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Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins
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Sequeira-Mendes, Joana (Centro de Biología Molecular Severo Ochoa) ;
Vergara, Zaida (Centro de Biología Molecular Severo Ochoa) ;
Peiró, Ramon (Centro de Biología Molecular Severo Ochoa) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Aragüez, Irene (Centro de Biología Molecular Severo Ochoa) ;
Costas, Celina (Centro de Biología Molecular Severo Ochoa) ;
Méndez Giráldez, Raúl (Centro de Biología Molecular Severo Ochoa) ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica) ;
Bastolla, Ugo (Centro de Biología Molecular Severo Ochoa) ;
Gutiérrez, Crisanto (Centro de Biología Molecular Severo Ochoa)
Eukaryotic genome replication depends on thousands of DNA replication origins (ORIs). A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. [...]
2019 -  10.1101/gr.240986.118
Genome research, Vol. 29, Issue 5 (May 2019) , p. 784-797
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9 p, 1.8 MB |
An improved assembly and annotation of the melon (Cucumis melo L.) reference genome
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Ruggieri, Valentino (Centre de Recerca en Agrigenòmica) ;
Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Pujol, Maria (Institut de Recerca i Tecnologia Agroalimentàries) ;
Yano, Ryoichi (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Nonaka, Satoko (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Ezura, Hiroshi (University of Tsukuba. Faculty of Life and Environmental Sciences) ;
Latrasse, David (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Boualem, Adnane (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Benhamed, Moussa (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Bendahmane, Abdelhafid (University of Evry. Institute of Plant Sciences Paris-Saclay (IPS2)) ;
Cigliano, Riccardo Aiese (Sequentia Biotech SL) ;
Sanseverino, Walter (Sequentia Biotech SL) ;
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica) ;
Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica)
We report an improved assembly (v3. 6. 1) of the melon (Cucumis melo L. ) genome and a new genome annotation (v4. 0). The optical mapping approach allowed correcting the order and the orientation of 21 previous scaffolds and permitted to correctly define the gap-size extension along the 12 pseudomolecules. [...]
2018 - 10.1038/s41598-018-26416-2
Scientific Reports, Vol. 8 (May 2018) , art. 8088
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12 p, 836.9 KB |
The evolutionary consequences of transposon-related pericentromer expansion in melon
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Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Tormo, Marc (Centre de Recerca en Agrigenòmica) ;
Alexiou, Konstantinos G. (Institut de Recerca i Tecnologia Agroalimentàries) ;
Vives, Cristina (Centre de Recerca en Agrigenòmica) ;
Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica) ;
Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica)
Transposable elements (TEs) are a major driver of plant genome evolution. A part frombeing a rich source of new genes and regulatory sequences, TEs can also affect plant genome evolution by modifying genome size and shaping chromosome structure. [...]
2018 - 10.1093/gbe/evy115
Genome Biology and Evolution, Vol. 10, Núm. 6 (June 2018) , p. 1584-1595
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60 p, 1.6 MB |
The Physcomitrella patens chromosome‐scale assembly reveals moss genome structure and evolution
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Lang, Daniel (Helmholtz Center Munich. Plant Genome and Systems Biology) ;
Ullrich, Kristian K. (University of Marburg. Faculty of Biology) ;
Murat, Florent (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals) ;
Fuchs, Jorg (Leibniz Institute of Plant Genetics and Crop Plant Research) ;
Jenkins, Jerry (HudsonAlpha Institute for Biotechnology) ;
Haas, Fabian B. (University of Marburg. Faculty of Biology) ;
Piednoel, M. (Max Planck Institute for Plant Breeding Research) ;
Gundlach, H. (Helmholtz Center Munich. Plant Genome and Systems Biology) ;
Van Bel, M. (VIB-UGent Center for Plant Systems Biology) ;
Meyberg, R. (University of Marburg. Faculty of Biology) ;
Vives, Cristina (Centre de Recerca en Agrigenòmica) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Symeonidi, Aikaterini (University of Marburg. Faculty of Biology) ;
Hiss, Manuel (University of Marburg. Faculty of Biology) ;
Muchero, Wellington (Oak Ridge National Laboratory. Biosciences Division) ;
Kamisugi, Yasuko (University of Leeds. Centre for Plant Sciences) ;
Saleh, Omar (University of Freiburg. Faculty of Biology) ;
Blanc, Guillaume (Aix-Marseille Université. Structural and Genomic Information Laboratory) ;
Decker, Eva L. (University of Freiburg. Faculty of Biology) ;
van Gessel, Nico (University of Freiburg. Faculty of Biology) ;
Grimwood, Jane (HudsonAlpha Institute for Biotechnology) ;
Hayes, Richard D. (DOE Joint Genome Institute) ;
Graham, Sean W. (University of British Columbia. Department of Botany) ;
Gunter, Lee E. (Oak Ridge National Laboratory. Biosciences Division) ;
McDaniel, Stuart F. (University of Florida. Department of Biology) ;
Hoernstein, Sebastian N.W. (University of Freiburg. Faculty of Biology) ;
Larsson, Anders (Uppsala University. Evolutionary Biology Centre) ;
Li, Fay-Wei (Boyce Thompson Institute) ;
Perroud, Pierre-François (University of Marburg. Faculty of Biology) ;
Phillips, Jeremy (DOE Joint Genome Institute) ;
Ranjan, Priya (Oak Ridge National Laboratory) ;
Rokshar, Daniel S. (DOE Joint Genome Institute) ;
Rothfels, Carl J. (University of California. Department of Integrative Biology) ;
Schneider, Lucas (University of Marburg. Faculty of Biology) ;
Shu, Shengqiang (DOE Joint Genome Institute) ;
Stevenson, Dennis W. (New York Botanical Garden) ;
Thümmler, Fritz (Vertis Biotechnologie AG) ;
Tillich, Michael (Max Planck Institute of Molecular Plant Physiology) ;
Villarreal Aguilar, Juan C. (Université Laval. Department of Biology) ;
Widiez, Thomas (University of Geneva. Department of Plant Biology) ;
Wong, Gane Ka-Shu (University of Alberta. Department of Biological Sciences) ;
Wymore, Ann (Oak Ridge National Laboratory) ;
Zhang, Yong (Shenzhen Huahan Gene Life Technology Co. Ltd) ;
Zimmer, Aandreas D. (University of Freiburg. Faculty of Biology) ;
Quatrano, Ralph S. (Washington University. Department of Biology) ;
Mayer, Klaus F. X. (Technical University Munich) ;
Goodstein, David (DOE Joint Genome Institute) ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica) ;
Vandepoele, Klaas (Ghent University. Department of Plant Biotechnology and Bioinformatics) ;
Reski, Ralph (University of Freiburg. Faculty of Biology) ;
Cuming, Andrew C. (University of Leeds. Faculty of Biological Sciences) ;
Tuskan, Gerald A. (Oak Ridge National Laboratory. Biosciences Division) ;
Maumus, Florian (Institut National de la Recherche Agronomique . Unité de Recherche Génomique Info) ;
Salse, Jerome (Institut national de la recherche agronomique. UMR 1095 Genetics. Diversity and Ecophysiology of Cereals) ;
Schmutz, Jeremy (DOE Joint Genome Institute) ;
Rensing, Stefan A. (University of Freiburg. BIOSS Centre for Biological Signalling Studies)
The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. [...]
2018 - 10.1111/tpj.13801
Plant journal, Vol. 93, issue 3 (Feb. 2018) , p. 515-533
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11 p, 563.4 KB |
Plant lineage-specific amplification of transcription factor binding motifs by miniature inverted-repeat transposable elements (MITEs)
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Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Marín Nieto, Fátima (Centre de Recerca en Agrigenòmica) ;
Payet, Jordi ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica)
Transposable elements are one of the main drivers of plant genome evolution. Transposon insertions can modify the gene coding capacity or the regulation of their expression, the latter being a more subtle effect, and therefore particularly useful for evolution. [...]
2018 - 10.1093/gbe/evy073
Genome biology and evolution, Vol. 10, issue 5 (May 2018) , p. 1210-1220
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38 p, 1.7 MB |
Transposon insertions, structural variations, and SNPs contribute to the evolution of the melon genome
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Sanseverino, Walter (Centre de Recerca en Agrigenòmica) ;
Hénaff, Elizabeth (Centre de Recerca en Agrigenòmica) ;
Vives, Cristina (Centre de Recerca en Agrigenòmica) ;
Pinosio, Sara (Universita degli studi di Udine. Dipartimento di szience agrarie e ambientali) ;
Burgos-Paz, William (Centre de Recerca en Agrigenòmica) ;
Morgante, Michele (Universita degli studi di Udine. Dipartimento di szience agrarie e ambientali) ;
Ramos-Onsins, Sebastián E. (Centre de Recerca en Agrigenòmica) ;
Garcia Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. (Centre de Recerca en Agrigenòmica)
The availability of extensive databases of crop genome sequences should allow analysis of crop variability at an unprecedented scale, which should have an important impact in plant breeding. However, up to now the analysis of genetic variability at the whole-genome scale has been mainly restricted to single nucleotide polymorphisms (SNPs). [...]
2015 - 10.1093/molbev/msv152
Molecular biology and evolution, Vol. 32, issue 10 (Oct. 2015) , p. 2760-74
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8 p, 198.0 KB |
Differential clinical characteristics and prognosis of intraventricular conduction defects in patients with chronic heart failure
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Cinca, Juan (Institut d'Investigació Biomèdica Sant Pau) ;
Mendez, Ana (Institut d'Investigació Biomèdica Sant Pau) ;
Puig, Teresa (Institut d'Investigació Biomèdica Sant Pau) ;
Ferrero, Andreu (Institut d'Investigació Biomèdica Sant Pau) ;
Roig, Eulalia (Institut d'Investigació Biomèdica Sant Pau) ;
Vazquez, Rafael (Servicio de Cardiología, Hospital Puerta del Mar, Cádiz, Spain) ;
Gonzalez-Juanatey, Jose R. (Servicio de Cardiología, Hospital Clínico, Santiago de Compostela, Spain) ;
Alonso-Pulpon, Luis (Servicio de Cardiología, Hospital Puerta de Hierro, Madrid, Spain) ;
Delgado, Juan (Servicio de Cardiología, Hospital 12 de Octubre, Madrid, Spain) ;
Brugada, Josep (Servicio de Cardiología, Hospital Clínic, Barcelona, Spain) ;
Pascual-Figal, Domingo (Servicio de Cardiología, Hospital Virgen de la Arrixaca, Murcia, Spain) ;
Brugada, J. (Hospital Clínic de Barcelona) ;
Batlle, M. (Hospital Clínic de Barcelona) ;
Berruezo, A. (Hospital Clínic de Barcelona) ;
Hevia, S. (Hospital Clínic de Barcelona) ;
Mont, L. (Hospital Clínic de Barcelona) ;
Pérez-Villa, F. (Hospital Clínic de Barcelona) ;
Cinca, J. (Hospital de la Santa Creu i Sant Pau) ;
Roig, E. (Hospital de la Santa Creu i Sant Pau) ;
Bayés de Luna, A. (Hospital de la Santa Creu i Sant Pau) ;
Borrás, X. (Hospital de la Santa Creu i Sant Pau) ;
Carreras, F. (Hospital de la Santa Creu i Sant Pau) ;
Ferrero, A. (Hospital de la Santa Creu i Sant Pau) ;
Guerra, J.M. (Hospital de la Santa Creu i Sant Pau) ;
Hove-Madsen, L. (Hospital de la Santa Creu i Sant Pau) ;
Jorge, E. (Hospital de la Santa Creu i Sant Pau) ;
Martínez, R. (Hospital de la Santa Creu i Sant Pau) ;
Padró, J. (Hospital de la Santa Creu i Sant Pau) ;
Puig, T. (Hospital de la Santa Creu i Sant Pau) ;
Ribas, N. (Hospital de la Santa Creu i Sant Pau) ;
Viñolas, X. (Hospital de la Santa Creu i Sant Pau) ;
Alvarez-Garcia, J. (Hospital de la Santa Creu i Sant Pau) ;
González-Juanatey, J.R. ;
Bandín, M. ;
Eiras, S. ;
Fernández-Hernández, L. ;
García-Acuña, J. ;
Gómez-Otero, I. ;
Grigorian-Shamagian, L. ;
Lago, F. ;
Manzón, P. ;
Moure, M. ;
Otero-Raviña, F. ;
Otero-Santiago, F. ;
Rodino Janeiro, B.K. ;
Rubio, J. ;
Salgado, A. ;
Seoane, A. ;
Varela, A. ;
Lear, P.V. ;
Fernández-Cruz, A. ;
Alvarez de Arcaya Vicente, A. ;
Avila, M. ;
Bordiu, E. ;
Calle, L. ;
Fernández-Pinilla, C. ;
Gómez-Garre, D. ;
González-Rubio, L. ;
Marco, J. ;
Martell, N. ;
Muñoz-Pacheco, P. ;
Ortega, A. ;
Patiño, R. ;
Pedrajas, J. ;
Reinares, L. ;
Pérez-Villacastín, J. ;
Bover, R. ;
Cobos, M. ;
García-Quintanilla, J. ;
Moreno, J. ;
Pérez-Castellano, N. ;
Pérez-Serrano, M. ;
Vila, I. ;
Delgado, J.F. ;
Arribas, F. ;
Escribano, P. ;
Flox, A. ;
Jiménez López-Guarch, C. ;
Paradina, M. ;
Ruiz-Cano, J. ;
Sáenz de la Calzada, C. ;
Salguero, R. ;
Sánchez-Sánchez, V. ;
Tello de Meneses, R. ;
Vicente-Hernández, M. ;
Alonso-Pulpón, L. ;
Fernández -Lozano, I. ;
García-Pavía, P. ;
García-Touchard, A. ;
Gómez-Bueno, M. ;
Márquez, J. ;
Segovia, J. ;
Silva, L. ;
Vázquez-Mosquera, M. ;
Valdés, M. ;
García-Alberola, A. ;
Garrido, I. ;
Pascual-Figal, D. A. ;
Pastor-Pérez, F.J. ;
Sánchez-Más, J. ;
Tornel, P. ;
Rivera, M. ;
Almenar, L. ;
Cortés, R. ;
Martínez-Dolz, L. ;
Montero, J. ;
Portolés, M. ;
Roselló-Lleti, E. ;
Salvador, A. ;
Vila, V. ;
Vázquez, R. ;
Cubero, J. ;
Fernández-Palacín, A. ;
García-Medina, D. ;
García-Rey, S. ;
Laguna, E. ;
Leal del Ojo, J. ;
Miñano, F. ;
Pastor-Torres, L. ;
Pavón, R. ;
Pérez-Navarro, A. ;
Villagómez, D. ;
Vázquez, R. ;
Arana, R. ;
Bartolomé, D. ;
Cabeza, P. ;
Calle-Pérez, G. ;
Camacho, F. ;
Cano, L. ;
Carrillo, A. ;
Díaz-Retamino, E. ;
Escolar, V. ;
Fernández-Rivero, R. ;
Gamaza, S. ;
Giráldes, A. ;
Hernández-Vicente, N. ;
Lagares, M. ;
López-Benítez, J. ;
Marante, M. ;
Otero, E. ;
Pedregal, J. ;
Sancho-Jaldón, M. ;
Sevillano, R. ;
Zayas, R. ;
Verdú, J.M. ;
Aguilar, S. ;
Aizpurúa, M. ;
Alguacil, F. ;
Casacuberta, J. ;
Cerain, J. ;
Domingo, M. ;
García-Lareo, M. ;
Herrero-Melechón, J. ;
López-Pareja, N. ;
Mena, A. ;
Pérez-Orcero, A. ;
Rodríguez- Cristóbal, J. ;
Rozas, M. ;
Sorribes, J. ;
Torán, P. ;
Worner, F. ;
Barta, L. ;
Bravo, C. ;
Cabau, J. ;
Casanova, J. ;
Daga, B. ;
De la Puerta, I. ;
Hernández-Martín, I. ;
Piñol, E. ;
Pueo, E. ;
Torres, G. ;
Troncoso, A. ;
Viles, D. ;
Bardají, Alfredo ;
Mercè, J. ;
Sanz-Girgas, E. ;
Valdovinos, P. ;
Aramburu, O. ;
Arias, J. ;
García-González, C. ;
Alonso, M. ;
Bischofberger, C. ;
Domínguez-De Pablos, G. ;
Jiménez-Cervantes, D. ;
Ureña, I. ;
Grau-Sepúlveda, A. ;
Fiol, C. ;
Pericas, P. ;
Villalonga, M. ;
Orosa, P. ;
Agüero, J. ;
Planas-Aymá, F. ;
Grau-Amoros, J. ;
Planas-Comes, F. ;
San Vicente, L.
Intraventricular conduction defects (IVCDs) can impair prognosis of heart failure (HF), but their specific impact is not well established. This study aimed to analyse the clinical profile and outcomes of HF patients with LBBB, right bundle branch block (RBBB), left anterior fascicular block (LAFB), and no IVCDs. [...]
2013 - 10.1093/eurjhf/hft042
European Journal of Heart Failure, Vol. 15 (march 2013) , p. 877-884
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