Browsing Center for Genomic Regulation (CRG) by Title

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  • A 3-way hybrid approach to generate a new high-quality chimpanzee reference genome (Pan_tro_3.0)
    Kuderna, Lukas, 1989-; Laayouni, Hafid, 1968-; García Pérez, Raquel, 1989-; Povolotskaya, Inna, 1986-; Serres Armero, Aitor, 1992-; Gómez Garrido, Jèssica; Alioto, Tyler; Navarro i Cuartiellas, Arcadi, 1969-; Bertranpetit, Jaume, 1952-; Marquès i Bonet, Tomàs, 1975- (Oxford University Press, 2017)
    The chimpanzee is arguably the most important species for the study of human origins. A key resource for these studies is a high-quality reference genome assembly; however, as with most mammalian genomes, the current ...
  • A benchmark for RNA-seq quantification pipelines
    Teng, Mingxiang; Love, Michael I.; Davis, Carrie A.; Djebali, Sarah; Dobin, Alexander; Graveley, Brenton R.; Li, Sheng; Mason, Christopher E.; Olson, Sara; Pervouchine, Dmitri D.; Sloan, Cricket A.; Wei, Xintao; Zhan, Lijun; Irizarry, Rafael A. (BioMed Central, 2016)
    Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, ...
  • A chromatin code for alternative splicing involving a putative association between CTCF and HP1alpha proteins
    Agirre Ortiz de Guzmán, Eneritz, 1983-; Bellora Pereyra, Nicolás; Alló, Mariano; Pagès Pinós, Amadís; Bertucci, Paola; Kornblihtt, Alberto R.; Eyras Jiménez, Eduardo (BioMed Central, 2015)
    BACKGROUND: Alternative splicing is primarily controlled by the activity of splicing factors and by the elongation of the RNA polymerase II (RNAPII). Recent experiments have suggested a new complex network of splicing ...
  • A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis
    de la Herrán, Roberto; Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Martínez, Paulino (Wiley, 2023)
    Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and ...
  • A community-based participatory framework to co-develop Patient Education Materials (PEMs) for rare diseases: A model transferable across diseases
    Falcão, Marta; Allocca, Mariateresa; Rodrigues, Ana Sofia; Granjo, Pedro; Francisco, Rita; Pascoal, Carlota; Rossi, Maria Grazia; Marques-da-Silva, Dorinda; Magrinho, Salvador C. M.; Jaeken, Jaak; Castro, Larisa Aragon; Freitas, Cláudia de; Videira, Paula A.; Andrés-Aguayo, Luísa de; Ferreira, Vanessa Miriam dos Reis (MDPI, 2023)
    At least 50% of chronic disease patients don't follow their care plans, leading to lower health outcomes and higher medical costs. Providing Patient Education Materials (PEMs) to individuals living with a disease can help ...
  • A comparative encyclopedia of DNA elements in the mouse genome
    Yue, Feng; Breschi, Alessandra, 1988-; Pervouchine, Dmitri D.; Djebali, Sarah; Prieto Barja, Pablo, 1986-; Lagarde, Julien; Bussotti, Giovanni, 1983-; Tanzer, Andrea; Notredame, Cedric; Guigó Serra, Roderic; Ren, Bing; The Mouse Encyclopedia of DNA Elements (ENCODE) Consortium (Nature Publishing Group, 2014)
    The laboratory mouse shares the majority of its protein-coding genes with humans, making it the premier model organism in biomedical research, yet the two mammals differ in significant ways. To gain greater insights into ...
  • A comparative genomics multitool for scientific discovery and conservation
    Zoonomia Consortium; Serres Armero, Aitor, 1992-; Juan, David; Kuderna, Lukas, 1989-; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2020)
    The Zoonomia Project is investigating the genomics of shared and specialized traits in eutherian mammals. Here we provide genome assemblies for 131 species, of which all but 9 are previously uncharacterized, and describe ...
  • A comparison of gene expression and DNA methylation patterns across tissues and species
    Blake, Lauren E.; Roux, Julien; Hernando Herráez, Irene, 1985-; Banovich, Nicholas E.; García Pérez, Raquel, 1989-; Hsiao, Chiaowen Joyce; Eres, Ittai; Cuevas, Claudia; Marquès i Bonet, Tomàs, 1975-; Gilad, Yoav (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    Previously published comparative functional genomic data sets from primates using frozen tissue samples, including many data sets from our own group, were often collected and analyzed using nonoptimal study designs and ...
  • A comparison of mechanistic signaling pathway activity analysis methods
    Amadoz, Alicia; Hidalgo, Marta R.; Çubut, Cankut; Carbonell-Caballero, Jose; Dopazo, Joaquín (Oxford University Press, 2019)
    Understanding the aspects of cell functionality that account for disease mechanisms or drug modes of action is a main challenge for precision medicine. Classical gene-based approaches ignore the modular nature of most human ...
  • A comparison of RNA-Seq results from paired formalin-fixed paraffin-embedded and fresh-frozen glioblastoma tissue samples
    Esteve-Codina, Anna; Arpí Llucià, Oriol; Martínez-García, Maria; Pineda, Estela; Mallo, Mar; Gut, Marta; Carrato, Cristina; Rovira Guerín, Ana; Lopez, Raquel; Tortosa, Avelina; Dabad, Marc; del Barco, Sonia; Heath, Simon; Bagué, Silvia; Ribalta, Teresa; Alameda Quitllet, Francisco; de la Iglesia, Nuria; Balaña, Carmen; GLIOCAT Group (Public Library of Science (PLoS), 2017)
    The molecular classification of glioblastoma (GBM) based on gene expression might better explain outcome and response to treatment than clinical factors. Whole transcriptome sequencing using next-generation sequencing ...
  • A complex secretory program orchestrated by the inflammasome controls paracrine senescence
    Acosta, Juan Carlos; Banito, Ana; Wuestefeld, Torsten; Georgilis, Athena; Janich, Peggy, 1981-; Morton, Jennifer P.; Athineos, Dimitris; Kang, Tae-Won; Lasitschka, Felix; Andrulis, Mindaugas; Pascual, Gloria; Morris, Kelly J.; Khan, Sadaf; Jin, Hong; Dharmalingam, Gopuraja; Snijders, Ambrosius P.; Carroll, Thomas; Capper, David; Pritchard, Catrin; Inman, Gareth J.; Longerich, Thomas; Sansom, Owen J.; Aznar Benitah, Salvador; Zender, Lars; Gil, Jesús (Nature Publishing Group, 2013)
    Oncogene-induced senescence (OIS) is crucial for tumour suppression. Senescent cells implement a complex pro-inflammatory response termed the senescence-associated secretory phenotype (SASP). The SASP reinforces senescence, ...
  • A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing
    Alioto, Tyler; Derdak, Sophia; Ribeca, Paolo; Castro Giner, Francesc; Beltran, Sergi; Raineri, Emanuele; Dabad, Marc; Heath, Simon; Gut, Marta; Gut, Ivo Glynne (Nature Research, 2015)
    As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different ...
  • A comprehensive proteomics-based interaction screen that links DYRK1A to RNF169 and to the DNA damage response
    Roewenstrunk, Julia Maria, 1981-; Di Vona, Chiara, 1981-; Chen, Jie; Borràs, Eva; Dong, Chao; Arató, Krisztina, 1981-; Sabidó Aguadé, Eduard, 1981-; Huen, Michael S. Y.; Luna Gargantilla, Susana de la (Nature Research, 2019)
    Dysregulation of the DYRK1A protein kinase has been associated with human disease. On the one hand, its overexpression in trisomy 21 has been linked to certain pathological traits of Down syndrome, while on the other, ...
  • A comprehensive view of the ß-arrestinome
    Crépieux, Pascale; Poupon, Anne; Langonné Gallay, Nathalie; Reiter, Éric R.; Delgado Blanco, Javier; Schaefer, Martin H.; Bourquard, Thomas; Serrano Pubull, Luis, 1982-; Kiel, Christina (Frontiers, 2017)
    G protein-coupled receptors (GPCRs) are membrane receptors critically involved in sensing the environment and orchestrating physiological processes. As such, they transduce extracellular signals such as hormone, ...
  • A computational approach for the discovery of protein-RNA networks
    Marchese, Domenica, 1986-; Livi, Carmen Maria; Tartaglia, Gian Gaetano (Humana Press (Springer Imprint), 2016)
    Protein–RNA interactions play important roles in a wide variety of cellular processes, ranging from transcriptional and posttranscriptional regulation of genes to host defense against pathogens. In this chapter we present ...
  • A computational clonal analysis of the developing mouse limb bud
    Marcon, Luciano, 1983-; Arqués, Carlos G.; Torres, Miguel S.; Sharpe, James (Public Library of Science (PLoS), 2011)
    A comprehensive spatio-temporal description of the tissue movements underlying organogenesis would be an extremely useful resource to developmental biology. Clonal analysis and fate mappings are popular experiments to study ...
  • A computational pipeline to learn gene expression predictive models from epigenetic information at enhancers or promoters
    González Ramírez, Mar, 1991-; Blanco, Enrique; Di Croce, Luciano (Elsevier, 2023)
    Here, we present a computational pipeline to obtain quantitative models that characterize the relationship of gene expression with the epigenetic marking at enhancers or promoters in mouse embryonic stem cells. Our protocol ...
  • A Concentration-Dependent Liquid Phase Separation Can Cause Toxicity upon Increased Protein Expression
    Bolognesi, Benedetta; Lorenzo Gotor, Maria de las Nieves; Dhar, Riddhiman; Cirillo, Davide; Baldrighi, Marta; Gaetano Tartaglia, Gian; Lehner, Ben, 1978- (Elsevier, 2016)
    Multiple human diseases are associated with a liquid-to-solid phase transition resulting in the formation of amyloid fibers or protein aggregates. Here, we present an alternative mechanism for cellular toxicity based on a ...
  • A conserved expression signature predicts growth rate and reveals cell & lineage-specific differences
    Jiang, Zhisheng; Generoso, Serena Francesca, 1988-; Badia, Marta; Payer, Bernhard; Carey, Lucas, 1980- (Public Library of Science (PLoS), 2021)
    Isogenic cells cultured together show heterogeneity in their proliferation rate. To determine the differences between fast and slow-proliferating cells, we developed a method to sort cells by proliferation rate, and performed ...
  • A coordinated response at the transcriptome and interactome level is required to ensure uropathogenic Escherichia coli survival during bacteremia
    Sanchez de Groot, Natalia; Torrent Burgas, Marc (MDPI, 2019)
    Localized infections or disruption of the skin barrier can enable the entry of bacteria into the bloodstream, possibly leading to acute inflammation and sepsis. There is currently no holistic view on how bacteria can survive ...

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