Browsing by Author "Cozzuto, Luca"

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  • A de novo nonsense mutation in MAGEL2 in a patient initially diagnosed as Opitz-C: similarities between Schaaf-Yang and Opitz-C syndromes
    Urreizti, Roser; Cueto González, Anna María; Franco Valls, Héctor; Mort Farre, Sílvia; Roca Ayats, Neus; Ponomarenko, Julia; Cozzuto, Luca; Company, Carlos; Bosio, Mattia; Ossowski, Stephan; Montfort, Magda; Hecht, Jochen; Tizzano, Eduardo F.; Cormand, Bru; Vilageliu, Lluïsa; Opitz, John M.; Neri, Giovanni; Grinberg, Daniel; Balcells, Susana (Nature Publishing Group, 2017)
    Opitz trigonocephaly C syndrome (OTCS) is a rare genetic disorder characterized by craniofacial anomalies, variable intellectual and psychomotor disability, and variable cardiac defects with a high mortality rate. Different ...
  • Age-associated inflammation inhibits epidermal stem cell function
    Doles, Jason; Storer, Mekayla, 1981-; Cozzuto, Luca; Roma, Guglielmo; Keyes, William M., 1973- (Cold Spring Harbor Laboratory Press (CSHL Press), 2012)
    Altered stem cell homeostasis is linked to organismal aging. However, the mechanisms involved remain poorly understood. Here we report novel alterations in hair follicle stem cells during skin aging, including increased ...
  • An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms
    Tapial Rodríguez, Javier, 1990-; Ha, Kevin C. H.; Sterne-Weiler, Thimothy; Gohr, André; Braunschweig, Ulrich; Hermoso Pulido, Antonio; Quesnel-Vallières, Mathieu; Permanyer, Jon; Sodaei, Reza, 1988-; Marquez, Yamile; Cozzuto, Luca; Wang, Xinchen; Gómez-Velázquez, Melisa; Rayon, Teresa; Manzanares, Miguel; Ponomarenko, Julia; Blencowe, Benjamin J.; Irimia Martínez, Manuel (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)
    Alternative splicing (AS) generates remarkable regulatory and proteomic complexity in metazoans. However, the functions of most AS events are not known, and programs of regulated splicing remain to be identified. To address ...
  • Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition
    Willis, Jesse R.; González-Torres, Pedro; Pittis, Alexandros, 1982-; Bejarano, Luis A.; Cozzuto, Luca; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Valentín, Antònia; Ksiezopolska, Ewa; Company, Carlos; Onywera, Harris; Montfort, Magda; Hermoso Pulido, Antonio; Iraola Guzmán, Susana; Saus Martínez, Ester; Labeeuw, Annick; Carolis, Carlo; Hecht, Jochen; Ponomarenko, Julia; Gabaldón Estevan, Juan Antonio, 1973- (BioMed Central, 2018)
    Background: The oral cavity comprises a rich and diverse microbiome, which plays important roles in health and disease. Previous studies have mostly focused on adult populations or in very young children, whereas the ...
  • Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species
    Willis, Jesse R.; Saus Martínez, Ester; Iraola Guzmán, Susana; Cabello-Yeves, Elena; Ksiezopolska, Ewa; Cozzuto, Luca; Bejarano, Luis A.; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Blanco, Andrea; Puig-Sola, Anna; Broglio, Elisabetta; Carolis, Carlo; Ponomarenko, Julia; Hecht, Jochen; Gabaldón Estevan, Juan Antonio, 1973- (Taylor & Francis, 2021)
    Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act ...
  • Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors
    Willis, Jesse R.; Saus Martínez, Ester; Iraola Guzmán, Susana; Ksiezopolska, Ewa; Cozzuto, Luca; Bejanaro, Luis A.; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Blanco, Andrea; Puig-Sola, Anna; Broglio, Elisabetta; Carolis, Carlo; Ponomarenko, Julia; Hecht, Jochen; Gabaldón Estevan, Juan Antonio, 1973- (Nature Research, 2022)
    The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and ...
  • Comparative "-omics" in mycoplasma pneumoniae clinical isolates reveals key virulence factors
    Lluch-Senar, Maria 1982-; Cozzuto, Luca; Cano, Jaime; Delgado Blanco, Javier; Lloréns Rico, Verónica, 1989-; Pereyre, Sabine; Bebear, Cécile; Serrano Pubull, Luis, 1982- (Public Library of Science (PLoS), 2015)
    The human respiratory tract pathogen M. pneumoniae is one of the best characterized minimal bacterium. Until now, two main groups of clinical isolates of this bacterium have been described (types 1 and 2), differing in the ...
  • Comparative transcriptomics of early dipteran development
    Jiménez Guri, Eva; Huerta Cepas, Jaime; Cozzuto, Luca; Wotton, Karl R.; Kang, Hui; Himmelbauer, Heinz; Roma, Guglielmo; Gabaldón Estevan, Juan Antonio, 1973-; Jaeger, Johannes, 1973- (BioMed Central, 2013)
    BACKGROUND: Modern sequencing technologies have massively increased the amount of data available for comparative genomics. Whole-transcriptome shotgun sequencing (RNA-seq) provides a powerful basis for comparative studies. ...
  • Controlled X-chromosome dynamics defines meiotic potential of female mouse in vitro germ cells
    Severino, Jacqueline, 1990-; Bauer, Moritz, 1987-; Mattimoe, Tom; Arecco, Niccolò; Cozzuto, Luca; Lorden, Patricia; Hamada, Norio; Nosaka, Yoshiaki; Nagaoka, So I.; Audergon, Pauline; Tarruell Pellegrin, Antonio,1990-; Heyn, Holger; Hayashi, Katsuhiko; Saitou, Mitinori; Payer, Bernhard (EMBO Press, 2022)
    The mammalian germline is characterized by extensive epigenetic reprogramming during its development into functional eggs and sperm. Specifically, the epigenome requires resetting before parental marks can be established ...
  • Cross talk between the upstream exon-intron junction and Prp2 facilitates splicing of non-consensus introns
    Hümmer, Stefan; Borao Arriazu, Sonia, 1993-; Guerra Moreno, Ángel; Cozzuto, Luca; Hidalgo Hernando, Elena; Ayté del Olmo, José (Elsevier, 2021)
    Splicing of mRNA precursors is essential in the regulation of gene expression. U2AF65 recognizes the poly-pyrimidine tract and helps in the recognition of the branch point. Inactivation of fission yeast U2AF65 (Prp2) blocks ...
  • Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing
    Conrad, Thomas; Ntini, Evgenia; Lang, Benjamin; Cozzuto, Luca; Andersen, Jesper B.; Marquardt, Jens U.; Ponomarenko, Julia; Tartaglia, Gian Gaetano; Vang Ørom, Ulf A. (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in ...
  • ExOrthist: a tool to infer exon orthologies at any evolutionary distance
    Márquez, Yamile; Mantica, Federica; Cozzuto, Luca; Burguera, Demián; Hermoso Pulido, Antonio; Ponomarenko, Julia; Roy, Scott W.; Irimia Martínez, Manuel (BioMed Central, 2021)
    Several bioinformatic tools have been developed for genome-wide identification of orthologous and paralogous genes. However, no corresponding tool allows the detection of exon homology relationships. Here, we present ...
  • Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx
    Abascal, Federico; Corvelo, André; Cruz, Fernando; Villanueva Cañas, José Luis, 1984-; Vlasova, Anna; Marcet Houben, Marina; Prieto Barja, Pablo, 1986-; Quilez Oliete, Javier; Frias, Leonor; Ribeca, Paolo; Capella Gutiérrez, Salvador Jesús, 1985-; Câmara Ferreira, Francisco; Lowy Gallego, Ernesto; Cozzuto, Luca; Erb, Ionas; Rodríguez Ales, José Luis; Ruiz Orera, Jorge, 1988-; Reverter, Ferran; Derdak, Sophia; Blanc, Julie; Gut, Marta; Lorente-Galdós, Belén, 1981-; Gut, Ivo Glynne; Guigó Serra, Roderic; Gabaldón Estevan, Juan Antonio, 1973-; Godoy, José A. (BioMed Central, 2016)
    Background: Genomic studies of endangered species provide insights into their evolution and demographic history, reveal patterns of genomic erosion that might limit their viability, and offer tools for their effective ...
  • Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes
    Vlasova, Anna; Capella Gutiérrez, Salvador Jesús, 1985-; Erb, Ionas; Cámara, Francisco; Prieto Barja, Pablo, 1986-; Kedra, Darek; González Navarrete, Irene, 1983-; Cozzuto, Luca; Gómez Garrido, Jèssica; Aguilar Morón, María Asunción; Andreu Somavilla, Núria; Zehnsdorf, Maik; Alioto, Tyler; Notredame, Cedric; Gabaldón Estevan, Juan Antonio, 1973-; Guigó Serra, Roderic (BioMed Central, 2016)
    Background: Legumes are the third largest family of angiosperms and the second most important crop class. Legume genomes have been shaped by extensive large-scale gene duplications, including an approximately 58 million ...
  • Genome-wide transcriptomic changes reveal the genetic pathways involved in insect migration
    Doyle, Toby; Jiménez Guri, Eva; Hawkes, Will L.S.; Massy, Richard; Mantica, Federica; Permanyer, Jon; Cozzuto, Luca; Hermoso Pulido, Antonio; Baril, Tobias; Hayward, Alexander; Irimia Martínez, Manuel; Chapman, Jason W.; Bass, Chris; Wotton, Karl R. (Wiley, 2022)
    Insects are capable of extraordinary feats of long-distance movement that have profound impacts on the function of terrestrial ecosystems. The ability to undertake these movements arose multiple times through the evolution ...
  • 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 ...
  • microRNA sequencing for biomarker detection in the diagnosis, classification and prognosis of Diffuse Large B Cell Lymphoma
    Larrabeiti Etxebarria, Ane; Bilbao Aldaiturriaga, Nerea; Arzuaga Mendez, Javier; Martin Arruti, Maialen; Cozzuto, Luca; Gaafar, Ayman; Ruiz Diaz, Irune; Guerra, Isabel; Martin Guerrero, Idoia; Lopez-Lopez, Elixabet; Gutierrez Camino, Angela (Nature Research, 2023)
    Despite being considered a single disease, Diffuse Large B Cell Lymphoma (DLBCL) presents with variable backgrounds, which results in heterogeneous outcomes among patients, with 40% of them still having primary refractory ...
  • MyMpn: a database for the systems biology model organism Mycoplasma pneumoniae
    Wodke, Judith A.H.; Alibés, Andreu; Cozzuto, Luca; Hermoso Pulido, Antonio; Yus, Eva; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982-; Roma, Guglielmo (Oxford University Press, 2015)
    MyMpn (http://mympn.crg.eu) is an online resource devoted to studying the human pathogen Mycoplasma pneumoniae, a minimal bacterium causing lower respiratory tract infections. Due to its small size, its ability to grow in ...
  • Oral microbiome in down syndrome and its implications on oral health
    Willis, Jesse R.; Iraola Guzmán, Susana; Saus Martínez, Ester; Ksiezopolska, Ewa; Cozzuto, Luca; Bejarano, Luis A.; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Puig, Anna; Blanco, Andrea; Broglio, Elisabetta; Carolis, Carlo; Hecht, Jochen; Ponomarenko, Julia; Gabaldón Estevan, Juan Antonio, 1973- (Taylor & Francis Open Access, 2020)
    Introduction: The oral cavity harbors an abundant and diverse microbial community (i.e. the microbiome), whose composition and roles in health and disease have been the focus of intense research. Down syndrome (DS) is ...
  • PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3
    Chung, Ho-Ryun; Xu, Chao; Fuchs, Alisa; Mund, Andreas; Lange, Martin; Staege, Hannah; Schubert, Tobias; Bian, Chuanbing; Dunkel, Ilona; Eberharter, Anton; Regnard, Catherine; Klinker, Henrike; Meierhofer, David; Cozzuto, Luca; Winterpacht, Andreas; Di Croce, Luciano; Min, Jinrong; Will, Hans; Kinkley, Sarah (eLife, 2016)
    PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate ...

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