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Browsing Articles (Center for Genomic Regulation (CRG)) by Title

Browsing Articles (Center for Genomic Regulation (CRG)) by Title

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  • Laezza, Chiara; D'Alessandro, Alba; Di Croce, Luciano; Picardi, Paola; Ciaglia, Elena; Pisanti, Simona; Malfitano, Anna Maria; Comegna, Marika; Faraonio, Raffaella; Gazzerro, Patrizia; Bifulco, Maurizio (Nature Publishing Group, 2015)
    The mevalonate (MVA) pathway is an important metabolic pathway implicated in multiple aspects of tumorigenesis. In this study, we provided evidence that p53 induces the expression of a group of enzymes of the MVA pathway ...
  • Arnan Ros, Carme; Ullrich, Sebastian, 1984-; Pulido-Quetglas, Carlos; Nurtdinov, Ramil; Esteban, Alexandre; Blanco-Fernandez, Joan; Aparicio-Prat, Estel; Johnson, Rory; Pérez-Lluch, Sílvia; Guigó Serra, Roderic (BioMed Central, 2022)
    CRISPR-Cas9 screening libraries have arisen as a powerful tool to identify protein-coding (pc) and non-coding genes playing a role along different processes. In particular, the usage of a nuclease active Cas9 coupled to a ...
  • Pengo, Thomas; Holden, Seamus J.; Manley, Suliana (Oxford University Press, 2015)
    During the past decade, localization microscopy (LM) has transformed into an accessible, commercially/navailable technique for life sciences. However, data processing can be challenging to the non-specialist and care is ...
  • 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 ...
  • Rodríguez Martín, Bernardo; PCAWG Structural Variation Working Group; PCAWG Consortium; Ossowski, Stephan (Nature Research, 2020)
    About half of all cancers have somatic integrations of retrotransposons. Here, to characterize their role in oncogenesis, we analyzed the patterns and mechanisms of somatic retrotransposition in 2,954 cancer genomes from ...
  • Miguel Escalada, Irene; Maestro, Miguel Ángel; Balboa, Diego; Elek, Anamaria; Bernal, Aina; Bernardo, Edgar; Grau, Vanessa; García-Hurtado, Javier; Sebé-Pedrós, Arnau; Ferrer, Jorge (Elsevier, 2022)
    Sequence variants in cis-acting enhancers are important for polygenic disease, but their role in Mendelian disease is poorly understood. Redundancy between enhancers that regulate the same gene is thought to mitigate the ...
  • Juan-Mateu, Jonàs; Bajew, Simon, 1994-; Miret-Cuesta, Marta; Íñiguez, Luis P.; Lopez-Pascual, Amaya; Bonnal, Sophie; Atla, Goutham; Bonàs-Guarch, Silvia; Ferrer, Jorge; Valcárcel, J. (Juan); Irimia Martínez, Manuel (Nature Research, 2023)
    Pancreatic islets control glucose homeostasis by the balanced secretion of insulin and other hormones, and their abnormal function causes diabetes or hypoglycaemia. Here we uncover a conserved programme of alternative ...
  • Torres Méndez, Antonio, 1992-; Pop, Sinziana; Bonnal, Sophie; Almudi, Isabel; Avola, Alida; Roberts, Ruairí J. V.; Paolantoni, Chiara; Alcaina-Caro, Ana; Martín-Anduaga, Ane; Haussmann, Irmgard U.; Morin, Violeta; Casares, Fernando; Soller, Matthias; Kadener, Sebastian; Roignant, Jean-Yves; Prieto-Godino, Lucia; Irimia Martínez, Manuel (American Association for the Advancement of Science (AAAS), 2022)
    Alternative splicing increases neuronal transcriptomic complexity throughout animal phylogeny. To delve into the mechanisms controlling the assembly and evolution of this regulatory layer, we characterized the neuronal ...
  • Brasó-Vives, Marina, 1990-; Marlétaz, Ferdinand; Echchiki, Amina; Mantica, Federica; Acemel, Rafael D.; Gómez Skarmeta, José Luis; Hartasánchez Frenk, Diego Andrés, 1982-; Le Targa, Lorlane; Pontarotti, Pierre; Tena, Juan J.; Maeso, Ignacio; Escriva, Hector; Irimia Martínez, Manuel; Robinson-Rechavi, Marc (BioMed Central, 2022)
    Background: Amphioxus are non-vertebrate chordates characterized by a slow morphological and molecular evolution. They share the basic chordate body-plan and genome organization with vertebrates but lack their 2R whole-genome ...
  • Schiavinato, Matteo; Marcet Houben, Marina; Dohm, Juliane C.; Gabaldón Estevan, Juan Antonio, 1973-; Himmelbauer, Heinz (Wiley-Blackwell, 2019)
    Nicotiana section Suaveolentes is an almost all-Australian clade of allopolyploid tobacco species including the important plant model Nicotiana benthamiana. The homology relationships of this clade and its formation are ...
  • Erb, Ionas (Elsevier, 2020)
    Partial correlations quantify linear association between two variables while adjusting for the influence of the remaining variables. They form the backbone for graphical models and are readily obtained from the inverse of ...
  • Montgomery, Sean A.; Berger, Frédéric (Wiley, 2024)
    We are becoming aware of a growing number of organisms that do not express genetic information equally from both parents as a result of an epigenetic phenomenon called genomic imprinting. Recently, it was shown that the ...
  • 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 ...
  • Pry, Jake; Chipungu, Jenala; Smith, Helene J.; Bolton Moore, Carolyn; Mutale, Jacob; Duran-Frigola, Miquel, 1985-; Savory, Theodora; Herce, Michael E. (Wiley Open Access, 2020)
    Introduction: In the current "test and treat" era, HIV programmes are increasingly focusing resources on linkage to care and same-day antiretroviral therapy (ART) initiation to meet UNAIDS 95-95-95 targets. After observing ...
  • di Domenico, Angelique; Carola, Giulia; Calatayud, Carles; Pons Espinal, Meritxell, 1986-; Muñoz, Juan Pablo; Richaud Patin, Yvonne; Fernández Carasa, Irene; Gut, Marta; Faella, Armida; Parameswaran, Janani, 1990-; Soriano, Jordi; Ferrer, Isidre; Tolosa, Eduard; Zorzano, Antonio; Cuervo, Ana Maria; Raya Chamorro, Ángel; Consiglio, Antonella (Elsevier, 2019)
    Parkinson's disease (PD) is associated with the degeneration of ventral midbrain dopaminergic neurons (vmDAns) and the accumulation of toxic α-synuclein. A non-cell-autonomous contribution, in particular of astrocytes, ...
  • Carreté Muñoz, Laia, 1990-; Ksiezopolska, Ewa; Pegueroles Queralt, Maria Cinta; Gómez-Molero, Emilia; Saus Martínez, Ester; Iraola Guzmán, Susana; Loska, Damian; Bader, Olivier; Fairhead, Cécile; Gabaldón Estevan, Juan Antonio, 1973- (Elsevier, 2018)
    Candida glabrata is an opportunistic fungal pathogen that ranks as the second most common cause of systemic candidiasis. Despite its genus name, this yeast is more closely related to the model yeast Saccharomyces cerevisiae ...
  • Li, Yilong; Roberts, Nicola D.; Wala, Jeremiah A.; Shapira, Ofer; Schumacher, Steven E.; Kumar, Kiran; Khurana, Ekta; Waszak, Sebastian; Korbel, Jan O.; Haber, James E.; Imielinski, Marcin; PCAWG Structural Variation Working Group; Weischenfeldt, Joachim; Beroukhim, Rameen; Campbell, Peter J.; PCAWG Consortium; Ossowski, Stephan (Nature Research, 2020)
    A key mutational process in cancer is structural variation, in which rearrangements delete, amplify or reorder genomic segments that range in size from kilobases to whole chromosomes1-7. Here we develop methods to group, ...
  • Ogando, Jesús; Sáez, María Eugenia; Santos, Javier; Nuevo-Tapioles, Cristina; Gut, Marta; Esteve-Codina, Anna; Heath, Simon; González-Pérez, Antonio; Cuezva, José M.; Lacalle, Rosa Ana; Mañes, Santos (BioMed Central, 2019)
    Background: Binding of the programmed death-1 (PD-1) receptor to its ligands (PD-L1/2) transduces inhibitory signals that promote exhaustion of activated T cells. Blockade of the PD-1 pathway is widely used for cancer ...
  • PDBe-KB consortium (Oxford University Press, 2020)
    The Protein Data Bank in Europe-Knowledge Base (PDBe-KB, https://pdbe-kb.org) is a community-driven, collaborative resource for literature-derived, manually curated and computationally predicted structural and functional ...
  • Varadi, Mihaly; Radusky, Leandro; Serrano Pubull, Luis, 1982-; Velankar, Sameer; PDBe-KB consortium (Oxford University Press, 2022)
    The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or ...

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