Browsing Center for Genomic Regulation (CRG) by Title

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  • BacFITBase: a database to assess the relevance of bacterial genes during host infection
    Macho Rendón, Javier; Lang, Benjamin; Tartaglia, Gian Gaetano; Torrent Burgas, Marc (Oxford University Press, 2020)
    Bacterial infections have been on the rise world-wide in recent years and have a considerable impact on human well-being in terms of attributable deaths and disability-adjusted life years. Yet many mechanisms underlying ...
  • Bacillus firmus strain I-1582, a nematode antagonist by itself and through the plant
    Ghahremani, Zahra; Escudero, Nuria; Beltrán Anadón, Daniel; Saus Martínez, Ester; Cunquero, Marina; Andilla, Jordi; Loza-Alvarez, Pablo; Gabaldón Estevan, Juan Antonio, 1973-; Sorribas, F. Javier (Frontiers, 2020)
    Bacillus firmus I-1582 is approved in Europe for the management of Meloidogyne on vegetable crops. However, little information about its modes of action and temperature requirements is available, despite the effect of these ...
  • Bacteria use structural imperfect mimicry to hijack the host interactome
    Sanchez de Groot, Natalia; Torrent Burgas, Marc (Public Library of Science (PLoS), 2020)
    Bacteria use protein-protein interactions to infect their hosts and hijack fundamental pathways, which ensures their survival and proliferation. Hence, the infectious capacity of the pathogen is closely related to its ...
  • Bacterial antisense RNAs are mainly the product of transcriptional noise
    Lloréns Rico, Verónica, 1989-; Cano, Jaime; Kamminga, Tjerko; Gil, Rosario; Latorre, Amparo; Chen, Wei-Hua; Bork, Peer; Glass, John I.; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (American Association for the Advancement of Science (AAAS), 2016)
    cis-Encoded antisense RNAs (asRNAs) are widespread along bacterial transcriptomes. However, the role of most of these RNAs remains unknown, and there is an ongoing discussion as to what extent these transcripts are the ...
  • Bacterial expression of a designed single-chain IL-10 prevents severe lung inflammation
    Montero-Blay, Ariadna, 1994-; Delgado Blanco, Javier; Rodriguez-Arce, Irene; Lastrucci, Claire; Piñero-Lambea, Carlos; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (EMBO Press, 2023)
    Interleukin-10 (IL-10) is an anti-inflammatory cytokine that is active as a swapped domain dimer and is used in bacterial therapy of gut inflammation. IL-10 can be used as treatment of a wide range of pulmonary diseases. ...
  • Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond
    Rambla de Argila, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Timothy; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita, 1986-; Spalding, J. Dylan; Törnoos, Juha; Vasallo, Claudia; Veal, Colin D.; Brookes, Anthony J. (Wiley, 2022)
    Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human ...
  • Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato
    Proietti, Silvia; Falconieri, Gaia Salvatore; Bertini, Laura; Pascale, Alberto; Bizzarri, Elisabetta; Morales Sanfrutos, Julia; Sabidó Aguadé, Eduard, 1981-; Ruocco, Michelina; Monti, Maurilia M.; Russo, Assunta; Dziurka, Kinga; Ceci, Marcello; Loreto, Francesco; Caruso, Carla (Oxford University Press, 2023)
    Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring ...
  • Behr syndrome and hypertrophic cardiomyopathy in a family with a novel UCHL1 deletion
    McMacken, Grace M.; Lochmüller, Hanns; Bansagi, Boglarka; Pyle, Angela; Lochmüller, Angela; Chinnery, Patrick F.; Laurie, Steven, 1973-; Beltran, Sergi; Matalonga, Leslie; Horvath, Rita (Springer, 2020)
    Background: Behr syndrome is a clinically distinct, but genetically heterogeneous disorder characterized by optic atrophy, progressive spastic paraparesis, and motor neuropathy often associated with ataxia. The molecular ...
  • Benchmarking of whole exome sequencing and ad hoc designed panels for genetic testing of hereditary cancer
    Feliubadaló, Lídia; Tonda, Raúl; Trotta, Jean-Remi; Gut, Marta; Gut, Ivo Glynne; Beltran, Sergi; Lázaro García, Conxi (Nature Research, 2017)
    Next generation sequencing panels have been developed for hereditary cancer, although there is some debate about their cost-effectiveness compared to exome sequencing. The performance of two panels is compared to exome ...
  • Benchmarking single-cell RNA sequencing protocols for cell atlas projects
    Mereu, Elisabetta; Lafzi, Atefeh; Moutinho, Catia; Gut, Marta; Gut, Ivo Glynne; Heyn, Holger (Nature Research, 2020)
    Single-cell RNA sequencing (scRNA-seq) is the leading technique for characterizing the transcriptomes of individual cells in a sample. The latest protocols are scalable to thousands of cells and are being used to compile ...
  • Best practice standards for circular RNA research
    Nielsen, Anne F.; Bindereif, Albrecht; Bozzoni, Irene; Hanan, Mor; Hansen, Thomas B.; Irimia Martínez, Manuel; Kadener, Sebastian; Kristensen, Lasse S.; Legnini, Ivano; Morlando, Mariangela; Jarlstad Olesen, Morten T.; Pasterkamp, Ronald Jeroen; Preibisch, Stephan; Rajewsky, Nicolaus; Suenkel, Christin; Kjems, Jørgen (Nature Research, 2022)
    Circular RNAs (circRNAs) are formed in all domains of life and via different mechanisms. There has been an explosion in the number of circRNA papers in recent years; however, as a relatively young field, circRNA biology ...
  • Beyond quiescent and active: Intermediate microglial transcriptomic states in a mouse model of down syndrome
    Fernández Blanco, Álvaro; Sierra, Cesar; Tejido, Clara; Dierssen, Mara (MDPI, 2024)
    Research on microglia in Down syndrome (DS) has shown that microglial activation, increased inflammatory gene expression, and oxidative stress occur at different ages in DS brains. However, most studies resulted in simplistic ...
  • Beyond the whole-genome duplication: phylogenetic evidence for an ancient interspecies hybridization in the Baker's yeast lineage
    Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Public Library of Science (PLoS), 2015)
    Whole-genome duplications have shaped the genomes of several vertebrate, plant, and fungal lineages. Earlier studies have focused on establishing when these events occurred and on elucidating their functional and evolutionary ...
  • Biallelic ADAM22 pathogenic variants cause progressive encephalopathy and infantile-onset refractory epilepsy
    van der Knoop, Marieke M.; Lochmüller, Hanns; Houlden, Henry (Oxford University Press, 2022)
    Pathogenic variants in A Disintegrin And Metalloproteinase (ADAM) 22, the postsynaptic cell membrane receptor for the glycoprotein leucine-rich repeat glioma-inactivated protein 1 (LGI1), have been recently associated with ...
  • Biallelic loss-of-function LACC1/FAMIN mutations presenting as rheumatoid factor-negative polyarticular juvenile idiopathic arthritis
    Rabionet, Raquel; Remesal, Agustín; Mensa Vilaró, Anna; Murías, Sara; Alcobendas, Rosa; González-Roca, Eva; Ruíz Ortiz, Estíbaliz; Antón, Jordi; Iglesias, Estibaliz; Modesto, Consuelo; Comas, David, 1969-; Puig, Anna; Drechsel, Oliver; Ossowski, Stephan; Yagüe, Jordi L.; Merino, Rosa; Estivill, Xavier, 1955-; Aróstegui Gorospe, Juan Ignacio (Nature Research, 2019)
    Juvenile idiopathic arthritis (JIA) is a complex rheumatic disease with both autoimmune and autoinflammatory components. Recently, familial cases of systemic-onset JIA have been attributed to mutations in LACC1/FAMIN. We ...
  • Biallelic TANGO1 mutations cause a novel syndromal disease due to hampered cellular collagen secretion
    Lekszas, Caroline; Foresti, Ombretta; Raote, Ishier; Liedtke, Daniel; König, Eva Maria; Nanda, Indrajit; Vona, Barbara; Coster, Peter de; Cauwels, Rita; Malhotra, Vivek; Haaf, Thomas (eLife, 2020)
    The transport and Golgi organization 1 (TANGO1) proteins play pivotal roles in the secretory pathway. Full length TANGO1 is a transmembrane protein localised at endoplasmic reticulum (ER) exit sites, where it binds bulky ...
  • bigSCale: an analytical framework for big-scale single-cell data
    Iacono, Giovanni; Mereu, Elisabetta; Guillaumet-Adkins, Amy; Corominas, Roser; Cuscó Martí, Ivon, 1973-; Rodríguez Esteban, Gustavo; Gut, Marta; Pérez Jurado, Luis Alberto; Gut, Ivo Glynne; Heyn, Holger (Cold Spring Harbor Laboratory Press (CSHL Press), 2018)
    Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers ...
  • Binding of the transcription factor Atf1 to promoters serves as a barrier to phase nucleosome arrays and avoid cryptic transcription
    García, Patrícia; Paulo Mirasol, Esther, 1984-; Gao, Jun; Wahls, Wayne P; Ayté del Olmo, José; Lowy Gallego, Ernesto; Hidalgo Hernando, Elena (Oxford University Press, 2014)
    Schizosaccharomyces pombe displays a large transcriptional response common to several stress conditions, regulated primarily by the transcription factor Atf1. Atf1-dependent promoters contain especially broad nucleosome ...
  • Binless normalization of Hi-C data provides significant interaction and difference detection independent of resolution
    Spill, Yannick G.; Castillo Andreo, David; Vidal, Enrique; Marti-Renom, Marc A. (Nature Research, 2019)
    Chromosome conformation capture techniques, such as Hi-C, are fundamental in characterizing genome organization. These methods have revealed several genomic features, such as chromatin loops, whose disruption can have ...
  • Bioactivity descriptors for uncharacterized chemical compounds
    Bertoni, Martino; Duran-Frigola, Miquel, 1985-; Badia-I-Mompel, Pau; Pauls, Eduardo; Orozco Ruiz, Modesto; Guitart Pla, Oriol; Alcalde, Víctor; Diaz, Víctor M.; Berenguer-Llergo, Antonio; Brun-Heath, Isabelle; Villegas, Núria; García de Herreros, Antonio; Aloy, Patrick, 1972- (Nature Research, 2021)
    Chemical descriptors encode the physicochemical and structural properties of small molecules, and they are at the core of chemoinformatics. The broad release of bioactivity data has prompted enriched representations of ...

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