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You searched for subject:(genomic features). Showing records 1 – 3 of 3 total matches.

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Penn State University

1. Campos Sanchez, Rebeca. Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure .

Degree: 2015, Penn State University

The topic of genome architecture is of great interest to evolutionary biologists. Small to large chromosome rearrangements have been reorganizing the genome information, including genes and heterochromatic regions such as centromeres and telomeres. Transposable elements (TEs) are an essential component of the genomes of all life forms studied until now, not only because of their abundance but also because of their influence on reshaping the genome architecture. Multiple studies have provided evidence that TEs are located in particular regions of the genome (e.g. GC-rich regions for Alus, or AT-rich regions for L1s). Here, using abundant genomic data and statistical methods as diverse as pair-wise non-parametric tests, multiple linear regression, multiple negative binomial regression, multiple logistic regression, interval testing procedure (ITP), and functional logistic regression (FLR), we addressed two questions about TE biology: 1. How do Alus’, DNA transposons’, and endogenous retroviruses’ (ERVs’) neighboring regions reflect integration site preferences and fixation processes for these TEs? What genomic features are associated with their presence genome-wide? 2. Can we capture integration site preferences alone using data from young, polymorphic or ex vivo integrations? The results from the TE analyses contributed to our understanding of fixation and integration site preferences genome-wide providing abundant information from diverse genomic features. This information is of great importance to direct studies of insertional mutagenesis and gene therapy. Additionally, we provided a set of statistical tools to analyze complex genomic datasets. Moreover, we explored the genes on the Y chromosome of gorilla. We performed this by first, generating Y-specific transcripts from testis RNAseq data; second, by evaluating their structure in the Y chromosome assembly; third, by using these transcripts to scaffold the Y chromosome assembly. Finally, we predicted novel genes from the assembly that could have been transposed from other chromosomes. This project allowed us to create a workflow to assemble Y transcripts from testis samples; this protocol will be applied in future studies. In addition, we proved the usefulness of transcriptome data to scaffold genomes. Advisors/Committee Members: Kateryna Dmytrivna Makova, Dissertation Advisor/Co-Advisor, Stephen Wade Schaeffer, Committee Chair/Co-Chair, Ross Cameron Hardison, Committee Member, Mark Shriver, Committee Member, Francesca Chiaromonte, Committee Member.

Subjects/Keywords: genome architecture; transposable elements; genomic features; testis transcriptome; Y chromosome genes

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Campos Sanchez, R. (2015). Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure . (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/27199

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Campos Sanchez, Rebeca. “Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure .” 2015. Thesis, Penn State University. Accessed December 04, 2020. https://submit-etda.libraries.psu.edu/catalog/27199.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Campos Sanchez, Rebeca. “Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure .” 2015. Web. 04 Dec 2020.

Vancouver:

Campos Sanchez R. Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure . [Internet] [Thesis]. Penn State University; 2015. [cited 2020 Dec 04]. Available from: https://submit-etda.libraries.psu.edu/catalog/27199.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Campos Sanchez R. Evolution of genome architecture: from transposable elements distribution to Y chromosome gene structure . [Thesis]. Penn State University; 2015. Available from: https://submit-etda.libraries.psu.edu/catalog/27199

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation


Iowa State University

2. Lu, Hong. Application of comparative genomics for detection of genomic features and transcriptional regulatory elements.

Degree: 2011, Iowa State University

In the wake of advanced DNA sequencing technology, a large number of bacterial, animal, and plant genomes have now been completely sequenced and deposited into public databases. The acceleration of genome (and transcriptome) sequence data accumulation remains unabated and poses considerable challenges for data storage, access, and transfer, with even greater challenges for comprehensive data mining to turn the genome information into knowledge. In particular, detailed genome annotation with respect to the encoded genes and their regulation is still largely confined to a few model species. Thus, important current research problems revolve around automated genome annotation and the related question of how widely applicable insights from the model species are with respect to novel genomes. For example, what features of genome organization are conserved across species? What differences in gene repertoire correlate with clade-specific traits or related species? To what extent are elements of transcriptional regulation shared? In this thesis, I discussed comparative genomics approaches to these questions. First, I described genome features of eight recently sequenced plant species, with standards for comparison provided by the well established model species for dicots (Arabidopsis) and monocots (rice). Secondly, I discussed software and statistical models for exploring possible cis-regulatory elements of co-regulated genes, with particular application to mapping gene expression data for a species with incomplete genome data to close model genomes.

Subjects/Keywords: Comparative Genomics; Genomic features; Cell and Developmental Biology; Genetics and Genomics

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Lu, H. (2011). Application of comparative genomics for detection of genomic features and transcriptional regulatory elements. (Thesis). Iowa State University. Retrieved from https://lib.dr.iastate.edu/etd/12151

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Lu, Hong. “Application of comparative genomics for detection of genomic features and transcriptional regulatory elements.” 2011. Thesis, Iowa State University. Accessed December 04, 2020. https://lib.dr.iastate.edu/etd/12151.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Lu, Hong. “Application of comparative genomics for detection of genomic features and transcriptional regulatory elements.” 2011. Web. 04 Dec 2020.

Vancouver:

Lu H. Application of comparative genomics for detection of genomic features and transcriptional regulatory elements. [Internet] [Thesis]. Iowa State University; 2011. [cited 2020 Dec 04]. Available from: https://lib.dr.iastate.edu/etd/12151.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Lu H. Application of comparative genomics for detection of genomic features and transcriptional regulatory elements. [Thesis]. Iowa State University; 2011. Available from: https://lib.dr.iastate.edu/etd/12151

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation


Brno University of Technology

3. Nétková, Barbora. Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features.

Degree: 2019, Brno University of Technology

This thesis deals with visualization of transposons' genomic features. The Genomic feature format (GFF) is an input file to visualisation. This type of file has strict definition and it is nowadays a de-facto standard format for genome description. Although there are several tools for GFF visualization, an open source application with advanced visualization features is missing. This work presents a design of such a tool. The application has a graphical user interface to simplify the user's work and combines the advantages of existing commercial products with free access. The application provides simple way to import user's biological data from a GFF file, creates hierarchical tree of individual elements including a detailed internal structure visualization in a subwindow. Advisors/Committee Members: Vogel, Ivan (advisor), Bendl, Jaroslav (referee).

Subjects/Keywords: vizualizace; transposony; hierarchický strom; GFF; genomické rysy; DNA; visualisation; transposons; hiararchical tree; GFF; genomic features; DNA

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APA · Chicago · MLA · Vancouver · CSE | Export to Zotero / EndNote / Reference Manager

APA (6th Edition):

Nétková, B. (2019). Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/56601

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Chicago Manual of Style (16th Edition):

Nétková, Barbora. “Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features.” 2019. Thesis, Brno University of Technology. Accessed December 04, 2020. http://hdl.handle.net/11012/56601.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

MLA Handbook (7th Edition):

Nétková, Barbora. “Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features.” 2019. Web. 04 Dec 2020.

Vancouver:

Nétková B. Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2020 Dec 04]. Available from: http://hdl.handle.net/11012/56601.

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

Council of Science Editors:

Nétková B. Vizualizace genomických rysů transposonů: Visualization of Transposons' Genomic Features. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/56601

Note: this citation may be lacking information needed for this citation format:
Not specified: Masters Thesis or Doctoral Dissertation

.