subject:(DNA Analysis)

Louisiana State University

1. Chen, Hui-Wen. Fully integrated microsystem for bacterial genotyping.

Degree: PhD, Chemistry, 2011, Louisiana State University

URL: etd-10252011-122025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3237

► Methods for bacterial detection and identification has garnered renewed interest in recent years due to the infections they may cause and the antimicrobial resistances they… (more)

▼ Methods for bacterial detection and identification has garnered renewed interest in recent years due to the infections they may cause and the antimicrobial resistances they can develop, the potential for bioterrorism threats and possible contamination of food/water supplies. Therefore, the rapid, specific and accurate detection of pathogens is crucial for the prevention of pathogen-related disease outbreaks and facilitating disease management as well as the containment of suspected contaminated food and/or water supplies. In this dissertation an integrated modular-based microfluidic system composed of a fluidic cartridge and a control instrument has been developed for bacterial pathogen detection. The integrated system can directly carry out the entire molecular processing pipeline in a single disposable fluidic cartridge and can detect sequence variations in selected genes to allow for the identification of the bacterial species and even its strain. The unique aspect of this fluidic cartridge is its modular format with a task-specific module interconnected to a fluidic motherboard to permit the selection of a material appropriate for the given processing step(s). In addition, to minimize the amount of finishing steps for assembling the fluidic cartridge, many of the functional components were produced during the polymer molding step used to create the fluidic network. The operation of the fluidic cartridge was provided by electronic, mechanical, optical and hydraulic controls located off-chip and assembled into a small footprint instrument. The fluidic cartridge was capable of performing cell lysis, solidphase extraction of genomic DNA from the whole cell lysate, continuous flow PCR amplification of specific gene fragments, continuous flow ligase detection reaction to discriminate sequence variations and universal DNA array readout, which consisted of DNA probes patterned onto a planar polymer waveguide for evanescent excitation. The performance of the fluidic system was demonstrated through its successful application to the genetic detection of bacterial pathogens, such as Escherichia coli O157:H7, Salmonella, methicillin-resistant Staphylococcus aureus and multi-drug resistant Mycobacterium tuberculosis, which are major threats for global heath. The modular system, which could successfully identify several strains of bacteria in <40 min with minimal human intervention and also perform strain identification, represents a significant contribution to pathogen detection.

Subjects/Keywords: DNA analysis; microfluidics

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APA (6^th Edition):

Chen, H. (2011). Fully integrated microsystem for bacterial genotyping. (Doctoral Dissertation). Louisiana State University. Retrieved from etd-10252011-122025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3237

Chicago Manual of Style (16^th Edition):

Chen, Hui-Wen. “Fully integrated microsystem for bacterial genotyping.” 2011. Doctoral Dissertation, Louisiana State University. Accessed January 28, 2021. etd-10252011-122025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3237.

MLA Handbook (7^th Edition):

Chen, Hui-Wen. “Fully integrated microsystem for bacterial genotyping.” 2011. Web. 28 Jan 2021.

Vancouver:

Chen H. Fully integrated microsystem for bacterial genotyping. [Internet] [Doctoral dissertation]. Louisiana State University; 2011. [cited 2021 Jan 28]. Available from: etd-10252011-122025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3237.

Council of Science Editors:

Chen H. Fully integrated microsystem for bacterial genotyping. [Doctoral Dissertation]. Louisiana State University; 2011. Available from: etd-10252011-122025 ; https://digitalcommons.lsu.edu/gradschool_dissertations/3237

Penn State University

2. Sun, Yazhou. DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.

Degree: 2012, Penn State University

URL: https://submit-etda.libraries.psu.edu/catalog/13771

► Understanding the sequential information coded in DNA, RNA and proteins is important for both basic and applied researches in life sciences. Extensive efforts have been… (more)

▼ Understanding the sequential information coded in DNA, RNA and proteins is important for both basic and applied researches in life sciences. Extensive efforts have been devoted to the research and development of DNA sequence analysis methods. The studies described in this dissertation explored new applications of existing methods in the context of the recent development of ultra-high throughput sequencing technologies. This dissertation also included new methods developed for studying gene families and human haplogroups. The theories, algorithms and tools for analyzing DNA sequence information concerning these studies are reviewed in Chapter 1 of this dissertation. With the recent development in DNA sequencing technologies, came many new research opportunities. Great challenges also came along, mainly because of the large data size of the latest high throughput sequencing technologies. The potential of these new technologies was exploited to complete a 100,000 years old ancient polar bear mitochondrial genome. With this and some additional modern bear data, the matrilineal polar bear’s divergence time was estimated to be around 130,000 years ago, which is significantly older than some recent estimates. This estimate indicated that modern polar bear matrilineal ancestors adapted to the niche polar environment within 30,000 years after the speciation event and propagated along the entire Arctic Circle for the next 100,000 years. This recent speciation and rapid expansion process is analogous to the evolution and migration of modern humans. The lineage characteristics of the latter were also briefly studied using the same technologies. (Chapter 2) Because of the increased efficiency from the latest sequencing technologies, more and more complete human mitochondrial genomes have been generated at an increasingly faster speed. Although mitochondrial haplogroups, and their classification and identification were widely used in human evolution and population studies, the current tools could not fully take advantage of the rapidly growing number of new mitochondrial genomes. An updated mitochondrial haplogroup classification system was thus developed with evolutionary models that incorporate the mitochondrial genomic variations within the human population. These variations have not been considered by previous methods, which could lead to incorrectly classified haplogroups. The variation parameters, including the whole-genome substitution rate (0.013 - 0.1 substitutions per generation), the rate heterogeneity among sites (Gamma distribution shape parameter α = 0.7078) and the percentage of invariant sites (64%), were estimated based on 7985 full-length human mitochondrial genome sequences. Haplogroups were then classified based on the corrected genetic distance estimation and modeled with position specific matrices. A new haplogroup identification system was developed based on the resulting matrices and the maximum-likelihood estimation (MLE) method, permitting fast and accurate haplogroup assignment for both known and new… Advisors/Committee Members: Hong Ma, Dissertation Advisor/Co-Advisor, Stephen Wade Schaeffer, Committee Chair/Co-Chair, Gong Chen, Committee Member, Naomi S Altman, Special Member, Anton Nekrutenko, Committee Member.

Subjects/Keywords: DNA sequence analysis; DNA sequence analysis methods; DNA sequence analysis applications

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APA (6^th Edition):

Sun, Y. (2012). DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. (Thesis). Penn State University. Retrieved from https://submit-etda.libraries.psu.edu/catalog/13771

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

Chicago Manual of Style (16^th Edition):

Sun, Yazhou. “DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.” 2012. Thesis, Penn State University. Accessed January 28, 2021. https://submit-etda.libraries.psu.edu/catalog/13771.

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

MLA Handbook (7^th Edition):

Sun, Yazhou. “DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups.” 2012. Web. 28 Jan 2021.

Vancouver:

Sun Y. DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. [Internet] [Thesis]. Penn State University; 2012. [cited 2021 Jan 28]. Available from: https://submit-etda.libraries.psu.edu/catalog/13771.

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

Council of Science Editors:

Sun Y. DNA sequence analysis: new applications with high throughput sequencing and new methods in studying gene families and human haplogroups. [Thesis]. Penn State University; 2012. Available from: https://submit-etda.libraries.psu.edu/catalog/13771

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

Hong Kong University of Science and Technology

3. Luo, Xiaoteng. Immobilization-free electrochemical DNA-based bio-analysis.

Degree: 2011, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7072 ; https://doi.org/10.14711/thesis-b1129759 ; http://repository.ust.hk/ir/bitstream/1783.1-7072/1/th_redirect.html

► DNA-based bio-analysis is important in the fields of molecular diagnostics, environmental and food safety monitoring, pathogen identification, forensic sciences, etc. Electrochemical DNA-based bio-analysis has the… (more)

▼ DNA-based bio-analysis is important in the fields of molecular diagnostics, environmental and food safety monitoring, pathogen identification, forensic sciences, etc. Electrochemical DNA-based bio-analysis has the advantages of high sensitivity, compatibility for miniaturization and easy operation. Most of existing electrochemical approaches require a probe immobilization step, which increases preparation time, lowers hybridization efficiency, requires washing steps, hampers multiplexing and therefore limits the application of the technology in point-of-care scenarios. This thesis describes a novel “immobilization-free” approach for electrochemical DNA-based bio-analysis in which no probe immobilization step is required and the hybridization or other interaction between the detection probe and the target occurs in a homogeneous solution phase. The approach takes advantage of the neutral backbone of a ferrocene-labeled peptide nucleic acid (Fc-PNA) probe, utilizing the electrostatic repulsion between the negatively-charged DNA backbone and a negatively-charged ITO electrode to transduce the hybridization between the target DNA and the Fc-PNA into a reduction of the electrochemical signal of Fc, therefore realizing an immobilization-free, signal-off electrochemical DNA detection. Based on the immobilization-free electrochemical DNA detection, an electrochemical melting curve analysis technique is developed, as well as a multiplex immobilization-free electrochemical DNA detection and quantification method. In order to produce more reliable results, the immobilization-free electrochemical DNA detection is transformed to the “signal-on” operating mode by introducing an additional DNA probe and solution-phase competitive hybridization into the system. Furthermore, the application of the immobilization-free electrochemical DNA detection strategy is expanded to the detection of DNA-modifying enzymes (exemplified with DNA polymerase) and aptamer-binding bio-molecules (exemplified with adenosine). Finally, the detection sensitivity of the immobilization-free electrochemical DNA-based bio-analytical platform is improved by using an electrode coated with a positively-charged conducing polymer as well as an interdigitated array electrode. The development of an immobilization-free detection platform is a great leap towards point-of-care applications of electrochemical DNA-based bio-analysis technologies.

Subjects/Keywords: Electrochemical analysis ; Biomolecules – Analysis ; DNA – Analysis

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APA (6^th Edition):

Luo, X. (2011). Immobilization-free electrochemical DNA-based bio-analysis. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7072 ; https://doi.org/10.14711/thesis-b1129759 ; http://repository.ust.hk/ir/bitstream/1783.1-7072/1/th_redirect.html

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

Chicago Manual of Style (16^th Edition):

Luo, Xiaoteng. “Immobilization-free electrochemical DNA-based bio-analysis.” 2011. Thesis, Hong Kong University of Science and Technology. Accessed January 28, 2021. http://repository.ust.hk/ir/Record/1783.1-7072 ; https://doi.org/10.14711/thesis-b1129759 ; http://repository.ust.hk/ir/bitstream/1783.1-7072/1/th_redirect.html.

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

MLA Handbook (7^th Edition):

Luo, Xiaoteng. “Immobilization-free electrochemical DNA-based bio-analysis.” 2011. Web. 28 Jan 2021.

Vancouver:

Luo X. Immobilization-free electrochemical DNA-based bio-analysis. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2011. [cited 2021 Jan 28]. Available from: http://repository.ust.hk/ir/Record/1783.1-7072 ; https://doi.org/10.14711/thesis-b1129759 ; http://repository.ust.hk/ir/bitstream/1783.1-7072/1/th_redirect.html.

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

Council of Science Editors:

Luo X. Immobilization-free electrochemical DNA-based bio-analysis. [Thesis]. Hong Kong University of Science and Technology; 2011. Available from: http://repository.ust.hk/ir/Record/1783.1-7072 ; https://doi.org/10.14711/thesis-b1129759 ; http://repository.ust.hk/ir/bitstream/1783.1-7072/1/th_redirect.html

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

University of Utah

4. Poulson, Matthew Dean. Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;.

Degree: MS;, Pathology;, 2006, University of Utah

URL: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/1530/rec/301

► Apolipoprotein E (ApoE) is a polymorphic glycoprotein consisting of 299 amino acids. ApoE is responsible for 5-15% of the total cholesterol level in the body… (more)

▼ Apolipoprotein E (ApoE) is a polymorphic glycoprotein consisting of 299 amino acids. ApoE is responsible for 5-15% of the total cholesterol level in the body and is strongly associated with coronary heart disease and specifically Type III hyperlipidemia. ApoE is also linked to Alzheimer’s disease (AD). The ApoE gene contains two single nucleotide polymorphisms (SNPs at amino acid positions 112 and 158 giving rise to 3 homozygous and 3 heterozygous genotypes for total of 6 different genotypes. ApoE has been the subject of much study since it was discovered in the early 1970s using a gel separation process called isoelectric focusing. Diagnostic testing for SNPs has continually evolved through the decades as new technologies emerge. One such advance was elucidation of the polymerase chain reaction. The polymerase chain reaction (PCR) has revolutionized the ability to examine DNA at the molecular level. The theoretical simplicity of the PCR has led to an ever expanding array of techniques and uses for PCR. One of these techniques is asymmetric PCR. Asymmetric PCR is used to selectively amplify on strand of the genomic DNA. Isolated probe-polymerase chain reaction (IP-PCR) is a new method that expands the usefulness of asymmetric PCR and unlabeled probes. IP-PCR separates the asymmetric PCR amplification and the detection of the unlabeled probes while maintaining a closed tub environment. This prevents the probes from interfering with the amplification of the DNA target. The closed tub format eliminates the possibility of amplicon contamination or sample carryover. To test this new technique DNA was isolated from 101-de-identified blood samples, obtained from ARUP. The DNA from these samples was genotyped using the IP-PCR technique using multiplexed unlabeled probes and high resolution melting analysis. The results from ARUP were de-blinded and compared to results obtained by IP-PCR. The IP-PCR results agreed in 96 out of 101 samples. The 5 discordant samples did not display any abnormal melting curve plots when compared to other samples tested. These 5 discordant samples were sequenced to determine the correct ApoE genotype. The sequencing results showed that IP-PCR and high resolution melting using unlabeled probes gave correct genotype in all five cases. Two samples (sample 20 and 36) out of the 101 samples displayed abnormal melting curve plots. However the abnormalities did not interfere with determining the genotype of these two samples. The 2 samples were also sequenced. The sequencing results showed no mutation under the unlabeled probe. The IPCR technique correctly genotyped every DNA sample use in the experiment.

Subjects/Keywords: Analysis; DNA

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APA (6^th Edition):

Poulson, M. D. (2006). Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;. (Masters Thesis). University of Utah. Retrieved from http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/1530/rec/301

Chicago Manual of Style (16^th Edition):

Poulson, Matthew Dean. “Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;.” 2006. Masters Thesis, University of Utah. Accessed January 28, 2021. http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/1530/rec/301.

MLA Handbook (7^th Edition):

Poulson, Matthew Dean. “Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;.” 2006. Web. 28 Jan 2021.

Vancouver:

Poulson MD. Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;. [Internet] [Masters thesis]. University of Utah; 2006. [cited 2021 Jan 28]. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/1530/rec/301.

Council of Science Editors:

Poulson MD. Determination of the six ApoE genotypes using an isolated probe-polymerase chain reaction technique combined with multiplexed unlabeled probes and high resolution melting analysis;. [Masters Thesis]. University of Utah; 2006. Available from: http://content.lib.utah.edu/cdm/singleitem/collection/etd1/id/1530/rec/301

Oregon State University

5. Basham, Beth E. The analysis and prediction of DNA structure.

Degree: PhD, Biochemistry and Biophysics, 1998, Oregon State University

URL: http://hdl.handle.net/1957/33950

► As genome sequencing projects begin to come to completion, the challenge becomes one of determining how to understand the information contained within the DNA. DNA… (more)

Subjects/Keywords: DNA – Analysis

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APA (6^th Edition):

Basham, B. E. (1998). The analysis and prediction of DNA structure. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/33950

Chicago Manual of Style (16^th Edition):

Basham, Beth E. “The analysis and prediction of DNA structure.” 1998. Doctoral Dissertation, Oregon State University. Accessed January 28, 2021. http://hdl.handle.net/1957/33950.

MLA Handbook (7^th Edition):

Basham, Beth E. “The analysis and prediction of DNA structure.” 1998. Web. 28 Jan 2021.

Vancouver:

Basham BE. The analysis and prediction of DNA structure. [Internet] [Doctoral dissertation]. Oregon State University; 1998. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/1957/33950.

Council of Science Editors:

Basham BE. The analysis and prediction of DNA structure. [Doctoral Dissertation]. Oregon State University; 1998. Available from: http://hdl.handle.net/1957/33950

Oregon State University

6. Hongtrakul, Vipa. The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis.

Degree: PhD, Genetics, 1997, Oregon State University

URL: http://hdl.handle.net/1957/33809

► Molecular DNA markers have become widely used in all areas of genetic research. The objectives of this thesis were to develop polymorphic markers in sunflower… (more)

▼ Molecular DNA markers have become widely used in all areas of genetic research. The objectives of this thesis were to develop polymorphic markers in sunflower and utilize the markers for genetic and candidate gene analyses. Amplified fragment length polymorphism (AFLP) markers were used to estimate genetic similarities and assess the genetic diversity among 24 public oilseed inbred lines of sunflower (Helianthus annuus L.). A total of 359 AFLP markers were scored by using six AFLP primer combinations. Genetic similarities ranged from 0.70 to 0.91, polymorphism rate ranged from 7 to 24%, and polymorphic information contents (PICs) ranged from 0.0 to 0.5. Principal coordinate and cluster analysis separated the lines into two groups, B-lines and R-lines, illustrating breeding history, basic heterotic pattern and the widespread practice of using each group to develop new lines. Δ9 stearoyl-ACP desaturase (SAD) and Δl2 oleate desaturase (OLD) cDNAs were cloned and sequenced. DNA fragment length polymorphism (DFLP), single strand conformational polymorphism (SSCP), and simple sequence repeat (SSR) markers were developed for the SAD6 and SAD17 genes among eight elite inbred lines. PICs for DFLP, SSCP, and SSR markers were 0.18, 0.37, and 0.30, respectively. Length variants were due to long monomeric repeats, insertions, and deletions in intron sequences, thereby producing polymorphic markers. OLD desaturates 18:1-PC (oleoyl phosphatidylcholine) to 18:2-PC, thereby converting oleic to linoleic acid. It is a likely candidate gene to be causing the high oleic phenotype in mutant sunflower. The expression of OLD7 in developing seeds was greatly reduced in mutant as opposed to wildtype backcross-derived lines. The restriction fragment length polymorphism (RFLP) patterns suggest that OLD7 is duplicated and rearranged in mutant lines. Utilizing sunflower SAD gene sequences and 27 inbred lines, intron fragment length polymorphism (IFLP) markers were developed for automated genotyping. These IFLP markers with ~470 to ~850 bp in length had a mean PIC score of 0.414, versus 0.336 for DFLP markers, and 0.582 for SSCP markers. One and two nucleotide length polymorphisms were reliably detected in PCR fragments up to ~150 and ~680 bp, respectively. Advisors/Committee Members: Knapp, Steven J. (advisor), Hayes, Patrick M. (committee member).

Subjects/Keywords: DNA – Analysis

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

APA (6^th Edition):

Hongtrakul, V. (1997). The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis. (Doctoral Dissertation). Oregon State University. Retrieved from http://hdl.handle.net/1957/33809

Chicago Manual of Style (16^th Edition):

Hongtrakul, Vipa. “The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis.” 1997. Doctoral Dissertation, Oregon State University. Accessed January 28, 2021. http://hdl.handle.net/1957/33809.

MLA Handbook (7^th Edition):

Hongtrakul, Vipa. “The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis.” 1997. Web. 28 Jan 2021.

Vancouver:

Hongtrakul V. The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis. [Internet] [Doctoral dissertation]. Oregon State University; 1997. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/1957/33809.

Council of Science Editors:

Hongtrakul V. The development and analysis of sequence-based DNA markers in sunflower for DNA fingerprinting and candidate gene analysis. [Doctoral Dissertation]. Oregon State University; 1997. Available from: http://hdl.handle.net/1957/33809

Hong Kong University of Science and Technology

7. Wang, Wentao. Systematic design and fabrication of DNA electrophoresis chip with nanostructures.

Degree: 2012, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-7805 ; https://doi.org/10.14711/thesis-b1198708 ; http://repository.ust.hk/ir/bitstream/1783.1-7805/1/th_redirect.html

► Separation of DNA molecules in micro electrophoresis chips with nanostructures has been shown great potential in DNA sequencing, genotyping, identification of DNA polymorphisms in human… (more)

▼ Separation of DNA molecules in micro electrophoresis chips with nanostructures has been shown great potential in DNA sequencing, genotyping, identification of DNA polymorphisms in human chromosomes and cancer-related genes genomics. The separation in these devices intrinsically involves multi-scale phenomena. The detailed mechanism of this type of separation is still not fully understood. In this study, we systematically investigate the electrophoretic mobility of large DNA molecules and then construct a macro model to predict spatiotemporal behavior of electrophoretic behavior based on the continuum mechanics. A novel Biased Reptation model with Electroosmosis (BRE) was developed to predict the electrophoretic mobility of long-chain DNA molecules in microchannels with a sub-micron pillar array. The BRE model incorporates effective electroosmosis into classical biased reptation models. The apparent electrophoretic mobilities of different sizes of long-chain DNA, T4 DNA, and lambda DNA at different electric fields were measured in a fabricated electrophoresis chip for the comparison with various theories. The proposed BRE model shows much better agreement with the experimental results compared to the classical BRM model and the Biased Reptation with Fluctuation (BRF). The average standard error between our proposed BRE model and experimental data is 8.13% without any fitting parameters, while the BRM is 343.01% and BRF is 17.54% with one fitting parameter. The BRE model can be only applied for low porosity sieving matrix (e < 0.5) with pillar spacing larger than twice of the persistence length of a DNA molecule with DNA length larger than 48 kbp. For DNA length smaller than 20 kbp, Ogston model can be applied. For DNA length between 20 kbp and 48 kbp, a hybrid model would need to be developed. For the micro electrophoresis on a silicon or glass wafer, the electroosmotic mobility of DNA buffers plays an important role in the BRE model. Therefore, theoretical analysis and nonlinear 2D numerical simulations are used to study the concentration difference and Peclet number effect on the measurement error of the electroosmotic mobility in microchannels. We propose a compact analytical model for this error as a function of normalized concentration difference and Peclet number in micro electroosmotic flow with experimental validation. The analytical predictions of the errors are consistent with the numerical simulations. Finally, the systematic model of DNA electrophoresis in the nanostructures can be used to optimize the design of micro-electrophoresis chip with embedded nanostructures. The optimized pillar spacing was found to be four times the length of persistence length and the separation limitation for large DNA molecules is around 48 kbp with resolution requirement of 0.5 per kbp. With the optimized pillar spacing, the silicon based micro-electrophoresis chip was designed and fabricated based micro-electrophoresis chip were designed and fabricated.

Subjects/Keywords: Electrophoresis ; DNA – Analysis ; Nanotechnology

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APA (6^th Edition):

Wang, W. (2012). Systematic design and fabrication of DNA electrophoresis chip with nanostructures. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-7805 ; https://doi.org/10.14711/thesis-b1198708 ; http://repository.ust.hk/ir/bitstream/1783.1-7805/1/th_redirect.html

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

Chicago Manual of Style (16^th Edition):

Wang, Wentao. “Systematic design and fabrication of DNA electrophoresis chip with nanostructures.” 2012. Thesis, Hong Kong University of Science and Technology. Accessed January 28, 2021. http://repository.ust.hk/ir/Record/1783.1-7805 ; https://doi.org/10.14711/thesis-b1198708 ; http://repository.ust.hk/ir/bitstream/1783.1-7805/1/th_redirect.html.

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

MLA Handbook (7^th Edition):

Wang, Wentao. “Systematic design and fabrication of DNA electrophoresis chip with nanostructures.” 2012. Web. 28 Jan 2021.

Vancouver:

Wang W. Systematic design and fabrication of DNA electrophoresis chip with nanostructures. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2012. [cited 2021 Jan 28]. Available from: http://repository.ust.hk/ir/Record/1783.1-7805 ; https://doi.org/10.14711/thesis-b1198708 ; http://repository.ust.hk/ir/bitstream/1783.1-7805/1/th_redirect.html.

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

Council of Science Editors:

Wang W. Systematic design and fabrication of DNA electrophoresis chip with nanostructures. [Thesis]. Hong Kong University of Science and Technology; 2012. Available from: http://repository.ust.hk/ir/Record/1783.1-7805 ; https://doi.org/10.14711/thesis-b1198708 ; http://repository.ust.hk/ir/bitstream/1783.1-7805/1/th_redirect.html

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

Hong Kong University of Science and Technology

8. Yu, Miao. Single-molecule DNA analysis in nanofluidic devices.

Degree: 2015, Hong Kong University of Science and Technology

URL: http://repository.ust.hk/ir/Record/1783.1-81387 ; https://doi.org/10.14711/thesis-b1514590 ; http://repository.ust.hk/ir/bitstream/1783.1-81387/1/th_redirect.html

► DNA is the central storage molecule of genetic information in humans and almost all other organisms. Analyzing the genetic information along the DNA molecule is… (more)

▼ DNA is the central storage molecule of genetic information in humans and almost all other organisms. Analyzing the genetic information along the DNA molecule is of great importance in life science and biomedical engineering. Recently, nanofluidics has been recognized as an efficient approach to study the behavior of DNA at the single-molecular level, which can unravel the phenomena that remain hidden in conventional bulk experiments. When confined in nanochannels, the coiled DNA molecules naturally stretch out as a combined result of the elastic properties and the excluded volume effects. Therefore, a reliable nanofluidic platform is the prerequisite for single-molecule DNA studies. This thesis focuses on the development of sub-100 nm disposable nanofluidic devices and the experimental demonstration of such devices for biomolecular detection and analysis. We first investigated various techniques for fabricating low-cost nanochannels on different substrates. We showed that the lithography-free nanocracking on a polystyrene substrate is a promising approach for lab-on-chip nano-manufacturing. Based on such nanocracking technology, an on-demand nanofluidic pre-concentrator was developed, which leveraged isolated droplets to avoid the sample diffusion and dispersion issues as compared to conventional devices. To prevent concentration decay during the sample ejection, a pressure-assisted strategy was introduced in the system for precisely positioning the concentrated sample plug at the ejecting nozzle. By integrating the ion concentration polarization with on-demand droplet generation, our system can adaptively encapsulate the highly concentrated sample and effectively enhance the long-term stability. We experimentally demonstrated the pre-concentration of a fluorescently labelled biomolecule, bovine serum albumin (BSA), by an amplification factor of 10,000. By adjusting the applied voltage, accumulation time, and pulsed pressure imposed on the control microchannel, our system can generate a droplet of desired volume with a target sample concentration at a prescribed time. Second, we developed a novel nanofluidic device to confine and align single-molecule DNA in dynamically formed nanochannels for optical analysis. By judiciously harnessing the microvalve control and the deformation of nanoslits made in the PDMS, we dynamically generated submillimeter-long uniform nanochannels with an effective confining dimension down to 20 nm based on low-cost soft lithography. Using such devices, we investigated DNA stretching and attained 80% of the contour length for DNA elongation. The curved edge of the microvalve smoothly bridges the different depths between the stretching nanochannels and the adjoining microchannels by more than 3 orders of magnitude, which greatly facilitates the introduction of DNA into the nanochannels without the need for high pressure or electric fields. Unlike traditional direct-bonded nanochannels, the sample nanochannels in our device recover in microscale when the pressure is released, eliminating…

Subjects/Keywords: Nanofluids ; Microfluidic devices ; DNA ; Analysis

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

APA (6^th Edition):

Yu, M. (2015). Single-molecule DNA analysis in nanofluidic devices. (Thesis). Hong Kong University of Science and Technology. Retrieved from http://repository.ust.hk/ir/Record/1783.1-81387 ; https://doi.org/10.14711/thesis-b1514590 ; http://repository.ust.hk/ir/bitstream/1783.1-81387/1/th_redirect.html

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

Chicago Manual of Style (16^th Edition):

Yu, Miao. “Single-molecule DNA analysis in nanofluidic devices.” 2015. Thesis, Hong Kong University of Science and Technology. Accessed January 28, 2021. http://repository.ust.hk/ir/Record/1783.1-81387 ; https://doi.org/10.14711/thesis-b1514590 ; http://repository.ust.hk/ir/bitstream/1783.1-81387/1/th_redirect.html.

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

MLA Handbook (7^th Edition):

Yu, Miao. “Single-molecule DNA analysis in nanofluidic devices.” 2015. Web. 28 Jan 2021.

Vancouver:

Yu M. Single-molecule DNA analysis in nanofluidic devices. [Internet] [Thesis]. Hong Kong University of Science and Technology; 2015. [cited 2021 Jan 28]. Available from: http://repository.ust.hk/ir/Record/1783.1-81387 ; https://doi.org/10.14711/thesis-b1514590 ; http://repository.ust.hk/ir/bitstream/1783.1-81387/1/th_redirect.html.

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

Council of Science Editors:

Yu M. Single-molecule DNA analysis in nanofluidic devices. [Thesis]. Hong Kong University of Science and Technology; 2015. Available from: http://repository.ust.hk/ir/Record/1783.1-81387 ; https://doi.org/10.14711/thesis-b1514590 ; http://repository.ust.hk/ir/bitstream/1783.1-81387/1/th_redirect.html

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

Western Carolina University

9. Stawski, Hilde. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.

Degree: 2013, Western Carolina University

URL: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16380

► Forensic DNA casework principally relies on the analysis of short tandem repeats (STRs) from nuclear DNA (nDNA). In cases where nDNA may not be suitable… (more)

▼ Forensic DNA casework principally relies on the analysis of short tandem repeats (STRs) from nuclear DNA (nDNA). In cases where nDNA may not be suitable for analysis (i.e., highly degraded DNA or DNA present in quantities too low to obtain an STR profile), mitochondrial DNA (mtDNA) is an excellent alternative. MtDNA is a circular genome of approximately 16.5 kb, is maternally derived, and is present in thousands of copies per cell versus two copies of nuclear DNA. The combined higher copy number, circular shape of the genome and protection by the double membrane of the mitochondrion allows for a greater probability to recover sufficient mtDNA for typing of degraded samples. Presently, forensic analysts sequence two or three hypervariable (HV) regions found in the non-coding control region of the mtGenome, since sequencing of the entire mitochondrial genome (mtGenome) is rather costly and labor-intensive. Additionally, difficulties sequencing through homopolymeric regions, as well as the presence of lowlevel mixtures in samples, can add complexity to the analysis of mtDNA in casework when traditional Sanger sequencing methods are used. These issues can be addressed with Next Generation Sequencing (NGS) technologies. NGS enables deeper analysis of the genome for identification of low-level mixtures, since clonal populations of molecules originating from a single template strand are sequenced. Moreover, this technology allows for the more cost-effective sequencing of whole mtGenomes compared to Sanger methods, since more sequences are obtained for the same sample. By expanding mtDNA analysis to the entire mtGenome, a better resolution in distinguishing between haplotypes is established. In forensic casework, amplification of challenging samples such as hair and aged bone is often performed differently than that of reference samples (buccal swabs, blood, etc.) due to the higher possibility of DNA degradation and limited mtDNA concentrations. For this study, two sample preparation approaches were developed including one method for robust reference samples, and one method for forensically relevant challenging samples. For NGS analysis of reference samples, DNA was extracted from buccal swabs obtained from eight donors. A long PCR approach, which refers to the amplification of DNA fragments of a size that may not be amplified using conventional PCR reagents, was successfully performed on these DNA extracts using a highly processive polymerase mixture and novel primer pairs to amplify the mtGenome in two independent PCR reactions, with overlap at the noncoding region. These samples were subsequently processed with Illumina® Nextera® XT. This NGS library preparation kit is designed exclusively for use with Illumina® instrumentation and employs an engineered Transposome™ to randomly fragment and tag amplicons and small genomes with Illumina® specific adapters. After library preparation, samples were sequenced on the Illumina® MiSeq™. This method generated whole mtGenome NGS data, which accurately reflected the Sanger… Advisors/Committee Members: Mark Wilson (advisor).

Subjects/Keywords: Mitochondrial DNA – Analysis – Data processing

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APA (6^th Edition):

Stawski, H. (2013). Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. (Masters Thesis). Western Carolina University. Retrieved from http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16380

Chicago Manual of Style (16^th Edition):

Stawski, Hilde. “Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.” 2013. Masters Thesis, Western Carolina University. Accessed January 28, 2021. http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16380.

MLA Handbook (7^th Edition):

Stawski, Hilde. “Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.” 2013. Web. 28 Jan 2021.

Vancouver:

Stawski H. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. [Internet] [Masters thesis]. Western Carolina University; 2013. [cited 2021 Jan 28]. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16380.

Council of Science Editors:

Stawski H. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. [Masters Thesis]. Western Carolina University; 2013. Available from: http://libres.uncg.edu/ir/listing.aspx?styp=ti&id=16380

University of Arizona

10. Hurliman, Eva Winter, 1941-. Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer .

Degree: 1965, University of Arizona

URL: http://hdl.handle.net/10150/318440

Subjects/Keywords: DNA – Analysis.

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APA (6^th Edition):

Hurliman, Eva Winter, 1. (1965). Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer . (Masters Thesis). University of Arizona. Retrieved from http://hdl.handle.net/10150/318440

Chicago Manual of Style (16^th Edition):

Hurliman, Eva Winter, 1941-. “Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer .” 1965. Masters Thesis, University of Arizona. Accessed January 28, 2021. http://hdl.handle.net/10150/318440.

MLA Handbook (7^th Edition):

Hurliman, Eva Winter, 1941-. “Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer .” 1965. Web. 28 Jan 2021.

Vancouver:

Hurliman, Eva Winter 1. Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer . [Internet] [Masters thesis]. University of Arizona; 1965. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/10150/318440.

Council of Science Editors:

Hurliman, Eva Winter 1. Changes in the molecular weight distribution of DNA sheared in a virtis homogenizer . [Masters Thesis]. University of Arizona; 1965. Available from: http://hdl.handle.net/10150/318440

Rutgers University

11. Swaminathan, Harish, 1989-. Computational methods for the interpretation of forensic DNA samples.

Degree: PhD, Computational and Integrative Biology, 2015, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/48160/

►

Interpretation of DNA profiles generated from STRs can be problematic because of dropout, allele overlap and artifacts like stutter. The goal of this research is… (more)

▼

Interpretation of DNA profiles generated from STRs can be problematic because of dropout, allele overlap and artifacts like stutter. The goal of this research is to develop computational methods for the analysis of STR profiles that are robust to these phenomena and that utilize quantitative peak height information captured in profiles. These methods are expected to improve significantly on existing methods for analysis of STR profiles, particularly in cases of low amounts of template DNA or where there are many contributors. In the first part of our research, we characterized the distribution of signal, noise and stutter peak heights and studied their dependence on template DNA amount. For the second part of our project, we developed a method to identify the number of contributors to a DNA sample. Our method, NOCIt, calculates the a posteriori probability on the number of contributors to a forensic sample taking into account signal peak heights, population allele frequencies, baseline noise, allele dropout and stutter. On the experimental samples tested, NOCIt had an accuracy of 83%, while the accuracy of the best pre-existing method was 72%. The accuracies of NOCIt and the best pre-existing method on the simulated profiles were 85% and 73%, respectively. We were able to reduce the running time of NOCIt by developing a faster method based on an importance sampling algorithm. In the third and final part of our research, we developed a computational tool (MatchIt) to directly compute a continuous Likelihood Ratio (LR) for a person of interest (POI), treating other contributors (if any) as interference. MatchIt also calculates the distribution of the LR along with the p-value, which is the probability a randomly chosen individual results in a LR at least as large as the LR obtained from the POI. We observed that the amount of template DNA from the contributor impacted the LR – small LRs resulted from contributors with low template masses. Moreover, we observed a decrease of p-values as the LR increased. A p-value of 10-9, the lowest possible in our testing, was achieved in all the cases where the LR was greater than 108.

Advisors/Committee Members: Lun, Desmond S (chair), Piccoli, Benedetto (internal member), Medard, Muriel (outside member), Grgicak, Catherine (outside member).

Subjects/Keywords: Forensic genetics; DNA – Analysis

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APA (6^th Edition):

Swaminathan, Harish, 1. (2015). Computational methods for the interpretation of forensic DNA samples. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/48160/

Chicago Manual of Style (16^th Edition):

Swaminathan, Harish, 1989-. “Computational methods for the interpretation of forensic DNA samples.” 2015. Doctoral Dissertation, Rutgers University. Accessed January 28, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/48160/.

MLA Handbook (7^th Edition):

Swaminathan, Harish, 1989-. “Computational methods for the interpretation of forensic DNA samples.” 2015. Web. 28 Jan 2021.

Vancouver:

Swaminathan, Harish 1. Computational methods for the interpretation of forensic DNA samples. [Internet] [Doctoral dissertation]. Rutgers University; 2015. [cited 2021 Jan 28]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48160/.

Council of Science Editors:

Swaminathan, Harish 1. Computational methods for the interpretation of forensic DNA samples. [Doctoral Dissertation]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48160/

Rutgers University

12. Arnold, Anurag, 1988-. Development of a computational tool for forensic DNA analysis.

Degree: MS, Computer Science, 2016, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/49070/

► Forensic DNA analysis consists of a DNA profiling process by a method called as STR Analysis, short for Short Tandem Repeats. By using the statistics… (more)

Subjects/Keywords: DNA – Analysis; Forensic genetics

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

APA (6^th Edition):

Arnold, Anurag, 1. (2016). Development of a computational tool for forensic DNA analysis. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/49070/

Chicago Manual of Style (16^th Edition):

Arnold, Anurag, 1988-. “Development of a computational tool for forensic DNA analysis.” 2016. Masters Thesis, Rutgers University. Accessed January 28, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/49070/.

MLA Handbook (7^th Edition):

Arnold, Anurag, 1988-. “Development of a computational tool for forensic DNA analysis.” 2016. Web. 28 Jan 2021.

Vancouver:

Arnold, Anurag 1. Development of a computational tool for forensic DNA analysis. [Internet] [Masters thesis]. Rutgers University; 2016. [cited 2021 Jan 28]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/49070/.

Council of Science Editors:

Arnold, Anurag 1. Development of a computational tool for forensic DNA analysis. [Masters Thesis]. Rutgers University; 2016. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/49070/

Rutgers University

13. Garg, Abhishek, 1987-. Development of a computational tool for forensic DNA analysis.

Degree: MS, Computer Science, 2015, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/48800/

► Forensic DNA analysis uses repetitive sequences in the human genome called Short Tandem Repeats (STRs) for human identification. This study has contributed to the building,… (more)

Subjects/Keywords: DNA – Analysis; Forensic pathology

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APA (6^th Edition):

Garg, Abhishek, 1. (2015). Development of a computational tool for forensic DNA analysis. (Masters Thesis). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/48800/

Chicago Manual of Style (16^th Edition):

Garg, Abhishek, 1987-. “Development of a computational tool for forensic DNA analysis.” 2015. Masters Thesis, Rutgers University. Accessed January 28, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/48800/.

MLA Handbook (7^th Edition):

Garg, Abhishek, 1987-. “Development of a computational tool for forensic DNA analysis.” 2015. Web. 28 Jan 2021.

Vancouver:

Garg, Abhishek 1. Development of a computational tool for forensic DNA analysis. [Internet] [Masters thesis]. Rutgers University; 2015. [cited 2021 Jan 28]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48800/.

Council of Science Editors:

Garg, Abhishek 1. Development of a computational tool for forensic DNA analysis. [Masters Thesis]. Rutgers University; 2015. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/48800/

Rutgers University

14. Sun, Die, 1986-. Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity.

Degree: PhD, Statistics and Biostatistics, 2017, Rutgers University

URL: https://rucore.libraries.rutgers.edu/rutgers-lib/52270/

► In this dissertation, we consider two research projects: deconvolution of transcript profiling data; and inferences for multivariate time series based on cross correlations, especially under… (more)

▼ In this dissertation, we consider two research projects: deconvolution of transcript profiling data; and inferences for multivariate time series based on cross correlations, especially under high dimensionality. The study of transcript profiling data such as macro-arrays or deep sequencing, has wide application in gene expression studies. A typical objective of gene expression study is to identify genes that are differentially expressed between groups of samples, such as normal vs. tumor tissue. However, most of the biological samples in scientific researches are heterogeneous: for the samples with identical cellular types, they may have very different proportions. Such variance in proportion will lead to confounding effects citep{Shen-Orr2013}. For example, the reflected gene expression variations are simply caused by the differences in proportions of cell subsets instead of the characteristic condition of a sample (e.g. disease). In order to eliminate the confounding effect, one solution might be to focus on the single cell subset. The isolation procedure, however, is limited by sample materials and financial budgets. Therefore, statistical deconvolution, which does not require any isolation, becomes necessary and practical. In the first project, we develop the Iterated Least Square (ILS) algorithms to estimate the cell specific signature and proportion matrix in complete blind case under homoscedasticity assumption, and theoretically justify the consistency of signature matrix estimate. We also find that the ILS estimate is equivalent to moment under homoscedasticity assumptions, and establish the central limit theorems for the moment estimates. In the heteroscedastic case, the ILS is no longer asymptotically unbiased. Thus, we propose to use the moment estimate, and develop the asymptotics of signature expression estimates. Both numerical examples and real data analysis are employed to illustrate the estimation methods and their asymptotic properties. Cross correlations are of fundamental importance in multivariate time series analysis. We consider tests for independence of component series based on sample cross correlations. We start with a study of cross correlations between two time series. We derive the central limit theorems for sample cross correlations at large lags, establish convergence rates for maximum sample cross correlations, and demonstrate how they can be used to identify the lead lag relationship for a bivariate time series. We also propose a window sum approach to reduce the computational cost when the series is long. As a second problem, we consider tests for independence of components series under high dimensionality. We propose to use the maximum sample cross correlation over a large range of lags as the test statistic. We also consider an extension to Ljung-Box type statistics. We show that the limiting distributions of the test statistics are extreme value distribution of type I. Our results allow both the number of series, and the range of lags to grow as powers of the sample size,… Advisors/Committee Members: Xiao, Han (chair), Chen, Rong (internal member), Kolassa, John (internal member), Lin, Xiaodong (outside member), Lu, Yuefeng (outside member).

Subjects/Keywords: Gene mapping; DNA – Analysis

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

APA (6^th Edition):

Sun, Die, 1. (2017). Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity. (Doctoral Dissertation). Rutgers University. Retrieved from https://rucore.libraries.rutgers.edu/rutgers-lib/52270/

Chicago Manual of Style (16^th Edition):

Sun, Die, 1986-. “Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity.” 2017. Doctoral Dissertation, Rutgers University. Accessed January 28, 2021. https://rucore.libraries.rutgers.edu/rutgers-lib/52270/.

MLA Handbook (7^th Edition):

Sun, Die, 1986-. “Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity.” 2017. Web. 28 Jan 2021.

Vancouver:

Sun, Die 1. Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity. [Internet] [Doctoral dissertation]. Rutgers University; 2017. [cited 2021 Jan 28]. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/52270/.

Council of Science Editors:

Sun, Die 1. Deconvolution of transcript profiling data and asymptotic inference of crosscorrelation in L infinity. [Doctoral Dissertation]. Rutgers University; 2017. Available from: https://rucore.libraries.rutgers.edu/rutgers-lib/52270/

15. NC DOCKS at Western Carolina University; Stawski, Hilde. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.

Degree: 2013, NC Docks

URL: http://libres.uncg.edu/ir/wcu/f/Stawski2013.pdf

► Forensic DNA casework principally relies on the analysis of short tandem repeats (STRs) from nuclear DNA (nDNA). In cases where nDNA may not be suitable… (more)

▼ Forensic DNA casework principally relies on the analysis of short tandem repeats (STRs) from nuclear DNA (nDNA). In cases where nDNA may not be suitable for analysis (i.e., highly degraded DNA or DNA present in quantities too low to obtain an STR profile), mitochondrial DNA (mtDNA) is an excellent alternative. MtDNA is a circular genome of approximately 16.5 kb, is maternally derived, and is present in thousands of copies per cell versus two copies of nuclear DNA. The combined higher copy number, circular shape of the genome and protection by the double membrane of the mitochondrion allows for a greater probability to recover sufficient mtDNA for typing of degraded samples. Presently, forensic analysts sequence two or three hypervariable (HV) regions found in the non-coding control region of the mtGenome, since sequencing of the entire mitochondrial genome (mtGenome) is rather costly and labor-intensive. Additionally, difficulties sequencing through homopolymeric regions, as well as the presence of lowlevel mixtures in samples, can add complexity to the analysis of mtDNA in casework when traditional Sanger sequencing methods are used. These issues can be addressed with Next Generation Sequencing (NGS) technologies. NGS enables deeper analysis of the genome for identification of low-level mixtures, since clonal populations of molecules originating from a single template strand are sequenced. Moreover, this technology allows for the more cost-effective sequencing of whole mtGenomes compared to Sanger methods, since more sequences are obtained for the same sample. By expanding mtDNA analysis to the entire mtGenome, a better resolution in distinguishing between haplotypes is established. In forensic casework, amplification of challenging samples such as hair and aged bone is often performed differently than that of reference samples (buccal swabs, blood, etc.) due to the higher possibility of DNA degradation and limited mtDNA concentrations. For this study, two sample preparation approaches were developed including one method for robust reference samples, and one method for forensically relevant challenging samples. For NGS analysis of reference samples, DNA was extracted from buccal swabs obtained from eight donors. A long PCR approach, which refers to the amplification of DNA fragments of a size that may not be amplified using conventional PCR reagents, was successfully performed on these DNA extracts using a highly processive polymerase mixture and novel primer pairs to amplify the mtGenome in two independent PCR reactions, with overlap at the noncoding region. These samples were subsequently processed with Illumina® Nextera® XT. This NGS library preparation kit is designed exclusively for use with Illumina® instrumentation and employs an engineered Transposome™ to randomly fragment and tag amplicons and small genomes with Illumina® specific adapters. After library preparation, samples were sequenced on the Illumina® MiSeq™. This method generated whole mtGenome NGS data, which accurately reflected the Sanger…

Subjects/Keywords: Mitochondrial DNA – Analysis – Data processing

Record Details Similar Records Cite « Share

❌

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

APA (6^th Edition):

NC DOCKS at Western Carolina University; Stawski, H. (2013). Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/wcu/f/Stawski2013.pdf

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

Chicago Manual of Style (16^th Edition):

NC DOCKS at Western Carolina University; Stawski, Hilde. “Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.” 2013. Thesis, NC Docks. Accessed January 28, 2021. http://libres.uncg.edu/ir/wcu/f/Stawski2013.pdf.

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

MLA Handbook (7^th Edition):

NC DOCKS at Western Carolina University; Stawski, Hilde. “Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT.” 2013. Web. 28 Jan 2021.

Vancouver:

NC DOCKS at Western Carolina University; Stawski H. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. [Internet] [Thesis]. NC Docks; 2013. [cited 2021 Jan 28]. Available from: http://libres.uncg.edu/ir/wcu/f/Stawski2013.pdf.

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

Council of Science Editors:

NC DOCKS at Western Carolina University; Stawski H. Preparing whole genome human mitochondrial DNA libraries for next generation sequencing using Illumina Nextera XT. [Thesis]. NC Docks; 2013. Available from: http://libres.uncg.edu/ir/wcu/f/Stawski2013.pdf

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

Brno University of Technology

16. Petrula, Jakub. Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation.

Degree: 2019, Brno University of Technology

URL: http://hdl.handle.net/11012/65450

► This bachelor’s thesis deals with design and optimalisation of custom biosensor for detection of methylated DNA. Teoretical part explains the mechanism and importance of DNA… (more)

Subjects/Keywords: DNA; metylácia; analýza DNA; detekcia DNA; elektrochémia; biosenzor; uhlíkové nanotrubice; DNA; methylation; DNA analysis; DNA detection; electrochemistry; biosensor; carbon nanotubes

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APA (6^th Edition):

Petrula, J. (2019). Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/65450

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

Chicago Manual of Style (16^th Edition):

Petrula, Jakub. “Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation.” 2019. Thesis, Brno University of Technology. Accessed January 28, 2021. http://hdl.handle.net/11012/65450.

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

MLA Handbook (7^th Edition):

Petrula, Jakub. “Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation.” 2019. Web. 28 Jan 2021.

Vancouver:

Petrula J. Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/11012/65450.

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

Council of Science Editors:

Petrula J. Elektrochemický biosenzor pro studium metylace DNA: Electrochemical biosensor for the study of DNA methylation. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/65450

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

George Mason University

17. Thoms, Kristen. Development of DNA Analysis for Forensic Animal Investigations .

Degree: 2012, George Mason University

URL: http://hdl.handle.net/1920/7883

► DNA Analysis has been an important tool for forensic investigations, used to scientifically link an individual to a crime, and provide statistical relevance to the… (more)

Subjects/Keywords: Wildlife Forensics; DNA Analysis; Animal DNA; Non-Human DNA Markers; Species Identification; Forensic DNA Identification

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APA (6^th Edition):

Thoms, K. (2012). Development of DNA Analysis for Forensic Animal Investigations . (Thesis). George Mason University. Retrieved from http://hdl.handle.net/1920/7883

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

Chicago Manual of Style (16^th Edition):

Thoms, Kristen. “Development of DNA Analysis for Forensic Animal Investigations .” 2012. Thesis, George Mason University. Accessed January 28, 2021. http://hdl.handle.net/1920/7883.

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

MLA Handbook (7^th Edition):

Thoms, Kristen. “Development of DNA Analysis for Forensic Animal Investigations .” 2012. Web. 28 Jan 2021.

Vancouver:

Thoms K. Development of DNA Analysis for Forensic Animal Investigations . [Internet] [Thesis]. George Mason University; 2012. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/1920/7883.

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

Council of Science Editors:

Thoms K. Development of DNA Analysis for Forensic Animal Investigations . [Thesis]. George Mason University; 2012. Available from: http://hdl.handle.net/1920/7883

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

Brno University of Technology

18. Martaus, Pavel. Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching.

Degree: 2019, Brno University of Technology

URL: http://hdl.handle.net/11012/72312

► This work is described in the theoretical part of repetitive DNA, their types and methods to search in DNA sequence. In the practical part is… (more)

Subjects/Keywords: Repetitivní DNA; analýza DNA sekvencí; Hammingova vzdálenost.; Repetitive DNA; analysis of DNA sequences; Hamming distance.

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APA (6^th Edition):

Martaus, P. (2019). Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching. (Thesis). Brno University of Technology. Retrieved from http://hdl.handle.net/11012/72312

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

Chicago Manual of Style (16^th Edition):

Martaus, Pavel. “Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching.” 2019. Thesis, Brno University of Technology. Accessed January 28, 2021. http://hdl.handle.net/11012/72312.

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

MLA Handbook (7^th Edition):

Martaus, Pavel. “Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching.” 2019. Web. 28 Jan 2021.

Vancouver:

Martaus P. Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching. [Internet] [Thesis]. Brno University of Technology; 2019. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/11012/72312.

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

Council of Science Editors:

Martaus P. Vyhledávání přesných a přibližných repetic v sekvenci DNA na základě porovnávaní znaků: Detecting exact and approximate repeats in DNA based on string matching. [Thesis]. Brno University of Technology; 2019. Available from: http://hdl.handle.net/11012/72312

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

Michigan State University

19. Doran, Ashley Elizabeth. Optimizing the analysis of trace DNA from fingernail evidence.

Degree: 2014, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:2949

►

Thesis M.S. Michigan State University. Forensic Science 2014.

During a physical assault, biological material can be transferred between an assailant and victim. When victims defend… (more)

Subjects/Keywords: Chemistry, Forensic; DNA fingerprinting – Technique; Fingernails – Analysis; DNA – Analysis; Criminology

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APA (6^th Edition):

Doran, A. E. (2014). Optimizing the analysis of trace DNA from fingernail evidence. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:2949

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

Chicago Manual of Style (16^th Edition):

Doran, Ashley Elizabeth. “Optimizing the analysis of trace DNA from fingernail evidence.” 2014. Thesis, Michigan State University. Accessed January 28, 2021. http://etd.lib.msu.edu/islandora/object/etd:2949.

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

MLA Handbook (7^th Edition):

Doran, Ashley Elizabeth. “Optimizing the analysis of trace DNA from fingernail evidence.” 2014. Web. 28 Jan 2021.

Vancouver:

Doran AE. Optimizing the analysis of trace DNA from fingernail evidence. [Internet] [Thesis]. Michigan State University; 2014. [cited 2021 Jan 28]. Available from: http://etd.lib.msu.edu/islandora/object/etd:2949.

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

Council of Science Editors:

Doran AE. Optimizing the analysis of trace DNA from fingernail evidence. [Thesis]. Michigan State University; 2014. Available from: http://etd.lib.msu.edu/islandora/object/etd:2949

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

Bond University

20. Hughes-Stamm, Sheree R. DNA Typing Methods for Highly Degraded Samples.

Degree: 2012, Bond University

URL: https://epublications.bond.edu.au/theses/69

► Highly degraded biological samples may be encountered in cases of mass disasters, missing persons cases, and forensic case work. As biological tissue degrades, DNA becomes… (more)

Subjects/Keywords: DNA damage; DNA damage Research Methodology; DNA Analysis; Forensic biology; Biology, Genetics (0369)

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APA (6^th Edition):

Hughes-Stamm, S. R. (2012). DNA Typing Methods for Highly Degraded Samples. (Thesis). Bond University. Retrieved from https://epublications.bond.edu.au/theses/69

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

Chicago Manual of Style (16^th Edition):

Hughes-Stamm, Sheree R. “DNA Typing Methods for Highly Degraded Samples.” 2012. Thesis, Bond University. Accessed January 28, 2021. https://epublications.bond.edu.au/theses/69.

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

MLA Handbook (7^th Edition):

Hughes-Stamm, Sheree R. “DNA Typing Methods for Highly Degraded Samples.” 2012. Web. 28 Jan 2021.

Vancouver:

Hughes-Stamm SR. DNA Typing Methods for Highly Degraded Samples. [Internet] [Thesis]. Bond University; 2012. [cited 2021 Jan 28]. Available from: https://epublications.bond.edu.au/theses/69.

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

Council of Science Editors:

Hughes-Stamm SR. DNA Typing Methods for Highly Degraded Samples. [Thesis]. Bond University; 2012. Available from: https://epublications.bond.edu.au/theses/69

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

Oklahoma State University

21. Smith, Byron Cody. Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex.

Degree: School of Forensic Sciences, 2011, Oklahoma State University

URL: http://hdl.handle.net/11244/10308

► DNA sample degradation is a common problem encountered in forensic DNA casework. In some instances the severity of sample degradation prevents the inclusion of an… (more)

▼ DNA sample degradation is a common problem encountered in forensic DNA casework. In some instances the severity of sample degradation prevents the inclusion of an evidentiary profile into the FBI CODIS database. In this study an end-point PCR quantitative assay is assessed to determine if human DNA targets of differing size can be used to predict DNA sample degradation in STR profiling. Primer sequences from a small male-specific target (SRY) and a large human target (Amelogenin) are multiplexed. These targets estimate the respective total-human and male-only quantities of sample DNA based on comparison to a standard curve prepared from known quantities of human DNA. The quantitative estimate of the small target versus the quantitative estimate of the large target can be compared in male samples to form a ratio. This ratio may indicate the probable amplification performance of large-target STR loci multiplexed in HID typing kits. A method was developed here to degrade DNA in a controlled manner for analysis with this quantitative assay. The resulting quantitative ratios were compared to HID ratios developed from the amplification performance of small and large CODIS core loci. In addition, a selection of male reference samples was also examined to evaluate the correlations of quantitative ratios and HID ratios obtained in actual casework. Regression analysis of the performance of the small and large targets amplified in the quantitative assay demonstrated a significant difference (p < 0.001) between both targets through the course of the in vitro degradation experiment. These results indicate that in degraded samples the small target will outperform the large target in the quantitative assay. Assessment of the quantitative ratios demonstrated significant degradation (p < 0.001) at and above the t=60 minute timepoint in the successive degradation of samples. This experimental model was applied to the quantitative and HID typing results obtained from male reference samples in actual casework. Statistical assessment of these samples indicates a strong correlation (r = 0.7478, p < 0.001) between the quantitative ratios and the HID ratios. This confirms the ability of the quantitative assay to assess large-target amplification performance via a ratio, which predicts the trend of sample degradation observed in HID profiling.

Subjects/Keywords: dna degradation; dna quantitation; forensic dna; in vitro degradation; pcr; str analysis

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

APA (6^th Edition):

Smith, B. C. (2011). Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex. (Thesis). Oklahoma State University. Retrieved from http://hdl.handle.net/11244/10308

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

Chicago Manual of Style (16^th Edition):

Smith, Byron Cody. “Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex.” 2011. Thesis, Oklahoma State University. Accessed January 28, 2021. http://hdl.handle.net/11244/10308.

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

MLA Handbook (7^th Edition):

Smith, Byron Cody. “Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex.” 2011. Web. 28 Jan 2021.

Vancouver:

Smith BC. Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex. [Internet] [Thesis]. Oklahoma State University; 2011. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/11244/10308.

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

Council of Science Editors:

Smith BC. Evaluating DNA Sample Degradation With a Quantitative Gender Typing End-Point PCR Multiplex. [Thesis]. Oklahoma State University; 2011. Available from: http://hdl.handle.net/11244/10308

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

Boston University

22. Wellner, Genevieve A. The examination of baseline noise and the impact on the interpretation of low-template DNA samples.

Degree: MS, Biomedical Forensic Sciences, 2014, Boston University

URL: http://hdl.handle.net/2144/14939

► It is common practice for DNA STR profiles to be analyzed using an analytical threshold (AT), but as more low template DNA (LT-DNA) samples are… (more)

▼ It is common practice for DNA STR profiles to be analyzed using an analytical threshold (AT), but as more low template DNA (LT-DNA) samples are tested it has become evident that these thresholds do not adequately separate signal from noise. In order to confidently examine LT-DNA samples, the behavior and characteristics of the background noise of STR profiles must be better understood. Thus, the background noise of single source LT-DNA STR profiles were examined to characterize the noise distribution and determine how it changes with DNA template mass and injection time. Current noise models typically assume the noise is independent of fragment size but, given the tendency of the baseline noise to increase with template amount, it is important to establish whether the baseline noise is randomly found throughout the capillary electrophoresis (CE) run or whether it is situated in specific regions of the electropherogram. While it has been shown that the baseline noise of negative samples does not behave similarly to the baseline noise of profiles generated using optimal levels of DNA, the ATs determined using negative samples have shown to be similar to those developed with near-zero, low template mass samples. The distinction between low-template samples, where the noise is consistent regardless of target mass, and standard samples could be made at approximately 0.063 ng for samples amplified using the Identifiler^TM Plus amplification kit (29 cycle protocol), and injected for 5 and 10 seconds. At amplification target masses greater than 0.063 ng, the average noise peak height increased and began to plateau between 0.5 and 1.0 ng for samples injected for 5 and 10 seconds. To examine the time dependent nature of the baseline noise, the baselines of over 400 profiles were combined onto one axis for each target mass and each injection time. Areas of reproducibly higher noise peak heights were identified as areas of potential non-specific amplified product. When the samples were injected for five seconds, the baseline noise did not appear to be time dependent. However, when the samples were injected for either 10 or 20 seconds, there were three areas that exhibited an increase in noise; these areas were identified at 118 bases in green, 231 bases in yellow, and 106 bases in red. If a probabilistic analysis or AT is to be employed for DNA interpretation, consideration must be given as to how the validation or calibration samples are prepared. Ideally the validation data should include all the variation seen within typical samples. To this end, a study was performed to examine possible sources of variation in the baseline noise within the electropherogram. Specifically, three samples were prepared at seven target masses using four different kit lots, four capillary lots, in four amplification batches or four injection batches. The distribution of the noise peak heights in the blue and green channels for samples with variable capillary lots, amplifications, and injections were similar, but the distribution of the noise…

Subjects/Keywords: Biology; STR profile; Baseline noise; Forensic DNA analysis; Low-template DNA

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

APA (6^th Edition):

Wellner, G. A. (2014). The examination of baseline noise and the impact on the interpretation of low-template DNA samples. (Masters Thesis). Boston University. Retrieved from http://hdl.handle.net/2144/14939

Chicago Manual of Style (16^th Edition):

Wellner, Genevieve A. “The examination of baseline noise and the impact on the interpretation of low-template DNA samples.” 2014. Masters Thesis, Boston University. Accessed January 28, 2021. http://hdl.handle.net/2144/14939.

MLA Handbook (7^th Edition):

Wellner, Genevieve A. “The examination of baseline noise and the impact on the interpretation of low-template DNA samples.” 2014. Web. 28 Jan 2021.

Vancouver:

Wellner GA. The examination of baseline noise and the impact on the interpretation of low-template DNA samples. [Internet] [Masters thesis]. Boston University; 2014. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/2144/14939.

Council of Science Editors:

Wellner GA. The examination of baseline noise and the impact on the interpretation of low-template DNA samples. [Masters Thesis]. Boston University; 2014. Available from: http://hdl.handle.net/2144/14939

Latrobe University

23. Young, Sylvia. Kernel methods in analysis of genetic markers and DNA microarrays.

Degree: PhD, 2012, Latrobe University

URL: http://hdl.handle.net/1959.9/517163

►

Thesis (Ph.D.) - La Trobe University, 2012

Submission note: "A thesis submitted in total fulfilment of the requirements for the degree of Doctor of Philosophy… (more)

Subjects/Keywords: Genetic markers.; DNA – Analysis – Mathematical models.; DNA microarrays.

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APA (6^th Edition):

Young, S. (2012). Kernel methods in analysis of genetic markers and DNA microarrays. (Doctoral Dissertation). Latrobe University. Retrieved from http://hdl.handle.net/1959.9/517163

Chicago Manual of Style (16^th Edition):

Young, Sylvia. “Kernel methods in analysis of genetic markers and DNA microarrays.” 2012. Doctoral Dissertation, Latrobe University. Accessed January 28, 2021. http://hdl.handle.net/1959.9/517163.

MLA Handbook (7^th Edition):

Young, Sylvia. “Kernel methods in analysis of genetic markers and DNA microarrays.” 2012. Web. 28 Jan 2021.

Vancouver:

Young S. Kernel methods in analysis of genetic markers and DNA microarrays. [Internet] [Doctoral dissertation]. Latrobe University; 2012. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/1959.9/517163.

Council of Science Editors:

Young S. Kernel methods in analysis of genetic markers and DNA microarrays. [Doctoral Dissertation]. Latrobe University; 2012. Available from: http://hdl.handle.net/1959.9/517163

Massey University

24. Waugh, William John. DNA barcoding the birds of New Zealand.

Degree: PhD, Molecular BioSciences, 2011, Massey University

URL: http://hdl.handle.net/10179/2665

► A comprehensive inventory of the life forms on earth is at the heart of any scientific study of evolution and biodiversity. The international "Barcode of… (more)

Subjects/Keywords: DNA analysis; Barcode of Life project; Mitochondrial DNA; Avian species identification

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APA (6^th Edition):

Waugh, W. J. (2011). DNA barcoding the birds of New Zealand. (Doctoral Dissertation). Massey University. Retrieved from http://hdl.handle.net/10179/2665

Chicago Manual of Style (16^th Edition):

Waugh, William John. “DNA barcoding the birds of New Zealand.” 2011. Doctoral Dissertation, Massey University. Accessed January 28, 2021. http://hdl.handle.net/10179/2665.

MLA Handbook (7^th Edition):

Waugh, William John. “DNA barcoding the birds of New Zealand.” 2011. Web. 28 Jan 2021.

Vancouver:

Waugh WJ. DNA barcoding the birds of New Zealand. [Internet] [Doctoral dissertation]. Massey University; 2011. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/10179/2665.

Council of Science Editors:

Waugh WJ. DNA barcoding the birds of New Zealand. [Doctoral Dissertation]. Massey University; 2011. Available from: http://hdl.handle.net/10179/2665

University of Cincinnati

25. Chen, Jiayao. Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks.

Degree: MDES, Design, Architecture, Art and Planning: Design, 2019, University of Cincinnati

URL: http://rave.ohiolink.edu/etdc/view?acc_num=ucin155421172489759

► Following the culturally-based product design methodology, this thesis project developed a new cultural product innovation process including the establishment of cultural DNA banks. To increase… (more)

Subjects/Keywords: Design; Cultural DNA Analysis; Product Innovation; Cultural DNA Bank; Guideline

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APA (6^th Edition):

Chen, J. (2019). Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks. (Masters Thesis). University of Cincinnati. Retrieved from http://rave.ohiolink.edu/etdc/view?acc_num=ucin155421172489759

Chicago Manual of Style (16^th Edition):

Chen, Jiayao. “Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks.” 2019. Masters Thesis, University of Cincinnati. Accessed January 28, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=ucin155421172489759.

MLA Handbook (7^th Edition):

Chen, Jiayao. “Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks.” 2019. Web. 28 Jan 2021.

Vancouver:

Chen J. Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks. [Internet] [Masters thesis]. University of Cincinnati; 2019. [cited 2021 Jan 28]. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin155421172489759.

Council of Science Editors:

Chen J. Cultural DNA and Product Innovation: A Guideline of Establishing and Utilizing Cultural DNA Banks. [Masters Thesis]. University of Cincinnati; 2019. Available from: http://rave.ohiolink.edu/etdc/view?acc_num=ucin155421172489759

26. McLamb, Jessica Marie. Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones.

Degree: 2017, NC Docks

URL: http://libres.uncg.edu/ir/wcu/f/McLamb2017.pdf

► Although DNA profiling techniques are considered a powerful method for identification, problems arise when low quantity and/or quality DNA is tested. Analyzing samples with low… (more)

▼ Although DNA profiling techniques are considered a powerful method for identification, problems arise when low quantity and/or quality DNA is tested. Analyzing samples with low template DNA using standard genotyping techniques like STR typing can yield no or an incomplete profile, making conclusive identification nearly impossible. One challenging forensic sample material is bone. For example, DNA within bone can be degraded due to harsh environmental conditions even when the structure of the bone appears to be relatively well preserved. Consequently, the amount of usable DNA in bones can be limited which complicates downstream applications for DNA profiling. This study investigated techniques that would improve obtaining a discriminating DNA profile from human bones. First, the performances of three commercial DNA extraction kits were evaluated for the recovery of genomic DNA from human bones. The PrepFiler® BTA Forensic DNA Extraction Kit recovered the highest DNA yield according to qPCR data and was used for additional bone extractions. Next, purified DNA from a total of 12 bone samples was subject to genotyping methods using capillary electrophoresis (CE) as well as massively parallel sequencing (MPS) to determine which strategy would produce the most discriminating DNA profile. The genotyping techniques evaluated were: CE-based STR analysis with the GlobalFiler® PCR Amplification Kit, whole genome amplification (WGA) with the REPLI-g® Mini Kit for improved CE-based STR detection, and MPS for STR/SNP analysis using the Ion PGM™ and MiSeq® FGx™ platforms. Random match probabilities were calculated to determine the discriminatory power of the resulting DNA profiles. Although the Ion PGM™ SNP profiles had the highest RMPs, the GlobalFiler® STR profiles produced similar discriminatory power. Considering the time and labor required for MPS, one could argue STR analysis using traditional CE may be better suited for DNA profiling of challenging bone samples. However, the MPS technologies provide additional information that CE-methods can’t, such as Y-haplogroup and biogeographical ancestry predictions from SNP analyses.

Subjects/Keywords: DNA fingerprinting; DNA – Analysis; Human remains (Archaeology); Forensic genetics

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APA (6^th Edition):

McLamb, J. M. (2017). Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones. (Thesis). NC Docks. Retrieved from http://libres.uncg.edu/ir/wcu/f/McLamb2017.pdf

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

Chicago Manual of Style (16^th Edition):

McLamb, Jessica Marie. “Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones.” 2017. Thesis, NC Docks. Accessed January 28, 2021. http://libres.uncg.edu/ir/wcu/f/McLamb2017.pdf.

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

MLA Handbook (7^th Edition):

McLamb, Jessica Marie. “Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones.” 2017. Web. 28 Jan 2021.

Vancouver:

McLamb JM. Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones. [Internet] [Thesis]. NC Docks; 2017. [cited 2021 Jan 28]. Available from: http://libres.uncg.edu/ir/wcu/f/McLamb2017.pdf.

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

Council of Science Editors:

McLamb JM. Application of enhancement strategies for the improvement of discriminating forensic DNA profiles from human bones. [Thesis]. NC Docks; 2017. Available from: http://libres.uncg.edu/ir/wcu/f/McLamb2017.pdf

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

Michigan State University

27. Peters, Shannon. The optimized use and recovery of DNA from tape lifts.

Degree: 2011, Michigan State University

URL: http://etd.lib.msu.edu/islandora/object/etd:653

►

Thesis M.S. Michigan State University. Forensic Science 2011.

The use of tape lifts for DNA recovery is becoming increasingly common in forensic laboratories, however there… (more)

Subjects/Keywords: DNA – Analysis; DNA fingerprinting – Research; Forensic sciences; Biology; Molecular biology

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APA (6^th Edition):

Peters, S. (2011). The optimized use and recovery of DNA from tape lifts. (Thesis). Michigan State University. Retrieved from http://etd.lib.msu.edu/islandora/object/etd:653

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

Chicago Manual of Style (16^th Edition):

Peters, Shannon. “The optimized use and recovery of DNA from tape lifts.” 2011. Thesis, Michigan State University. Accessed January 28, 2021. http://etd.lib.msu.edu/islandora/object/etd:653.

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

MLA Handbook (7^th Edition):

Peters, Shannon. “The optimized use and recovery of DNA from tape lifts.” 2011. Web. 28 Jan 2021.

Vancouver:

Peters S. The optimized use and recovery of DNA from tape lifts. [Internet] [Thesis]. Michigan State University; 2011. [cited 2021 Jan 28]. Available from: http://etd.lib.msu.edu/islandora/object/etd:653.

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

Council of Science Editors:

Peters S. The optimized use and recovery of DNA from tape lifts. [Thesis]. Michigan State University; 2011. Available from: http://etd.lib.msu.edu/islandora/object/etd:653

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

University of Hong Kong

28. 翁海珠. Rapid and direct DNA extraction from saliva for personalized medicine.

Degree: 2010, University of Hong Kong

URL: http://hdl.handle.net/10722/134794

Subjects/Keywords: DNA - Analysis.; Pharmacogenetics.

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APA (6^th Edition):

翁海珠.. (2010). Rapid and direct DNA extraction from saliva for personalized medicine. (Thesis). University of Hong Kong. Retrieved from http://hdl.handle.net/10722/134794

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

Chicago Manual of Style (16^th Edition):

翁海珠.. “Rapid and direct DNA extraction from saliva for personalized medicine.” 2010. Thesis, University of Hong Kong. Accessed January 28, 2021. http://hdl.handle.net/10722/134794.

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

MLA Handbook (7^th Edition):

翁海珠.. “Rapid and direct DNA extraction from saliva for personalized medicine.” 2010. Web. 28 Jan 2021.

Note: this citation may be lacking information needed for this citation format:
Author name may be incomplete

Vancouver:

翁海珠.. Rapid and direct DNA extraction from saliva for personalized medicine. [Internet] [Thesis]. University of Hong Kong; 2010. [cited 2021 Jan 28]. Available from: http://hdl.handle.net/10722/134794.

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

Council of Science Editors:

翁海珠.. Rapid and direct DNA extraction from saliva for personalized medicine. [Thesis]. University of Hong Kong; 2010. Available from: http://hdl.handle.net/10722/134794

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

Drexel University

29. Young, Eleanor A. Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing.

Degree: 2019, Drexel University

URL: https://idea.library.drexel.edu/islandora/object/idea%3A10993

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Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population… (more)

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Detailed comprehensive knowledge of the structures of individual long-range telomere-terminal haplotypes are needed to understand their impact on telomere function, and to delineate the population structure and evolution of subtelomere regions. However, the abundance of large evolutionarily recent segmental duplications and high levels of large structural variations have complicated both the mapping and sequence characterization of human subtelomere regions. Here, I use a highly automated whole genome mapping technology in nano-channel arrays to analyze large terminal human chromosome segments extending from chromosome-specific subtelomere sequences through subtelomeric repeat regions to terminal (TTAGGG)n repeat tracts. I analyzed 154 human genomes from 26 populations to present a comprehensive look at human subtelomere structure and variation. The results catalog many novel long-range subtelomere haplotypes and determine the frequencies and contexts of specific subtelomeric duplicons on each chromosome arm, helping to clarify the currently ambiguous nature of many specific subtelomere structures as represented in the current reference sequence (hg38). The organization and content of some duplicons in subtelomeres appear to show both chromosome arm and population-specific trends. Based upon these trends, I estimate a timeline for the spread of these duplication blocks. The highly repetitive and variable short repeat elements (SREs) in subtelomeric regions present the significant challenges to complete the sequence assembly, as many additional copies of the blocks found through these methods are lacking in the current human reference. More often, the sequence reads (even the long PacBio reads) are aligned to the wrong locations in SRE regions as evidenced by high sequencing read coverage, and unusual allele distribution patterns in the aligned reads. Reads belonging to chromosomes lacking a reference copy of a block have been aligned to copies on other chromosomes that are present in the reference. I present a method for realigning and assigning these sequence reads to correct SREs. Long PacBio sequencing reads from each reference copy of these SRE blocks were pooled into consensus haplotypes based on allele distributions and combinations. Haplotypes were reassigned to the correct chromosome arms by evaluating their similarity to the reference copies of the block. I also used 10x Genomics Linked-Read sequencing data to assign the haplotypes to the extra SRE copies that are not present in hg38 by linking unassigned consensus haplotypes to the unique, single copy regions of the chromosome arms. This work also provides a better foundation for clinical diagnostics and understanding variants in subtelomeric regions.

Ph.D., Biomedical Engineering – Drexel University, 2019

Advisors/Committee Members: Xiao, Ming (Advisor), School of Biomedical Engineering, Science, and Health Systems (College).

Subjects/Keywords: Biomedical engineering; DNA – Analysis; Genomics; Gene mapping

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

APA (6^th Edition):

Young, E. A. (2019). Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing. (Thesis). Drexel University. Retrieved from https://idea.library.drexel.edu/islandora/object/idea%3A10993

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

Chicago Manual of Style (16^th Edition):

Young, Eleanor A. “Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing.” 2019. Thesis, Drexel University. Accessed January 28, 2021. https://idea.library.drexel.edu/islandora/object/idea%3A10993.

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

MLA Handbook (7^th Edition):

Young, Eleanor A. “Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing.” 2019. Web. 28 Jan 2021.

Vancouver:

Young EA. Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing. [Internet] [Thesis]. Drexel University; 2019. [cited 2021 Jan 28]. Available from: https://idea.library.drexel.edu/islandora/object/idea%3A10993.

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

Council of Science Editors:

Young EA. Comprehensive Analysis of Subtelomeres by Genome Mapping and Sequencing. [Thesis]. Drexel University; 2019. Available from: https://idea.library.drexel.edu/islandora/object/idea%3A10993

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

30. Nayak, Shreenath. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.

Degree: Botany, 2014, Visva Bharti University

URL: http://shodhganga.inflibnet.ac.in/handle/10603/19542

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A thermostable DNA polymerase gene (DNA pol) was isolated from the genomic DNA of Geobacillus sp.WBI by polymerase chain reaction (PCR). PCR amplification with the… (more)

Subjects/Keywords: Geobacillus; Sequence analysis; Thermostable DNA polymerase

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

APA (6^th Edition):

Nayak, S. (2014). Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. (Thesis). Visva Bharti University. Retrieved from http://shodhganga.inflibnet.ac.in/handle/10603/19542

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

Chicago Manual of Style (16^th Edition):

Nayak, Shreenath. “Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.” 2014. Thesis, Visva Bharti University. Accessed January 28, 2021. http://shodhganga.inflibnet.ac.in/handle/10603/19542.

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

MLA Handbook (7^th Edition):

Nayak, Shreenath. “Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI.” 2014. Web. 28 Jan 2021.

Vancouver:

Nayak S. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. [Internet] [Thesis]. Visva Bharti University; 2014. [cited 2021 Jan 28]. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/19542.

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

Council of Science Editors:

Nayak S. Cloning sequence analysis and characterization of DNA polymerase from Geobacillus sp. WBI. [Thesis]. Visva Bharti University; 2014. Available from: http://shodhganga.inflibnet.ac.in/handle/10603/19542

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

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Open Access Theses and Dissertations