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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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  • Li, Li; Gómez, Antonio; Hakem, Razq (American Society for Clinical Investigation, 2018)
    Storage and consumption of neutral lipids in lipid droplets (LDs) are essential for energy homeostasis and tightly coupled to cellular metabolism. However, how metabolic cues are integrated in the life cycle of LDs is ...
  • Brouwer, Rutger W.; Hout, Mirjam C. van den; IJcken, Wilfred F. van; Soler, Eric; Stadhouders, Ralph (Humana Press (Springer Imprint), 2017)
    The development and widespread implementation of chromosome conformation capture (3C) technology has allowed unprecedented new insight into how chromosomes are folded in three-dimensional (3D) space. 3C and its derivatives ...
  • 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 ...
  • García González, Laura; Martí Sarrias, Andrea; Puertas, Maria C.; Bayón-Gil, Ángel; Resa Infante, Patricia; Martinez Picado, Javier; Navarro i Cuartiellas, Arcadi, 1969-; Acosta, Sandra (Company of Biologists, 2023)
    As early as in the acute phase of the coronavirus disease 2019 (COVID-19) pandemic, the research community voiced concerns about the long-term implications of infection. Severe acute respiratory syndrome coronavirus 2 ...
  • Cheng, Chao; Alexander, Roger; Min, Renqiang; Leng, Jing; Yip, Kevin Y.; Rozowsky, Joel S.; Yan, Koon-Kiu; Dong, Xianjun; Djebali, Sarah; Ruan, Yijun; Davis, Carrie A.; Carninci, Piero; Lassmann, Timo; Gingeras, Thomas R.; Guigó Serra, Roderic; Birney, Ewan; Weng, Zhiping; Snyder, Michael; Gerstein, Mark B. (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Statistical models have been used to quantify the relationship between gene expression and transcription factor (TF) binding signals. Here we apply the models to the large-scale data generated by the ENCODE project to study ...
  • Pryszcz, Leszek Piotr, 1985-; Németh, Tibor; Gácser, Attila; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2013)
    Invasive candidiasis is the most commonly reported invasive fungal infection worldwide. Although Candida albicans remains the main cause, the incidence of emerging Candida species, such as C. parapsilosis is increasing. ...
  • Ciampi, Ludovica; Serrano Pubull, Luis, 1982-; Irimia Martínez, Manuel (Wiley, 2024)
    Alternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal ...
  • Verde, Gaetano; De Llobet, Lara Isabel; Wright, Roni H.G.; Quilez Oliete, Javier; Peiró Sales, Sandra; Le Dily, François; Beato, Miguel (MDPI, 2018)
    Breast cancer prognosis and response to endocrine therapy strongly depends on the expression of the estrogen and progesterone receptors (ER and PR, respectively). Although much is known about ERα gene (ESR1) regulation ...
  • Martínez-Useros, Javier; Georgiev Hristov, Tihomir; Fernández Aceñero, María Jesús; Borrero-Palacios, Aurea; Indacochea Cusirramos, Alberto; Guerrero Jijon, Santiago Xavier; Li, Weiyao; Cebrián, Arancha; del Pulgar, Teresa Gómez; Puime Otín, Alberto; Puerto Nevado, Laura del; Rodríguez Remírez, María; Pérez, Núria; Celdrán Uriarte, Ángel; Gebauer, Fátima; García-Foncillas, Jesús (Public Library of Science (PLoS), 2017)
    Pancreatic ductal adenocarcinoma is an aggressive form of pancreatic cancer and the fourth leading cause of cancer-related death. When possible, curative approaches are based on surgical resection, though not every patient ...
  • Wurth, Laurence; Papasaikas, Panagiotis; Olmeda, David; Bley, Nadine; Calvo, Guadalupe T.; Guerrero Jijon, Santiago Xavier; Cerezo-Wallis, Daniela; Martínez-Useros, Javier; García-Fernández, María; Hüttelmaier, Stefan; Soengas, María S.; Gebauer, Fátima (Elsevier, 2016)
    RNA binding proteins (RBPs) modulate cancer progression through poorly understood mechanisms. Here we show that the RBP UNR/CSDE1 is overexpressed in melanoma tumors and promotes invasion and metastasis. iCLIP sequencing, ...
  • Agraz-Doblas, Antonio; Bueno, Clara; Bashford-Rogers, Rachael; Roy, Anindita; Schneider, Pauline; Bardini, Michela; Ballerini, Paola; Cazzaniga, Gianni; Moreno, Thaidy; Revilla, Carlos; Gut, Marta; Valsecchi, Maria G.; Roberts, Irene; Pieters, Rob; De Lorenzo, Paola; Varela, Ignacio; Menéndez, Pablo; Stam, Ronald W. (Ferrata Storti Foundation, 2019)
    B-cell acute lymphoblastic leukemia is the commonest childhood cancer. In infants, B-cell acute lymphoblastic leukemia remains fatal, especially in patients with t(4;11), present in ~80% of cases. The pathogenesis of ...
  • Miravet Verde, Samuel; Ferrar, Tony; Espadas, Guadalupe; Mazzolini, Rocco; Gharrab, Anas; Sabidó Aguadé, Eduard, 1981-; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (Wiley Open Access, 2019)
    Identification of small open reading frames (smORFs) encoding small proteins (≤ 100 amino acids; SEPs) is a challenge in the fields of genome annotation and protein discovery. Here, by combining a novel bioinformatics tool ...
  • Cantó-Santos, Judith; Valls-Roca, Laura; Tobías, Ester; García-García, Francesc Josep; Guitart-Mampel, Mariona; Esteve-Codina, Anna; Martín-Mur, Beatriz; Casado, Mercedes; Artuch, Rafael; Solsona-Vilarrasa, Estel; Fernandez-Checa, José Carlos; García-Ruiz, Carmen; Rentero, Carles; Enrich, Carlos; Moreno-Lozano, Pedro J.; Milisenda, José César; Cardellach, Francesc; Grau-Junyent, Josep M.; Garrabou, Glòria (Wiley, 2023)
    Inclusion body myositis (IBM) is an inflammatory myopathy clinically characterized by proximal and distal muscle weakness, with inflammatory infiltrates, rimmed vacuoles and mitochondrial changes in muscle histopathology. ...
  • Blanco Picazo, Pedro; Fernández Orth, Dietmar; Brown Jaque, Maryury; Miró, Elisenda; Espinal, Paula; Rodríguez Rubio, Lorena; Muniesa, Maite; Navarro, Ferran (Nature Research, 2020)
    Bacteriophages are abundant in human biomes and therefore in human clinical samples. Although this is usually not considered, they might interfere with the recovery of bacterial pathogens at two levels: 1) by propagating ...
  • Durán, Elisa; Djebali, Sarah; González, Santi; Flores, Oscar; Mercader Bigas, Josep Maria; Guigó Serra, Roderic; Torrents, David; Soler López, Montserrat; Orozco, Modesto (Oxford University Press, 2013)
    Although protein recognition of DNA motifs in promoter regions has been traditionally considered as a critical regulatory element in transcription, the location of promoters, and in particular transcription start sites ...
  • Declercq, Arthur; Bouwmeester, Robbin; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Hirschler, Aurélie; Carapito, Christine; Martens, Lennart; Degroeve, Sven; Gabriels, Ralf (Oxford University Press, 2023)
    Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such ...
  • Stratakis, Nikos; Maitre, Léa; Fernández-Barrés, Sílvia; Basagaña Flores, Xavier; Casas Sanahuja, Maribel; Fossati, Serena; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Urquiza, José M.; Vrijheid, Martine; Chatzi, Leda (eLife, 2022)
    Urinary metabolic profiling is a promising powerful tool to reflect dietary intake and can help understand metabolic alterations in response to diet quality. Here, we used 1H NMR spectroscopy in a multicountry study in ...
  • Erb, Ionas; González-Vallinas Rostes, Juan, 1983-; Bussotti, Giovanni, 1983-; Blanco, Enrique; Eyras Jiménez, Eduardo; Notredame, Cedric (Oxford University Press, 2012)
    We address the challenge of regulatory sequence alignment with a new method, Pro-Coffee, a multiple aligner specifically designed for homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated ...
  • Borràs, Eva; Pastor, Olga; Sabidó Aguadé, Eduard, 1981- (American Chemical Society (ACS), 2021)
    The need for a better understanding of cellular heterogeneity has pushed mass spectrometry technologies to the analysis of single-cell and single-cell-type proteomes, although several challenges still limit their widespread ...
  • Fernández Rodríguez, Juana; Morales la Madrid, Andrés; Gel, Bernat; Castañeda Heredia, Alicia; Salvador, Héctor; Martínez Iniesta, María; Moutinho, Catia; Morata, Jordi; Heyn, Holger; Blanco, Ignacio; Creus Bachiller, Edgar; Capellá, Gabriel; Farré, Lourdes; Vidal, August; Soldado, Francisco; Krauel, Lucas; Suñol, Mariona; Serra, Eduard; Villanueva, Alberto; Lázaro García, Conxi (SAGE Publications, 2020)
    Background: The aim of this study was to test the feasibility and utility of developing patient-derived orthotopic xenograft (PDOX) models for patients with malignant peripheral nerve sheath tumors (MPNSTs) to aid therapeutic ...

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