínez-Jiménez, F., Muiños, F., Sentís, I., Deu-Pons, J., Reyes-Salazar, I., Arnedo-Pac, C., Mularoni, L., Pich, O., Bonet, J., Kranas, H., Gonzalez-Perez, A., & Lopez-Bigas, N. (2020). A compendium of mutational cancer driver genes. Nature Reviews. Cancer, 20(10), 555. https://doi.org/10.1038/s41568-020-0290-x Cite