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Dissertations / Theses on the topic 'DNA microarrays'

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Published: 4 June 2021

Last updated: 30 July 2024

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1

Stephens, Nathan W. "A comparison of genetic microarray analyses : a mixed models approach versus the significance analysis of microarrays /." Diss., CLICK HERE for online access, 2006. http://contentdm.lib.byu.edu/ETD/image/etd1604.pdf.

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2

Brunner, Thomas. "Designing oligonucleotides for DNA microarrays /." Zürich : ETH, Eidgenössische Technische Hochschule Zürich, Department of Computer Science, 2003. http://e-collection.ethbib.ethz.ch/show?type=dipl&nr=116.

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3

Smith, Kaleigh. "Towards quality control in DNA microarrays." Thesis, McGill University, 2003. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=79129.

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We present a framework for detecting degenerate probes in a DNA microarray that may add to measurement error in hybridization experiments. We consider four types of behaviour: secondary structure formation, self-dimerization, cross-hybridization and dimerization. The framework uses a well-established model of nucleic acid sequence hybridization and a novel method for the detection of patterns in hybridization experiment data. Our primary result is the identification of unique patterns in hybridization experiment data that are correlated with each type of degenerate probe behaviour. The framework also contains a machine learning technique to learn from the hybridization experiment data. We implement the components of the framework and evaluate the ability of the framework to detect degenerate probes in the Affymetrix HuGeneFL GeneChip.

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4

Arrais, Joel Perdiz. "Sistemas de informação para DNA microarrays." Doctoral thesis, Universidade de Aveiro, 2010. http://hdl.handle.net/10773/2232.

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Doutoramento em Engenharia Informática
O projecto de sequenciação do genoma humano veio abrir caminho para o surgimento de novas áreas transdisciplinares de investigação, como a biologia computacional, a bioinformática e a bioestatística. Um dos resultados emergentes desde advento foi a tecnologia de DNA microarrays, que permite o estudo do perfil da expressão de milhares de genes, quando sujeitos a perturbações externas. Apesar de ser uma tecnologia relativamente consolidada, continua a apresentar um conjunto vasto de desafios, nomeadamente do ponto de vista computacional e dos sistemas de informação. São exemplos a optimização dos procedimentos de tratamento de dados bem como o desenvolvimento de metodologias de interpretação semi-automática dos resultados. O principal objectivo deste trabalho consistiu em explorar novas soluções técnicas para agilizar os procedimentos de armazenamento, partilha e análise de dados de experiências de microarrays. Com esta finalidade, realizou-se uma análise de requisitos associados às principais etapas da execução de uma experiência, tendo sido identificados os principais défices, propostas estratégias de melhoramento e apresentadas novas soluções. Ao nível da gestão de dados laboratoriais, é proposto um LIMS (Laboratory Information Management System) que possibilita a gestão de todos os dados gerados e dos procedimentos realizados. Este sistema integra ainda uma solução que permite a partilha de experiências, de forma a promover a participação colaborativa de vários investigadores num mesmo projecto, mesmo usando LIMS distintos. No contexto da análise de dados, é apresentado um modelo que facilita a integração de algoritmos de processamento e de análise de experiências no sistema desenvolvido. Por fim, é proposta uma solução para facilitar a interpretação biológica de um conjunto de genes diferencialmente expressos, através de ferramentas que integram informação existente em diversas bases de dados biomédicas.
The sequencing of the human genome paved the way for the emergence of new transdisciplinary research areas, such as computational biology, bioinformatics and biostatistics. One example of such is the advent of DNA microarray technology, which allows the study of the expression of thousands of genes when subjected to an external disturbance. Despite being a well-established technology, it continues to present a wide range of challenges, particularly in terms of computing and information systems. Examples include the optimization of procedures for processing data as well as the development of methodologies for semi-automated interpretation of results. The main objective of this study was to explore new technical solutions to streamline the procedures for storing, sharing and analyzing the data from microarray experiments. To this end, it was performed an analysis of the key steps from the experiment, having been identified the major deficits, proposed strategies for improving and presented new solutions. Regarding the management of laboratory data we propose a LIMS (Laboratory Information Management System) that allows the storage of all data generated and procedures performed in the laboratory. This system also includes a solution that enables the sharing of experiments in order to promote collaborative participation of several researchers in the same project, even using different LIMS. In the context of data analysis, it is presented a model that allows the simplified integration of processing and analysis algorithms in the developed system. Finally, it is proposed a solution to facilitate the biological interpretation of a set of differentially expressed genes, using tools that integrate information from several public biomedical databases.

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5

Harness, Denise. "A Comparison of Unsupervised Methods for DNA Microarray Leukemia Data." Digital Commons @ East Tennessee State University, 2018. https://dc.etsu.edu/asrf/2018/schedule/106.

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Advancements in DNA microarray data sequencing have created the need for sophisticated machine learning algorithms and feature selection methods. Probabilistic graphical models, in particular, have been used to identify whether microarrays or genes cluster together in groups of individuals having a similar diagnosis. These clusters of genes are informative, but can be misleading when every gene is used in the calculation. First feature reduction techniques are explored, however the size and nature of the data prevents traditional techniques from working efficiently. Our method is to use the partial correlations between the features to create a precision matrix and predict which associations between genes are most important to predicting Leukemia diagnosis. This technique reduces the number of genes to a fraction of the original. In this approach, partial correlations are then extended into a spectral clustering approach. In particular, a variety of different Laplacian matrices are generated from the network of connections between features, and each implies a graphical network model of gene interconnectivity. Various edge and vertex weighted Laplacians are considered and compared against each other in a probabilistic graphical modeling approach. The resulting multivariate Gaussian distributed clusters are subsequently analyzed to determine which genes are activated in a patient with Leukemia. Finally, the results of this are compared against other feature engineering approaches to assess its accuracy on the Leukemia data set. The initial results show the partial correlation approach of feature selection predicts the diagnosis of a Leukemia patient with almost the same accuracy as using a machine learning algorithm on the full set of genes. More calculations of the precision matrix are needed to ensure the set of most important genes is correct. Additionally more machine learning algorithms will be implemented using the full and reduced data sets to further validate the current prediction accuracy of the partial correlation method.

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6

Chow, Brian 1978. "Photoelectromechanical synthesis of low-cost DNA microarrays." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/42405.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, School of Architecture and Planning, Program in Media Arts and Sciences, 2008.
Includes bibliographical references.
Recent advances in de novo gene synthesis, library construction, and genomic selection for target sequencing using DNA from custom microarrays have demonstrated that microarrays can effectively be used as the world's cheapest sources of complex oligonucleotide pools. Unfortunately, commercial custom microarrays are expensive and not easily accessible to academic researchers, and technical challenges still exist for dealing with the small amount of DNA synthesized on a chip. Genomic research would certainly benefit from the creation of cheaper custom microarrays with larger oligonucleotide concentrations per spot. This thesis presents the development of a novel DNA microarray synthesis platform based on semiconductor photoelectrochemistry (PEC) designed with these needs in mind. An amorphous silicon photoconductor is activated by an optical projection system to create "virtual electrodes" that electrochemically generate protons in a site-selective manner, thereby cleaving acid-labile dimethoxytrityl protecting groups with the spatial selectivity that is required for in-situ DNA synthesis. This platform has the potential to be particularly low-cost since it employs standard phosphoramidite reagents, visible wavelength optics, and a cheaply microfabricated and reusable substrate. By incorporating a porous thin-film glass that dramatically increases the DNA quantity produced by over an order of magnitude per chip, this platform may also simplify the handling of DNA cleaved from chip and drive down the cost per base synthesized. The hybridization detection of single-base errors was successfully demonstrated on PEC synthesized microarrays. This thesis also reports a suite of new surface chemistries and high-resolution techniques for patterning biological molecules.
by Brian Yichiun Chow.
Ph.D.

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7

Horschinek, Andreas. "DNA-Microarrays zur therapiebegleitenden Prognose bei Brustkrebs." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-27654.

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8

Xue, Mei. "Array based integrated DNA identification system for genetic chip application /." View Abstract or Full-Text, 2002. http://library.ust.hk/cgi/db/thesis.pl?ELEC%202002%20XUE.

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9

Peeters, Justine Kate. "Microarray bioinformatics and applications in oncology." [S.l.] : Rotterdam : [The Author] ; Erasmus University [Host], 2008. http://hdl.handle.net/1765/12618.

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10

Karanam, Suresh Kumar. "Automation of comparative genomic promoter analysis of DNA microarray datasets." Thesis, Available online, Georgia Institute of Technology, 2004:, 2003. http://etd.gatech.edu/theses/available/etd-04062004-164658/unrestricted/karanam%5Fsuresh%5Fk%5F200312%5Fms.pdf.

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11

Goh, Liang. "Computational methods for microarray gene expression analysis through integration and knowledge discovery a thesis submitted to Auckland University of Technology in partial fulfillment of the degree of Doctor of Philosophy, 2005." Full thesis. Abstract, 2005. http://puka2.aut.ac.nz/ait/theses/GohL.pdf.

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12

Leung, Yuk-yee. "An integrated framework for feature selection and classification in microarray data analysis." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43278632.

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13

Farcomeni, Alessio. "Multiple testing procedures under dependence, with applications." Doctoral thesis, La Sapienza, 2005. http://hdl.handle.net/11573/917424.

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14

Dickman, Rebekah. "Thermodynamic Effects of 5' and 3' Single Strand Dangling Ends on Short Duplex DNA." PDXScholar, 2010. https://pdxscholar.library.pdx.edu/open_access_etds/94.

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Differential scanning calorimetry (DSC) melting analysis was performed on 27 short double stranded DNA duplexes containing 15 to 25 base pairs and short single stranded overhangs from one to 10 bases, on both ends. Molecules have two 5' dangling ends or one 5' and one 3' dangling end. For these molecules the duplex region was incrementally reduced from 25 to 15 base pairs with increased length of the dangling ends from one to 10 bases. A third set of molecules contained 21 base pair duplexes with a four base dangling end on either the 5' or 3' end. Blunt ended duplexes from 15 to 25 base pairs were also examined and served as control duplexes. DSC melting curves were measured in solution containing 85 mM, 300 mM or 1.0 M Na+. From these measurements, thermodynamic parameters for 5' and 3' dangling ends as a function of end length were evaluated. Results showed the 5' ends were slightly stabilizing, and this stability was essentially constant with end length, while the 3' ends were generally destabilizing with increasing length of the end. This finding of lower stability for the 3' ends is consistent with results of published studies that have found 5' dangling ends to be more than or equally as stabilizing as 3' dangling ends. Our finding that 3' dangling ends are actually destabilizing for duplex DNA contrasts with published results. The 3' ends also display a stronger dependence on the [Na+]. In the lower Na+ environment the 3' ends are more destabilizing than at the higher salt environments. Analysis of the thermodynamic parameters of the dangling-ended duplexes as a function [Na+] indicated the 3' dangling end molecules behave differently compared to 5' dangling ended and blunt ended duplexes. The net counterion release per phosphate upon melting the molecules having one 5' and one 3' end was approximately 15% smaller as a function of end length compared to the duplex having two 5' ends. Further analysis of the DSC evaluated thermodynamic transition parameter, ΔHcal, and its relationship to the measured transition temperatures of the DNA molecules, provided an estimate on the excess heat capacity differences, ΔCp, between duplex and melted single strands for the dangling-ended molecules. The analysis revealed the molecules with one 5' and one 3' dangling end had very different ΔCp values compared to the blunt-ended molecule; while the molecules with two 5' ends have ΔCp that are essentially the same as the blunt-ended duplex. These observations are interpreted as differences in the interactions with Na+, solvent and the terminal base pairs of the duplex for the 5' versus 3' dangling ends.

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15

Pascault, Jean-Roland Eric. "A finite element study of the DNA hybridization kinetics on the surface of microfluidic devices." Link to electronic thesis, 2007. http://www.wpi.edu/Pubs/ETD/Available/etd-043007-170242/.

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16

Tate, Catriona Mary. "Effect of probe-target sequence mismatches on the results of microarray hybridisations : position-dependence, modelling and impact of evolutionary distance." Thesis, University of Manchester, 2010. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.529202.

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17

Loo, Lit-Hsin Kam Moshe. "Identifying differentially expressed genes in DNA microarray data /." Philadelphia, Pa. : Drexel University, 2004. http://dspace.library.drexel.edu/handle/1860/375.

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18

Guo, Ruijuan. "Sample comparisons using microarrays: - Application of False Discovery Rate and quadratic logistic regression." Digital WPI, 2008. https://digitalcommons.wpi.edu/etd-theses/28.

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In microarray analysis, people are interested in those features that have different characters in diseased samples compared to normal samples. The usual p-value method of selecting significant genes either gives too many false positives or cannot detect all the significant features. The False Discovery Rate (FDR) method controls false positives and at the same time selects significant features. We introduced Benjamini's method and Storey's method to control FDR, applied the two methods to human Meningioma data. We found that Benjamini's method is more conservative and that, after the number of the tests exceeds a threshold, increase in number of tests will lead to decrease in number of significant genes. In the second chapter, we investigate ways to search interesting gene expressions that cannot be detected by linear models as t-test or ANOVA. We propose a novel approach to use quadratic logistic regression to detect genes in Meningioma data that have non-linear relationship within phenotypes. By using quadratic logistic regression, we can find genes whose expression correlates to their phenotypes both linearly and quadratically. Whether these genes have clinical significant is a very interesting question, since these genes most likely be neglected by traditional linear approach.

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19

Tjaden, Brian C. "Computational methods for transcription anlysis using oligonucleotide microarrays /." Thesis, Connect to this title online; UW restricted, 2003. http://hdl.handle.net/1773/6907.

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20

Au, Siu Kie. "Gene expression profiling of non-small cell lung cancer using cDNA microarrays /." access full-text access abstract and table of contents, 2009. http://libweb.cityu.edu.hk/cgi-bin/ezdb/thesis.pl?phd-bch-b23749490f.pdf.

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Thesis (Ph.D.)--City University of Hong Kong, 2009.
"Submitted to Department of Biology and Chemistry in partial fulfillment of the requirements for the degree of Doctor of Philosophy." Includes bibliographical references (leaves 133-147)

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21

Wang, Tao. "Statistical design and analysis of microarray experiments." Connect to this title online, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1117201363.

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Thesis (Ph. D.)--Ohio State University, 2005.
Title from first page of PDF file. Document formatted into pages; contains ix, 146 p.; also includes graphics (some col.) Includes bibliographical references (p. 145-146). Available online via OhioLINK's ETD Center

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22

Engelmann, Julia Cathérine. "DNA microarrays: applications and novel approaches for analysis and interpretation." kostenfrei, 2008. http://www.opus-bayern.de/uni-wuerzburg/volltexte/2008/2974/.

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23

Lemuth, Karin. "Transkriptomanalyse von Escherichia coli unter Kohlenhydrat-Limitierung mittels DNA-Microarrays." [S.l. : s.n.], 2006. http://nbn-resolving.de/urn:nbn:de:bsz:93-opus-28479.

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24

Consolandi, C. "Development of DNA microarrays for human single nucleotide polymorphisms detection." Doctoral thesis, Università degli Studi di Milano, 2004. http://hdl.handle.net/2434/62035.

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One major goal of genetic research is to understand the role of genetic variation. By far the most common type of such variation in humans involves single DNA bases, and is termed single nucleotide polymorphism (SNP). In order that DNA chip technology continue to emerge as an alterative to conventional DNA diagnostic methods, questions about the conformation and activity of DNA on surfaces must be addressed. We developed three robust chemical methods for the covalent attachment of amino-modified oligonucleotides on glass surfaces based on polymeric coatings, providing robust platforms to prepare oligonucleotide arrays. We explored the feasibility of using oligonucleotide-array methods for molecular typing of a highly polymorphic genomic region by using the PCR-LDR strategy. We set up a low resolution microarray-based molecular tool for allele discrimination, which is of interest in clinical applications. Our goal was the identification of Single Nucleotide Polymorphisms in the Human LeukocyteAntigen gene. The methodology we proposed presents interesting features as genotyping tool: the reaction principle is robust, the assay easily automated, thereaction format flexible and capable to analyse different samples in parallel.

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25

Fujita, André. "Análise de dados de expressão gênica: normalização de microarrays e modelagem de redes regulatórias." Universidade de São Paulo, 2007. http://www.teses.usp.br/teses/disponiveis/95/95131/tde-14092007-173758/.

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A análise da expressão gênica através de dados gerados em experimentos de microarrays de DNA vem possibilitando uma melhor compreensão da dinâmica e dos mecanismos envolvidos nos processos celulares ao nível molecular. O aprimoramento desta análise é crucial para o avanço do conhecimento sobre as bases moleculares das neoplasias e para a identificação de marcadores moleculares para uso em diagnóstico, desenho de novos medicamentos em terapias anti-tumorais. Este trabalho tem como objetivos o desenvolvimento de modelos de análise desses dados, propondo uma nova forma de normalização de dados provenientes de microarrays e dois modelos para a construção de redes regulatórias de expressão gênica, sendo uma baseada na conectividade dinâmica entre diversos genes ao longo do ciclo celular e a outra que resolve o problema da dimensionalidade, em que o número de experimentos de microarrays é menor que o número de genes. Apresenta-se, ainda, um pacote de ferramentas com uma interface gráfica de fácil uso contendo diversas técnicas de análise de dados já conhecidas como também as abordagens propostas neste trabalho.
The analyses of DNA microarrays gene expression data are allowing a better comprehension of the dynamics and mechanisms involved in cellular processes at the molecular level. In the cancer field, the improvement of gene expression interpretation is crucial to better understand the molecular basis of the neoplasias and to identify molecular markers to be used in diagnosis and in the design of new anti-tumoral drugs. The main goals of this work were to develop a new method to normalize DNA microarray data and two models to construct gene expression regulatory networks. One method analyses the dynamic connectivity between genes through the cell cycle and the other solves the dimensionality problem in regulatory networks, meaning that the number of experiments is lower than the number of genes. We also developed a toolbox with a user-friendly interface, displaying several established statistical methods implemented to analyze gene expression data as well as the new approaches presented in this work.

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26

Li, Shuzhao. "A genomic screen for Zic1 target genes in neural development." Thesis, Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/li/LiS0806.pdf.

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27

Srivastava, Gyan Prakash Xu Dong. "Genome scale meta analysis of microarrays for biological inferences." Diss., Columbia, Mo. : University of Missouri--Columbia, 2009. http://hdl.handle.net/10355/6841.

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Title from PDF of title page (University of Missouri--Columbia, viewed on April 5, 2010). The entire thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file; a non-technical public abstract appears in the public.pdf file. Dissertation advisor: Dr. Dong Xu. Vita. Includes bibliographical references.

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28

Szeto, Lap Keung. "Clustering analysis of microarray gene expression data /." access full-text access abstract and table of contents, 2005. http://libweb.cityu.edu.hk/cgi-bin/ezdb/thesis.pl?mphil-it-b19885817a.pdf.

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Thesis (M.Phil.)--City University of Hong Kong, 2005.
"Submitted to Department of Computer Engineering and Information Technology in partial fulfillment of the requirements for the degree of Master of Philosophy" Includes bibliographical references (leaves 70-79)

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29

Thompson, Liz. "A label free DNA hybridization sensor." Thesis, Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/26968.

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30

Wong, Tsz-yeung. "Molecular characterization of IBDV-induced apoptosis in vitro using cDNA microarrays." Click to view the E-thesis via HKUTO, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36375998.

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31

Alleyne, Renikko. "Tool for the identification of differentially expressed genes using a user-defined threshold /." Link to online version, 2006. https://ritdml.rit.edu/dspace/handle/1850/2363.

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32

Gelmi, Claudio A. "A novel probabilistic framework for microarray data analysis from fundamental probability models to experimental validation /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 177 p, 2007. http://proquest.umi.com/pqdweb?did=1257806411&sid=6&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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33

Leung, Yuk-yee, and 梁玉儀. "An integrated framework for feature selection and classification in microarray data analysis." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43278632.

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34

Pendleton, Carly R. "A simulation-based approach for evaluating gene expression analyses /." Diss., CLICK HERE for online access, 2007. http://contentdm.lib.byu.edu/ETD/image/etd1753.pdf.

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35

Chen, Ilene Y. "Microarray bioinformatics and its applications to clinical research." Phd thesis, Faculty of Engineering and Information Technologies, 2009. http://hdl.handle.net/2123/9327.

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36

Lönnstedt, Ingrid. "Empirical Bayes methods for DNA microarray data /." Uppsala : Matematiska institutionen, Univ. [distributör], 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-5865.

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37

Castells, Domingo Xavier. "Towards Objective Human Brain Tumours Classiﬁcation using DNA microarrays." Doctoral thesis, Universitat Autònoma de Barcelona, 2009. http://hdl.handle.net/10803/3624.

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Els tumors de cervell humans (HBTs) són uns dels càncers més agressius i intractables. El sistema actual de diagnosi i prognosi dels HBTs es basa en l'examinació histològica d'un tall de biòpsia, el qual es considera el sistema de referència ("gold¬standard"). A més de ser invasiva, aquesta tècnica no és prou acurada per a diferenciar els graus de malignitat de determinats HBTs i la correlació amb la resposta del pacient a la teràpia sol ser variable. En aquest context, les signatures gèniques obtingudes a partir de microarrays de DNA poden millorar els resultats del "gold-standard".
En aquesta tesi, vaig recollir 333 biòpsies de varis tipus de HBTs. Com un 38% de les mostres tenien l'RNA degradat, vam avaluar si el tipus de HBTs, el contingut aparent de sang de la biòpsia i el medi de recollida de la biòpsia hi afectaven. Com no vam determinar cap relació, hipotetitzo que un temps variable d'isquèmia a temperatura normal del cos abans de l'extracció de la biòpsia podria induir la degradació de l'RNA. Això va ser avaluat en un tumor glial pre-clínic desenvolupat en ratolí. Es va detectar que 30 minuts de temps d'isquèmia afecta la integritat del RNA en tumors no necròtics, però no en els necròtics.
Una part crucial de la tesi va ser la demostració com una "prova de principis" de l'habilitat de les signatures gèniques per a predir objectivament els HBTs. Això es va mostrar mitjançant una predicció perfecta de glioblastoma multiforme (Gbm) i meningioma meningotelial (Mm) utilitzant microarrays de cDNA i microchips d'Affymetrix. Els histopatòlegs poden discriminar perfectament aquests dos tipus de tumors, però aquest treball demostra una predicció perfecta utilitzant una fórmula matemàtica objectiva.
Un cop es va demostrar això, em vaig sentir confiat per a predir diferents graus de malignitat i possibles subtipus moleculars de tumors glials. En aquest sentit, es va descriure una signatura gènica basada en l'expressió de 59 transcrits, la qual va distingir dos grups de glioblastomes. Finalment, una anàlisi inicial de les dades clíniques associades suggereix que la signatura gènica podria correlacionar amb glioblastomes primaris i secundaris.
Human brain tumours (HBTs) are among the most aggressive and intractable cancers. The current system for diagnosis and prognosis of HBTs is based on the histological examination of a biopsy slice, which is considered the 'gold standard'. Apart from being invasive, this technique is not accurate enough to differentiate malignancy grades of some HBTs and it provides a variable correlation with response to therapy of the patient. In this context, gene signatures from DNA microarray experiments can improve the results of the 'gold standard'.
In this thesis, I collected 333 biopsies from various types of HBTs. As 38% of samples displayed degraded RNA, I evaluated whether the HBT type, the apparent blood content and the collection medium of the biopsy could play a role in this. As no relationship was found, I hypothesized that the variable ischaemia time at normal body temperature prior to removal of the biopsy may induce degradation of RNA. This was tested in a preclinical glial tumour model in mice. It was detected that 30 minutes ischaemia time affects the integrity of the RNA in non-necrotic tumours, but not in the necrotic ones.
A crucial part of this thesis was the demonstration of proof-of-principle of the ability of gene signatures for objective prediction of HBTs. This was shown by perfect prediction of glioblastoma multiforme (Gbm) and meningothelial meningioma (Mm) using cDNA and Affymetrix microarrays. Histopathologists perfectly discriminates both tumour types, but this work demonstrated perfect prediction using a simple mathematical formula.
Once this was demonstrated, I felt confident to predict different malignancy grades and possible molecular subtypes of glial tumours. In this respect, a gene signature based on the expression of 59 transcripts, which distinguished two groups of glioblastomas, was described. Finally, a crude initial analysis of associated clinical data suggests that this gene signature may correlate to primary and secondary glioblastomas.

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38

Kurz, Sebastian Gerhard. "Analyse des Transkriptoms von Neisseria meningitidis Serogruppe B mit DNA-Microarrays." Doctoral thesis, [S.l.] : [s.n.], 2005. http://deposit.ddb.de/cgi-bin/dokserv?idn=975613944.

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39

Effati, Pedram. "Survey Of Genes Of Escherichia Coli Causing Bovine Mastitis With DNA Microarrays." Thesis, Uppsala universitet, Institutionen för medicinsk biokemi och mikrobiologi, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-154988.

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Background: Mastitis in dairy cattle is a common ailment worldwide. A cause of mastitis can be bacteria such as Escherichia coli. Mastitis is not a deadly ailment and sometimes the dairy cows show no symptoms but if certain virulence genes are present in the bacteria that cause the mastitis, the bacteria can be transmitted to humans and cause severe diseases. The potential presence of enterohemorrhagic Escherichia coli (EHEC) in particular would be a major concern for human health. Aim: The aim for this study was to analyze the presence of virulence genes known to be present in E.coli strains isolated from dairy cows with mastitis in Sweden. Method: A Qiagen BIO ROBOT EZ1 was used to purify DNA from 90 bacterial cultures. A panel of virulence genes were amplified and biotinylated from the purified DNA by PCR and an E.coli based DNA microarray was used to detect presumed virulence genes in E.coli. Result: There were no samples that had all the genes traditionally used to classify E.coli as EHEC or potential EHEC. 63 samples were analyzed without any problems but 27 samples were not fully analyzed. Conclusion: The DNA based microarray proved to be a reliable method to detect genes from pathogenic bacteria but it needed high concentration of purified DNA which was not always easy to obtain. There were some samples in this study that contained virulence genes.

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Gurrala, Rajesh. "DNA microarrays as a toll in the investigation of animal viral diseases." Thesis, University of Surrey, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.549464.

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McGinley, Susan. "DNA Chips Boost Dairy Research: Gene Microarrays Target Heat Stress in Cows." College of Agriculture and Life Sciences, University of Arizona (Tucson, AZ), 2001. http://hdl.handle.net/10150/622262.

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Dawany, Noor Tozeren Aydin. "Large-scale integration of microarray data : investigating the pathologies of cancer and infectious diseases /." Philadelphia, Pa. : Drexel University, 2010. http://hdl.handle.net/1860/3251.

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Kirk, Michael School of Biotechnology &amp Biomolecular Science UNSW. "Bioinformatic analyses of microarray experiments on genetic control of gene expression level." Awarded by:University of New South Wales. School of Biotechnology and Biomolecular Science, 2006. http://handle.unsw.edu.au/1959.4/25986.

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The advent of microarray technology, allowing measurement of gene expression levels for thousands of genes in parallel, has made possible experiments designed to investigate the genetic control of variation in gene expression level (described in the literature as ???genetical genomics??? or ???eQTL??? experiments). Published results from these studies, in yeast and in mice, show that genetic variation is an important factor in gene regulation, and furthermore that individual polymorphisms modify the expression level of many genes. The concern of this thesis is the bioinformatic analyses of the expression level and genotype data sets that are the raw material for these studies. In particular this thesis addresses the two issues of detection of artefactual effects, and maximizing the information that can be extracted from the data. It is shown that while a polymorphism affecting the expression of many genes may be readily detected, care must be taken to determine whether the detected effect is genuinely one of genetic control of expression level, rather than the effect of correlations in measured expression level not of genetic cause. A significance test is devised to distinguish between these cases. The detection of artefactual correlation is explored further in the reanalysis of the published data from a large yeast study. A critique is given of the permutation method used to ascribe genetic control as the cause of inter gene expression level correlation. The presence of some degree of artefactual correlation is shown, and novel methods are presented for identifying such artefacts. To extend the analyses that may be applied to eQTL data, an algorithm is presented for determining secondary eQTLs for gene expression level (as opposed to a single primary QTL), along with a significance test for the putative QTL found. The technique is demonstrated on a large public data set. In addition to the use for which they are intended, the data sets generated for eQTL studies provide opportunities for additional analyses. In this thesis a method is developed for calculating a genome wide map of meiotic recombination frequency from the genotype data for multiple segregant strains. The method is demonstrated on the published genotype data generated for a large yeast eQTL study.

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Maughan, Michele Nancy. "Molecular detection and identification of avian influenza viruses by cDNA microarray." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 141 p, 2007. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&res_dat=xri:pqdiss&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&rft_dat=xri:pqdiss:1440635.

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Guo, Ruijuan. "Sample comparisons using microarrays -- application of false discovery rate and quadratic logistic regression." Worcester, Mass. : Worcester Polytechnic Institute, 2007. http://www.wpi.edu/Pubs/ETD/Available/etd-010808-173747/.

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Ghanekar, Ruchi. "Cross chip probe matching tool a tool for linking probes from microarrays within and across species /." Birmingham, Ala. : University of Alabama at Birmingham, 2006. https://www.mhsl.uab.edu/dt/2008r/ghanekar.pdf.

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Jiang, Ying, and 蔣穎. "Studies of gene regulation using microarray data." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B29976388.

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Cheung, Kin Lok. "Investigation of (3-mercaptopropyl) trimethoxysilane (MPTS)-modified surface and DNA microarray for genotyping of traditional Chinese medicinal plants /." View Abstract or Full-Text, 2003. http://library.ust.hk/cgi/db/thesis.pl?BIOL%202003%20CHEUNGK.

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Thesis (M. Phil.)--Hong Kong University of Science and Technology, 2003.
Includes bibliographical references (leaves 103-111). Also available in electronic version. Access restricted to campus users.

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Ferguson, Jane A. "Fiber optic chemical sensors : the evolution of high-density fiber-optic DNA microarrays /." Thesis, Connect to Dissertations & Theses @ Tufts University, 2001.

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Thesis (Ph.D.)--Tufts University, 2001.
Adviser: David R. Walt. Submitted to the Dept. of Chemistry, Includes bibliographical references (leaves 197-208). Access restricted to members of the Tufts University community. Also available via the World Wide Web;

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Wong, Tsz-yeung, and 王子揚. "Molecular characterization of IBDV-induced apoptosis in vitro using cDNA microarrays." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36375998.

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