Index Catalog // ScholarsArchive@OSU

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Creator:: Bollmann, Annette, Sedlacek, Christopher J., Norton, Jeanette, Laanbroek, Hendrikus J., Suwa, Yuichi, Stein, Lisa Y., Klotz, Martin G., Arp, Daniel J., Sayavedra-Soto, Luis, Lu, Megan, Bruce, David, Detter, Chris, Tapia, Roxanne, Han, James, Woyke, Tanja, Pitluck, Sam, Pennacchio, Len, Nolan, Matt, Land, Miriam L., Huntemann, Marcel, Deshpande, Shweta, Han, Cliff, Chen, Amy, Kyrpides, Nikos, Movromatis, Konstantinos, Markowitz, Victor, Szeto, Ernest, Ivonova, Natalia, Mikhailova, Natalia, Pagani, Ioanna, Pati, Amrita, Peters, Lin, Ovchinnikova, Galina, Goodwin, Lynne A., and Lucas, Susan M.
Abstract:: Nitrosomonas sp. Is79 is a chemolithoautotrophic ammonia-oxidizing bacterium that belongs to the family Nitrosomonadaceae within the phylum Proteobacteria. Ammonia oxidation is the first step of nitrification, an important process in the global nitrogen cycle ultimately resulting in the production of nitrate. Nitrosomonas sp. Is79 is an ammonia oxidizer of high...
Resource Type:: Article
Full Text:: recommended by JGI (Bacterial genomic DNA isolation using CTAB). Size and quality of the bulk DNA was

Genomic characterization of a novel leporid Herpes simplex virus

Creator:: Babra, Bobby A.
Abstract:: The viral family Herpesviridae consists of large double stranded DNA viruses including eight species that infect humans with varying pathology from benign rashes to cancerous cell transformation. From three subfamilies, alpha-, beta- and gammaherpes, the alphaherpes contains the genera iltovirus, mardivirus, varicellovirus and simplex, two of which, the human simplex...
Resource Type:: Dissertation
Full Text:: infected with HSV. Comparative genomics revealed a high degree of sequence similarity and genome

Using Culture-independent Genomics as a Means for Understanding Chlamydial Biology

Creator:: Putman, Timothy E.
Abstract:: The chlamydiae are a family of obligate intracellular bacteria that have a unique bi-phasic developmental cycle, unique cellular properties, and a unique set of challenges to studying its biology. While genetic manipulation is becoming routine in Chlamydia, there are significant challenges to working with this intracellular parasite. The body of...
Resource Type:: Dissertation
Full Text:: tools and methods for improving the comparative genomic research

Gramene 2013: comparative plant genomics resources

Creator:: Monaco, Marcela K., Stein, Joshua, Naithani, Sushma, Wei, Sharon, Dharmawardhana, Palitha, Kumari, Sunita, Amarasinghe, Vindhya, Youens-Clark, Ken, Thomason, James, Preece, Justin, Pasternak, Shiran, Olson, Andrew, Jiao, Yinping, Lu, Zhenyuan, Bolser, Dan, Kerhornou, Arnaud, Staines, Dan, Walts, Brandon, Wu, Guanming, D'Eustachio, Peter, Haw, Robin, Croft, David, Kersey, Paul J., Stein, Lincoln, Jaiswal, Pankaj, and Ware, Doreen
Abstract:: Gramene (http://www.gramene.org) is a curated online resource for comparative functional genomics in crops and model plant species, currently hosting 27 fully and 10 partially sequenced reference genomes in its build number 38. Its strength derives from the application of a phylogenetic framework for genome comparison and the use of ontologies...
Resource Type:: Article

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 for genetic, genomic and comparative genomics data for the major crop species, including rice

Advances in Freshwater Cyanobacterial Genomics

Creator:: Brown, Nathaniel M.
Abstract:: Limnology is undergoing a transition to high-throughput -omic analysis of freshwater bacterial communities. An important first step in making the transition is to characterize several genomes that can be used as references to guide metagenome assembly and analysis. Here I characterize four new freshwater cyanobacterial genomes, a pair of lake...
Resource Type:: Dissertation
Full Text:: comparative genomic analysis with other members of the Nostocaceae is car- ried out, and its capacity to

Gramene: a resource for comparative grass genomics

Creator:: Ware, Doreen, Jaiswal, Pankaj, Ni, Junjian, Pan, Xiaokang, Chang, Kuan, Clark, Kenneth, Teytelman, Leonid, Schmidt, Steve, Zhao, Wei, Cartinhour, Samuel, McCouch, Susan, and Stein, Lincoln
Abstract:: Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on...
Resource Type:: Article
Full Text:: more limited scope that also focused on rice and comparative genomics for agriculturally important

The Pursuit of Hoppiness : Propelling Hop into the Genomic Era

Creator:: Hill, Steven T.
Abstract:: Hop (Humulus lupulus L. var lupulus) is a plant of great cultural significance, used as a medicinal herb for thousands of years, and for flavor and as a preservative in brewing beer. Studies of the medicinal effects of the unique compounds produced by hop have led to interest from the...
Resource Type:: Masters Thesis
Full Text:: studies for many different traits have been performed, and as the genomic resources increase, the

Strategies for Altering Energy Flux in Thalassiosira pseudonana Elucidated by Transcriptomics

Creator:: Pombrol, Michelle
Abstract:: Diatoms play a major role in ocean biogeochemical cycles and are important tools in bioengineering for natural products and nanotechnology. Diatoms and other algae growing at varying resource-limited growth rates allocate carbon to different metabolic pathways to optimize growth; however, the molecular mechanisms controlling these pathway gating strategies are not...
Resource Type:: Masters Thesis
Full Text:: functional annotation of diatom genomes. Several genes involved in the TCA and glyoxylate cycles

Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing

Creator:: Bellinger, M. Renee
Abstract:: Substantial scientific investment has been directed towards understanding factors that influence distribution patterns and animals' remarkable ability for precise orientation and navigation, yet fundamental gaps in our knowledge remain. In my dissertation, I applied emerging genetic technologies to conduct a top-down and bottom-up investigation of animal movement and cue perception....
Resource Type:: Dissertation
Full Text:: genomics education and guidance during the Keck proposal process. Many thanks to the Hatfield Marine

ScholarsArchive@OSU

Complete genome sequence of Nitrosomonas sp. Is79, an ammonia oxidizing bacterium adapted to low ammonium concentrations

Genomic characterization of a novel leporid Herpes simplex virus

Using Culture-independent Genomics as a Means for Understanding Chlamydial Biology

Gramene 2013: comparative plant genomics resources

Gramene: a growing plant comparative genomics resource

Advances in Freshwater Cyanobacterial Genomics

Gramene: a resource for comparative grass genomics

The Pursuit of Hoppiness : Propelling Hop into the Genomic Era

Strategies for Altering Energy Flux in Thalassiosira pseudonana Elucidated by Transcriptomics

Genomics of migration : from marine distributions of salmonids to mechanisms of olfactory and magnetic cue perception for natal homing

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