Browsing Center for Genomic Regulation (CRG) by Title

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  • p53 regulates the mevalonate pathway in human glioblastoma multiforme
    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 ...
  • Paired guide RNA CRISPR-Cas9 screening for protein-coding genes and lncRNAs involved in transdifferentiation of human B-cells to macrophages
    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 ...
  • PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy
    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 ...
  • 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 analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition
    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 ...
  • Pancreas agenesis mutations disrupt a lead enhancer controlling a developmental enhancer cluster
    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 ...
  • Pancreatic microexons regulate islet function and glucose homeostasis
    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 ...
  • Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals
    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 ...
  • Parallel evolution of amphioxus and vertebrate small-scale gene duplications
    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 ...
  • Parental origin of the allotetraploid tobacco Nicotiana benthamiana
    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 ...
  • Partial correlations in compositional data analysis
    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 ...
  • Paternal imprinting in Marchantia polymorpha
    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 ...
  • 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 ...
  • Patient-reported reasons for declining same-day antiretroviral therapy initiation in routine HIV care settings in Lusaka, Zambia: results from a mixed-effects regression analysis
    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 ...
  • Patient-specific iPSC-derived astrocytes contribute to non-cell-autonomous neurodegeneration in Parkinson's disease
    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, ...
  • Patterns of genomic variation in the opportunistic pathogen candida glabrata suggest the existence of mating and a secondary association with humans
    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 ...
  • Patterns of somatic structural variation in human cancer genomes
    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, ...
  • PD-1 signaling affects cristae morphology and leads to mitochondrial dysfunction in human CD8+ T lymphocytes
    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: a community-driven resource for structural and functional annotations
    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 ...
  • PDBe-KB: collaboratively defining the biological context of structural data
    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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