Browsing by Author "Gonzalez-Perez, Abel"

Sort by: Order: Results:

  • Analyses of non-coding somatic drivers in 2,658 cancer whole genomes
    Rheinbay, Esther; Sabarinathan, Radhakrishnan; Mularoni, Loris; Gonzalez-Perez, Abel; Pich, Oriol; Tamborero Noguera, David; López Bigas, Núria; Getz, Gad; PCAWG Consortium (Nature Research, 2020)
    The discovery of drivers of cancer has traditionally focused on protein-coding genes1-4. Here we present analyses of driver point mutations and structural variants in non-coding regions across 2,658 genomes from the ...
  • DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
    Bonet, Jose; Chen, Mandi; Dabad, Marc; Heath, Simon; Gonzalez-Perez, Abel; López Bigas, Núria; Lagergren, Jens (Oxford University Press, 2021)
    Motivation: DNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational ...
  • High p16 expression and heterozygous RB1 loss are biomarkers for CDK4/6 inhibitor resistance in ER+ breast cancer
    Palafox, Marta; Gonzalez-Perez, Abel; Arribas, Joaquín; López Bigas, Núria; Serra, Violeta (Nature Research, 2022)
    CDK4/6 inhibitors combined with endocrine therapy have demonstrated higher antitumor activity than endocrine therapy alone for the treatment of advanced estrogen receptor-positive breast cancer. Some of these tumors are ...
  • LOXL2-mediated H3K4 oxidation reduces chromatin accessibility in triple-negative breast cancer cells
    Cebrià i Costa, Joan Pau, 1989-; Pascual-Reguant, Laura; Gonzalez-Perez, Abel; Serra Bardenys, Gemma, 1992-; Querol, J.; Cosín, M.; Verde, Gaetano; Cigliano, Riccardo Aiese; Sanseverino, Walter; Segura-Bayona, Sandra; Iturbide Martínez de Albéniz, Ane, 1989-; Andreu Martínez, David; Nuciforo, Paolo G.; Bernado-Morales, C.; Rodilla, Verónica; Arribas, Joaquín; Yélamos López, José; García de Herreros, Antonio; Stracker, Travis; Peiró Sales, Sandra (Nature Research, 2020)
    Oxidation of H3 at lysine 4 (H3K4ox) by lysyl oxidase-like 2 (LOXL2) generates an H3 modification with an unknown physiological function. We find that LOXL2 and H3K4ox are higher in triple-negative breast cancer (TNBC) ...
  • Network, transcriptomic and genomic features differentiate genes relevant for drug response
    Piñero González, Janet, 1977-; Gonzalez-Perez, Abel; Guney, Emre; Aguirre Plans, Joaquim, 1993-; Sanz, Ferran; Oliva Miguel, Baldomero; Furlong, Laura I., 1971- (Frontiers, 2018)
    Understanding the mechanisms underlying drug therapeutic action and toxicity is crucial for the prevention and management of drug adverse reactions, and paves the way for a more efficient and rational drug design. The ...
  • Nucleotide excision repair is impaired by binding of transcription factors to DNA
    Sabarinathan, Radhakrishnan; Mularoni, Loris; Deu-Pons, Jordi; Gonzalez-Perez, Abel; López Bigas, Núria (Nature Publishing Group, 2016)
    Somatic mutations are the driving force of cancer genome evolution. The rate of somatic mutations appears to be greatly variable across the genome due to variations in chromatin organization, DNA accessibility and replication ...
  • Pan-cancer analysis of whole genomes
    ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium; Demidov, German, 1990-; Drechsel, Oliver; Ossowski, Stephan; Estivill, Xavier, 1955-; Escaramís, Geòrgia; Bosio, Mattia; Holik, Aliaksei Z.; Sušak, Hana, 1985-; Rabionet, Raquel; Stobbe, Miranda D.; Marquès i Bonet, Tomàs, 1975-; Navarro i Cuartiellas, Arcadi, 1969-; Gut, Ivo Glynne; Beltran, Sergi; Gut, Marta; Trotta, Jean-Remi; Whalley, Justin P.; Heath, Simon; Prasad, Aparna; Heredia Genestar, José María, 1985-; Sabarinathan, Radhakrishnan; Pich, Oriol; Gonzalez-Perez, Abel; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David; Mularoni, Loris; Deu-Pons, Jordi; Muiños, Ferran; Muyas Remolar, Francesc, 1992- (Nature Research, 2020)
    Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale . Here we report the integrative analysis of 2,658 ...
  • Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes
    Leiserson, Mark D.M.; Vandin, Fabio; Wu, Hsin-Ta; Dobson, Jason R.; Eldridge, Jonathan V.; Thomas, Jacob L.; Papoutsaki, Alexandra; Kim, Younhun; Niu, Beifang; McLellan, Michael; Lawrence, Michael S.; Gonzalez-Perez, Abel; Tamborero Noguera, David; Cheng, Yuwei; Ryslik, Gregory A.; López Bigas, Núria; Getz, Gad; Ding, Li; Raphael, Benjamin J. (Nature Research, 2015)
    Cancers exhibit extensive mutational heterogeneity, and the resulting long-tail phenomenon complicates the discovery of genes and pathways that are significantly mutated in cancer. We perform a pan-cancer analysis of mutated ...
  • Pathway and network analysis of cancer genomes
    Creixell, Pau; Gonzalez-Perez, Abel; López Bigas, Núria; Mutation Consequences and Pathway Analysis Working Group of the International Cancer Genome Consortium (Nature Research, 2015)
    Genomic information on tumors from 50 cancer types cataloged by the International Cancer Genome Consortium (ICGC) shows that only a few well-studied driver genes are frequently mutated, in contrast to many infrequently ...
  • Reduced mutation rate in exons due to differential mismatch repair
    Frigola, Joan; Sabarinathan, Radhakrishnan; Mularoni, Loris; Muiños, Ferran; Gonzalez-Perez, Abel; López Bigas, Núria (Nature Publishing Group, 2017)
    While recent studies have identified higher than anticipated heterogeneity of mutation rate across genomic regions, mutations in exons and introns are assumed to be generated at the same rate. Here we find fewer somatic ...
  • Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples
    Bailey, Matthew H.; Drechsel, Oliver; Gut, Ivo Glynne; Ossowski, Stephan; Stobbe, Miranda D.; Gonzalez-Perez, Abel; PCAWG Consortium (Nature Research, 2020)
    The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part ...
  • Sex differences in oncogenic mutational processes
    Li, Constance H.; Stobbe, Miranda D.; Déu Pons, Jordi; Gonzalez-Perez, Abel; Muiños, Ferran; Mularoni, Loris; Pich Roselló, Oriol, 1992-; Rubio Pérez, Carlota, 1990-; Sabarinathan, Radhakrishnan; Tamborero Noguera, David; Heredia Genestar, José María, 1985-; Marquès i Bonet, Tomàs, 1975-; Navarro i Cuartiellas, Arcadi, 1969-; Bosio, Mattia; Demidov, German, 1990-; Drechsel, Oliver; Escaramís, Geòrgia; Estivill, Xavier, 1955-; Holik, Aliaksei Z.; Muyas Remolar, Francesc, 1992-; Ossowski, Stephan; Rabionet, Raquel; Sušak, Hana, 1985-; PCAWG Consortium (Nature Research, 2020)
    Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features ...