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1.
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10 p, 5.6 MB |
Antimicrobial Peptides Can Generate Tolerance by Lag and Interfere with Antimicrobial Therapy
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Sandín, Daniel (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular) ;
Valle García, Javier (Universitat Pompeu Fabra) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Andreu Martínez, David (Universitat Pompeu Fabra) ;
Torrent Burgas, Marc (Universitat Autònoma de Barcelona. Departament de Bioquímica i de Biologia Molecular)
Antimicrobial peptides (AMPs) are widely distributed molecules secreted mostly by cells of the innate immune system to prevent bacterial proliferation at the site of infection. As with classic antibiotics, continued treatment with AMPs can create resistance in bacteria. [...]
2022 -  10.3390/pharmaceutics14102169
Pharmaceutics, Vol. 14, Núm. 10 (October 2022) , art. 2169
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2.
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15 p, 2.1 MB |
Novel class of viral ankyrin proteins targeting the host E3 ubiquitin ligase Cullin-2
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Odon, Valerie (University of Surrey. Department of Microbial Sciences) ;
Georgana, Iliana (University of Surrey. Department of Microbial Sciences) ;
Holley, Joe (University of Surrey. Department of Microbial Sciences) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Maluquer De Motes, Carlos (University of Surrey. Department of Microbial Sciences)
Ankyrin repeat (ANK) domains are among the most abundant motifs in eukaryotic proteins. ANK proteins are rare amongst viruses, with the exception of poxviruses, which presumably acquired them from the host via horizontal gene transfer. [...]
2018 - 10.1128/JVI.01374-18
Journal of Virology, Vol. 92, Issue 23 (December 2018) , art. e01374
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3.
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50 p, 962.3 KB |
Transposons played a major role in the diversification between the closely related almond and peach genomes : Results from the almond genome sequence
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Alioto, Tyler Scott (Centre de Regulació Genòmica) ;
Alexiou, Konstantinos G. (Centre de Recerca en Agrigenòmica) ;
Bardil, Amélie (Centre de Recerca en Agrigenòmica) ;
Barteri, Fabio (Centre de Recerca en Agrigenòmica) ;
Castanera, Raúl (Centre de Recerca en Agrigenòmica) ;
Cruz, Fernando (Centre de Regulació Genòmica) ;
Dhingra, Amit (Washington State University. Department of Horticulture) ;
Duval, Henri (Institut National de la Recherche Agronomique (França)) ;
Fernández i Martí, Angel (University of California) ;
Frias, Leonor (Centre de Regulació Genòmica) ;
Galán, Beatriz (Consejo Superior de Investigaciones Científicas) ;
García, José Luis (Consejo Superior de Investigaciones Científicas) ;
Howad, Werner (Centre de Recerca en Agrigenòmica) ;
Gómez-Garrido, Jessica (Centre de Regulació Genòmica) ;
Gut, Marta (Centre de Regulació Genòmica) ;
Julca, Irene (Centre de Regulació Genòmica) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ;
Ribeca, Paolo (Centre de Regulació Genòmica) ;
Rubio Cabetas, María José (Centro de Investigación y Tecnología Agroalimentaria de Aragón) ;
Vlasova, Anna (Centre de Regulació Genòmica) ;
Wirthensohn, Michelle (The University of Adelaide. School of Agriculture, Food and Wine) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Gabaldón, Toni (Centre de Regulació Genòmica) ;
Casacuberta i Suñer, Josep M. 1962- (Centre de Recerca en Agrigenòmica) ;
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica)
We sequenced the genome of the highly heterozygous almond Prunus dulcis cv. Texas combining short and long-read sequencing. We obtained a genome assembly totaling 227. 6 Mb of the estimated 238 Mb almond genome size, of which 91% is anchored to eight pseudomolecules corresponding to its haploid chromosome complement, and annotated 27,969 protein-coding genes and 6,747 non-coding transcripts. [...]
2020 - 10.1111/tpj.14538
The Plant journal, Vol. 101, Issue 2 (January 2020) , p. 455-472
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4.
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38 p, 5.4 MB |
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, Ramón (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. 1962- (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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5.
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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 Abajo, Marta (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)) ;
Aiese Cigliano, Riccardo (Sequentia Biotech SL) ;
Sanseverino, Walter (Sequentia Biotech SL) ;
Puigdomènech, Pere, 1948- (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (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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6.
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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, Sebastian (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Casacuberta i Suñer, Josep M. 1962- (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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7.
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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. 1962- (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 (França)) ;
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
The Plant journal, Vol. 93, issue 3 (Feb. 2018) , p. 515-533
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8.
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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. 1962- (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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9.
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14 p, 1.7 MB |
Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly
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Argyris, Jason (Centre de Recerca en Agrigenòmica) ;
Ruiz-Herrera Moreno, Aurora (Universitat Autònoma de Barcelona. Departament de Biologia Cel·lular, de Fisiologia i d'Immunologia) ;
Madriz-Masis, Pablo (Centre de Recerca en Agrigenòmica) ;
Sanseverino, Walter (Centre de Recerca en Agrigenòmica) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Pujol Abajo, Marta (Centre de Recerca en Agrigenòmica) ;
Ramos-Onsins, Sebastian (Centre de Recerca en Agrigenòmica) ;
Garcia-Mas, Jordi (Centre de Recerca en Agrigenòmica) ;
Universitat Autònoma de Barcelona.
Institut de Biotecnologia i de Biomedicina "Vicent Villar Palasí"
Background: The genome of the melon (Cucumis melo L. ) double-haploid line DHL92 was recently sequenced, with 87. 5 and 80. 8% of the scaffold assembly anchored and oriented to the 12 linkage groups, respectively. [...]
2015
BMC genomics, Vol. 16 (Jan. 2015) , art. 4
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10.
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28 p, 1.7 MB |
Molecular dynamics study of naturally existing cavity couplings in proteins
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Barbany, Montserrat (Institut de Recerca Biomèdica de Lleida) ;
Meyer, Tim (Max-Planck-Institut für biophysikalische Chemie) ;
Hospital, Adam (Institut de Recerca Biomèdica) ;
Faustino, Ignacio (Institut de Recerca Biomèdica) ;
D'Abramo, Marco (Università degli Studi di Roma "La Sapienza". Dipartimento di Chimica) ;
Morata, Jordi (Centre de Recerca en Agrigenòmica) ;
Orozco, Modesto (Institut de Recerca Biomèdica) ;
de la Cruz, Xavier (Institució Catalana de Recerca i Estudis Avançats)
Couplings between protein sub-structures are a common property of protein dynamics. Some of these couplings are especially interesting since they relate to function and its regulation. In this article we have studied the case of cavity couplings because cavities can host functional sites, allosteric sites, and are the locus of interactions with the cell milieu. [...]
2015 - 10.1371/journal.pone.0119978
BMC genomics, Vol. 10, issue 3 (March 2015) , e0119978
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