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You searched for +publisher:"Dalhousie University" +contributor:("Dr. Joseph Bielawski"). Showing records 1 – 3 of 3 total matches.

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Dalhousie University

1. Bay, Rachael. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.

Degree: MS, Department of Biology, 2010, Dalhousie University

Lineages of the cyanobacteria Prochlorococcus marinus have diverged into two genetically distinct ‘ecotypes,’ high-light adapted (HL) and low-light adapted (LL), which thrive under different environmental conditions. This type of niche differentiation in prokaryotes is often accompanied by genetic and genomic divergence. Differential selection pressure associated with ecotype divergence can be analyzed using models of codon evolution. However, some characteristics of the Prochlorococcus genome violate underlying assumptions of these models. For example, high levels of recombination between bacterial strains are known to cause false positives for codon models. Therefore, it is important that statistical methods for detecting recombination be reliable. In Chapter 2, I evaluate a set of recombination detection methods under four different scenarios related to functional divergence: 1) varying tree shape, 2) positive selection, 3) non-stationary evolution, and 4) varying levels of recombination and divergence. Advisors/Committee Members: Dr. Jonathan Wright (external-examiner), Dr. Hal Whitehead (graduate-coordinator), Dr. Katherine Dunn (thesis-reader), Dr. Andrew Roger (thesis-reader), Dr. Joseph Bielawski (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Not Applicable (copyright-release).

Subjects/Keywords: Cyanobacteria; Recombination; Natural Selection

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APA (6th Edition):

Bay, R. (2010). Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/13021

Chicago Manual of Style (16th Edition):

Bay, Rachael. “Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.” 2010. Masters Thesis, Dalhousie University. Accessed May 09, 2021. http://hdl.handle.net/10222/13021.

MLA Handbook (7th Edition):

Bay, Rachael. “Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus.” 2010. Web. 09 May 2021.

Vancouver:

Bay R. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. [Internet] [Masters thesis]. Dalhousie University; 2010. [cited 2021 May 09]. Available from: http://hdl.handle.net/10222/13021.

Council of Science Editors:

Bay R. Analysis of Functional Constraint and Recombination in Gene Sequences of the Cyanobacteria Prochlorococcus. [Masters Thesis]. Dalhousie University; 2010. Available from: http://hdl.handle.net/10222/13021


Dalhousie University

2. Urquhart, Caroline. Analysis of Prokaryotic Metabolic Networks.

Degree: MS, Department of Mathematics & Statistics - Statistics Division, 2011, Dalhousie University

Establishing group structure in complex networks is potentially very useful since nodes belonging to the same module can often be related by commonalities in their biological function. However, module detection in complex networks poses a challenging problem and has sparked a great deal of interest in various disciplines in recent years [5]. In real networks, which can be quite complex, we have no idea about the true number of modules that exist. Furthermore, the structure of the modules may be hierarchical meaning they may be further divided into sub-modules and so forth. Many attempts have been made to deal with these problems and because the involved methods vary considerably they have been difficult to compare [5]. The objectives of this thesis are (i) to create and implement a new algorithm that will identify modules in complex networks and reconstruct the network in such a way so as to maximize modularity, (ii) to evaluate the performance of a new method, and compare it to a popular method based on a simulated annealing algorithm, and (iii) to apply the new method, and a comparator method, to analyze the metabolic network of the bacterial genus Listeria, an important pathogen in both agricultural and human clinical settings. Advisors/Committee Members: n/a (external-examiner), Dr. Bruce Smith (graduate-coordinator), Dr. David Hamilton (thesis-reader), Dr. Hong Gu, Dr. Joseph Bielawski (thesis-supervisor), Not Applicable (ethics-approval), Yes (manuscripts), Not Applicable (copyright-release).

Subjects/Keywords: Complex networks; metabolism; metabolic networks; modularity; module identification methods; simulated annealing; schematic searching algorithm; Listeria monocytogenes; multinomial regression analysis; divergent selection pressure

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

APA (6th Edition):

Urquhart, C. (2011). Analysis of Prokaryotic Metabolic Networks. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/13319

Chicago Manual of Style (16th Edition):

Urquhart, Caroline. “Analysis of Prokaryotic Metabolic Networks.” 2011. Masters Thesis, Dalhousie University. Accessed May 09, 2021. http://hdl.handle.net/10222/13319.

MLA Handbook (7th Edition):

Urquhart, Caroline. “Analysis of Prokaryotic Metabolic Networks.” 2011. Web. 09 May 2021.

Vancouver:

Urquhart C. Analysis of Prokaryotic Metabolic Networks. [Internet] [Masters thesis]. Dalhousie University; 2011. [cited 2021 May 09]. Available from: http://hdl.handle.net/10222/13319.

Council of Science Editors:

Urquhart C. Analysis of Prokaryotic Metabolic Networks. [Masters Thesis]. Dalhousie University; 2011. Available from: http://hdl.handle.net/10222/13319


Dalhousie University

3. Chen, Wei Jr. The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics.

Degree: MS, Department of Mathematics & Statistics - Statistics Division, 2012, Dalhousie University

It is possible that the maximum likelihood method can give an inconsistent result when the DNA sequences are generated under a tree topology which is in the Felsentein Zone and analyzed with a misspeci ed model. Therefore, it is important to select a good substitution model. This thesis rst explores the e ects of di erent degrees and types of model misspeci cation on the maximum likelihood estimates. The results are presented for tree selection and branch length estimates based on simulated data sets. Next, two Pearson's goodness-of- t tests are developed based on binning of site patterns. These two tests are used for testing the adequacy of substitution models and their performances are studied on both simulated data sets and empirical data. Advisors/Committee Members: n/a (external-examiner), Dr. David Hamilton (graduate-coordinator), Dr. Edward Susko (thesis-reader), Dr. Toby Kenney (thesis-reader), Dr. Hong Gu and Dr. Joseph Bielawski (thesis-supervisor), Not Applicable (ethics-approval), Not Applicable (manuscripts), Not Applicable (copyright-release).

Subjects/Keywords: model misspecification; statistical test

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

APA (6th Edition):

Chen, W. J. (2012). The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics. (Masters Thesis). Dalhousie University. Retrieved from http://hdl.handle.net/10222/15705

Chicago Manual of Style (16th Edition):

Chen, Wei Jr. “The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics.” 2012. Masters Thesis, Dalhousie University. Accessed May 09, 2021. http://hdl.handle.net/10222/15705.

MLA Handbook (7th Edition):

Chen, Wei Jr. “The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics.” 2012. Web. 09 May 2021.

Vancouver:

Chen WJ. The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics. [Internet] [Masters thesis]. Dalhousie University; 2012. [cited 2021 May 09]. Available from: http://hdl.handle.net/10222/15705.

Council of Science Editors:

Chen WJ. The Exploration of Effect of Model Misspecification and Development of an Adequacy-Test for Substitution Model in Phylogenetics. [Masters Thesis]. Dalhousie University; 2012. Available from: http://hdl.handle.net/10222/15705

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