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Browsing Faculty Research Publications (Botany and Plant Pathology) by Title

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Browsing Faculty Research Publications (Botany and Plant Pathology) by Title

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  • Nomenclature report on rice WRKY’s - Conflict regarding gene names and its solution 
    Shen, Qingxi J.; Yu, Diqiu; Jeon, Jong-Seong; Piffanelli, Pietro; Abbruscato, Pamela; Guo, Ze-Jian; Zhang, Yuanji; Itoh, Takeshi; Lee, Sung S.; Buell, C. Robin; Nagato, Yasuo; McCouch, Susan; Yano, Masahiro; Wang, Guo-liang; Jena, Kshirod K.; Xiong, Lizhong; Meyers, Blake; Jaiswal, Pankaj; Yamazaki, Yukiko (Springer, 2012-02-27)
    Background: Since whole genome sequences of rice were made publically accessible, the number of articles on new rice genes has increased remarkably. The Committee on Gene Symbolization, Nomenclature and Linkage (CGSNL) o ...
  • Non-parametric habitat models with automatic interactions 
    McCune, Bruce (IAVS Opulus Press, Uppsala, 2006)
    Questions: Can a statistical model be designed to represent more directly the nature of organismal response to multiple interacting factors? Can multiplicative ernel smoothers be used for this purpose? What advantages do ...
  • Ontologies as Integrative Tools for Plant Science 
    Walls, Ramona L.; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A.; Jaiswal, Pankaj; Mungall, Christopher J.; Preece, Justin; Rensing, Stefan; Smith, Barry; Stevenson, Dennis W. (Botanical Society of America, 2012-08)
    Premise of the study: Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregati ...
  • Orbilia ultrastructure, character evolution and phylogeny of Pezizomycotina 
    Kumar, T.K. Arun; Healy, Rosanne; Spatafora, Joseph W.; Blackwell, Meredith; McLaughlin, David J. (The Mycological Society of America, 2012-03)
    Molecular phylogenctic analyses indicate that the monophyletic classes Orbiliomycetes and Pezizomycetes are among the earliest diverging branches of Pezizomycotina, the largest subphylum of the Ascomycota. Although Orbil ...
  • An overview of the BioCreative 2012 Workshop Track III: interactive text mining task 
    Arighi, Cecilia N.; Carterette, Ben; Cohen, K. Bretonnel; Krallinger, Martin; Wilbur, W. John; Fey, Petra; Dodson, Robert; Cooper, Laurel; Van Slyke, Ceri E.; Dahdul, Wasila; Mabee, Paula; Li, Donghui; Harris, Bethany; Gillespie, Marc; Jimenez, Silvia; Roberts, Phoebe; Matthews, Lisa; Becker, Kevin; Drabkin, Harold; Bello, Susan; Licata, Luana; Chatr-aryamontri, Andrew; Schaeffer, Mary L.; Park, Julie; Haendel, Melissa; Van Auken, Kimberly; Li, Yuling; Chan, Juancarlos; Muller, Hans-Michael; Cui, Hong; Balhoff, James P.; Wu, Johnny Chi-Yang; Lu, Zhiyong; Wei, Chih-Hsuan; Tudor, Catalina O.; Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar; Cejuela, Juan Miguel; Dubey, Pratibha; Wu, Cathy (Oxford University Press, 2013-01-17)
    In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literat ...
  • The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes 
    Floudas, Dimitrios; Binder, Manfred; Riley, Robert; Barry, Kerrie; Blanchette, Robert A.; Henrissat, Bernard; Martínez, Angel T.; Otillar, Robert; Spatafora, Joseph W.; Yadav, Jagjit S.; Aerts, Andrea; Benoit, Isabelle; Boyd, Alex; Carlson, Alexis; Copeland, Alex; Coutinho, Pedro M.; de Vries, Ronald P.; Ferreira, Patricia; Findley, Keisha; Foster, Brian; Gaskell, Jill; Glotzer, Dylan; Gorecki, Pawel; Heitman, Joseph; Hesse, Cedar; Hori, Chiaki; Igarashi, Kiyohiko; Jurgens, Joel A.; Kallen, Nathan; Kersten, Phil; Kohler, Annegret; Kues, Ursula; Kumar, T. K. Arun; Kuo, Alan; LaButti, Kurt; Larrondo, Luis F.; Lindquist, Erika; Ling, Albee; Lombard, Vincent; Lucas, Susan; Lundell, Taina; Martin, Rachael; McLaughlin, David J.; Morgenstern, Ingo; Morin, Emanuelle; Murat, Claude; Nagy, Laszlo G.; Nolan, Matt; Ohm, Robin A.; Patyshakuliyeva, Aleksandrina; Rokas, Antonis; Ruiz-Duenas, Francisco J.; Sabat, Grzegorz; Salamov, Asaf; Samejima, Masahiro; Schmutz, Jeremy; Slot, Jason C.; St. John, Franz; Stenlid, Jan; Sun, Hui; Sun, Sheng; Syed, Khajamohiddin; Tsang, Adrian; Wiebenga, Ad; Young, Darcy; Pisabarro, Antonio; Eastwood, Daniel C.; Martin, Francis; Cullen, Dan; Grigoriev, Igor V.; Hibbett, David S. (American Association for the Advancement of Science, 2012-06-29)
    Wood is a major pool of organic carbon that is highly resistant to decay, owing largely to the presence of lignin. The only organisms capable of substantial lignin decay are white rot fungi in the Agaricomycetes, which a ...
  • Pararaucaria carrii sp nov., anatomically preserved evidence for the conifer family cheirolepidiaceae in the northern hemisphere 
    Stockey, Ruth A.; Rothwell, Gar W. (University of Chicago Press, 2013-03)
    A cylindrical permineralized conifer seed cone has been identified from the Officer Member of the Trowbridge Formation, near Izee, in east-central Oregon. The cone is preserved in a Middle Jurassic (Callovian) marine cal ...
  • Pararaucaria delfueyoi sp nov from the late jurassic canadon calcareo formation, chubut, argentina: Insights into the evolution of the cheirolepidiaceae 
    Escapa, Ignacio H.; Cuneo, Nestor R.; Rothwell, Gar; Stockey, Ruth A. (University of Chicago Press, 2013-03)
    The discovery of 16 cylindrical conifer seed cones at the Estancia Vilan locality in the Late Jurassic Canadon Calcareo Formation of Chubut Province, Patagonia, Argentina, provides anatomically preserved specimens, allow ...
  • Parmelina yalungana resurrected and reported from Alaska, China and Russia 
    Nelson, Peter R.; Kepler, Ryan; Walton, James; Fankhauser, John; Nelson, Laura; Song, Wang Li (The American Bryological and Lichenological Society, Inc., 2012-11-15)
    Parmelina quercina is a well-studied foliose macro-lichen found on rocks and trees in the Northern Hemisphere. Recent studies support multiple species within P. quercina based on material from Europe, North America and w ...
  • Particulate optical scattering coefficients along an Atlantic Meridional Transect 
    Dall Olmo, G.; Boss, E.; Behrenfeld, M.J.; Westberry, T.K. (Optical Society of America, 2012-09-10)
    See article for abstract.
  • A Perithecial Sordariomycete (Ascomycota, Diaporthales) from the Lower Cretaceous of Vancouver Island, British Columbia, Canada 
    Bronson, Allison W.; Klymiuk, Ashley A.; Stockey, Ruth A.; Tomescu, Alexandru M. F. (The University of Chicago Press, 2013-03)
    A perithecial ascomycete, Spataporthe taylori gen. et sp. nov., represented by >70 sporocarps is preserved by cellular permineralization in marine carbonate concretions dated at the Valanginian-Hauterivian boundary (Ear ...
  • The Personal Sequence Database: a suite of tools to create and maintain web-accessible sequence databases 
    Givan, Scott A.; Sullivan, Christopher M.; Carrington, James C. (BioMed Central, 2007-12-18)
    Background: Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller seq ...
  • Phenotypic Plasticity of the Hydrasperman Seed Fern Tetrastichia bupatides Gordon (Lyginopteridaceae) 
    Dunn, Michael T.; Rothwell, Gar W. (University of Chicago Press, 2012-09)
    Fifty-nine stems of Tetrastichia bupatides, numerous frond segments, and roots from Oxroad Bay, Scotland, have recently been analyzed. They reveal that many characters originally used to describe this species exhibit a w ...
  • Phylogenetic insights into the correlates of dioecy in meadow-rues (Thalictrum, Ranunculaceae) 
    Soza, Valerie L.; Brunet, Johanne; Liston, Aaron; Smith, Patricia Salles; Di Stilio, Veronica S. (Elsevier, 2012-04)
    Numerous studies have examined the evolution of sexual systems in angiosperms, but few explore the interaction between these and the evolution of pollination mode. Wind pollination is often associated with unisexual fl ...
  • Phylogenetic placement of the ectomycorrhizal genus Cenococcum in Gloniaceae (Dothideomycetes) 
    Spatafora, Joseph W.; Owensby, C. Alisha; Douhan, Greg W.; Boehm, Eric W. A.; Schoch, Conrad L. (The Mycological Society of America, 2012-05)
    Cenococcum is a genus of ectomycorrhizal Ascomycota that has a broad host range and geographic distribution. It is not known to produce either meiotic or mitotic spores and is known to exist only in the form of hyphae, s ...
  • Phytophthora borealis and Phytophthora riparia, new species in Phytophthora ITS Clade 6 
    Hansen, Everett M.; Reeser, Paul W.; Sutton, Wendy (The Mycological Society of America, 2012-09)
    Phytophthora borealis and Phytophthora riparia, identified in recent Phytophthora surveys of forest streams in Oregon, California and Alaska, are described as new species in Phytophthora ITS Glade 6. They are similar in ...
  • Phytophthora obscura sp nov., a new species of the novel Phytophthora subclade 8d 
    Gruenwald, N. J.; Werres, S.; Goss, E. M.; Taylor, C. R.; Fieland, V. J. (Wiley-Blackwell, 2011-10-09)
    A new Phytophthora species was detected (i) in the USA, infecting foliage of Kalmia latifolia, (ii) in substrate underneath Pieris, and (iii) in Germany in soil samples underneath Aesculus hippocastanum showing disease s ...
  • The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses 
    Cooper, Laurel; Walls, Ramona L.; Elser, Justin; Gandolfo, Maria A.; Stevenson, Dennis W.; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J.; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z.; Li, Donghui; Huala, Eva; Schaeffer, Mary; Menda, Naama; Arnaud, Elizabeth; Shrestha, Rosemary; Yamazaki, Yukiko; Jaiswal, Pankaj (Oxford University Press on behalf of Japanese Society of Plant Physiologists, 2013-02)
    The Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology ...
  • Population Density and Phenology of Tetranychus urticae (Acari: Tetranychidae) in Hop is Linked to the Timing of Sulfur Applications 
    Woods, J. L.; Dreves, A. J.; Fisher, G. C.; James, D. G.; Wright, L. C.; Gent, D. H. (Entomological Society of America, 2012-06)
    The twospotted spider mite, Tetranychus urticae Koch, is a worldwide pest of numerous agronomic and horticultural plants. Sulfur fungicides are known to induce outbreaks of this pest on several crops, although mechanisms ...
  • Population structure and genetic diversity of Botrychium pumicola (Ophioglossaceae) based on inter-simple sequence repeats (ISSR) 
    Camacho, Francisco J.; Liston, Aaron (Botanical Society of America, Inc., 2001-06)
    Species of Botrychium reproduce by spores that form subterranean gametophytes and a few, like B. pumicola, also reproduce asexually with subterranean sporophytic gemmae. The goal of this study was to examine the genetic ...

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