Browsing Center for Genomic Regulation (CRG) by Title

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  • Identification and analysis of splicing quantitative trait loci across multiple tissues in the human genome
    Garrido Martín, Diego, 1992-; Borsari, Beatrice, 1992-; Calvo, Miquel (Calvo Llorca); Reverter, Ferran; Guigó Serra, Roderic (Nature Research, 2021)
    Alternative splicing (AS) is a fundamental step in eukaryotic mRNA biogenesis. Here, we develop an efficient and reproducible pipeline for the discovery of genetic variants that affect AS (splicing QTLs, sQTLs). We use it ...
  • Identification of a de novo splicing variant in the Coffin-Siris gene, SMARCE1, in a patient with Angelman-like syndrome
    Aguilera, Cinthia; Gabau, Elisabeth; Laurie, Steven, 1973-; Baena, Neus; Derdak, Sophia; Capdevila, Núria; Ramirez, Ariadna; Delgadillo, Veronica; García-Catalan, Maria Jesus; Brun i Gasca, Carme; Guitart, Miriam; Ruiz, Anna (Wiley, 2019)
    Background: Patients affected by Angelman syndrome (AS) present severe intellectual disability, lack of speech, ataxia, seizures, abnormal electroencephalography (EEG), and a characteristic behavioral phenotype. Around 10% ...
  • Identification of ALK gene alterations in urothelial carcinoma
    Bellmunt Molins, Joaquim, 1959-; Selvarajah, Shamini; Rodig, Scott; Salido Galeote, Marta; Muga, Silvia de; Costa, Irmgard; Bellosillo Paricio, Beatriz; Werner, Lillian; Mullane, Stephanie A.; Fay, André P.; O’Brien, Robert; Barretina, Jordi; Minoche, André E.; Signoretti, Sabina; Montagut Viladot, Clara; Himmelbauer, Heinz; Berman, David M.; Kantoff, Philip; Choueiri, Toni K.; Rosenberg, Jonathan E. (Public Library of Science (PLoS), 2014)
    Anaplastic lymphoma kinase (ALK) genomic alterations have emerged as a potent predictor of benefit from treatment with ALK inhibitors in several cancers. Currently, there is no information about ALK gene alterations in ...
  • Identification of autosomal cis expression quantitative trait methylation (cis eQTMs) in children's blood
    Ruiz-Arenas, Carlos; Hernandez-Ferrer, Carles, 1987-; Vives Usano, Marta, 1990-; Marí, Sergi; Casas Sanahuja, Maribel; Vafeiadi, Marina, 1983-; Vrijheid, Martine; González Ruiz, Juan Ramón; Bustamante Pineda, Mariona (eLife Sciences Publications, 2022)
    Background: The identification of expression quantitative trait methylation (eQTMs), defined as associations between DNA methylation levels and gene expression, might help the biological interpretation of epigenome-wide ...
  • Identification of bovine sperm surface proteins involved in carbohydrate-mediated fertilization interactions
    Defaus, Sira; Avilés, Manuel; Andreu Martínez, David; Gutiérrez Gallego, Ricardo, 1968- (Elsevier, 2016)
    Glycan-protein interactions play a key role in mammalian fertilization, but data on the composition and identities of protein complexes involved in fertilization events are scarce, with the added complication that the ...
  • Identification of chromatin loops from Hi-C interaction matrices by CTCF-CTCF topology classification
    Galan Martínez, Silvia, 1992-; Serra, François; Marti-Renom, Marc A. (Oxford University Press, 2022)
    Genome-wide profiling of long-range interactions has revealed that the CCCTC-Binding factor (CTCF) often anchors chromatin loops and is enriched at boundaries of the so-called Topologically Associating Domains, which ...
  • Identification of constrained sequence elements across 239 primate genomes
    Kuderna, Lukas, 1989-; Valenzuela, Alejandro; Navarro i Cuartiellas, Arcadi, 1969-; Marquès i Bonet, Tomàs, 1975-; Kai-How Farh, Kyle (Nature Research, 2023)
    Noncoding DNA is central to our understanding of human gene regulation and complex diseases1,2, and measuring the evolutionary sequence constraint can establish the functional relevance of putative regulatory elements in ...
  • Identification of enhancer-promoter contacts in embryoid bodies by quantitative chromosome conformation capture (4C)
    Tian, Tian V.; Vidal Ocabo, Enrique; Graf, T. (Thomas); Stik, Grégoire (MyJove Corporation, 2020)
    During mammalian development, cell fates are determined through the establishment of regulatory networks that define the specificity, timing, and spatial patterns of gene expression. Embryoid bodies (EBs) derived from ...
  • Identification of gene mutations and fusion genes in patients with Sézary syndrome.
    Prasad, Aparna; Rabionet, Raquel; Espinet Solà, Blanca; Zapata Ortiz, Luis, 1985-; Puiggros Metje, Anna Maria; Melero Vilella, Maria Carme; Puig, Anna; Sarria-Trujillo, Yaris; Ossowski, Stephan; Garcia-Muret, Maria P.; Estrach, Teresa; Servitje, Octavio; Lopez-Lerma, Ingrid; Gallardo Hernández, Fernando; Pujol Vallverdú, Ramon Maria; Estivill, Xavier, 1955- (Elsevier, 2016)
    Sézary syndrome is a leukemic form of cutaneous T-cell lymphoma with an aggressive clinical course. The genetic etiology of the disease is poorly understood, with chromosomal abnormalities and mutations in some genes being ...
  • Identification of genetic variants associated with alternative splicing using sQTLseekeR
    Monlong, Jean; Calvo, Miquel (Calvo Llorca); Ferreira, Pedro G.; Guigó Serra, Roderic (Nature Publishing Group, 2014)
    Identification of genetic variants affecting splicing in RNA sequencing population studies is still in its infancy. Splicing phenotype is more complex than gene expression and ought to be treated as a multivariate phenotype ...
  • Identification of leukemic and pre-leukemic stem cells by clonal tracking from single-cell transcriptomics
    Velten, Lars; Story, Benjamin A.; Hernández-Malmierca, Pablo; Raffel, Simon; Leonce, Daniel R.; Milbank, Jennifer; Paulsen, Malte; Demir, Aykut; Szu-Tu, Chelsea; Frömel, Robert; Lutz, Christoph; Novak, Daniel; Jann, Johann-Christoph; Pabst, Caroline; Boch, Tobias; Hofmann, Wolf-Karsten; Müller-Tidow, Carsten; Trumpp, Andreas; Haas, Simon; Steinmetz, Lars M. (Nature Research, 2021)
    Cancer stem cells drive disease progression and relapse in many types of cancer. Despite this, a thorough characterization of these cells remains elusive and with it the ability to eradicate cancer at its source. In acute ...
  • Identification of long non-coding RNAs and RNA binding proteins in breast cancer subtypes
    Cava, Claudia; Armaos, Alexandros, 1989-; Lang, Benjamin; Tartaglia, Gian Gaetano; Castiglioni, Isabella (Nature Research, 2022)
    Breast cancer is a heterogeneous disease classified into four main subtypes with different clinical outcomes, such as patient survival, prognosis, and relapse. Current genetic tests for the differential diagnosis of BC ...
  • Identification of protein-damaging mutations in 10 swine taste receptors and 191 appetite-reward genes
    Clop, Alex; Sharaf, Abdoallah; Castelló, Anna; Ramos-Onsins, Sebastián; Cirera, Susanna; Mercadé, Anna; Derdak, Sophia; Beltran, Sergi; Huisman, Abe; Fredholm, Merete; van As, Pieter; Sánchez, Armand (BioMed Central, 2016)
    Background: Taste receptors (TASRs) are essential for the body’s recognition of chemical compounds. In the tongue, TASRs sense the sweet and umami and the toxin-related bitter taste thus promoting a particular eating ...
  • Identification of tipifarnib sensitivity biomarkers in T-cell acute lymphoblastic leukemia and T-cell lymphoma
    Alonso Alonso, Ruth; Mondéjar, Rufino; Martínez, Nerea; García Diaz, Nuria; Pérez, Cristina; Merino, David; Rodríguez, Marta; Esteve-Codina, Anna; Fusté, Berta; Gut, Marta; Burrows, Francis; Scholz, Catherine; Vaqué, José Pedro; Gualberto, Antonio; Piris, Miguel A. (Nature Research, 2020)
    Patients diagnosed with T-cell leukemias and T-cell lymphomas (TCLs) still have a poor prognosis and an inadequate response to current therapies, highlighting the need for targeted treatments. We have analyzed the potential ...
  • Identification of tissue-specific and common methylation quantitative trait loci in healthy individuals using MAGAR
    Scherer, Michael; Gasparoni, Gilles; Rahmouni, Souad; Shashkova, Tatiana; Arnoux, Marion; Louis, Edward J.; Nostaeva, Arina; Avalos, Diana; Dermitzakis, Emmanuouil T.; Aulchenko, Yurii S.; Lengauer, Thomas; Lyons, Paul A.; Georges, Michel; Walter, Jörn (BioMed Central, 2021)
    Background: Understanding the influence of genetic variants on DNA methylation is fundamental for the interpretation of epigenomic data in the context of disease. There is a need for systematic approaches not only for ...
  • Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data
    Marot-Lassauzaie, Valérie; Beneyto Calabuig, Sergi; Obermayer, Benedikt; Velten, Lars; Beule, Dieter; Haghverdi, Laleh (Oxford University Press, 2024)
    Motivation: Single-cell RNA sequencing (scRNA-seq) data are widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it ...
  • Identifying clinically useful biomarkers in neurodegenerative disease through a collaborative approach: the NeuroToolKit
    Johnson, Sterling C.; Suárez-Calvet, Marc; Suridjan, Ivonne; Minguillón, Carolina; Gispert López, Juan Domingo; Jonaitis, Erin; Michna, Agatha; Carboni, Margherita; Bittner, Tobias; Rabe, Christina; Kollmorgen, Gwendlyn; Zetterberg, Henrik; Blennow, Kaj (BioMed Central, 2023)
    Background: Alzheimer's disease (AD) is a complex and heterogeneous disease, which requires reliable biomarkers for diagnosis and monitoring disease activity. Preanalytical protocol and technical variability associated ...
  • Identifying miRNA-mRNA regulatory networks on extreme n-6/n-3 polyunsaturated fatty acid ratio expression profiles in porcine skeletal muscle
    Manaig, Yron Joseph Yabut; Criado-Mesas, Lourdes; Esteve-Codina, Anna; Mármol-Sánchez, Emilio; Castelló, Anna; Sánchez, Armand; Folch, Josep M. (Public Library of Science (PLoS), 2023)
    Omega-3 (n-3) and omega-6 (n-6) polyunsaturated fatty acids (PUFAs) are essential fatty acids with antagonistic inflammatory functions that play vital roles in metabolic health and immune response. Current commercial swine ...
  • Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis
    Senthivel, Vivek Raj, 1983-; Sturrock, Marc; Piedrafita, Gabriel; Isalan, Mark (Nature Publishing Group, 2016)
    Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like ...
  • Identity noise and adipogenic traits characterize dermal fibroblast aging
    Aznar Benitah, Salvador; Lafzi, Atefeh; Berenguer-Llergo, Antonio; Youssif, Catrin; Castellanos, Andrés; Solanas, Guiomar; Peixoto, Francisca Oliveira; Stephan-Otto Attolini, Camille; Prats, Neus; Aguilera, Mònica; Martín Caballero, Juan; Heyn, Holger; Aznar Benitah, Salvador (Elsevier, 2018)
    During aging, stromal functions are thought to be impaired, but little is known whether this stems from changes of fibroblasts. Using population- and single-cell transcriptomics, as well as long-term lineage tracing, we ...

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