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Dissertations / Theses on the topic 'Microarray Probes'

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Published: 4 June 2021

Last updated: 1 February 2022

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1

Almeida, Pedro Rafael de Sousa Gomes de. "Automatic design of microarray probes for mutations detection." Master's thesis, Universidade de Aveiro, 2007. http://hdl.handle.net/10773/1902.

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Mestrado em Engenharia Biomédica - Instrumentação, Sinal e Imagem Médica<br>A Utilização de microarrays para detecção de mutações genómicas é uma das vastas aplicações desta tecnologia em biologia e medicina. Mutações são alterações em genes a nivel dos nucleótidos que podem ser tão pequenas como uma diferença de apenas um nucleótido entre duas sequências, as quais neste caso se dá o nome de Polimorfismo Nucleotidico Simples (SNP). É possivel detectar tais mutações recorrendo a tecnologia de microarrays, apesar de que requer um extenso e moroso procedimento (trabalho) associado ao desenho de s

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Kapur, Karen Anita. "Low-level analysis of microarray probes on exon-targeting microarrays : modeling background, gene expression and cross-hybridization /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.

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3

Fairley, Susan Lynn. "Mapping microarray probes to the rat genome using a persistent index." Thesis, University of Glasgow, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.438089.

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4

Nordberg, Eric Kinsley. "Creating Scientific Software, with Application to Phylogenetics and Oligonucleotide Probe Design." Diss., Virginia Tech, 2015. http://hdl.handle.net/10919/64366.

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The demands placed on scientific software are different from those placed on general purpose software, and as a result, creating software for science and for scientists requires a specialized approach. Much of software engineering practices have developed in situations in which a tool is desired to perform some definable task, with measurable and verifiable outcomes. The users and the developers know what the tool "should" do. Scientific software often uses unproven or experimental techniques to address unsolved problems. The software is often run on "experimental" High Performance Computing h

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5

Kamisetty, Nagendra Kumar. "Development of advanced DNA microarray system by high density amine functionalization of solid surface and functional design of DNA probes." Kyoto University, 2007. http://hdl.handle.net/2433/135562.

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Kyoto University (京都大学)<br>0048<br>新制・課程博士<br>博士(エネルギー科学)<br>甲第12717号<br>エネ博第145号<br>新制||エネ||35(附属図書館)<br>UT51-2007-C253<br>京都大学大学院エネルギー科学研究科エネルギー社会・環境科学専攻<br>(主査)教授牧野圭祐, 教授尾形幸生, 助教授小瀧努<br>学位規則第4条第1項該当

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6

Banér, Johan. "Genetic Analyses using Rolling Circle or PCR Amplified Padlock Probes." Doctoral thesis, Uppsala University, Department of Genetics and Pathology, 2003. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-3339.

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<p>Padlock probes are useful in a variety of genetic applications, some of which require that the probes are amplified in order to generate detectable signals. Two general padlock amplification methods, RCA and PCR, are discussed in this thesis.</p><p>The isothermal rolling circle amplification (RCA) mechanism is described in detail as well as how a target strand affects primer extension. A mechanism to resolve the topological constraint imposed by the target strand, to which a padlock probe has been linked, is also discussed. We also present a more powerful amplification technique, termed ser

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7

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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8

Kennedy, Richard Ellis. "Probe Level Analysis of Affymetrix Microarray Data." VCU Scholars Compass, 2008. http://hdl.handle.net/10156/1637.

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9

Shukla, Maulik. "GeneSieve: A Probe Selection Strategy for cDNA Microarrays." Thesis, Virginia Tech, 2004. http://hdl.handle.net/10919/10114.

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The DNA microarray is a powerful tool to study expression levels of thousands of genes simultaneously. Often, cDNA libraries representing expressed genes of an organism are available, along with expressed sequence tags (ESTs). ESTs are widely used as the probes for microarrays. Designing custom microarrays, rich in genes relevant to the experimental objectives, requires selection of probes based on their sequence. We have designed a probe selection method, called GeneSieve, to select EST probes for custom microarrays. To assign annotations to the ESTs, we cluster them into contigs using PHRAP.

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10

Ratushna, Vladyslava G. "Incorporation of Physico-Chemical Parameters Into Design of Microarray Experiments." Thesis, Virginia Tech, 2005. http://hdl.handle.net/10919/32989.

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Microarrays containing long oligonucleotides provide sensitive and specific detection of gene expression and are becoming a popular experimental platform. In the process of designing an oligonucleotide microarray for Brucella, we optimized the overall design of the array and created probes to distinguish among the known Brucella species. A 3-way genome comparison identified a set of genes which occur uniquely in only one or two of the sequenced Brucella genomes. Reverse transcriptase PCR assays of over one hundred unique and pairwise-differential regions identified in Brucella revealed sever

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11

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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12

Marconi, Daniela <1979&gt. "New approaches to open problems in gene expression microarray data." Doctoral thesis, Alma Mater Studiorum - Università di Bologna, 2008. http://amsdottorato.unibo.it/842/.

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In the past decade, the advent of efficient genome sequencing tools and high-throughput experimental biotechnology has lead to enormous progress in the life science. Among the most important innovations is the microarray tecnology. It allows to quantify the expression for thousands of genes simultaneously by measurin the hybridization from a tissue of interest to probes on a small glass or plastic slide. The characteristics of these data include a fair amount of random noise, a predictor dimension in the thousand, and a sample noise in the dozens. One of the most exciting areas to which

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13

Ericsson, Olle. "Biomolecular Analysis by Dual-Tag Microarrays and Single Molecule Amplification." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8475.

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14

Lee, Kyeong Eun. "Bayesian models for DNA microarray data analysis." Diss., Texas A&M University, 2005. http://hdl.handle.net/1969.1/2465.

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Selection of signi?cant genes via expression patterns is important in a microarray problem. Owing to small sample size and large number of variables (genes), the selection process can be unstable. This research proposes a hierarchical Bayesian model for gene (variable) selection. We employ latent variables in a regression setting and use a Bayesian mixture prior to perform the variable selection. Due to the binary nature of the data, the posterior distributions of the parameters are not in explicit form, and we need to use a combination of truncated sampling and Markov Chain Monte Carlo (MCMC)

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15

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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16

Valles-Miret, Mariona. "Synthesis and applications of trifluoromethyl aryldiazirine photophore." Thesis, University of Edinburgh, 2011. http://hdl.handle.net/1842/5756.

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Photoreactive groups have been used in photoaffinity labelling of chemical macromolecules via the generation of highly reactive species upon short wave light irradiation. One of the most efficient photoreactive functional groups is trifluoromethyl aryldiazirine (TFMAD). This compound was synthesised as part of the work discussed in this thesis, making use of microwave irradiation to shorten reaction times (Chapter I). An investigation of properties allowed the development of three different applications for conjugation to biomolecules. The first application consisted of the development of an a

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17

Pratt, Kyle Evan. "The Effects of Mismatches and Probe Tethering Configurations on the Stability of DNA Duplexes on Surfaces." BYU ScholarsArchive, 2013. https://scholarsarchive.byu.edu/etd/4056.

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DNA microarrays are chip-based, analysis tools which can perform hundreds of thousands of parallel assays to determine the identity of genes or gene expression levels present in a sample. They have been identified as a key technology in genomic sciences and emergent medical techniques; however, despite their abundant use in research laboratories, microarrays have not been used in the clinical setting to the fullest potential due to the difficulty of obtaining reproducible results. Microarrays work on the principle of DNA hybridization, and can only be as accurate as this process is robust. Fun

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18

Bae, Kyounghwa. "Bayesian model-based approaches with MCMC computation to some bioinformatics problems." Texas A&M University, 2005. http://hdl.handle.net/1969.1/2396.

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Bioinformatics applications can address the transfer of information at several stages of the central dogma of molecular biology, including transcription and translation. This dissertation focuses on using Bayesian models to interpret biological data in bioinformatics, using Markov chain Monte Carlo (MCMC) for the inference method. First, we use our approach to interpret data at the transcription level. We propose a two-level hierarchical Bayesian model for variable selection on cDNA Microarray data. cDNA Microarray quantifies mRNA levels of a gene simultaneously so has thousands of genes in on

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19

Wang, Yuker, Victoria Carlton, George Karlin-Neumann, et al. "High quality copy number and genotype data from FFPE samples using Molecular Inversion Probe (MIP) microarrays." BioMed Central, 2009. http://hdl.handle.net/10150/610039.

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BACKGROUND:A major challenge facing DNA copy number (CN) studies of tumors is that most banked samples with extensive clinical follow-up information are Formalin-Fixed Paraffin Embedded (FFPE). DNA from FFPE samples generally underperforms or suffers high failure rates compared to fresh frozen samples because of DNA degradation and cross-linking during FFPE fixation and processing. As FFPE protocols may vary widely between labs and samples may be stored for decades at room temperature, an ideal FFPE CN technology should work on diverse sample sets. Molecular Inversion Probe (MIP) technology ha

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20

Jaziri, Faouzi. "Conception et analyse des biopuces à ADN en environnements parallèles et distribués." Thesis, Clermont-Ferrand 2, 2014. http://www.theses.fr/2014CLF22465/document.

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Les microorganismes constituent la plus grande diversité du monde vivant. Ils jouent un rôle clef dans tous les processus biologiques grâce à leurs capacités d’adaptation et à la diversité de leurs capacités métaboliques. Le développement de nouvelles approches de génomique permet de mieux explorer les populations microbiennes. Dans ce contexte, les biopuces à ADN représentent un outil à haut débit de choix pour l'étude de plusieurs milliers d’espèces en une seule expérience. Cependant, la conception et l’analyse des biopuces à ADN, avec leurs formats de haute densité actuels ainsi que l’immen

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21

Pelve, Erik A. "Unique Solutions to Universal Problems : Studies of the Archaeal Cell." Doctoral thesis, Uppsala universitet, Molekylär evolution, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-162886.

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Archaea is one of the three domains of life and studies of archaeal biology are important for understanding of life in extreme environments, fundamental biogeochemical processes, the origin of life, the eukaryotic cell and their own, unique biology. This thesis presents four studies of the archaeal cell, using the extremophilic Sulfolobus and ocean living Nitrosopumilus as model systems. Cell division in crenarchaea is shown to be carried out by a previously unknown system named Cdv (cell division). The system shares homology with the eukaryotic ESCRT-III system which is used for membrane reor

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22

Hundewale, Nisar. "CAD Tools for DNA Micro-Array Design, Manufacture and Application." Digital Archive @ GSU, 2006. http://digitalarchive.gsu.edu/cs_diss/13.

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Motivation: As the human genome project progresses and some microbial and eukaryotic genomes are recognized, numerous biotechnological processes have attracted increasing number of biologists, bioengineers and computer scientists recently. Biotechnological processes profoundly involve production and analysis of highthroughput experimental data. Numerous sequence libraries of DNA and protein structures of a large number of micro-organisms and a variety of other databases related to biology and chemistry are available. For example, microarray technology, a novel biotechnology, promises to monito

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23

Parisot, Nicolas. "Détermination de sondes oligonucléotidiques pour l'exploration à haut débit de la diversité taxonomique et fonctionnelle d'environnements complexes." Thesis, Clermont-Ferrand 2, 2014. http://www.theses.fr/2014CLF22498/document.

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Les microorganismes, par leurs fascinantes capacités d’adaptation liées à l’extraordinaire diversité de leurs capacités métaboliques, jouent un rôle fondamental dans tous les processus biologiques. Jusqu’à récemment, la mise en culture était l’étape préliminaire obligatoire pour réaliser l’inventaire taxonomique et fonctionnel des microorganismes au sein des environnements. Cependant ces techniques ne permettent d’isoler qu’une très faible fraction des populations microbiennes et tendent donc à être remplacées par des outils moléculaires haut-débit. Dans ce contexte, l’évolution des techniques

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24

Terrat, Sébastien. "Nouveau design de sondes pour biopuces ADN fonctionnelles et caractérisation des capacités de biodégradation des communautés bactériennes de sols pollués par des hydrocarbures." Phd thesis, Université Blaise Pascal - Clermont-Ferrand II, 2010. http://tel.archives-ouvertes.fr/tel-00629656.

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Les activités humaines sont à l'origine de nombreuses pollutions par des hydrocarbures au niveau des écosystèmes, et plus particulièrement au niveau des sols. Afin de préserver la santé humaine et environnementale, il est nécessaire d'éliminer les polluants présents. Dans ce but, les techniques de bioremédiation apparaissent aujourd'hui comme de réelles alternatives aux techniques classiques, invasives et onéreuses. Cependant, l'utilisation optimale de tels procédés nécessite une meilleure connaissance des capacités métaboliques des communautés microbiennes impliquées dans la biodégradation de

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25

Gardeux, Vincent. "Conception d'heuristiques d'optimisation pour les problèmes de grande dimension : application à l'analyse de données de puces à ADN." Phd thesis, Université Paris-Est, 2011. http://tel.archives-ouvertes.fr/tel-00676449.

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Cette thèse expose la problématique récente concernant la résolution de problèmes de grande dimension. Nous présentons les méthodes permettant de les résoudre ainsi que leurs applications, notamment pour la sélection de variables dans le domaine de la fouille de données. Dans la première partie de cette thèse, nous exposons les enjeux de la résolution de problèmes de grande dimension. Nous nous intéressons principalement aux méthodes de recherche linéaire, que nous jugeons particulièrement adaptées pour la résolution de tels problèmes. Nous présentons ensuite les méthodes que nous avons dévelo

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26

Wu, Chia-Lin, and 吳佳霖. "Target-Activated Streptavidin-Biotin Control Binding Probes for Microarray." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/b474ug.

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27

Liu, Xuan-yu, and 劉軒宇. "Synthesis of Boronic Acid-Tosyl Chemical Probes and It''s Applications in Glycoprotein Microarray." Thesis, 2014. http://ndltd.ncl.edu.tw/handle/6678t2.

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碩士<br>國立中山大學<br>化學系研究所<br>102<br>Protein microarray is a high-throughput screening platform in the study of protein-protein interaction. However, the orientation and structure integrity of immobilized proteins can considerably affect the corresponding biological activity. To date this end, amino-cyclooctyne and a series of boronic acid (BA)-tosyl chemical probes have been synthesized, and used in the fabrication of glycoprotein microarray. Accordingly, strain-promoted azide-alkyne cycloaddition under homogeneous condition have been shown to improve the efficiency of BA-tosyl chemical probe mod

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28

Schneider, Stephanie G. "Reannotation and consolidation of microarray probes for the meta-analysis of gene expression across multiple cell types." Thesis, 2014. https://hdl.handle.net/2144/14151.

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Recent advances in global gene expression measurement and the development of large- scale public repositories for storage of such data have made a wealth of information available to researchers. While one gene expression study may lack sufficient replicates to make statistically significant pronouncements, the combination of studies through meta-analysis can yield results with a much greater likelihood of accuracy. In order to combine multiple sets of data, one must first address the issue of cross-comparison between global gene expression platforms, as well as resolve the issue of repeated me

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29

Cheng, Kuang-Hong, and 鄭光泓. "Surface Morphology Study of cDNA Microarray Probe Spots." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/62397073134800143095.

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碩士<br>國立清華大學<br>生醫工程與環境科學系<br>96<br>AbstractcDNA microarray contains densely packed spots with known DNA sequences. The deposited DNA sample is referred to as the probe. After the fluorescently-labeled target DNA is hybridized to its complementary probe strand, the microarray was scanned to measure the intensity of the fluorescent signals on each spot. The intensity of each spot represents the expression level of a specific gene. However, the DNA distribution within each spot will influence the analysis of the fluorescent signals. This research aims at applying the spectral images technology a

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30

Glomb, Torsten. "Sequence specific probe signals on SNP microarrays." 2010. https://ul.qucosa.de/id/qucosa%3A16542.

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Single nucleotide polymorphism (SNP) arrays are important tools widely used for genotyping and copy number estimation. This technology utilizes the specific affinity of fragmented DNA for binding to surface-attached oligonucleotide DNA probes. This thesis contemplates the variability of the probe signals of Affymetrix GeneChip SNP arrays as a function of the probe sequence to identify relevant sequence motifs which potentially cause systematic biases of genotyping and copy number estimates.

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31

Warren, Liling. "Probe design and data analysis for gene expression microarrays." 2002. http://www.lib.ncsu.edu/theses/available/etd-01062003-203515/unrestricted/etd.pdf.

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32

Kim, Joohoon 1976. "Development of microdevices for applications to bioanalysis." Thesis, 2007. http://hdl.handle.net/2152/3286.

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The development of microdevices for applications related to bioanalysis is described. There are two types of microdevices involved in this study: DNA (or RNA) microarrays and bead-based microfluidic devices. First, a new method to fabricate DNA microarrays is developed: replication of DNA microarrays. It was shown that oligonucleotides immobilized on a glass master can hybridize with their biotin-modified complements, and then the complements can be transferred to a streptavidinfunctionalized replica surface. This results in replication of the master DNA array. Several innovative aspects of re

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33

JONG, HSU WEI, and 許維中. "Evaluation and Analysis of Cross Hybridization Effects of Probes on cDNA Microarrays." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/51467682302329602672.

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碩士<br>長庚大學<br>資訊管理研究所<br>93<br>Microarray have been extensively used to studying genome-wide expression analysis. A potential problem with microarray research is that probes of an array might have segments of similar sequence that resulted form gene families, homologous genes and highly similar sequences may cause cross hybridization. Cross hybridization effects can be a source of error and reducing the reliability of DNA microarray results. The objective of this research is to discuss observations of cross hybridiztaion on an existing set of cDNA microarrays that are currently used by Chang G

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Zhang, Mingquan. "Label-free Detection of Oligonucleotide Microarrays by the Scanning Kelvin Nanoprobe." Thesis, 2008. http://hdl.handle.net/1807/17252.

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The Kelvin measurement is a sensitive and label-free method based on work function measurements. Work function, the minimum energy required to extract an electron from a metallic material, can be shifted by ionic charges and dipoles present on the surface. The scanning Kelvin nanoprobe (SKN), a probe-based microscopic imaging device, was used in the detection of work function changes induced by surface-immobilized oligonucleotide / DNA microarrays. The scanning Kelvin nanoprobe was able to study DNA microarrays smaller than 100 µm in size, produced with solution concentrations lower than 10 µ

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35

Jiang, Kai-Ren, and 姜凱仁. "Efficiency Enhancement of DNA Hybridization by Pre-Hybridization on Microarrayed Gene Probes." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/36560509115769990082.

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碩士<br>中原大學<br>化學工程研究所<br>97<br>The effect of pre-hybridizing genetic DNA target on the hybridization efficiency of the second target samples is studied on two probe configurations and various probe concentrations. Three sets of microarrayed DNA probes and their complementary samples are utilized. Each set contains a pair of DNA probes and a pair of their complementary samples labeled with two distinct fluorescent dyes. The sequence of each probe is especially designed so that two targets are simultaneously complementary to two adjacent sections of the probe. The molecular steric effect on th

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Cheng, Hsiao-Ping, and 鄭筱萍. "Rapid Fabrication Technology of Microarray-based DNA Computers for Solving SAT Problems." Thesis, 2005. http://ndltd.ncl.edu.tw/handle/72129618445384681228.

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碩士<br>國立中山大學<br>機械與機電工程學系研究所<br>93<br>This paper presents a novel MEMS based DNA computer for solving SAT problems. No time-consuming sample preparation procedures and delicate sample applying equipment were required for the computing process. Moreover, experimental results show the bound DNA sequences can sustain the chemical solutions during computing processes such that the proposed method shall be useful in dealing with large scale problems. An algorithm based on a modified sticker model accompanied with a state-of-the-art MEMS-based microarray experiment is demonstrated to solve SAT probl

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Yang, Deng-Kai, and 楊登凱. "Enhancement of Target-DNA Hybridization Efficiency by Pre-hybridization on Sequence Orientated Microarrayed Probes." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/17781946118706984023.

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碩士<br>中原大學<br>化學工程研究所<br>96<br>The enhancement of hybridization efficiency of deoxyribose nucleic acid (DNA) targets by oigonucleotide pre-hybridization is studied on two sequence-inversed microarrayed probes. The sequences of both pre-hybridizing oligo and target DNA are designed to be fully complementary to their shared DNA probe in a coaxial stacking configuration; i.e. they hybridize immediately next to each other along the continuous complement probe strand. The pre-hybridizing oligo and target DNA are differentiated by labeling with two distinct fluorescent dyes, and the cooperative effe

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38

Huang, Min-Tzu, and 黃敏慈. "Comparison of Bayesian Binary Regression (BBR) and Prediction Analysis of Microarray (PAM) in Classification Problems." Thesis, 2010. http://ndltd.ncl.edu.tw/handle/88838164886719151273.

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碩士<br>國立清華大學<br>統計學研究所<br>98<br>Using microarray gene expression data as a tool for disease classification has been recognized as a useful method. There have been many methods proposed for analyzing these data. Among which PAM (Prediction Analysis of Microarray) is a popular method in recent years. Similar problem arose in the area of text classification and BBR (Bayesian Binary Regression) was proposed recently. In the first part of this study, we used BBR to analyze gene expression datasets and compared the performance with that of PAM. The performance is based on the error rates of both tra

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39

Lin, Wan-Ting, and 林婉婷. "A study of automatic selection of probe sets avoiding cross-hybridization for DNA microarrays based on suffix tree algorithms." Thesis, 2007. http://ndltd.ncl.edu.tw/handle/25002944411148926237.

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碩士<br>中華大學<br>資訊工程學系碩士班<br>95<br>DNA microarrays are very useful for analyzing gene expression of entire bacterial transcriptomes. Thousands of hybridizations can be run at the same time on a microarray. It offers a systemic view of gene expression of cells in response to certain stimuli. The purpose of this paper is to design the software for automatic genome-scale probe selection for DNA microarrays. There are 5 constraints are considered for selection of probes, such as GC content, melting temperature, probe length, self-complementarity, and cross-hybridization. The purpose of software is t

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40

Αργυρόπουλος, Χρήστος. "Στατιστική ανακάλυψη και πειραματική επιβεβαίωση μεταγραφικών παραγόντων που ελέγχουν την ενεργοποίηση των λεμφοκυττάρων σε άνοσες καταστάσεις". 2002. http://nemertes.lis.upatras.gr/jspui/handle/10889/383.

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Σκοπός της παρούσης διατριβής είναι να προτείνει ένα τυπικό πλαίσιο για μια μεθοδολογία ανάλυσης που να ενσωματώνει ποσοτικά, και λειτουργικά δεδομένα και στοχεύει στο σχεδιασμό πειραμάτων για την επιβέβαιωση μεταγραφικών παραγόντων που δεσμεύονται σε ένα λειτουργικά ενεργό μοτίβο στον υποκινητή γονιδίων. Το πλαίσιο αυτό που βασίζεται στη Bayesian πιθανοκρατική θεωρία όπως αυτή θεμελιώνεται στη θεωρία λήψης αποφάσεων, εφαρμόζεται σε ένα πρόβλημα από το ερευνητικό πεδίο της ανοσοβιολογίας. Συγκεκριμένα μελετούμε την ανίχνευση μεταγραφικών παραγόντων που ενέχονται στην αρνητική ρύθμιση της γονιδ

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