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You searched for +publisher:"University of Notre Dame" +contributor:("Scott J. Emrich, Committee Chair"). Showing records 1 – 3 of 3 total matches.

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University of Notre Dame

1. Allison Ann Penner Regier. A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>.

Degree: PhD, Computer Science and Engineering, 2011, University of Notre Dame

Genome sequencing technologies have revolutionized biology in the past two decades, yet data analysis has lagged behind data production. In this thesis, we present a framework for analyzing genomic data in more flexible ways than previous techniques. First, the framework allows researchers to design analyses that compare genomic samples directly instead of relying on reference-relative variant calls, as most current tools do. Second, we provide utilities to look at both assembly data and resequencing data in the same analysis, where previous tools were restricted to either looking at an assembly or at resequencing data. Finally, our framework allows researchers to flexibly incorporate alignments to arbitrarily many reference sequences into their analysis. We describe FlexReseq, the software implementation of this framework. FlexReseq allows researchers to easily customize resequencing analyses using a simple configuration file to define positions of interest. We give results from applications of these tools such as genotyping strains of Plasmodium falciparum, finding diversity and divergence between strains of Anopheles gambiae, detecting inversions based on assembly and alignment information from A. gambiae, and exploring resequencing analysis using alignments to multiple reference sequences. Advisors/Committee Members: Mihai Pop, Committee Member, Scott J. Emrich, Committee Chair, Frank Collins, Committee Member, Kevin Bowyer, Committee Member, Nora Besansky, Committee Member.

Subjects/Keywords: anopheles gambiae; plasmodium falciparum; bioinformatics

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

APA (6th Edition):

Regier, A. A. P. (2011). A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>. (Doctoral Dissertation). University of Notre Dame. Retrieved from https://curate.nd.edu/show/0k225b01f48

Chicago Manual of Style (16th Edition):

Regier, Allison Ann Penner. “A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>.” 2011. Doctoral Dissertation, University of Notre Dame. Accessed April 22, 2019. https://curate.nd.edu/show/0k225b01f48.

MLA Handbook (7th Edition):

Regier, Allison Ann Penner. “A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>.” 2011. Web. 22 Apr 2019.

Vancouver:

Regier AAP. A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>. [Internet] [Doctoral dissertation]. University of Notre Dame; 2011. [cited 2019 Apr 22]. Available from: https://curate.nd.edu/show/0k225b01f48.

Council of Science Editors:

Regier AAP. A Flexible Comparative Genomics Framework for Integrating Heterogeneous Sequence Data</h1>. [Doctoral Dissertation]. University of Notre Dame; 2011. Available from: https://curate.nd.edu/show/0k225b01f48


University of Notre Dame

2. Shawn Thomas O'Neil. Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>.

Degree: PhD, Computer Science and Engineering, 2012, University of Notre Dame

Transcriptome sequencing (sequencing only from the protein coding genes of a genome) has multiplied our ability to understand the biology of life on Earth. While full genome sequencing is still prohibitively expensive for many species, sequencing of genes only provides direct access to the most functional elements of a genome for a fraction of the cost. This advance brings broad genetic resources to those studying species of even the most specialized interest. We use these techniques to answer an important ecological question: How will species react to climate change? It has been assumed that as climate warms, populations will simply shift poleward to compensate. Unfortunately, previous reseach shows that some populations (of two butterflies) are adapted to local conditions and may not respond this way. To discover the genetic basis of these results, we first sequenced, assembled, annotated, and analyzed the butterfly transcriptomes. Because sequences were sampled from wild-caught populations, we developed novel methods to ensure high quality results in this setting. We then designed custom microarrays to measure how much of every gene is expressed in a given experimental setting. These, coupled with a robust experimental design, revealed a variety of genes and functional categories carrying the signature of local adaptation to climate. The bioinformatic difficulties associated with such projects are many. In particular, transcriptome assembly presents unique challenges, and it is not yet clear how to quantitatively evaluate assemblies. By simulating sequencing and comparing assembler results to those of perfect assemblies, we evaluate a number of commonly used and novel quality metrics. This study reveals that some quality metrics reflect biological accuracy while others (such as contig N50 length) do not and provides vital information for researchers making use of transcriptome data. Finally, when sequences are sourced from many genetically diverse individuals, our tools would ideally reveal this diversity rather than produce a simple genetic consensus. To this end, we develop algorithms to seperately assemble diverse sequences (haplotypes) accurately in the face of both sequencing error and data ambiguity. These methods will help reveal biodiversity in applications ranging from community ecology to epidemiology. Advisors/Committee Members: Jessica J. Hellmann, Committee Co-Chair, Michael Pfrender, Committee Member, Laurel Riek, Committee Member, Scott J. Emrich, Committee Chair, Kevin W. Bowyer, Committee Member, Jason McLachlan, Committee Member.

Subjects/Keywords: assembly; bioinformatics; transcriptome

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

APA (6th Edition):

O'Neil, S. T. (2012). Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>. (Doctoral Dissertation). University of Notre Dame. Retrieved from https://curate.nd.edu/show/2514nk33w4v

Chicago Manual of Style (16th Edition):

O'Neil, Shawn Thomas. “Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>.” 2012. Doctoral Dissertation, University of Notre Dame. Accessed April 22, 2019. https://curate.nd.edu/show/2514nk33w4v.

MLA Handbook (7th Edition):

O'Neil, Shawn Thomas. “Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>.” 2012. Web. 22 Apr 2019.

Vancouver:

O'Neil ST. Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>. [Internet] [Doctoral dissertation]. University of Notre Dame; 2012. [cited 2019 Apr 22]. Available from: https://curate.nd.edu/show/2514nk33w4v.

Council of Science Editors:

O'Neil ST. Non-Model Transcriptomics: Applications, Assessments, and Algorithms</h1>. [Doctoral Dissertation]. University of Notre Dame; 2012. Available from: https://curate.nd.edu/show/2514nk33w4v


University of Notre Dame

3. Allison A.P. Regier. Challenges in working with draft genomes</h1>.

Degree: MSin Computer Science and Engineering, Computer Science and Engineering, 2008, University of Notre Dame

As the cost of DNA sequencing falls, the relative cost of finishing steps (e.g., error correction and gap-closing) is increasing. As a result, many completed genome projects are only completed to draft stages and may not provide full information about the location of sequences on the chromosome. Further, they may contain gaps and assembly errors. Whether draft or finished, the output of a genome sequence project serves as the input to a host of analysis tools such as gene finding or variation analysis. Many of these tools have been designed for and tested on high-quality, finished genomes such as human or the fruit fly Drosophila melanogaster. In this thesis we discuss specific challenges in working with draft genomes and show how methods can be adapted to be more effective in draft genomes. First, we examine computational methods for finding errors in draft assemblies. Next, we modify a technique for finding DNA inversions between two genomes to account for gaps in the genomes. Finally, we develop a pipeline to construct chromosomes out of draft scaffolds using a closely related reference genome. We use examples from three different species of importance to global health: the body louse (Pediculus humanus), a malaria mosquito (Anopheles gambiae), and the human malaria parasite (Plasmodium falciparum). Advisors/Committee Members: Scott J Emrich, Committee Chair, Kevin W Bowyer, Committee Chair.

Subjects/Keywords: structural variation; comparative genomics; assembly validation

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

APA (6th Edition):

Regier, A. A. (2008). Challenges in working with draft genomes</h1>. (Masters Thesis). University of Notre Dame. Retrieved from https://curate.nd.edu/show/h415p843h2t

Chicago Manual of Style (16th Edition):

Regier, Allison A.P.. “Challenges in working with draft genomes</h1>.” 2008. Masters Thesis, University of Notre Dame. Accessed April 22, 2019. https://curate.nd.edu/show/h415p843h2t.

MLA Handbook (7th Edition):

Regier, Allison A.P.. “Challenges in working with draft genomes</h1>.” 2008. Web. 22 Apr 2019.

Vancouver:

Regier AA. Challenges in working with draft genomes</h1>. [Internet] [Masters thesis]. University of Notre Dame; 2008. [cited 2019 Apr 22]. Available from: https://curate.nd.edu/show/h415p843h2t.

Council of Science Editors:

Regier AA. Challenges in working with draft genomes</h1>. [Masters Thesis]. University of Notre Dame; 2008. Available from: https://curate.nd.edu/show/h415p843h2t

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