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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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  • van Oevelen, Chris; Collombet, Samuel; Vicent, Guillermo Pablo; Hoogenkamp, Maarten; Lepoivre, Cyrille; Badeaux, Aimee; Bussmann, Lars; Sardina, Jose Luis; Thieffry, Denis; Beato, Miguel; Shi, Yang; Bonifer, Constanze; Graf, T. (Thomas) (Elsevier, 2015)
    Transcription-factor-induced somatic cell conversions are highly relevant for both basic and clinical research yet their mechanism is not fully understood and it is unclear whether they reflect normal differentiation ...
  • Nacht, A. Silvina; Ferrari, Roberto; Zaurín Quer, Roser; Scabia, Valentina; Carbonell-Caballero, Jose; Le Dily, François; Quilez Oliete, Javier; Leopoldi, Alexandra; Brisken, Cathrin; Beato, Miguel; Vicent, Guillermo Pablo (EMBO Press, 2019)
    Steroid hormones are key gene regulators in breast cancer cells. While estrogens stimulate cell proliferation, progestins activate a single cell cycle followed by proliferation arrest. Here, we use biochemical and genome-wide ...
  • Barteri, Fabio; Valenzuela, Alejandro; Farré, Xavier; Juan, David; Muntané, Gerard; Esteve Altava, Borja; Navarro i Cuartiellas, Arcadi, 1969- (Oxford University Press, 2023)
    Motivation: Coincidence of Convergent Amino Acid Substitutions (CAAS) with phenotypic convergences allow pinpointing genes and even individual mutations that are likely to be associated with trait variation within their ...
  • Blume, Julia von; Alleaume, Anne-Marie; Kienzle, Christine; Carreras Sureda, Amado, 1986-; Valverde, M. A. (Miguel Ángel), 1963-; Malhotra, Vivek (Rockefeller University Press, 2012)
    Ca(2+) import into the lumen of the trans-Golgi network (TGN) by the secretory pathway calcium ATPase1 (SPCA1) is required for the sorting of secretory cargo. How is Ca(2+) retained in the lumen of the Golgi, and what is ...
  • Ruíz Romero, Marina; Blanco, Enrique; Paricio, Nuria; Serras Rigalt, Florenci; Corominas Guiu, Montserrat (EMBO Press, 2015)
    The Drosophila transcription factor Cabut/dTIEG (Cbt) is a growth regulator, whose expression is modulated by different stimuli. Here, we determine Cbt association with chromatin and identify Yorkie (Yki), the transcriptional ...
  • Schiffer, Jodie A.; Servello, Francesco A.; Heath, William R.; Amrit, Francis Raj Ghandi; Stumbur, Stephanie V; Eder, Matthias; Martin, Olivier M. F.; Johnsen, Sean B.; Stanley, Julia A.; Tam, Hannah; Brennan, Sara J.; McGowan, Natalie G.; Vogelaar, Abigail L.; Xu, Yuyan; Serkin, William T.; Ghazi, Arjumand; Stroustrup, Nicholas; Apfeld, Javier (eLife, 2020)
    Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated ...
  • Filion, Guillaume; Cortini, Ruggero; Zorita, Eduard (Frontiers, 2020)
    The increasing throughput of DNA sequencing technologies creates a need for faster algorithms. The fate of most reads is to be mapped to a reference sequence, typically a genome. Modern mappers rely on heuristics to gain ...
  • Hernández, Sergi; Franco, Luís; Calvo Vidal, Verónica Alejandra; Ferragut, Gabriela; Hermoso Pulido, Antonio; Amela, Isaac; Gómez, Antonio; Querol, Enrique; Cedano, Juan (Portland Press, 2014)
    Protein multitasking or moonlighting is the capability of certain proteins to execute two or more unique biological functions. This ability to perform moonlighting functions helps us to understand one of the ways used by ...
  • Carlevaro-Fita, Joana; Lanzós, Andrés; Feuerbach, Lars; Hong, Chen; Mas Ponte, David; Pedersen, Jackob S.; PCAWG Drivers and Functional Interpretation Working Group; Johnson, Rory; PCAWG Consortium (Nature Research, 2020)
    Long non-coding RNAs (lncRNAs) are a growing focus of cancer genomics studies, creating the need for a resource of lncRNAs with validated cancer roles. Furthermore, it remains debated whether mutated lncRNAs can drive ...
  • Serra Musach, Jordi; Capdevila Busquets, Eva; Jaeger, Samira; Aloy, Patrick, 1972-; Pujana, Miguel Angel (BioMed Central, 2016)
    Background: Cancer patients often show no or only modest benefit from a given therapy. This major problem in oncology is generally attributed to the lack of specific predictive biomarkers, yet a global measure of cancer ...
  • Park, Solip; Lehner, Ben, 1978- (Wiley Blackwell, 2015)
    Cancers, like many diseases, are normally caused by combinations of genetic alterations rather than by changes affecting single genes. It is well established that the genetic alterations that drive cancer often interact ...
  • Pekmezovic, Marina; Hovhannisyan, Hrant, 1992-; Gresnigt, Mark S.; Iracane, Elise; Oliveira Pacheco, João; Siscar Lewin, Sofía; Seemann, Eric; Qualmann, Britta; Kalkreuter, Till; Müller, Sylvia; Kamradt, Thomas; Mogavero, Selene; Brunke, Sascha; Butler, Geraldine; Gabaldón Estevan, Juan Antonio, 1973-; Hube, Bernhard (Nature Research, 2021)
    Vaginal candidiasis is an extremely common disease predominantly caused by four phylogenetically diverse species: Candida albicans; Candida glabrata; Candida parapsilosis; and Candida tropicalis. Using a time course infection ...
  • Navarro-Romero, Alba; Vázquez-Oliver, Anna; Gomis González, Maria, 1988-; Garzón-Montesinos, Carlos; Falcón-Moya, Rafael; Pastor, Antonio; Martín García, Elena, 1975-; Pizarro Lozano, Mª Nieves; Busquets Garcia, Arnau, 1985-; Revest, Jean-Michel; Piazza, Pier Vincenzo; Bosch, Fatima; Dierssen, Mara; Torre Fornell, Rafael de la; Rodríguez-Moreno, Antonio; Maldonado, Rafael, 1961-; Ozaita Mintegui, Andrés, 1969- (Elsevier, 2019)
    Intellectual disability is the most limiting hallmark of Down syndrome, for which there is no gold-standard clinical treatment yet. The endocannabinoid system is a widespread neuromodulatory system involved in multiple ...
  • Aulicino, Francesco, 1987-; Pedone, Elisa, 1985-; Sottile, Francesco, 1988-; Lluis Viñas, Frederic; Marucci, Lucia; Cosma, Maria Pia (Elsevier, 2020)
    The Wnt/β-catenin signaling pathway is a key regulator of embryonic stem cell (ESC) self-renewal and differentiation. Constitutive activation of this pathway has been shown to increase mouse ESC (mESC) self-renewal and ...
  • Torcal Garcia, Guillem, 1991-; Kowenz-Leutz, Elisabeth; Tian, Tian V.; Klonizakis, Antonios; Lerner, Jonathan; Andrés Aguayo, Luisa de; Sapozhnikova, Valeriia; Berenguer, Clara; Plana Carmona, Marcos, 1993-; Vila-Casadesús, Maria; Bulteau, Romain; Francesconi, Mirko; Peiró Sales, Sandra; Mertins, Philipp; Zaret, Kenneth S.; Leutz, Achim; Graf, T. (Thomas) (eLife, 2023)
    Here, we describe how the speed of C/EBPα-induced B cell to macrophage transdifferentiation (BMT) can be regulated, using both mouse and human models. The identification of a mutant of C/EBPα (C/EBPαR35A) that greatly ...
  • Ounzain, Samir; Micheletti, Rudi; Arnan Ros, Carme; Plaisance, Isabelle; Cecchi, Dario; Schroen, Blanche; Reverter, Ferran; Alexanian, Michael; Gonzales, Christine; Ng, Shi Yan; Bussotti, Giovanni, 1983-; Pezzuto, Iole; Notredame, Cedric; Heymans, Stephane; Guigó Serra, Roderic; Johnson, Rory; Pedrazzini, Thierry (Elsevier, 2015)
    Long noncoding RNAs (lncRNAs) are emerging as important regulators of developmental pathways. However, their roles in human cardiac precursor cell (CPC) remain unexplored. To characterize the long noncoding transcriptome ...
  • Schorling, David; Kölbel, Heike; Hentschel, Andreas; Pechmann, Astrid; Meyer, Nancy; Wirth, Brunhilde; Rombo, Roman; SMArtCARE consortium; Sickmann, Albert; Kirschner, Janbernd; Schara-Schmidt, Ulrike; Lochmüller, Hanns; Roos, Andreas (Wiley, 2022)
    Background and purpose: The therapeutic landscape of spinal muscular atrophy (SMA) has changed dramatically during the past 4 years, but treatment responses differ remarkably between individuals, and therapeutic decision-making ...
  • Agostini, Federico, 1985-; Zanzoni, Andreas; Klus, Petr, 1985-; Marchese, Domenica, 1986-; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2013)
    SUMMARY: Here we introduce catRAPID omics, a server for large-scale calculations of protein-RNA interactions. Our web server allows (i) predictions at proteomic and transcriptomic level; (ii) use of protein and RNA sequences ...
  • Livi, Carmen Maria; Klus, Petr, 1985-; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano (Oxford University Press, 2016)
    MOTIVATION: Recent technological advances revealed that an unexpected large number of proteins interact with transcripts even if the RNA-binding domains are not annotated. We introduce catRAPID signature to identify ...
  • Bauer, Moritz, 1987-; Payer, Bernhard; Filion, Guillaume (Wiley, 2022)
    The spatial organization of genomes is becoming increasingly understood. In mammals, where it is most investigated, this organization ties in with transcription, so an important research objective is to understand whether ...

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