Browsing by Author "González-Pérez, Abel"

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  • Tamborero Noguera, David; López Bigas, Núria; González-Pérez, Abel (Public Library of Science (PLoS), 2013)
    A well-established approach for detecting genes involved in tumorigenesis due to copy number alterations (CNAs) is to assess the recurrence of the alteration across multiple samples. Expression data can be used to filter ...
  • Tamborero Noguera, David; González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2015-11)
    OncodriveCLUST is a method aimed to identify genes whose mutations are biased towards a large spatial clustering. This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often ...
  • González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2015-10)
    OncodriveFM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).This novel approach ...
  • Mularoni, Loris; Sabarinathan, Radhakrishnan; González-Pérez, Abel; López Bigas, Núria; Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-06-06)
    Method to identify genomic regions, both coding and non-coding, bearing mutations with significant shift towards high functional impact across a cohort of tumos (FMbias), which are candidates to function as cancer drivers, ...
  • Mularoni, Loris; Sabarinathan, Radhakrishnan; Déu Pons, Jordi; González-Pérez, Abel; López Bigas, Núria (BioMed Central, 2016)
    Distinguishing the driver mutations from somatic mutations in a tumor genome is one of the major challenges of cancer research. This challenge is more acute and far from solved for non-coding mutations. Here we present ...
  • Tamborero Noguera, David; Rubio Pérez, Carlota; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets, Ignasi; Albanell Mestres, Joan; Rodon, Jordi; Tabernero Cartula, Josep; Dienstman, Rodrigo; González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2016-01)
    Bioinformatics method to identify individual driver mutations.
  • Schroeder, Michael Philipp, 1986-; Rubio Pérez, Carlota; Tamborero Noguera, David; González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2014-06)
    Machine-learning based approach to classify cancer driver genes into to Activating or Loss of Function roles for cancer gene development.
  • 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 ...
  • Tamborero Noguera, David; López Bigas, Núria; González-Pérez, Abel; Rubio Pérez, Carlota; Déu Pons, Jordi (Universitat Pompeu Fabra, 2016-10-16)
    A tool aimed at the rational design of cancer gene panels. It estimates the cost-effectiveness of the designed panel on a cohort of tumors and provides reports on the importance of individual mutations for tumorigenesis ...
  • Ng, Sam; Collisson, Eric A.; Sokolov, Artem; Goldstein, Theodore; González-Pérez, Abel; López Bigas, Núria; Benz, Christopher; Haussler, David; Stuart, Joshua M. (Oxford University Press, 2012)
    MOTIVATION: A current challenge in understanding cancer processes is to pinpoint which mutations influence the onset and progression of disease. Toward this goal, we describe a method called PARADIGM-SHIFT that can predict ...
  • 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 ...
  • Tamborero Noguera, David; Rubio Pérez, Carlota; Déu Pons, Jordi; Schroeder, Michael Philipp, 1986-; Vivancos Prellezo, Ana; Rovira Guerín, Ana; Tusquets, Ignasi; Albanell Mestres, Joan; Rodon, Jordi; Tabernero Cartula, Josep; Dienstman, Rodrigo; González-Pérez, Abel; López Bigas, Núria (Universitat Pompeu Fabra, 2016-10)
    CGI drug prescription assigns targeted drugs to a tumor, based on its genomic alterations, according different levels of evidence (from pre-clinical assays to clinical guidelines).
  • Ferreira, Pedro G.; González-Pérez, Abel; Knowles, David G.; Monlong, Jean; Johnson, Rory; Djebali, Sarah; Papasaikas, Panagiotis; Tamborero Noguera, David; Gouin, Anaïs; López Bigas, Núria; Guigó Serra, Roderic (Cold Spring Harbor Laboratory Press (CSHL Press), 2014)
    Chronic lymphocytic leukemia (CLL) has heterogeneous clinical and biological behavior. Whole-genome and -exome sequencing has contributed to the characterization of the mutational spectrum of the disease, but the underlying ...
  • Piñero González, Janet, 1977-; Berenstein, Ariel José; González-Pérez, Abel; Chernomoretz, Ariel; Furlong, Laura I., 1971- (Nature Publishing group, 2016)
    Characterizing the behavior of disease genes in the context of biological networks has the potential to shed light on disease mechanisms, and to reveal both new candidate disease genes and therapeutic targets. Previous ...
  • Schroeder, Michael Philipp, 1986-; González-Pérez, Abel; López Bigas, Núria (BioMed Central, 2013)
    Cancer genomics projects employ high-throughput technologies to identify the complete catalog of somatic alterations that characterize the genome, transcriptome and epigenome of cohorts of tumor samples. Examples include ...