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Filtering by: Has journal Genome Research Remove constraint Has journal: Genome Research Non-Academic Affiliation Oregon State University. Center for Genome Research and Biocomputing Remove constraint Non-Academic Affiliation: Oregon State University. Center for Genome Research and Biocomputing

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Assessing De Novo transcriptome assembly metrics for consistency and utility

Creator:

O’Neil, Shawn T. and Emrich, Scott J.

Abstract:

Background: Transcriptome sequencing and assembly represent a great resource for the study of non-model species, and many metrics have been used to evaluate and compare these assemblies. Unfortunately, it is still unclear which of these metrics accurately reflect assembly quality. Results: We simulated sequencing transcripts of Drosophila melanogaster. By assembling...

Resource Type:

Article

Full Text:

://www.biomedcentral.com/1471-2164/14/465 RESEARCH ARTICLE Open Access Assessing De Novo transcriptome assembly metrics
Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:

Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.

Abstract:

Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...

Resource Type:

Article

Full Text:

untitled Genome-Wide Profiling and Analysis of Arabidopsis
Creating High Throughput Low Cost Analysis of Different Labor-Intensive Repetitive Research Processes

Creator:

Sullivan, Christopher M.

Abstract:

Many research projects suffer from limited data causing poor statistical analysis or limited results. The movement to high throughput methods has been building for many years and cross many different disciplines. Lots of these methods start out using pathways that generate large amounts of data but have limited methods to...

Resource Type:

Masters Thesis

Full Text:

to the Center for Genome Research and Biocomputing for all the computational resources. The author
De novo Discovery of Novel Long Noncoding RNAs in the North American Beaver

Creator:

Kashyap, Amita

Abstract:

Long noncoding RNAs (lncRNAs) are RNA molecules that are at least 200 nucleotides long and do not encode proteins. lncRNAs have roles in gene regulation, chromatin epigenetics, and molecular scaffolding. In light of mounting evidence implicating species-specific noncoding RNAs and gene regulatory mechanisms in species adaptations, it is reasonable to...

Resource Type:

Honors College Thesis

Full Text:

Research, College of Agricultural Sciences 2Center for Genome Research and Biocomputing 3Department of
Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

Creator:

Wiemann, Philipp, Sieber, Christian M. K., von Bargen, Katharina W., Studt, Lena, Niehaus, Eva- Maria, Espino, Jose J., Huß, Kathleen, Michielse, Caroline B., Albermann, Sabine, Wagner, Dominik, Bergner, Sonja V., Connolly, Lanelle R., Fischer, Andreas, Reuter, Gunter, Kleigrewe, Karin, Bald, Till, Wingfield, Brenda D., Ophir, Ron, Freeman, Stanley, Hippler, Michael, Smith, Kristina M., Brown, Daren W., Proctor, Robert H., Munsterkotter, Martin, Freitag, Michael, Humpf, Hans-Ulrich, Guldener, Ulrich, and Tudzynski, Bettina

Abstract:

The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we...

Resource Type:

Article

Full Text:

, Münster, Germany, 5 Department of Biochemistry and Biophysics, Center for Genome Research and
The Genome and Development-Dependent Transcriptomes of Pyronema confluens: A Window into Fungal Evolution

Creator:

Traeger, Stefanie, Altegoer, Florian, Freitag, Michael, Gabaldon, Toni, Kempken, Frank, Kumar, Abhishek, Marcet-Houben, Marina, Poggeler, Stefanie, Stajich, Jason E., and Nowrousian, Minou

Abstract:

Fungi are a large group of eukaryotes found in nearly all ecosystems. More than 250 fungal genomes have already been sequenced, greatly improving our understanding of fungal evolution, physiology, and development. However, for the Pezizomycetes, an early-diverging lineage of filamentous ascomycetes, there is so far only one genome available, namely...

Resource Type:

Article

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-Universität Bochum, Bochum, Germany, 2 Center for Genome Research and Biocomputing, Department of
The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Creator:

Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.

Abstract:

The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...

Resource Type:

Article

Full Text:

America, 3 Center for Genome Research & Biocomputing, Oregon State University, Corvallis, Oregon, United
Analysis of Genome Sequences from Plant Pathogenic Rhodococcus Reveals Genetic Novelties in Virulence Loci

Creator:

Creason, Allison L., Vandeputte, Olivier M., Savory, Elizabeth A., Davis, Edward W., II, Putnam, Melodie L., Hu, Erdong, Swader-Hines, David, Mol, Adeline, Baucher, Marie, Prinsen, Els, Zdanowska, Magdalena, Givan, Scott A., El Jaziri, Mondher, Loper, Joyce E., Mahmud, Taifo, and Chang, Jeff H.

Abstract:

Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus, some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with...

Resource Type:

Article
Dissecting a Hidden Gene Duplication: The Arabidopsis thaliana SEC10 Locus

Creator:

Vukašinović, Nemanja, Cvrčková, Fatima, Eliáš, Marek, Cole, Rex A., Fowler, John E., Žárský, Viktor, and Synek, Lukáš

Abstract:

Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we...

Resource Type:

Article
Transcriptomic Analyses of Crop Plants using Next-Generation Sequencing Technology

Creator:

Geniza, Matthew J.

Abstract:

Advancements in molecular biology and computer science have enabled researchers the ability to investigate the transcriptome – the quantification of an organism’s RNA transcripts in response to its environment on a system wide scale. The collective chapters of this thesis utilize high-throughput RNA sequencing, which produces hundreds of millions of...

Resource Type:

Dissertation

Full Text:

you, the first year of core classes would have been much harder. To the Center for Genome Research

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Academic Affiliation

Botany and Plant Pathology16
Biochemistry and Biophysics5
Statistics3
College of Pharmacy2
Environmental and Molecular Toxicology2
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Advisor

Banks, Michael A.1
Brander, Susanne M.1
Curtin, Chris D.1
Dallas, David C.1
Jaiswal, Pankaj1
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Commencement Year

Commencement Year range begin – Commencement Year range end

Current results range from 2018 to 2023

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Unknown 25

Committee Member

Hendrix, David3
Fowler, John2
Sidlauskas, Brian2
Anderson, Jeffrey C.1
Barreto, Felipe1
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Creator

Chang, Jeff H.5
Cumbie, Jason S.5
Freitag, Michael5
Carrington, James C.4
Fahlgren, Noah4
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Contributor

Barreto, Felipe1
Bermudez, Luiz E.1
Bernell, David A.1
Carroll, Kirstin M. A.1
Filtz, Theresa M.1
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Date

Date range begin – Date range end

Current results range from 2007 to 2023

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Decade

2020-20297
2010-201929
2000-20092

Degree Field

Molecular and Cellular Biology5
Toxicology3
Food Science and Technology2
BioResource Research1
Fisheries Science1
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Degree Level

Doctoral7
Master's4
Bachelor's2

Degree Name

Doctor of Philosophy (Ph.D.)7
Master of Science (M.S.)4
Honors Bachelor of Science (H.B.S.)2

Language

English [eng]38
Spanish; Castilian [spa]1

License

Attribution 3.0 United States13
All rights reserved12
Attribution 4.0 (CC BY 4.0)8
CC0 1.0 Universal4
Attribution-NonCommercial-NoDerivatives 4.0 (CC BY-NC-ND 4.0)1

Non-Academic Affiliation

Oregon State University. Center for Genome Research and Biocomputing[remove]38
Oregon State University. Honors College2
Hatfield Marine Science Center1
Oregon State University. Bioresource Research1
Oregon State University. Graduate School1

Peer Reviewed

Yes24
No13

Resource Type

Article23
Dissertation7
Masters Thesis4
Honors College Thesis2
Dataset1
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Rights Statement

In Copyright33
No Copyright - United States4
In Copyright - Non-Commercial Use Permitted1

Subject

Membrane proteins2
Alternative toxicity testing1
Education -- Study and teaching (Graduate)1
Fluorescent protein1
Gene expression1
more Subjects »

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