Browsing by Author "Mularoni, Loris"

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  • 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 ...
  • 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 ...
  • Comparative genomics of amino acid tandem repeats
    Mularoni, Loris (Universitat Pompeu Fabra, 2009-07-28)
    Tandem amino acid repeats, also known as homopolimeric tract or homopeptides, are very common features of eukaryotic genomes and are present in nearly one-fifth of human encoded proteins. These structures have attracted ...
  • Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features
    Lanzos Camaioni, Andrés Arturo; Carlevaro-Fita, Joana; Mularoni, Loris; Reverter, Ferran; Palumbo, Emilio; Guigó Serra, Roderic; Johnson, Rory (Nature Publishing Group, 2017)
    Long noncoding RNAs (lncRNAs) represent a vast unexplored genetic space that may hold missing drivers of tumourigenesis, but few such “driver lncRNAs” are known. Until now, they have been discovered through changes in ...
  • Integrative pathway enrichment analysis of multivariate omics data
    Paczkowska, Marta; Barenboim, Jonathan; Sintupisut, Nardnisa; Fox, Natalie S.; Zhu, Helen; Abd-Rabbo, Diala; Mee, Miles W.; Boutros, Paul C.; PCAWG Drivers and Functional Interpretation Working Group; Reimand, Jüri; PCAWG Consortium; Deu-Pons, Jordi; González Pérez, Abel; Gut, Ivo Glynne; Muiños, Ferran; Mularoni, Loris; Pich, Oriol; Rubio Pérez, Carlota; Sabarinathan, Radhakrishnan; Tamborero Noguera, David (Nature Research, 2020)
    Multi-omics datasets represent distinct aspects of the central dogma of molecular biology. Such high-dimensional molecular profiles pose challenges to data interpretation and hypothesis generation. ActivePathways is an ...
  • Mutation patterns of amino acid tandem repeats in the human proteome
    Mularoni, Loris; Guigó Serra, Roderic; Albà Soler, Mar (BioMed Central, 2006)
    Background: Amino acid tandem repeats are found in nearly one-fifth of human proteins. Abnormal expansion of these regions is associated with several human disorders. To gain further insight into the mutational mechanisms ...
  • 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 ...
  • OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers
    Arnedo Pac, Claudia; Mularoni, Loris; Muiños, Ferran; González Pérez, Abel; López Bigas, Núria (Oxford University Press, 2019)
    Motivation: Identification of the genomic alterations driving tumorigenesis is one of the main goals in oncogenomics research. Given the evolutionary principles of cancer development, computational methods that detect ...
  • OncodriveFML
    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, ...
  • OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations
    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 ...
  • 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 ...
  • 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 ...
  • 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 evolution of relapse of adult T cell acute lymphoblastic leukemia
    Sentís, Inés; González, Santi; Genescà, Eulalia; García Hernández, Violeta; Muiños, Ferran; González, Celia; López Arribillaga, Erika, 1986-; González, Jessica; Fernández-Ibarrondo, Lierni; Mularoni, Loris; Espinosa-Anke, Luis; Bellosillo Paricio, Beatriz; Ribera, Josep Maria; Bigas Salvans, Anna; González Pérez, Abel; López Bigas, Núria (BioMed Central, 2020)
    Background: Adult T cell acute lymphoblastic leukemia (T-ALL) is a rare disease that affects less than 10 individuals in one million. It has been less studied than its cognate pediatric malignancy, which is more prevalent. ...
  • The Pancreatic Islet Regulome Browser
    Mularoni, Loris; Ramos-Rodríguez, Mireia; Pasquali, Lorenzo (Frontiers, 2017)
    The pancreatic islet is a highly specialized tissue embedded in the exocrine pancreas whose primary function is that of controlling glucose homeostasis. Thus, understanding the transcriptional control of islet-cell may ...