Index Catalog // ScholarsArchive@OSU

ASRP: the Arabidopsis Small RNA Project Database

Creator:: Gustafson, Adam M., Allen, Edwards, Givan, Scott, Smith, Daniel, Carrington, James C., and Kasschau, Kristin D.
Abstract:: ABSTRACT Eukaryotes produce functionally diverse classes of small RNAs (20–25 nt). These include microRNAs (miRNAs), which act as regulatory factors during growth and development, and short-interfering RNAs (siRNAs), which function in several epigenetic and post-transcriptional silencing systems. The Arabidopsis Small RNA Project (ASRP) seeks to characterize and functionally analyze the...
Resource Type:: Article
Full Text:: , Database issue D637–D640 doi:10.1093/nar/gki127 composed of web pages delivered by an apache HTTP

MyroldDavidCropSoilSciFOAMFunctionalOntologyAssignments.pdf

Creator:: Prestat, Emmanuel, David, Maude M., Hultman, Jenni, Myrold, David D., and et al.
Abstract:: A new functional gene database, FOAM (Functional Ontology Assignments for Metagenomes), was developed to screen environmental metagenomic sequence datasets. FOAM provides a new functional ontology dedicated to classify gene functions relevant to environmental microorganisms based on Hidden Markov Models (HMMs). Sets of aligned protein sequences (i.e. ‘profiles’) were tailored to...
Full Text:: Research, 42(19), e145. doi:10.1093/nar/gku702 10.1093/nar/gku702 Oxford University Press Version of

Mass Spectrometry-based Analysis of Superwarfarins and their Metabolites and the Investigation of Novel Treatments for Poisoned Victims

Creator:: Nosal, Daniel Grzegorz
Abstract:: Superwarfarins are anticoagulant rodenticides that are 100 times more potent and 15 times more persistent than warfarin. They have been used since the 1980s and cause over 10,000 cases of accidental and intentional poisonings per year. Apart from inducing uncontrollable bleeding, by inhibiting the vitamin K cycle, superwarfarins can disrupt...
Resource Type:: Dissertation
Full Text:: , Chicago, IL 60612, USA J. AOAC. Int., 2020, 103(3), 770 – 778 DOI: 10.1093/jaoacint

OneFish: One Internet Portal, All Fisheries Research

Creator:: Bostock, Tim, Baron, Joan, and Searle, Greg
Abstract:: OneFish is a Web based knowledge management system that draws together a broad cross section of stakeholders within the fisheries and aquatic research community. The primary aim of oneFish is to raise the profile of fisheries and aquatic research and reinforce its impact on responsible fisheries development. oneFish represents a...
Resource Type:: Conference Proceeding

Responses of bush snap bean cultivars (Phaseolus vulgaris L.) to plant population densities

Creator:: Stang, Jack Rudolf
Abstract:: The effects of plant population densities on the growth and development of six cultivars of bush snap beans (Phaseolus vulgaris L.) were studied in two field experiments. A systematic planting design was used to achieve a range of densities from 21- to 110 plants per m² and a rectangularity of...
Resource Type:: Dissertation
Full Text:: (NAR) per unit increase in their LAI; however, at any given LAI the highest yielding cultivars had

Gramene: a growing plant comparative genomics resource

Creator:: Liang, Chengzhi, Jaiswal, Pankaj, Hebbard, Claire, Avraham, Shuly, Buckler, Edward S., Casstevens, Terry, Hurwitz, Bonnie, McCouch, Susan, Ni, Junjian, Pujar, Anuradha, Ravenscroft, Dean, Ren, Liya, Spooner, William, Tecle, Isaak, Thomason, Jim, Tung, Chih-wei, Wei, Xuehong, Yap, Immanuel, Youens-Clark, Ken, Ware, Doreen, and Stein, Lincoln
Abstract:: Gramene (www.gramene.org) is a curated resource for genetic, genomic and comparative genomics data for the major crop species, including rice, maize, wheat and many other plant (mainly grass) species. Gramene is an open-source project. All data and software are freely downloadable through the ftp site (ftp.gramene.org/pub/gramene) and available for use...
Resource Type:: Article
Full Text:: resource. Nucleic Acids Research, 36, D947-D953. doi:10.1093/nar/gkm968 10.1093/nar/gkm968 Oxford

Tello-RuizGramene2016Comparative.pdf

Creator:: Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Full Text:: , 2016, Vol. 44, Database issue D1133–D1140 doi: 10.1093/nar/gkv1179 Gramene 2016: comparative plant

Tello-RuizGramene2016ComparativeSupplementaryTablesS1-S6.pdf

Creator:: Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...

Gramene 2016: comparative plant genomics and pathway resources

Creator:: Tello-Ruiz, Marcela K., Stein, Joshua, Wei, Sharon, Preece, Justin, Olson, Andrew, Naithani, Sushma, Amarasinghe, Vindhya, Dharmawardhana, Palitha, Jiao, Yinping, Mulvaney, Joseph, Kumari, Sunita, Chougule, Kapeel, Elser, Justin, Wang, Bo, Thomason, James, Bolser, Daniel M., Kerhornou, Arnaud, Walts, Brandon, Fonseca, Nuno A., Huerta, Laura, Keays, Maria, Tanga, Y. Amy, Parkinson, Helen, Fabregat, Antonio, McKay, Sheldon, Weiser, Joel, D'Eustachio, Peter, Stein, Lincoln, Petryszak, Robert, Kersey, Paul J., Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is an online resource for comparative functional genomics in crops and model plant species. Its two main frameworks are genomes (collaboration with Ensembl Plants) and pathways (The Plant Reactome and archival BioCyc databases). Since our last NAR update, the database website adopted a new Drupal management platform. The...
Resource Type:: Article

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

Creator:: Chatterjee, Saikat, Koslicki, David, Dong, Siyuan, Innocenti, Nicholas, Cheng, Lu, Lan, Yueheng, Vehkaperä, Mikko, Skoglund, Mikael, Rasmussen, Lars, K., Aurell, Erik, and Corander, Jukka
Abstract:: MOTIVATION: Estimation of bacterial community composition from a high-throughput sequenced sample is an important task in metagenomics applications. Since the sample sequence data typically harbors reads of variable lengths and different levels of biological and technical noise, accurate statistical analysis of such data is challenging. Currently popular estimation methods are...
Resource Type:: Article
Full Text:: . Bioinformatics, 30(17), 2423-2431. doi:10.1093/bioinformatics/btu320 10.1093/bioinformatics/btu320 Oxford

ScholarsArchive@OSU

ASRP: the Arabidopsis Small RNA Project Database

MyroldDavidCropSoilSciFOAMFunctionalOntologyAssignments.pdf

Mass Spectrometry-based Analysis of Superwarfarins and their Metabolites and the Investigation of Novel Treatments for Poisoned Victims

OneFish: One Internet Portal, All Fisheries Research

Responses of bush snap bean cultivars (Phaseolus vulgaris L.) to plant population densities

Gramene: a growing plant comparative genomics resource

Tello-RuizGramene2016Comparative.pdf

Tello-RuizGramene2016ComparativeSupplementaryTablesS1-S6.pdf

Gramene 2016: comparative plant genomics and pathway resources

SEK: sparsity exploiting k-mer-based estimation of bacterial community composition

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