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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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  • Vlasova, Anna; Hermoso Pulido, Antonio; Camara, Francisco; Ponomarenko, Julia; Guigó Serra, Roderic (MDPI, 2021)
    Functional annotation allows adding biologically relevant information to predicted features in genomic sequences, and it is, therefore, an important procedure of any de novo genome sequencing project. It is also useful for ...
  • Gutierrez-Zotes, Alfonso; Gallardo-Pujol, David; Labad, Javier; Martín Santos, Rocío; García-Esteve, Luisa; Gelabert, Estel; Jover, Manuel; Guillamat, Roser; Mayoral Cleries, Fermín; Gornemann, Isolde; Canellas, Francesca; Gratacós Mayora, Mònica; Guitart, Miriam; Roca, Miquel; Costas, Javier; Ivorra, Jose Luis; Navinés, Ricard; Diego, Yolanda de; Vilella, Elisabet; Sanjuan, Julio (Fundación López Ibor, 2018)
    INTRODUCTION: The Edinburgh Postnatal Depression Scale (EPDS) is considered the gold standard in screening for postpartum depression. Although the Spanish version has been widely used, its factorial structure has not yet ...
  • Vonesch, Sibylle C.; Li, Shengdi; Szu-Tu, Chelsea; Henning, Bianca P.; Dobrev, Nikolay; Steinmetz, Lars M. (Oxford University Press, 2021)
    Through the increase in the capacity of sequencing machines massively parallel sequencing of thousands of samples in a single run is now possible. With the improved throughput and resulting drop in the price of sequencing, ...
  • Derrien, Thomas; Estellé, Jordi; Marco Sola, Santiago; Knowles, David G.; Raineri, Emanuele; Guigó Serra, Roderic; Ribeca, Paolo (Public Library of Science (PLoS), 2012)
    We present a fast mapping-based algorithm to compute the mappability of each region of a reference genome up to a specified number of mismatches. Knowing the mappability of a genome is crucial for the interpretation of ...
  • Miravet Verde, Samuel; Burgos, Raul; Delgado Blanco, Javier; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (Oxford University Press, 2020)
    Transposon sequencing is commonly applied for identifying the minimal set of genes required for cellular life; a major challenge in fields such as evolutionary or synthetic biology. However, the scientific community has ...
  • Jiménez-Izquierdo, Rafael; Morrugares, Rosario; Suanes-Cobos, Lucía; Correa-Sáez, Alejandro; Garrido-Rodríguez, Martín; Cerero-Tejero, Laura; Khan, Omar M.; Luna, Susana de la; Sancho, Rocío; Calzado, Marco A. (Springer, 2023)
    FBXW7 is a member of the F-box protein family, which functions as the substrate recognition component of the SCF E3 ubiquitin ligase. FBXW7 is a main tumor suppressor due to its ability to control proteasome-mediated ...
  • Fiume, Marc; Rambla de Argila, Jordi; Torre, Sabela de la; Scollen, Serena (Nature Research, 2019)
  • Ramos-Romero, Sara; Ponomarenko, Julia; Amézqueta, Susana; Hereu, Mercè; Miralles-Pérez, Bernat; Romeu, Marta; Méndez, Lucía; Medina, Isabel; Torres, Josep Lluís (MDPI, 2022)
    The goal of this work is to explore if the changes induced by d-fagomine in the gut microbiota are compatible with its effect on body weight and inflammation markers in rats. Methods: Sprague Dawley rats were fed a standard ...
  • Riemschoss, Katrin; Arndt, Verena; Bolognesi, Benedetta; von Eisenhart-Rothe, Philipp; Liu, Shu; Buravlova, Oleksandra; Duernberger, Yvonne; Paulsen, Lydia; Hornberger, Annika; Hossinger, André; Lorenzo Gotor, Maria de las Nieves; Hogl, Sebastian; Müller, Stephan A.; Tartaglia, Gian Gaetano; Lichtenthaler, Stefan F.; Vorberg, Ina M. (Life Science Alliance, 2019)
    Prions of lower eukaryotes are self-templating protein aggregates that replicate by converting homotypic proteins into stable, tightly packed beta-sheet-rich protein assemblies. Propagation is mediated by prion domains, ...
  • Elsik, Christine G; Cámara, Francisco; Honey Bee Genome Sequencing Consortium (BioMed Central, 2014)
    Background: The first generation of genome sequence assemblies and annotations have had a significant impact upon our understanding of the biology of the sequenced species, the phylogenetic relationships among species, the ...
  • Maceda Porto, Iago, 1986-; Martín Álvarez, Miguel; Athanasiadis, Georgios; Tonda, Raúl; Camps-Puchadas, Jordi; Beltran, Sergi; Camps, Agustí; Fàbrega, Jordi; Felisart, Josefina; Grané, Joan; Remón, José Luis; Serra, Jordi; Moral, Pedro; Lao Grueso, Oscar, 1976- (Springer Nature, 2021)
    The area of the Spanish Pyrenees is particularly interesting for studying the demographic dynamics of European rural areas given its orography, the main traditional rural condition of its population and the reported higher ...
  • Chipman, Ariel D; Capella Gutiérrez, Salvador Jesús, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic; Mariotti, Marco, 1984-; Richards, Stephan (Public Library of Science (PLoS), 2014)
    Myriapods (e.g., centipedes and millipedes) display a simple homonomous body plan relative to other arthropods. All members of the class are terrestrial, but they attained terrestriality independently of insects. Myriapoda ...
  • Soo, Valerie W. C.; Swadling, Jacob B.; Faure, Andre J.; Warnecke, Tobias (Public Library of Science (PLoS), 2021)
    RNA structures are dynamic. As a consequence, mutational effects can be hard to rationalize with reference to a single static native structure. We reasoned that deep mutational scanning experiments, which couple molecular ...
  • Esnaola, Mikel; Puig, Pedro; González, David; Castelo Valdueza, Robert; González Ruiz, Juan Ramón (BioMed Central, 2013)
    Background: High-throughput RNA sequencing (RNA-seq) offers unprecedented power to capture the real dynamics of gene expression. Experimental designs with extensive biological replication present a unique opportunity to ...
  • Kuderna, Lukas, 1989-; Solís Moruno, Manuel, 1993-; Batlle Masó, Laura, 1993-; Julià, Eva; Lizano González, Esther, 1974-; Anglada Busquets, Roger; Ramírez Bautista, Eva; Bote, Alex; Tormo, Marc; Marquès i Bonet, Tomàs, 1975-; Fornas Carreño, Oscar; Casals López, Ferran (Frontiers Media, 2020)
    Sorting of individual chromosomes by Flow Cytometry (flow-sorting) is an enrichment method to potentially simplify genome assembly by isolating chromosomes from the context of the genome. We have recently developed a ...
  • Arias, Adrian; Manubens-Gil, Linus, 1989-; Dierssen, Mara (Frontiers, 2022)
    A paradigm shift is occurring in neuroscience and in general in life sciences converting biomedical research from a descriptive discipline into a quantitative, predictive, actionable science. Living systems are becoming ...
  • Delgado Blanco, Javier; Radusky, Leandro; Cianferoni, Damiano; Serrano Pubull, Luis, 1982- (Oxford University Press, 2019)
    SUMMARY: A new version of FoldX, whose main new features allows running classic FoldX commands on structures containing RNA molecules and includes a module that allows parametrization of ligands or small molecules (ParamX) ...
  • Delgado Blanco, Javier; Radusky, Leandro; Climente González, Héctor; Serrano Pubull, Luis, 1982- (Oxford University Press, 2018)
    The speed at which new genomes are being sequenced highlights the need for genome-wide methods capable of predicting protein-DNA interactions. Here, we present PADA1, a generic algorithm that accurately models structural ...
  • Banse, Paul; Luiselli, Juliette; Parsons, David P.; Grohens, Théotime; Foley, Marco; Trujillo, Leonardo; Rouzaud-Cornabas, Jonathan; Knibbe, Carole; Beslon, Guillaume (Wiley, 2023)
    While chromosomal rearrangements are ubiquitous in all domains of life, very little is known about their evolutionary significance, mostly because, apart from a few specifically studied and well-documented mechanisms ...
  • Cuypers, Bart; Meysman, Pieter; Erb, Ionas; Bittremieux, Wout; Valkenborg, Dirk; Baggerman, Geert; Mertens, Inge; Sundar, Shyam; Khanal, Basudha; Notredame, Cedric; Dujardin, Jean-Claude; Domagalska, Malgorzata A.; Laukens, Kris (Public Library of Science (PLoS), 2022)
    Aneuploidy causes system-wide disruptions in the stochiometric balances of transcripts, proteins, and metabolites, often resulting in detrimental effects for the organism. The protozoan parasite Leishmania has an unusually ...

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