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1.
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10 p, 1.6 MB |
The genome of woodland strawberry (Fragaria vesca)
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Shulaev, Vladimir (University of North Texas. Department of Biological Sciences) ;
Sargent, Daniel J. (East Malling Research) ;
Crowhurst, Ross (New Zealand Institute for Plant and Food Research Limited) ;
Mockler, Todd C. (Oregon State University. Center for Genome Research and Biocomputing) ;
Folkerts, Otto (Chromatin Inc.) ;
Delcher, Arthur L. (University of Maryland. Center for Bioinformatics and Computational Biology) ;
Jaiswal, Pankaj (Oregon State University. Department of Botany and Plant Pathology) ;
Mockaitis, Keithanne (Indiana University. Center for Genomics and Bioinformatics) ;
Liston, Aaron (Oregon State University. Department of Botany and Plant Pathology) ;
Mane, Shrinivasrao P. (Virginia Bioinformatics Institute) ;
Burns, Paul (Joint Georgia Tech and Emory Wallace H. Coulter. Department of Biomedical Engineering) ;
Davis, Thomas M. (University of New Hampshire. Department of Biological Sciences) ;
Slovin, Janet P. (Henry Wallace Beltsville Agricultural Research Center) ;
Bassil, Nahla (National Clonal Germplasm Repository) ;
Hellens, Roger P. (New Zealand Institute for Plant and Food Research Limited) ;
Evans, Clive (State University. Virginia Bioinformatics Institute) ;
Harkins, Tim (Roche Diagnostics. Roche Applied Science) ;
Kodira, Chinnappa (Roche Diagnostics. Roche Applied Science) ;
Desany, Brian (Roche Diagnostics. Roche Applied Science) ;
Crasta, Oswald R. (Chromatin Inc.) ;
Jensen, Roderick V. (Virginia Tech. Department of Biological Sciences) ;
Allan, Andrew C. (New Zealand Institute for Plant and Food Research Limited) ;
Michael, Todd P. (State University of New Jersey. Waksman Institute of Microbiology) ;
Setubal, Joao Carlos (Virginia Tech. Department of Computer Science) ;
Celton, Jean-Marc (University of the Western Cape. Department of Biotechnology) ;
Rees, D. Jasper G. (University of the Western Cape. Department of Biotechnology) ;
Williams, Kelly P. (State University. Virginia Bioinformatics Institute) ;
Holt, Sarah H. (Institute for Sustainable and Renewable Resources) ;
Rojas, Juan Jairo (State University. Virginia Polytechnic Institute. Department of Horticulture) ;
Chatterjee, Mithu (University of Florida. Graduate Program for Plant Molecular and Cellular Biology) ;
Liu, Bo (University of New Hampshire. Department of Biological Sciences) ;
Silva, Herman (University of Chile. Millennium Nucleus in Plant Cell Biotechnology) ;
Meisel, Lee (Universidad Andres Bello. Millennium Nucleus in Plant Cell Biotechnology) ;
Adato, Avital (Weizmann Institute of Science (Israel). Department of Plant Sciences) ;
Filichkin, Sergei A. (Oregon State University. Center for Genome Research and Biocomputing) ;
Troggio, Michela (Foundation Edmund Mach. Istituto Agrario San Michele all'Adige () ;
Viola, Roberto (Istituto Agrario San Michele all'Adige (IASMA). Research and Innovation Centre. Foundation Edmund Mach) ;
Ashman, Tia-Lynn (University of Pittsburgh. Department of Biological Sciences) ;
Wang, Hao (University of Georgia. Department of Genetics) ;
Dharmawardhana, Palitha (Oregon State University. Department of Botany and Plant Pathology) ;
Elser, Justin (Oregon State University. Department of Botany and Plant Pathology) ;
Raja, Rajani (Oregon State University. Department of Botany and Plant Pathology) ;
Priest, Henry D. (Oregon State University. Center for Genome Research and Biocomputing) ;
Bryant, Douglas W. (Oregon State University. Center for Genome Research and Biocomputing) ;
Fox, Samuel E. (Oregon State University. Center for Genome Research and Biocomputing) ;
Givan, Scott A. (Oregon State University. Center for Genome Research and Biocomputing) ;
Wilhelm, Larry J. (Oregon State University. Center for Genome Research and Biocomputing) ;
Naithani, Sushma (Oregon State University. Department of Horticulture) ;
Christoffels, Alan (University of the Western Cape. South African National Bioinformatics Institute) ;
Salama, David Y. (University of Florida. Horticultural Sciences Department) ;
Carter, Jade (Indiana University. Center for Genomics and Bioinformatics) ;
Girona, Elena L. (East Malling Research) ;
Zdepski, Anna (State University of New Jersey. Waksman Institute of Microbiology) ;
Wang, Wenqin (State University of New Jersey. Waksman Institute of Microbiology) ;
Kerstetter, Randall A. (State University of New Jersey. Waksman Institute of Microbiology) ;
Schwab, Wilfried (Technical University München. Biotechnology of Natural Products) ;
Korban, Schuyler S. (University of Illinois. Department of Natural Resources and Environmental Sciences) ;
Davik, Jahn (Norwegian Institute for Agricultural and Environmental Research. Genetics and Biotechnology) ;
Monfort, Amparo (Centre de Recerca en Agrigenòmica) ;
Denoyes, Beatrice (Institut National de la Recherche Agronomique (França)) ;
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica) ;
Mittler, Ron (University of North Texas. Department of Biological Sciences) ;
Flinn, Barry (Institute for Sustainable and Renewable Resources. Institute for Advanced Learning and Research) ;
Aharoni, Asaph (Universidad Andres Bello. Millennium Nucleus in Plant Cell Biotechnology. Centro de Biotecnología Vegetal.) ;
Bennetzen, Jeffrey L. (University of Georgia. Department of Genetics) ;
Salzberg, Steven L. (University of Maryland. Center for Bioinformatics and Computational Biology) ;
Dickerman, Allan W. (State University. Virginia Bioinformatics Institute. Virginia Polytechnic Institute) ;
Velasco, Riccardo (Foundation Edmund Mach. Istituto Agrario San Michele all'Adige) ;
Borodovsky, Mark (Georgia Tech. School of Computational Science and Engineering) ;
Veilleux, Richard E. (State University. Virginia Polytechnic Institute. Department of Horticulture) ;
Folta, Kevin M. (University of Florida. Graduate Program for Plant Molecular and Cellular Biology)
The woodland strawberry, Fragaria vesca (2n = 2x = 14), is a versatile experimental plant system. This diminutive herbaceous perennial has a small genome (240 Mb), is amenable to genetic transformation and shares substantial sequence identity with the cultivated strawberry (Fragaria Ã- ananassa) and other economically important rosaceous plants. [...]
2011 -  10.1038/ng.740
Nature genetics, Vol. 43, Issue 2 (February 2011) , p. 109-116
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2.
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12 p, 2.1 MB |
Whole genome comparisons of Fragaria, Prunus and Malus reveal different modes of evolution between Rosaceous subfamilies
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Jung, Sook (Washington State University. Department of Horticulture and Landscape Architecture) ;
Cestaro, Alessandro (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Troggio, Michela (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Main, Dorrie (Washington State University. Department of Horticulture and Landscape Architecture) ;
Zheng, Ping (Washington State University. Department of Horticulture and Landscape Architecture) ;
Cho, Ilhyung (Saginaw Valley State University. Department of Computer Science and Information Systems) ;
Folta, Kevin M. (University of Florida. Horticultural Sciences Department) ;
Sosinski, Bryon (North Carolina State University. Department of Horticultural Science) ;
Abbott, Albert G. (Clemson University. Department of Genetics and Biochemistry) ;
Celton, Jean-Marc (Institut National de la Recherche Agronomique (França)) ;
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica) ;
Shulaev, Vladimir (University of North Texas. Department of Biological Sciences) ;
Verde, Ignazio (Centro di Ricerca per la Frutticoltura) ;
Morgante, Michele (Istituto di Genomica Applicata (Udine, Itàlia)) ;
Rokhsar, Daniel (United States. Department of Energy. Joint Genome Institute) ;
Velasco, Riccardo (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Sargent, Daniel James (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige)
Background: Rosaceae include numerous economically important and morphologically diverse species. Comparative mapping between the member species in Rosaceae have indicated some level of synteny. Recently the whole genome of three crop species, peach, apple and strawberry, which belong to different genera of the Rosaceae family, have been sequenced, allowing in-depth comparison of these genomes. [...]
2012 - 10.1186/1471-2164-13-129
BMC genomics, Vol. 13 (April 2012) , art. 129
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3.
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9 p, 435.9 KB |
Prediction of overall survival in stage II and III colon cancer beyond TNM system : a retrospective, pooled biomarker study
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Dienstmann, Rodrigo. (Hospital Universitari Vall d'Hebron) ;
Mason, M. J. (Computational Oncology, Sage Bionetworks, Seattle, USA) ;
Sinicrope, F. A. (Mayo Clinic and Mayo Comprehensive Cancer Center, Rochester, USA) ;
Phipps, A. I. (Fred Hutchinson Cancer Research Center, Seattle, USA) ;
Tejpar, Sabine (University Hospitals Gasthuisberg (Leuven, Bélgica)) ;
Nesbakken, A. (Oslo University Hospital (Oslo, Noruega)) ;
Danielsen, S. A. (Oslo University Hospital (Oslo, Noruega)) ;
Sveen, A. (Oslo University Hospital (Oslo, Noruega)) ;
Buchanan, Daniel D (The University of Melbourne) ;
Clendenning, M. (The University of Melbourne) ;
Rosty, C. (The University of Melbourne) ;
Bot, Brian M (Computational Oncology, Sage Bionetworks, Seattle, USA) ;
Alberts, S. R. (Mayo Clinic and Mayo Comprehensive Cancer Center, Rochester, USA) ;
Milburn Jessup, J. (National Cancer Institute (Rockville, Estats Units d'Amèrica)) ;
Lothe, R. A. (Oslo University Hospital (Oslo, Noruega)) ;
Delorenzi, Mauro (SIB Swiss Institute Bioinformatics, Lausanne, Switzerland) ;
Newcomb, P. A. (Fred Hutchinson Cancer Research Center, Seattle, USA) ;
Sargent, D. (Mayo Clinic, Rochester, USA) ;
Guinney, J. (Computational Oncology, Sage Bionetworks, Seattle, USA) ;
Universitat Autònoma de Barcelona
TNM staging alone does not accurately predict outcome in colon cancer (CC) patients who may be eligible for adjuvant chemotherapy. It is unknown to what extent the molecular markers microsatellite instability (MSI) and mutations in BRAF or KRAS improve prognostic estimation in multivariable models that include detailed clinicopathological annotation. [...]
2017 - 10.1093/annonc/mdx052
Annals of oncology, Vol. 28 (february 2017) , p. 1023-1031
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5.
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5 p, 238.6 KB |
The development and characterisation of a bacterial artificial chromosome library for Fragaria vesca
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Bonet Gigante, Julio (Centre de Recerca en Agrigenòmica) ;
López Girona, Elena (East Malling Research) ;
Sargent, Daniel J. (East Malling Research) ;
Muñoz Torres, Monica C. (Clemson University. Department of Genetics and Biochemistry) ;
Monfort, Amparo (Centre de Recerca en Agrigenòmica) ;
Abbott, Albert G. (Clemson University. Department of Genetics and Biochemistry) ;
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica) ;
Simpson, David W. (East Malling Research) ;
Davik, Jahn (Bioforsk Midt-Norge)
BACKGROUND: the cultivated strawberry Fragaria xananassa is one of the most economically-important soft-fruit species. Few structural genomic resources have been reported for Fragaria and there exists an urgent need for the development of physical mapping resources for the genus. [...]
2009 - 10.1186/1756-0500-2-188
BMC research notes, Vol. 2 (Set. 2009) , art. 188
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6.
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13 p, 1.3 MB |
Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family
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Illa, Eudald (Centre de Recerca en Agrigenòmica) ;
Sargent, Daniel J. (East Malling Research) ;
López Girona, Elena (East Malling Research) ;
Bushakra, Jill (The New Zealand Institute for Plant & Food Research Ltd) ;
Cestaro, Alessandro (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Crowhurst, Ross (The New Zealand Institute for Plant & Food Research Ltd) ;
Pindo, Massimo (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Cabrera, Antonio (The Ohio State University. Department of Horticulture and Crop Science) ;
Van der Knaap, Esther (The Ohio State University. Department of Horticulture and Crop Science) ;
Iezzoni, Amy (Michigan State University. Department of Horticulture) ;
Gardiner, Susan (The New Zealand Institute for Plant & Food Research Ltd) ;
Velasco, Riccardo (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige) ;
Arús i Gorina, Pere (Centre de Recerca en Agrigenòmica) ;
Chagné, David (The New Zealand Institute for Plant & Food Research Ltd) ;
Troggio, Michela (Fondazione Edmund Mach. Istituto agrario di San Michele all'Adige)
Background. comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. [...]
2011 - 10.1186/1471-2148-11-9
BMC evolutionary biology, Vol. 11 (January 2011) , art. 9
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30 p, 3.7 MB |
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
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Bassil, Nahla (United States Department of Agriculture. National Clonal Germplasm Repository) ;
Davis, Thomas M. (University of New Hampshire) ;
Zhang, Hailong (University of New Hampshire) ;
Ficklin, Stephen (Washington State University) ;
Mittmann, Mike (Affymetrix) ;
Webster, Teresa (Affymetrix) ;
Mahoney, Lise (University of New Hampshire) ;
Wood, David (University of New Hampshire) ;
Alperin, Elisabeth S. (United States Department of Agriculture. National Clonal Germplasm Repository) ;
Rosyara, Umesh R. (Michigan State University) ;
Koehorst-vanc Putten, Herma (Wageningen UR. Plant Breeding) ;
Monfort, Amparo (Centre de Recerca en Agrigenòmica) ;
Sargent, Daniel J. (Fondazione Edmund Mach, Centro di Ricerca e Innovazione) ;
Amaya, Iraida (Instituto de Investigación y Formación Agraria y Pesquera) ;
Denoyes, Beatrice (Institut national de la recherche agronomique (França). Biologie du Fruit et Pathologie) ;
Bianco, Luca (Fondazione Edmund Mach, Centro di Ricerca e Innovazione) ;
Van Dijk, Thijs (Wageningen UR. Plant Breeding) ;
Pirani, Ali (Affymetrix) ;
Iezzoni, Amy (Michigan State University) ;
Main, Dorrie (Washington State University) ;
Peace, Cameron (Washington State University) ;
Yang, Yilong (University of New Hampshire) ;
Vance Whitaker, Vance (University of Florida) ;
Verma, Sujeet · (University of Florida) ;
Bellon, Laurent (Affymetrix) ;
Brew, Fiona (Affymetrix) ;
Herrera, Raul (Universidad de Talca. Instituto Ciencias Biologicas) ;
Van de Weg, Eric (Wageningen UR. Plant Breeding)
Background: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca 'Hawaii 4' reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation into a 90 K Affymetrix® Axiom® array. [...]
2015 - 10.1186/s12864-015-1310-1
BMC genomics, Vol. 16 (2015) art. 155
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