Index Catalog // ScholarsArchive@OSU

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks

Creator:: Hanumappa, Mamatha, Preece, Justin, Elser, Justin, Nemeth, Denise, Bono, Gina, Wu, Kenny, and Jaiswal, Pankaj
Abstract:: Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
Resource Type:: Article
Full Text:: Hanumappa, Justin Preece, Justin Elser, Denise Nemeth, Gina Bono, Kenny Wu and Pankaj Jaiswal* Abstract

Ontologies as Integrative Tools for Plant Science

Creator:: Walls, Ramona L., Athreya, Balaji, Cooper, Laurel, Elser, Justin, Gandolfo, Maria A., Jaiswal, Pankaj, Mungall, Christopher J., Preece, Justin, Rensing, Stefan, Smith, Barry, and Stevenson, Dennis W.
Abstract:: 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 aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web....
Resource Type:: Article
Full Text:: . WALLS 2,9 , BALAJI ATHREYA 3 , LAUREL COOPER 3,9 , JUSTIN ELSER 3

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf

Creator:: Fox, Samuel E., Geniza, Matthew, Hanumappa, Mamatha, Naithani, Sushma, Sullivan, Chris, Preece, Justin, Tiwari, Vijay K., Elser, Justin, Leonard, Jeffrey M., Sage, Abigail, Jaiswal, Pankaj, and et al.
Abstract:: BACKGROUND: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
Full Text:: Sullivan1,3, Justin Preece1, Vijay K. Tiwari4¤b, Justin Elser1, Jeffrey M. Leonard4, Abigail Sage1, Cathy

NaithaniFragariaCycMetabolicPathway.pdf

Creator:: Naithani, Sushma, Partipilo, Christina M., Raja, Rajani, Elser, Justin L., and Jaiswal, Pankaj
Abstract:: FragariaCyc is a strawberry-specific cellular metabolic network based on the annotated genome sequence of Fragaria vesca L. ssp. vesca, accession Hawaii 4. It was built on the Pathway-Tools platform using MetaCyc as the reference. The experimental evidences from published literature were used for supporting/editing existing entities and for the addition...
Full Text:: . Partipilo, Rajani Raja, Justin L. Elser and Pankaj Jaiswal Department of Botany and Plant Pathology, Oregon

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

Creator:: Quandt, C. Alisha, Di, Yanming, Elser, Justin, Jaiswal, Pankaj, and Spatafora, Joseph W.
Abstract:: This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Resource Type:: Article
Full Text:: ophioglossoides C. Alisha Quandt,*,1 Yanming Di,† Justin Elser,* Pankaj Jaiswal,* and Joseph W. Spatafora

AISO: Annotation of Image Segments with Ontologies

Creator:: Lingutla, Nikhil Tej, Preece, Justin, Todorovic, Sinisa, Cooper, Laurel, Moore, Laura, and Jaiswal, Pankaj
Abstract:: BACKGROUND: Large quantities of digital images are now generated for biological collections, including those developed in projects premised on the high-throughput screening of genome-phenome experiments. These images often carry annotations on taxonomy and observable features, such as anatomical structures and phenotype variations often recorded in response to the environmental factors...
Resource Type:: Article
Full Text:: with Ontologies AISO: Annotation of Image Segments with Ontologies Lingutla, N. T., Preece, J

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

Creator:: Smita, Shuchi, Lenka, Sangram Keshari, Katiyar, Amit, Jaiswal, Pankaj, Preece, Justin, and Bansal, Kailash Chander
Abstract:: The QlicRice database is designed to host publicly accessible, abiotic stress responsive quantitative trait loci (QTLs) in rice (Oryza sativa) and their corresponding sequenced gene loci. It provides a platform for the data mining of abiotic stress responsive QTLs, as well as browsing and annotating associated traits, their location on...
Resource Type:: Article
Full Text:: , Amit Katiyar1, Pankaj Jaiswal3, Justin Preece3 and Kailash Chander Bansal1,4,* 1National Research

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

Creator:: Naithani, Sushma, Raja, Rajani, Waddell, Elijah N., Elser, Justin, Gouthu, Satyanarayana, Deluc, Laurent G., and Jaiswal, Pankaj
Abstract:: We have developed VitisCyc, a grapevine-specific metabolic pathway database that allows researchers to (i) search and browse the database for its various components such as metabolic pathways, reactions, compounds, genes and proteins, (ii) compare grapevine metabolic networks with other publicly available plant metabolic networks, and (iii) upload, visualize and analyze...
Resource Type:: Article
Full Text:: vinifera) Naithani, S., Raja, R., Waddell, E. N., Elser, J., Gouthu, S., Deluc, L. G., & Jaiswal, P

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Creator:: 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, and Jaiswal, Pankaj
Abstract:: 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 and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and...
Resource Type:: Article
Full Text:: Plant Anatomy and Genomic Analyses Laurel Cooper1,16,17, Ramona L. Walls2,16,17, Justin Elser1,17, Maria

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Creator:: Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj
Abstract:: PREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum (slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis, Oregon, USA. METHODS AND RESULTS: More than 350 million sequence reads from the mRNA libraries...
Resource Type:: Article
Full Text:: sylvaticum (Poaceae) Fox, S. E., Preece, J., Kimbrel, J. A., Marchini, G. L., Sage, A., Youens-Clark, K

ScholarsArchive@OSU

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks

Ontologies as Integrative Tools for Plant Science

GenizaMatthewMolecularCellularBiologyDeNovoTranscriptome.pdf

NaithaniFragariaCycMetabolicPathway.pdf

Differential Expression of Genes Involved in Host Recognition, Attachment, and Degradation in the Mycoparasite Tolypocladium ophioglossoides

AISO: Annotation of Image Segments with Ontologies

QlicRice: a web interface for abiotic stress responsive QTL and loci interaction channels in rice

VitisCyc: a metabolic pathway knowledgebase for grapevine (Vitis vinifera)

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

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