Browsing by Author "Rubio Pérez, Carlota, 1990-"

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  • Cancer Genome Interpreter annotates the biological and clinical relevance of tumor alterations
    Tamborero Noguera, David; Rubio Pérez, Carlota, 1990-; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets Trias de Bes, Ignacio; Albanell Mestres, Joan; Rodon, Jordi; Tabernero Cartula, Josep; Torres, Carmen de; Dienstmann, Rodrigo; González-Pérez, Abel; López Bigas, Núria (BioMed Central, 2018)
    While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Interpreter, a ...
  • Combined burden and functional impact tests for cancer driver discovery using DriverPower
    Shuai, Shimin; PCAWG Drivers and Functional Interpretation Working Group; Gallinger, Steven; Stein, Lincoln D.; PCAWG Consortium; Deu-Pons, Jordi; Gut, Ivo Glynne; Muiños, Ferran; Mularoni, Loris; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David (Nature Research, 2020)
    The discovery of driver mutations is one of the key motivations for cancer genome sequencing. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing ...
  • Genetic and functional characterization of disease associations explains comorbidity
    Rubio Pérez, Carlota, 1990-; Güney, Emre, 1983-; Aguilar, Daniel; Piñero González, Janet, 1977-; García-García, Javier, 1982-; Iadarola, Barbara; Sanz, Ferran; Fernández Fuentes, Narcís; Furlong, Laura I., 1971-; Oliva Miguel, Baldomero (Nature Publishing Group, 2017)
    Understanding relationships between diseases, such as comorbidities, has important socio-economic implications, ranging from clinical study design to health care planning. Most studies characterize disease comorbidity using ...
  • In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities
    Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David; Schroeder, Michael Philipp, 1986-; Antolín Hernández, Albert, 1984-; Déu Pons, Jordi; Pérez Llamas, Christian, 1976-; Mestres i López, Jordi; González-Pérez, Abel; López Bigas, Núria (Elsevier, 2015)
    Large efforts dedicated to detect somatic alterations across tumor genomes/exomes are expected to produce significant improvements in precision cancer medicine. However, high inter-tumor heterogeneity is a major obstacle ...
  • Independent component analysis uncovers the landscape of the bladder tumor transcriptome and reveals insights into luminal and basal subtypes
    Biton, Anne; Bernard-Pierrot, Isabelle; Lou, Yinjun; Krucker, Clémentine; Chapeaublanc, Elodie; Rubio Pérez, Carlota, 1990-; López Bigas, Núria; Kamoun, Aurélie; Neuzillet, Yann; Gestraud, Pierre; Grieco, Luca; Rebouissou, Sandra; deReyniès, Aurélien; Benhamou, Simone; Lebret, Thierry; Southgate, Jennifer; Barillot, Emmanuel; Allory, Yves; Zinovyev, Andrei; Radvanyi, François (Elsevier, 2014)
    Extracting relevant information from large-scale data offers unprecedented opportunities in cancerology. We applied independent component analysis (ICA) to bladder cancer transcriptome data sets and interpreted the components ...
  • Integrating genomic alterations in diffuse large B-cell lymphoma identifies new relevant pathways and potential therapeutic targets
    Karube, Kennosuke; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David; Salar Silvestre, Antonio; Colomo Saperas, Luis Alberto; López Bigas, Núria; Miyoshi, Hiroaki (Nature Publishing Group, 2018)
    Genome studies of diffuse large B-cell lymphoma (DLBCL) have revealed a large number of somatic mutations and structural alterations. However, the clinical significance of these alterations is still not well defined. In ...
  • OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action
    Schroeder, Michael Philipp, 1986-; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David; González-Pérez, Abel; López Bigas, Núria (Oxford University Press, 2014)
    MOTIVATION: Several computational methods have been developed to identify cancer drivers genes-genes responsible for cancer development upon specific alterations. These alterations can cause the loss of function (LoF) of ...
  • 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 ...
  • Pathway and network analysis of more than 2500 whole cancer genomes
    Reyna, Matthew A.; Haan, David; Paczkowska, Marta; Verbeke, Lieven P.C.; Vazquez, Miguel; Kahraman, Abdullah; Pulido-Tamayo, Sergio; Barenboim, Jonathan; Wadi, Lina; Dhingra, Priyanka; Shrestha, Raunak; Getz, Gad; Lawrence, Michael S.; Pedersen, Jackob S.; Rubin, Mark A.; Wheeler, David A.; Brunak, Søren; Izarzugaza, Jose M.G.; PCAWG Drivers and Functional Interpretation Working Group; PCAWG Consortium; Deu-Pons, Jordi; Gut, Ivo Glynne; Muiños, Ferran; Mularoni, Loris; Rubio Pérez, Carlota, 1990-; Tamborero Noguera, David (Nature Research, 2020)
    The catalog of cancer driver mutations in protein-coding genes has greatly expanded in the past decade. However, non-coding cancer driver mutations are less well-characterized and only a handful of recurrent non-coding ...
  • Rational design of cancer gene panels with OncoPaD
    Rubio Pérez, Carlota, 1990-; Déu Pons, Jordi; Tamborero Noguera, David; López Bigas, Núria; González-Pérez, Abel (BioMed Central, 2016)
    BACKGROUND: Profiling the somatic mutations of genes which may inform about tumor evolution, prognostics and treatment is becoming a standard tool in clinical oncology. Commercially available cancer gene panels rely on ...
  • 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 ...
  • The DYRK family of kinases in cancer: molecular functions and therapeutic opportunities
    Boni, Jacopo, 1987-; Rubio Pérez, Carlota, 1990-; López Bigas, Núria; Fillat i Fonts, Cristina; Luna, Susana de la (MDPI, 2020)
    DYRK (dual-specificity tyrosine-regulated kinases) are an evolutionary conserved family of protein kinases with members from yeast to humans. In humans, DYRKs are pleiotropic factors that phosphorylate a broad set of ...

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