Browsing Center for Genomic Regulation (CRG) by Title

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  • Obesity is associated with shorter telomeres in 8 year-old children
    Clemente Batalha Pardal, Diana, 1990-; Maitre, Léa; Bustamante Pineda, Mariona; Chatzi, Leda; Roumeliotaki, Theano; Fossati, Serena; Gražulevičienė, Regina; Gützkow, Kristine B.; Lepeule, Johanna; Martens, Dries S.; McEachan, Rosemary R.C.; Meltzer, Helle Margrete; Petraviciene, Inga; Slama, Rémy; Tamayo-Uria, Ibon; Urquiza, José M.; Vafeiadi, Marina, 1983-; Wright, John; Nawrot, Tim S.; Vrijheid, Martine (Nature Research, 2019)
    Telomere length is considered a biomarker of biological aging. Shorter telomeres and obesity have both been associated with age-related diseases. To evaluate the association between various indices of obesity with leukocyte ...
  • omiXcore: a web server for prediction of protein interactions with large RNA
    Armaos, Alexandros, 1989-; Cirillo, Davide; Tartaglia, Gian Gaetano (Oxford University Press, 2017)
    SUMMARY: Here we introduce omiXcore, a server for calculations of protein binding to large RNAs (> 500 nucleotides). Our webserver allows (i) use of both protein and RNA sequences without size restriction, (ii) pre-compiled ...
  • Omnipose: a high-precision morphology-independent solution for bacterial cell segmentation
    Cutler, Kevin J.; Stringer, Carsen; Lo, Teresa W.; Rappez, Luca; Stroustrup, Nicholas; Peterson, S. Brook; Wiggins, Paul A.; Mougous, Joseph D. (Nature Research, 2022)
    Advances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately ...
  • OneD: increasing reproducibility of Hi-C samples with abnormal karyotypes
    Vidal Ocabo, Enrique; Le Dily, François; Quilez Oliete, Javier; Stadhouders, Ralph; Cuartero, Yasmina; Graf, T. (Thomas); Martí Renom, Marc A.; Beato, Miguel; Filion, Guillaume (Oxford University Press, 2018)
    The three-dimensional conformation of genomes is an essential component of their biological activity. The advent of the Hi-C technology enabled an unprecedented progress in our understanding of genome structures. However, ...
  • Oocytes maintain ROS-free mitochondrial metabolism by suppressing complex I
    Rodríguez-Nuevo, Aida; Torres-Sanchez, Ariadna; Duran, Juan M.; De Guirior, Cristian; Martínez-Zamora, Maria Angeles; Böke, Elvan (Nature Research, 2022)
    Oocytes form before birth and remain viable for several decades before fertilization1. Although poor oocyte quality accounts for most female fertility problems, little is known about how oocytes maintain cellular fitness, ...
  • Opposite phenotypes of muscle strength and locomotor function in mouse models of partial trisomy and monosomy 21 for the proximal Hspa13-App region
    Brault, Véronique; Duchon, Arnaud; Romestaing, Caroline; Sahún, Ignasi; Pothion, Stéphanie; Karout, Mona; Borel, Christelle; Dembele, Doulaye; Bizot, Jean-Charles; Messaddeq, Nadia; Sharp, Andrew J.; Roussel, Damien; Antonarakis, Stylianos E.; Dierssen, Mara; Hérault, Yann (Public Library of Science (PLoS), 2015)
    The trisomy of human chromosome 21 (Hsa21), which causes Down syndrome (DS), is the most common viable human aneuploidy. In contrast to trisomy, the complete monosomy (M21) of Hsa21 is lethal, and only partial monosomy or ...
  • Optical and physical mapping with local finishing enables megabase-scale resolution of agronomically important regions in the wheat genome
    Keeble-Gagnère, Gabriel; Câmara Ferreira, Francisco; Appels, Rudi (BioMed Central, 2018)
    Background: Numerous scaffold-level sequences for wheat are now being released and, in this context, we report on a strategy for improving the overall assembly to a level comparable to that of the human genome. Results: ...
  • Oral microbiome in down syndrome and its implications on oral health
    Willis, Jesse R.; Iraola Guzmán, Susana; Saus Martínez, Ester; Ksiezopolska, Ewa; Cozzuto, Luca; Bejarano, Luis A.; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Puig, Anna; Blanco, Andrea; Broglio, Elisabetta; Carolis, Carlo; Hecht, Jochen; Ponomarenko, Julia; Gabaldón Estevan, Juan Antonio, 1973- (Taylor & Francis Open Access, 2020)
    Introduction: The oral cavity harbors an abundant and diverse microbial community (i.e. the microbiome), whose composition and roles in health and disease have been the focus of intense research. Down syndrome (DS) is ...
  • ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins
    Mas, Aina Maria; Goñi, Enrique; Ruiz de Los Mozos, Igor; Arcas Mantas, Aida; Statello, Luisa; González, Jovanna; Blázquez, Lorea; Lee, Wei Ting Chelsea; Gupta, Dipika; Sejas, Álvaro; Hoshina, Shoko; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano; Waga, Shou; Ule, Jernej; Rothenberg, Eli; Gómez, María; Huarte, Maite (Nature Research, 2023)
    Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in ...
  • Origin and evolution of eukaryotic transcription factors
    de Mendoza, Alex; Sebé-Pedrós, Arnau (Elsevier, 2019)
    Transcription factors (TFs) have a central role in genome regulation directing gene transcription through binding specific DNA sequences. Eukaryotic genomes encode a large diversity of TF classes, each defined by unique ...
  • Origin and evolution of metabolic sub-cellular compartmentalization in eukaryotes
    Gabaldón Estevan, Juan Antonio, 1973-; Pittis, Alexandros, 1982- (Elsevier, 2016)
    A high level of subcellular compartmentalization is a hallmark of eukaryotic cells. This intricate internal organization was present already in the common ancestor of all extant eukaryotes, and the determination of the ...
  • Origin of exon skipping-rich transcriptomes in animals driven by evolution of gene architecture
    Grau Bové, Xavier; Ruiz Trillo, Iñaki; Irimia Martínez, Manuel (BioMed Central, 2018)
    Background: Alternative splicing, particularly through intron retention and exon skipping, is a major layer of pre-translational regulation in eukaryotes. While intron retention is believed to be the most prevalent mode ...
  • Origins of de novo genes in human and chimpanzee
    Ruiz Orera, Jorge, 1988-; Hernández Rodríguez, Jéssica, 1983-; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Kondova, Ivanela; Bontrop, Ronald E.; Marquès i Bonet, Tomàs, 1975-; Albà Soler, Mar (Public Library of Science, 2015)
    The birth of new genes is an important motor of evolutionary innovation. Whereas many new genes arise by gene duplication, others originate at genomic regions that did not contain any genes or gene copies. Some of these ...
  • Orthology clusters from gene trees with possvm
    Grau Bové, Xavier; Sebé-Pedrós, Arnau (Oxford University Press, 2021)
    Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL [Markov clustering algorithm]) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and ...
  • Osteogenic commitment of Wharton's jelly mesenchymal stromal cells: mechanisms and implications for bioprocess development and clinical application
    Cabrera Pérez, Raquel; Monguió Tortajada, Marta; Gámez Valero, Ana; Rojas Márquez, Raquel; Borràs, Francesc Enric; Roura, Santiago; Vives, Joaquim (BioMed Central, 2019)
    Background: Orthopaedic diseases are one of the major targets for regenerative medicine. In this context, Wharton’s jelly (WJ) is an alternative source to bone marrow (BM) for allogeneic transplantation since its isolation ...
  • Outcome of the first wwPDB Hybrid/Integrative Methods Task Force Workshop
    Sali, Andrej; Martí Renom, Marc A.; Westbrook, John D. (Elsevier, 2015)
    Structures of biomolecular systems are increasingly computed by integrative modeling that relies on varied types of experimental data and theoretical information. We describe here the proceedings and conclusions from the ...
  • Overexpression of Dyrk1A, a down syndrome candidate, decreases excitability and impairs gamma oscillations in the prefrontal cortex
    Ruiz Mejias, Marcel; Martínez de Lagrán Cabredo, María; Mattia, Maurizio; Castaño Prat, Patricia; Pérez Mendez, Lorena; Ciria Suarez, Laura; Gener, Thomas; Sancristóbal, Belen; García Ojalvo, Jordi; Gruart, Agnès; Delgado García, José María; Sanchez-Vives, Maria V.; Dierssen, Mara (Society for Neuroscience, 2016)
    The dual-specificity tyrosine phosphorylation-regulated kinase DYRK1A is a serine/threonine kinase involved in neuronal differentiation and synaptic plasticity and a major candidate of Down syndrome brain alterations and ...
  • Overexpression of Reelin prevents the manifestation of behavioral phenotypes related to schizophrenia and bipolar disorder
    Teixeira, Cátia M.; Martín, Eduardo D.; Sahún, Ignasi; Masachs, Nuria; Pujadas, Lluís; Corvelo, André; Bosch, Carles; Rossi, Daniela; Martínez, Albert; Maldonado, Rafael, 1961-; Dierssen, Mara; Soriano, Eduardo (Nature Publishing Group, 2011)
    Despite the impact of schizophrenia and mood disorders, which in extreme cases can lead to death, recent decades have brought little progress in the development of new treatments. Recent studies have shown that Reelin, an ...
  • Overexpression of α3/α5/β4 nicotinic receptor subunits modifies impulsive-like behavior
    Viñals Álvarez, Xavier, 1985-; Molas Casacuberta, Susanna, 1985-; Gallego, Xavier; Fernández Montes, Rubén D.; Robledo, Patricia, 1958-; Dierssen, Mara; Maldonado, Rafael, 1961- (Elsevier, 2012)
    Recent studies have revealed that sequence variants in genes encoding the α3/α5/β4 nicotinic acetylcholine receptor subunits are associated with nicotine dependence. In this study, we evaluated two specific aspects of ...
  • 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 ...

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