Articles (Center for Genomic Regulation (CRG)): Recent submissions

  • Pokusaeva, Victoria O.; Usmanova, Dinara R.; Putintseva, Ekaterina V.; Espinar, Lorena; Sarkisyan, Karen S.; Mishin, Alexander S.; Bogatyreva, Natalya S.; Ivankov, Dmitry N.; Akopyan, Arseniy V.; Avvakumov, Sergey Ya; Povolotskaya, Inna, 1986-; Filion, Guillaume; Carey, Lucas; Kondrashov, Fyodor A., 1979- (Public Library of Science (PLoS), 2019)
    Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the ...
  • Han, Sojung; Andrés Morán, Aida; Marquès i Bonet, Tomàs, 1975-; Kuhlwilm, Martin (Oxford University Press, 2019)
    Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but the two species show distinct behavioral and physiological differences, particularly regarding female reproduction. ...
  • Küpers, Leanne K.; Salas Díaz, Lucas Andrés, 1980-; Bustamante, Mariona; Kogevinas, Manolis; Vrijheid, Martine; Sunyer Deu, Jordi; Felix, Janine Frédérique (Nature Research, 2019)
    Birthweight is associated with health outcomes across the life course, DNA methylation may be an underlying mechanism. In this meta-analysis of epigenome-wide association studies of 8,825 neonates from 24 birth cohorts in ...
  • Galván-Femenía, Iván; Guindo Martínez, Marta; Duran Jordà, Xavier, 1974-; Calabuig-Fariñas, Sílvia; Mercader Bigas, Josep Maria; Ramirez, Jose Luis; Rosell, Rafael; Torrents, David; Carreras, Anna; Kohno, Takashi; Jantus-Lewintre, Eloisa; Camps, Carlos; Perucho, Manuel; Sumoy Van Dyck, Lauro; Yokota, Jun; Cid Ibeas, Rafael de (Elsevier, 2018)
    Objective: The aim of the study was to investigate the relationship between germline variations as a prognosis biomarker in patients with advanced Non-Small-Cell-Lung-Cancer (NSCLC) subjected to first-line platinum-based ...
  • Gutierrez-Zotes, Alfonso; Gallardo-Pujol, David; Labad, Javier; Martín Santos, Rocío; García-Esteve, Luisa; Gelabert, Estel; Jover, Manuel; Guillamat, Roser; Mayoral, 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 ...
  • Scherbaum, Samantha; Hellmann, Nadja; Fernández, Rosa; Pick, Christian; Burmester, Thorsten (BioMed Central, 2018)
    Background: Hemocyanin transports O2 in the hemolymph of many arthropod species. Such respiratory proteins have long been considered unnecessary in Myriapoda. As a result, the presence of hemocyanin in Myriapoda has long ...
  • Julca, Irene; Marcet Houben, Marina; Vargas Gómez, Pablo; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2018)
    Background: Polyploidization is one of the major evolutionary processes that shape eukaryotic genomes, being particularly common in plants. Polyploids can arise through direct genome doubling within a species (autopolypl ...
  • Sanz, Hector; Valim, Clarissa; Vegas Lozano, Esteban; Oller, Josep M.; Reverter Comes, Ferran (BioMed Central, 2018)
    Background: Support vector machines (SVM) are a powerful tool to analyze data with a number of predictors approximately equal or larger than the number of observations. However, originally, application of SVM to analyze ...
  • Garrido Martín, Diego; Pazos, Florencio (BioMed Central, 2018)
    Background: The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was ...
  • Díaz-Gay, Marcos; Vila-Casadesús, Maria; Franch-Expósito, Sebastià; Hernández-Illán, Eva; Lozano, Juan José; Castellví Bel, Sergi (BioMed Central, 2018)
    Background: Mutational signatures have been proved as a valuable pattern in somatic genomics, mainly regarding cancer, with a potential application as a biomarker in clinical practice. Up to now, several bioinformatic ...
  • Conte, Claudia; Baird, Michelle A.; Davidson, Michael W.; Griffis, Eric R. (Company of Biologists, 2018)
    Dynein is the sole processive minus-end-directed microtubule motor found in animals. It has roles in cell division, membrane trafficking, and cell migration. Together with dynactin, dynein regulates centrosomal orientation ...
  • Hidalgo, Marta R.; Amadoz, Alicia; Çubut, Cankut; Carbonell-Caballero, Jose; Dopazo, Joaquín (BioMed Central, 2018)
    Background: Despite the progress in neuroblastoma therapies the mortality of high-risk patients is still high (40–50%) and the molecular basis of the disease remains poorly known. Recently, a mathematical model was used ...
  • Forslund, Kristoffer; Pereira, Cecile; Capella Gutiérrez, Salvador Jesús, 1985-; Sousa da Silva, Alan; Altenhoff, Adrian M.; Huerta Cepas, Jaime; Muffato, Matthieu; Patricio, Mateus; Vandepoele, Klaas; Ebersberger, Ingo; Blake, Judith; Fernández Breis, Jesualdo Tomás; Quest for Orthologs consortium; Boeckmann, Brigitte; Gabaldón Estevan, Juan Antonio, 1973-; Sonnhammer, Erik; Dessimoz, Christophe; Lewis, Suzanna E. (Oxford University Press, 2018)
    The Quest for Orthologs (QfO) is an open collaboration framework for experts in comparative phylogenomics and related research areas who have an interest in highly accurate orthology predictions and their applications. We ...
  • Usmanova, Dinara R.; Bogatyreva, Natalya S.; Ariño Bernad, Joan; Eremina, Aleksandra A.; Gorshkova, Anastasiya A.; Kanevskiy, German M.; Lonishin, Lyubov R.; Meister, Alexander V.; Yakupova, Alisa G.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2018)
    Motivation: Computational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic ...
  • Quinn, Thomas P.; Erb, Ionas; Richardson, Mark F.; Crowley, Tamsyn M. (Oxford University Press, 2018)
    Motivation: Although seldom acknowledged explicitly, count data generated by sequencing platforms exist as compositions for which the abundance of each component (e.g. gene or transcript) is only coherently interpretable ...
  • Merkel, Angelika; Fernández Callejo, Marcos; Casals, Eloi; Marco Sola, Santiago; Schuyler, Ronald P.; Gut, Ivo Glynne; Heath, Simon (Oxford University Press, 2019)
    Motivation: DNA methylation is essential for normal embryogenesis and development in mammals and can be captured at single base pair resolution by whole genome bisulfite sequencing (WGBS). Current available analysis tools ...
  • Díaz-Gay, Marcos; Park, Solip; Parra Farré, Genís; Laurie, Steven, 1973-; Beltran, Sergi; Castellví Bel, Sergi (MDPI, 2019)
    Colorectal cancer (CRC) shows aggregation in some families but no alterations in the known hereditary CRC genes. We aimed to identify new candidate genes which are potentially involved in germline predisposition to familial ...
  • Brial, Francois; Le Lay, Aurélie; Hedjazi, Lyamine; Tsang, Tsz; Fearnside, Jane F.; Otto, Georg W.; Alzaid, Fawaz; Wilder, Steven P.; Venteclef, Nicolas; Cazier, Jean-Baptiste; Nicholson, Jeremy K.; Day, Chris; Burt, Alastair D.; Gut, Ivo Glynne; Lathrop, Mark; Dumas, Marc-Emmanuel; Gauguier, Dominique (Nature Research, 2019)
    Non-alcoholic fatty liver disease (NAFLD) is often associated with obesity and type 2 diabetes. To disentangle etiological relationships between these conditions and identify genetically-determined metabolites involved in ...
  • Quintana-Gallardo, Lucía; Martín-Benito, Jaime; Marcilla, Miguel; Espadas, Guadalupe; Sabidó Aguadé, Eduard, 1981-; Valpuesta, José M. (Nature Research, 2019)
    Some molecular chaperones are involved not only in assisting the folding of proteins but also, given appropriate conditions, in their degradation. This is the case for Hsp70 and Hsp90 which, in concert with the cochaperone ...
  • Souriant, Shanti; Lastrucci, Claire; Vérollet, Christel (Elsevier, 2019)
    The tuberculosis (TB) bacillus, Mycobacterium tuberculosis (Mtb), and HIV-1 act synergistically; however, the mechanisms by which Mtb exacerbates HIV-1 pathogenesis are not well known. Using in vitro and ex vivo cell culture ...

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