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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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  • MACF1 links Rapsyn to microtubule- and actin-binding proteins to maintain neuromuscular synapses
    Oury, Julien; Liu, Yun; Töpf, Ana; Todorovic, Slobodanka; Hoedt, Esthelle; Preethish-Kumar, Veeramani; Neubert, Thomas A.; Lin, Weichun; Lochmüller, Hanns; Burden, Steven J. (Rockefeller University Press, 2019)
    Complex mechanisms are required to form neuromuscular synapses, direct their subsequent maturation, and maintain the synapse throughout life. Transcriptional and post-translational pathways play important roles in synaptic ...
  • Machine learning identifies stemness features associated with oncogenic dedifferentiation
    Malta, Tathiane M.; Heyn, Holger; Wiznerowicz, Maciej (Elsevier, 2018)
    Cancer progression involves the gradual loss of a differentiated phenotype and acquisition of progenitor and stem-cell-like features. Here, we provide novel stemness indices for assessing the degree of oncogenic ...
  • Machine learning methods applied to genotyping data capture interactions between single nucleotide variants in late onset Alzheimer's disease
    Arnal, Magdalena; Bini, Giorgio; Fernández Orth, Dietmar; Samaras, Eleftherios; Kassis, Maya; Aisopos, Fotis; Rambla de Argila, Jordi; Paliouras, George; Garrard, Peter; Giambartolomei, Claudia; Tartaglia, Gian Gaetano (Wiley Open Access, 2022)
    Introduction: Genome-wide association studies (GWAS) in late onset Alzheimer's disease (LOAD) provide lists of individual genetic determinants. However, GWAS do not capture the synergistic effects among multiple genetic ...
  • Machine learning: how much does it tell about protein folding rates?
    Corrales, Marc; Cuscó, Pol; Usmanova, Dinara R.; Chen, Heng-Chang; Bogatyreva, Natalya S.; Filion, Guillaume; Ivankov, Dmitry N. (Public Library of Science (PLoS), 2015)
    The prediction of protein folding rates is a necessary step towards understanding the principles of protein folding. Due to the increasing amount of experimental data, numerous protein folding models and predictors of ...
  • Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease
    Garrido Trigo, Alba; Marchese, Domenica, 1986-; Caratù, Ginevra; Heyn, Holger; Salas, Azucena (Nature Research, 2023)
    Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains ...
  • MAF amplification licenses ERα through epigenetic remodelling to drive breast cancer metastasis
    Llorente, Alicia; Ballaré, Cecilia Julia; Blanco, Enrique; Di Croce, Luciano; Gomis, Roger R. (Nature Research, 2023)
    MAF amplification increases the risk of breast cancer (BCa) metastasis through mechanisms that are still poorly understood yet have important clinical implications. Oestrogen-receptor-positive (ER+) BCa requires oestrogen ...
  • Major roles for pyrimidine dimers, nucleotide excision repair, and ATR in the alternative splicing response to UV irradiation
    Muñoz, Manuel Javier; Nieto Moreno, Nicolás; Giono, Luciana E.; Cambindo Botto, Adrián E.; Dujardin, Gwendal; Bastianello, Giulia; Lavore, Stefania; Torres Méndez, Antonio; Menck, Carlos Frederico Martins; Blencowe, Benjamin J.; Irimia Martínez, Manuel; Foiani, Marco; Kornblihtt, Alberto R. (Elsevier, 2017)
    We have previously found that UV irradiation promotes RNA polymerase II (RNAPII) hyperphosphorylation and subsequent changes in alternative splicing (AS). We show now that UV-induced DNA damage is not only necessary but ...
  • Making sense of big data in health research: Towards an EU action plan
    Auffray, Charles; Gut, Ivo Glynne; Zanetti, Gianluigi (BioMed Central, 2016)
    Medicine and healthcare are undergoing profound changes. Whole-genome sequencing and high-resolution imaging technologies are key drivers of this rapid and crucial transformation. Technological innovation combined with ...
  • Mammalian HP1 isoforms have specific roles in heterochromatin structure and organization
    Bosch Presegué, Laia; Raurell Vila, Helena; Thackray, Joshua K.; González, Jessica; Casal, Carmen; Kane-Goldsmith, Noriko; Vizoso, Miguel; Brown, Jeremy P.; Gómez, Antonio; Ausió, Juan; Zimmermann, Timo; Esteller, Manel; Schotta, Gunnar; Singh, Prim B.; Serrano, Lourdes; Vaquero, Alejandro (Elsevier, 2017)
    HP1 is a structural component of heterochromatin. Mammalian HP1 isoforms HP1α, HP1β, and HP1γ play different roles in genome stability, but their precise role in heterochromatin structure is unclear. Analysis of Hp1α-/-, ...
  • Mammalian neuronal mRNA transport complexes: the few knowns and the many unknowns
    Rodrigues, Elsa C.; Grawenhoff, Julia; Baumann, Sebastian; Lorenzon, Nicola; Maurer, Sebastian (Frontiers, 2021)
    Hundreds of messenger RNAs (mRNAs) are transported into neurites to provide templates for the assembly of local protein networks. These networks enable a neuron to configure different cellular domains for specialized ...
  • Mapping the energetic and allosteric landscapes of protein binding domains.
    Faure, Andre J.; Domingo Espinós, Júlia, 1991-; Schmiedel, Jörn M.; Hidalgo-Carcedo, Cristina; Diss, Guillaume; Lehner, Ben, 1978- (2022)
    Allosteric communication between distant sites in proteins is central to biological regulation but still poorly characterized, limiting understanding, engineering and drug development1-6. An important reason for this is ...
  • MapToCleave: High-throughput profiling of microRNA biogenesis in living cells
    Kang, Wenjing; Fromm, Bastian; Houben, Anna J.; Høye, Eirik; Bezdan, Daniela; Arnan Ros, Carme; Thrane, Kim; Asp, Michaela; Johnson, Rory; Biryukova, Inna; Friedländer, Marc R. (Elsevier, 2021)
    Previous large-scale studies have uncovered many features that determine the processing of microRNA (miRNA) precursors; however, they have been conducted in vitro. Here, we introduce MapToCleave, a method to simultaneously ...
  • Mass spectrometry identification of biomarkers in extracellular vesicles from plasmodium vivax liver hypnozoite infections
    Gualdrón-López, Melisa; Díaz Varela, Míriam; Aparici-Herraiz, Iris; Cuscó Pons, Pol, 1987-; González, Juan Ramón; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Fernandez-Becerra, Carmen; del Portillo, Hernando A. (Elsevier, 2022)
    Latent liver stages termed hypnozoites cause relapsing Plasmodium vivax malaria infection and represent a major obstacle in the goal of malaria elimination. Hypnozoites are clinically undetectable, and presently, there are ...
  • Massive gene presence-absence variation shapes an open pan-genome in the Mediterranean mussel
    Gerdol, Marco; Cruz, Fernando; Gómez-Garrido, Jèssica; Vlasova, Anna; Naranjo Ortiz, Miguel Ángel, 1989-; Corvelo, André; Frias, Leonor; Gut, Marta; Gabaldón Estevan, Juan Antonio, 1973-; Alioto, Tyler; Figueras, Antonio (BioMed Central, 2020)
    Background: The Mediterranean mussel Mytilus galloprovincialis is an ecologically and economically relevant edible marine bivalve, highly invasive and resilient to biotic and abiotic stressors causing recurrent massive ...
  • MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets
    Choi, Meena; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Vitek, Olga (Nature Research, 2020)
    MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational ...
  • MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets
    Cozzuto, Luca; Liu, Huanle; Pryszcz, Leszek Piotr, 1985-; Hermoso Pulido, Antonio; Delgado-Tejedor, Anna; Ponomarenko, Julia; Novoa, Eva Maria (Frontiers Media, 2020)
    The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is ...
  • Maternal and fetal genetic contribution to gestational weight gain
    Warrington, Nicole M.; Espinosa Díaz, Ana; Guxens Junyent, Mònica; Kogevinas, Manolis; Bustamante Pineda, Mariona; Lawlor, Deborah (Nature Research, 2018)
    Background: Clinical recommendations to limit gestational weight gain (GWG) imply high GWG is causally related to adverse outcomes in mother or offspring, but GWG is the sum of several inter-related complex phenotypes ...
  • Maternal and neonatal immune response to SARS-CoV-2, IgG transplacental transfer and cytokine profile
    Rubio, Rocío; Aguilar, Ruth; Bustamante Pineda, Mariona; Muñoz, Erica; Vázquez-Santiago, Miquel; Santano, Rebeca; Vidal, Marta; Rodrigo Melero, Natalia; Parras, Daniel; Serra, Pau; Santamaria, Pere; Carolis, Carlo; Izquierdo, Luis; Gómez-Roig, María Dolores; Dobaño, Carlota; Moncunill, Gemma; Mazarico, Edurne (Frontiers, 2022)
    SARS-CoV-2 infected pregnant women are at increased risk of severe COVID-19 than non-pregnant women and have a higher risk of adverse pregnancy outcomes like intrauterine/fetal distress and preterm birth. However, little ...
  • Maternal co-ordinate gene regulation and axis polarity in the scuttle fly Megaselia abdita
    Wotton, Karl R.; Jiménez Guri, Eva; Jaeger, Johannes, 1973- (Public Library of Science (PLoS), 2015)
    Axis specification and segment determination in dipteran insects are an excellent model system for comparative analyses of gene network evolution. Antero-posterior polarity of the embryo is established through systems of ...
  • Maternal pluripotency factors initiate extensive chromatin remodelling to predefine first response to inductive signals
    Gentsch, George E.; Spruce, Thomas; Owens, Nick D.L.; Smith, James (Nature Research, 2019)
    Embryonic development yields many different cell types in response to just a few families of inductive signals. The property of signal-receiving cells that determines how they respond to inductive signals is known as ...

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