Browsing Center for Genomic Regulation (CRG) by Title

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  • Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies
    Naranjo Ortiz, Miguel Ángel, 1989-; Molina, Manuel; Fuentes Palacios, Diego; Mixão, Verónica; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2022)
    Background: Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, ...
  • KChIP3 coupled to Ca2+ oscillations exerts a tonic brake on baseline mucin release in the colon
    Cantero Recasens, Gerard, 1984-; Butnaru, Cristian M.; Valverde, M. A. (Miguel Ángel), 1963-; Naranjo, José R.; Brouwers, Nathalie; Malhotra, Vivek (eLife, 2018)
    Regulated mucin secretion from specialized goblet cells by exogenous agonist-dependent (stimulated) and -independent (baseline) manner is essential for the function of the epithelial lining. Over extended periods, baseline ...
  • Key features of turing systems are determined purely by network topology
    Diego, Xavier; Marcon, Luciano, 1983-; Müller, Patrick; Sharpe, James (American Physical Society, 2018)
    Turing’s theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry, and biology. Essential properties of a Turing system, such as the conditions for the existence ...
  • Key Role of Amino Acid Repeat Expansions in the Functional Diversification of Duplicated Transcription Factors.
    Radó i Trilla, Núria, 1985-; Arató, Krisztina, 1981-; Pegueroles Queralt, Maria Cinta; Raya, Alicia; Luna, Susana de la; Albà Soler, Mar (Open University Press, 2015)
    The high regulatory complexity of vertebrates has been related to two rounds of whole genome duplication (2R-WGD) that occurred before the divergence of the major vertebrate groups. Following these events, many developmental ...
  • Kinesin-5/Eg5 is important for transport of CARTS from the trans-Golgi network to the cell surface
    Wakana, Yuichi; Villeneuve, Julien; Galen, Josse van; Cruz-Garcia, David; Tagaya, Mitsuo; Malhotra, Vivek (Rockefeller University Press, 2013)
    Here we report that the kinesin-5 motor Klp61F, which is known for its role in bipolar spindle formation in mitosis, is required for protein transport from the Golgi complex to the cell surface in Drosophila S2 cells. ...
  • Kinesin-8 and Dis1/TOG collaborate to limit spindle elongation from prophase to anaphase A for proper chromosome segregation in fission yeast
    Pinder, Corinne; Matsuo, Yuzy; Maurer, Sebastian; Toda, Takashi (Company of Biologists, 2019)
    High-fidelity chromosome segregation relies on proper microtubule regulation. Kinesin-8 has been shown to destabilise microtubules to reduce metaphase spindle length and chromosome movements in multiple species. XMAP215/chTOG ...
  • Kinetics in signal transduction pathways involving promiscuous oligomerizing receptors can be determined by receptor specificity: apoptosis induction by TRAIL
    Szegezdi, Eva; van der Sloot, Almer M.; Mahalingam, Devalingam; O'Leary, Lynda; Cool, Robbert H.; Muñoz, Inés G.; Montoya, Guillermo; Quax, Wim J.; Jong, Steven M. de, 1962-; Samali, Afshin; Serrano Pubull, Luis, 1982- (American Society for Biochemistry and Molecular Biology (ASBMB), 2012)
    Here we show by computer modeling that kinetics and outcome of signal transduction in case of hetero-oligomerizing receptors of a promiscuous ligand largely depend on the relative amounts of its receptors. Promiscuous ...
  • Knock-down of AHCY and depletion of adenosine induces DNA damage and cell cycle arrest
    Belužić, Lucija; Grbeša, Ivana; Belužić, Robert; Park, Jong Hoon; Kong, Hyun Kyung; Kopjar, Nevenka; Espadas, Guadalupe; Sabidó Aguadé, Eduard, 1981-; Lepur, Adriana; Rokić, Filip; Jerić, Ivanka; Brkljačić, Lidija; Vugrek, Oliver (Nature Research, 2018)
    Recently, functional connections between S-adenosylhomocysteine hydrolase (AHCY) activity and cancer have been reported. As the properties of AHCY include the hydrolysis of S-adenosylhomocysteine and maintenance of the ...
  • Knockout of RNA binding protein MSI2 impairs follicle development in the mouse ovary: characterization of MSI1 and MSI2 during folliculogenesis
    Sutherland, Jessie M.; Sobinoff, Alexander P.; Gunter, Kara M.; Fraser, Barbara A.; Pye, Victoria; Bernstein, Ilana R.; Boon, Evan; Siddall, Nicole A.; Andrés, Luisa De; Hime, Gary R.; Holt, Janet E.; Graf, T. (Thomas); McLaughlin, Eileen A. (MDPI, 2015)
    Characterizing the mechanisms underlying follicle development in the ovary is crucial to understanding female fertility and is an area of increasing research interest. The RNA binding protein Musashi is essential for ...
  • L amino acid transporter structure and molecular bases for the asymmetry of substrate interaction
    Errasti-Murugarren, Ekaitz; Fort, Joana; Bartoccioni, Paola; Díaz, Lucía; Pardon, Els; Carpena, Xavier; Espino Guarch, Meritxell; Zorzano, Antonio; Ziegler, Christine; Steyaert, Jan; Fernández Recio, Juan; Fita, Ignacio; Palacín Mateo, Manuel (Nature Research, 2019)
    L-amino acid transporters (LATs) play key roles in human physiology and are implicated in several human pathologies. LATs are asymmetric amino acid exchangers where the low apparent affinity cytoplasmic side controls the ...
  • Labelled regulatory elements are pervasive features of the macrophage genome and are dynamically utilized by classical and alternative polarization signals
    Horvath, Attila; Daniel, Bence; Szeles, Lajos; Cuaranta-Monroy, Ixchelt; Czimmerer, Zsolt; Ozgyin, Lilla; Steiner, Laszlo; Kiss, Mate; Simandi, Zoltan; Poliska, Szilard; Giannakis, Nikolas; Raineri, Emanuele; Gut, Ivo Glynne; Nagy, Benedek; Nagy, Laszlo (Oxford University Press, 2019)
    The concept of tissue-specific gene expression posits that lineage-determining transcription factors (LDTFs) determine the open chromatin profile of a cell via collaborative binding, providing molecular beacons to ...
  • Lack of support for the association between facial shape and aggression: a reappraisal based on a worldwide population genetics perspective
    Gómez-Valdés, Jorge; Hünemeier, Tábita; Quinto-Sánchez, Mirsha; Paschetta, Carolina; de Azevedo, Soledad; González, Marina F.; Martínez Abadías, Neus; Esparza, Mireia; Pucciarelli, Héctor M.; Salzano, Francisco Mauro; Bau, Claiton H. D.; Bortolini, Maria Cátira; González-José, Rolando (Public Library of Science (PLoS), 2013)
    Antisocial and criminal behaviors are multifactorial traits whose interpretation relies on multiple disciplines. Since these interpretations may have social, moral and legal implications, a constant review of the evidence ...
  • Lack of tailless leads to an increase in expression variability in Drosophila embryos
    Janssens, Hilde; Crombach, Anton; Wotton, Karl R.; Cicin Sain, Damjan; Surkova, Svetlana; Lim, Chea Lu; Samsonova, Maria; Akam, Michael; Jaeger, Johannes, 1973- (Elsevier, 2013)
    Developmental processes are robust, or canalised: dynamic patterns of gene expression across space and time are regulated reliably and precisely in the presence of genetic and environmental perturbations. It remains unclear ...
  • Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host
    Echeverz, Maite; García, Begoña M.; Sabalza, Amaia; Valle, Jaione; Gabaldón Estevan, Juan Antonio, 1973-; Solano, Cristina; Lasa, Iñigo (Public Library of Science (PLoS), 2017)
    Many bacteria build biofilm matrices using a conserved exopolysaccharide named PGA or PNAG (poly-β-1,6-N-acetyl-D-glucosamine). Interestingly, while E. coli and other members of the family Enterobacteriaceae encode the ...
  • Lamin B1 mapping reveals the existence of dynamic and functional euchromatin lamin B1 domains
    Pascual-Reguant, Laura; Blanco, Enrique; Galan Martínez, Silvia, 1992-; Le Dily, François; Cuartero, Yasmina; Serra Bardenys, Gemma, 1992-; Di Carlo, Valerio; Iturbide Martínez de Albéniz, Ane, 1989-; Cebrià i Costa, Joan Pau, 1989-; Nonell Mazelon, Lara, 1972-; García de Herreros, Antonio; Di Croce, Luciano; Marti-Renom, Marc A.; Peiró Sales, Sandra (Nature Publishing Group, 2018)
    Lamins (A/C and B) are major constituents of the nuclear lamina (NL). Structurally conserved lamina-associated domains (LADs) are formed by genomic regions that contact the NL. Lamins are also found in the nucleoplasm, ...
  • Lamivudine, a reverse transcriptase inhibitor, rescues cognitive deficits in a mouse model of down syndrome
    Martínez de Lagrán Cabredo, María; Elizalde-Torrent, Aleix; Paredes, Roger; Clotet, Bonaventura; Dierssen, Mara (Wiley, 2022)
    An elevated activity of retrotransposons is increasingly recognized to be implicated in a wide range of neurodegenerative and neurodevelopmental diseases. Down syndrome (DS) is the most common genetic disorder associated ...
  • Landscape of transcription in human cells
    Djebali, Sarah; Merkel, Angelika; Tanzer, Andrea; Lagarde, Julien; Röder, Maik; Curado, Joao; Derrien, Thomas; Ferreira, Pedro G.; González, David; Johnson, Rory; Kingswood, Colin; Ribeca, Paolo; Sammeth, Michael; Skancke, Jorgen; Tilgner, Hagen, 1980-; Guigó Serra, Roderic; Gingeras, Thomas R. (Nature Publishing Group, 2012)
    Eukaryotic cells make many types of primary and processed RNAs that are found either in specific subcellular compartments or throughout the cells. A complete catalogue of these RNAs is not yet available and their characteristic ...
  • Landscape of X chromosome inactivation across human tissues
    Tukiainen, Taru; Guigó Serra, Roderic; MacArthur, Daniel G.; Genotype-Tissue Expression (GTEx) Consortium (Nature Publishing Group, 2017)
    X chromosome inactivation (XCI) silences transcription from one of the two X chromosomes in female mammalian cells to balance expression dosage between XX females and XY males. XCI is, however, incomplete in humans: up to ...
  • Large expert-curated database for benchmarking document similarity detection in biomedical literature search
    Brown, Peter; Raote, Ishier; RELISH Consortium; Zhou, Yaoqi (Oxford University Press, 2019)
    Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that ...
  • Large-scale analysis of genome and transcriptome alterations in multiple tumors unveils novel cancer-relevant splicing networks
    Sebestyén, Endre; Singh, Babita, 1986-; Miñana Gómez, Belén; Pagès Pinós, Amadís; Mateo, Francesc; Pujana, Miguel Angel; Valcárcel, J. (Juan); Eyras Jiménez, Eduardo (Cold Spring Harbor Laboratory Press (CSHL Press), 2016)
    Alternative splicing is regulated by multiple RNA-binding proteins and influences the expression of most eukaryotic genes. However, the role of this process in human disease, and particularly in cancer, is only starting ...

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