Relevant bibliographies by topics / Microarray Probes

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  2. Dissertations / Theses
  3. Books
  4. Book chapters
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Academic literature on the topic 'Microarray Probes'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Microarray Probes"

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Zhao, Jianmei, Xuecang Li, Jincheng Guo, et al. "ReCirc: prediction of circRNA expression and function through probe reannotation of non-circRNA microarrays." Molecular Omics 15, no. 2 (2019): 150–63. http://dx.doi.org/10.1039/c8mo00252e.

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Mecham, Brigham H., Daniel Z. Wetmore, Zoltan Szallasi, Yoel Sadovsky, Isaac Kohane, and Thomas J. Mariani. "Increased measurement accuracy for sequence-verified microarray probes." Physiological Genomics 18, no. 3 (2004): 308–15. http://dx.doi.org/10.1152/physiolgenomics.00066.2004.

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Microarrays have been extensively used to investigate genome-wide expression patterns. Although this technology has been tremendously successful, it has suffered from suboptimal individual measurement precision. Significant improvements in this respect have been recently made. In an effort to further explore the underlying variability, we have attempted to globally assess the accuracy of individual probe sequences used to query gene expression. For mammalian Affymetrix microarrays, we identify an unexpectedly large number of probes (greater than 19% of the probes on each platform) that do not correspond to their appropriate mRNA reference sequence (RefSeq). Compared with data derived from inaccurate probes, we find that data derived from sequence-verified probes show 1) increased precision in technical replicates, 2) increased accuracy translating data from one generation microarray to another, 3) increased accuracy translating data from oligonucleotide to cDNA microarrays, and 4) improved capture of biological information in human clinical specimens. The logical conclusion of this work is that probes containing the most reliable sequence information provide the most accurate results. Our data reveal that the identification and removal of inaccurate probes can significantly improve this technology.
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Ranjbar, Reza, Payam Behzadi, and Caterina Mammina. "Respiratory Tularemia: Francisella Tularensis and Microarray Probe Designing." Open Microbiology Journal 10, no. 1 (2016): 176–82. http://dx.doi.org/10.2174/1874285801610010176.

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Background:Francisella tularensis(F. tularensis) is the etiological microorganism for tularemia. There are different forms of tularemia such as respiratory tularemia. Respiratory tularemia is the most severe form of tularemia with a high rate of mortality; if not treated. Therefore, traditional microbiological tools and Polymerase Chain Reaction (PCR) are not useful for a rapid, reliable, accurate, sensitive and specific diagnosis. But, DNA microarray technology does. DNA microarray technology needs to appropriate microarray probe designing.Objective:The main goal of this original article was to design suitable long oligo microarray probes for detection and identification ofF. tularensis.Method:For performing this research, the complete genomes ofF. tularensissubsp.tularensisFSC198,F. tularensissubsp.holarcticaLVS,F. tularensissubsp.mediasiatica,F. tularensissubsp.novicida(F. novicidaU112), andF. philomiragiasubsp.philomiragiaATCC 25017 were studiedviaNCBI BLAST tool, GView and PanSeq Servers and finally the microarray probes were produced and processedviaAlleleID 7.7 software and Oligoanalyzer tool, respectively.Results:In thisin silicoinvestigation, a number of long oligo microarray probes were designed for detecting and identifyingF. tularensis. Among these probes, 15 probes were recognized as the best candidates for microarray chip designing.Conclusion:Calibrated microarray probes reduce the biasis of DNA microarray technology as an advanced, rapid, accurate and cost-effective molecular diagnostic tool with high specificity and sensitivity. Professional microarray probe designing provides us with much more facility and flexibility regarding preparation of a microarray diagnostic chip.
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Russell, R. "Designing microarray oligonucleotide probes." Briefings in Bioinformatics 4, no. 4 (2003): 361–67. http://dx.doi.org/10.1093/bib/4.4.361.

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Paredes, Carlos J., Ryan S. Senger, Iwona S. Spath, Jacob R. Borden, Ryan Sillers, and Eleftherios T. Papoutsakis. "A General Framework for Designing and Validating Oligomer-Based DNA Microarrays and Its Application to Clostridium acetobutylicum." Applied and Environmental Microbiology 73, no. 14 (2007): 4631–38. http://dx.doi.org/10.1128/aem.00144-07.

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ABSTRACT While DNA microarray analysis is widely accepted as an essential tool for modern biology, its use still eludes many researchers for several reasons, especially when microarrays are not commercially available. In that case, the design, construction, and use of microarrays for a sequenced organism constitute substantial, time-consuming, and expensive tasks. Recently, it has become possible to construct custom microarrays using industrial manufacturing processes, which offer several advantages, including speed of manufacturing, quality control, no up-front setup costs, and need-based microarray ordering. Here, we describe a strategy for designing and validating DNA microarrays manufactured using a commercial process. The 22K microarrays for the solvent producer Clostridium acetobutylicum ATCC 824 are based on in situ-synthesized 60-mers employing the Agilent technology. The strategy involves designing a large library of possible oligomer probes for each target (i.e., gene or DNA sequence) and experimentally testing and selecting the best probes for each target. The degenerate C. acetobutylicum strain M5 lacking the pSOL1 megaplasmid (with 178 annotated open reading frames [genes]) was used to estimate the level of probe cross-hybridization in the new microarrays and to establish the minimum intensity for a gene to be considered expressed. Results obtained using this microarray design were consistent with previously reported results from spotted cDNA-based microarrays. The proposed strategy is applicable to any sequenced organism.
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Chandler, Darrell P., Gregory J. Newton, Jonathan A. Small, and Don S. Daly. "Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays." Applied and Environmental Microbiology 69, no. 5 (2003): 2950–58. http://dx.doi.org/10.1128/aem.69.5.2950-2958.2003.

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ABSTRACT A two-probe proximal chaperone detection system consisting of a species-specific capture probe for the microarray and a labeled, proximal chaperone probe for detection was recently described for direct detection of intact rRNAs from environmental samples on oligonucleotide arrays. In this study, we investigated the physical spacing and nucleotide mismatch tolerance between capture and proximal chaperone detector probes that are required to achieve species-specific 16S rRNA detection for the dissimilatory metal and sulfate reducer 16S rRNAs. Microarray specificity was deduced by analyzing signal intensities across replicate microarrays with a statistical analysis-of-variance model that accommodates well-to-well and slide-to-slide variations in microarray signal intensity. Chaperone detector probes located in immediate proximity to the capture probe resulted in detectable, nonspecific binding of nontarget rRNA, presumably due to base-stacking effects. Species-specific rRNA detection was achieved by using a 22-nt capture probe and a 15-nt detector probe separated by 10 to 14 nt along the primary sequence. Chaperone detector probes with up to three mismatched nucleotides still resulted in species-specific capture of 16S rRNAs. There was no obvious relationship between position or number of mismatches and within- or between-genus hybridization specificity. From these results, we conclude that relieving secondary structure is of principal concern for the successful capture and detection of 16S rRNAs on planar surfaces but that the sequence of the capture probe is more important than relieving secondary structure for achieving specific hybridization.
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Liu, Hongfang. "Microarray probes and probe sets." Frontiers in Bioscience E2, no. 1 (2010): 325–38. http://dx.doi.org/10.2741/e93.

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KARYAGYNA, ANNA S., MICHAIL O. VASSILIEV, ANNA S. ERSHOVA, RAMIL N. NURTDINOV, and ILYA S. LOSSEV. "PROBE-LEVEL UNIVERSAL SEARCH (PLUS) ALGORITHM FOR GENDER DIFFERENTIATION IN AFFYMETRIX DATASETS." Journal of Bioinformatics and Computational Biology 08, no. 03 (2010): 553–77. http://dx.doi.org/10.1142/s0219720010004823.

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Affymetrix microarrays measure gene expression based on the intensity of hybridization of a panel of oligonucleotide probes (probe set) with mRNA. The signals from all probes within a probe set are converted into a single measure that represents the expression value of a gene. This step diminishes the number of independently measured parameters and eliminates from consideration individual "good-working" probes. We propose a new feature selection algorithm (Probe Level Universal Search or PLUS algorithm) for probe-level analysis of gene expression datasets. The algorithm evaluates the intensities of perfect-match Affymetrix probes individually and selects probes that allow one to distinguish two given classes of samples. The algorithm was used to differentiate the samples according to their gender ("gender differentiation"). The universal gender differentiating set of 3' Gene Affymetrix microarray probes was selected; the set consists of 38 probes from XIST gene of X-chromosome and 17 probes from five Y-chromosome genes: RPS4Y1, EIF1A, DDX3Y, JARID1D and USP9Y. The selection procedure based on the probes selected by PLUS algorithm differentiates the sex chromosome karyotype of the sample, reveals samples with incorrect gender labels and samples from patients with hereditary syndromes or cancer-associated chromosome abnormalities.
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Metfies, Katja, and Linda K. Medlin. "Feasibility of Transferring Fluorescent In Situ Hybridization Probes to an 18S rRNA Gene Phylochip and Mapping of Signal Intensities." Applied and Environmental Microbiology 74, no. 9 (2008): 2814–21. http://dx.doi.org/10.1128/aem.02122-07.

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ABSTRACT DNA microarray technology offers the possibility to analyze microbial communities without cultivation, thus benefiting biodiversity studies. We developed a DNA phylochip to assess phytoplankton diversity and transferred 18S rRNA probes from dot blot or fluorescent in situ hybridization (FISH) analyses to a microarray format. Similar studies with 16S rRNA probes have been done determined that in order to achieve a signal on the microarray, the 16S rRNA molecule had to be fragmented, or PCR amplicons had to be <150 bp in length to minimize the formation of a secondary structure in the molecule so that the probe could bind to the target site. We found different results with the 18S rRNA molecule. Four out of 12 FISH probes exhibited false-negative signals on the microarray; eight exhibited strong but variable signals using full-length 18S RNA molecules. A systematic investigation of the probe's accessibility to the 18S rRNA gene was made using Prymenisum parvum as the target. Fourteen additional probes identical to this target covered the regions not tested with existing FISH probes. Probes with a binding site in the first 900 bp of the gene generated positive signals. Six out of nine probes binding in the last 900 bp of the gene produced no signal. Our results suggest that although secondary structure affected probe binding, the effect is not the same for the 18S rRNA gene and the 16S rRNA gene. For the 16S rRNA gene, the secondary structure is stronger in the first half of the molecule, whereas in the 18S rRNA gene, the last half of the molecule is critical. Probe-binding sites within 18S rRNA gene molecules are important for the probe design for DNA phylochips because signal intensity appears to be correlated with the secondary structure at the binding site in this molecule. If probes are designed from the first half of the 18S rRNA molecule, then full-length 18S rRNA molecules can be used in the hybridization on the chip, avoiding the fragmentation and the necessity for the short PCR amplicons that are associated with using the 16S rRNA molecule. Thus, the 18S rRNA molecule is a more attractive molecule for use in environmental studies where some level of quantification is desired. Target size was a minor problem, whereas for 16S rRNA molecules target size rather than probe site was important.
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Ranjbar, Reza, Payam Behzadi, Ali Najafi, and Raheleh Roudi. "DNA Microarray for Rapid Detection and Identification of Food and Water Borne Bacteria: From Dry to Wet Lab." Open Microbiology Journal 11, no. 1 (2017): 330–38. http://dx.doi.org/10.2174/1874285801711010330.

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Background:A rapid, accurate, flexible and reliable diagnostic method may significantly decrease the costs of diagnosis and treatment. Designing an appropriate microarray chip reduces noises and probable biases in the final result.Objective:The aim of this study was to design and construct a DNA Microarray Chip for a rapid detection and identification of 10 important bacterial agents.Method:In the present survey, 10 unique genomic regions relating to 10 pathogenic bacterial agents includingEscherichia coli (E.coli), Shigella boydii, Sh.dysenteriae, Sh.flexneri, Sh.sonnei, Salmonella typhi, S.typhimurium, Brucella sp., Legionella pneumophila,andVibrio cholerawere selected for designing specific long oligo microarray probes. For this reason, the in-silico operations including utilization of the NCBI RefSeq database, Servers of PanSeq and Gview, AlleleID 7.7 and Oligo Analyzer 3.1 was done. On the other hand, thein-vitropart of the study comprised stages of robotic microarray chip probe spotting, bacterial DNAs extraction and DNA labeling, hybridization and microarray chip scanning. In wet lab section, different tools and apparatus such as Nexterion® Slide E, Qarrayminispotter, NimbleGen kit, TrayMixTMS4, and Innoscan 710 were used.Results:A DNA microarray chip including 10 long oligo microarray probes was designed and constructed for detection and identification of 10 pathogenic bacteria.Conclusion:The DNA microarray chip was capable to identify all 10 bacterial agents tested simultaneously. The presence of a professional bioinformatician as a probe designer is needed to design appropriate multifunctional microarray probes to increase the accuracy of the outcomes.
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Dissertations / Theses on the topic "Microarray Probes"

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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 sondas, devido a determinadas propriedades comuns que todas as sondas têm de respeitar e ainda o facto de terem de ser únicas. Depois de avaliado diverso software de desenho de sondas, foi detectada uma evidente falta de ferramentas bioinformáticas para desenho automático de sondas para detecção de mutações. Analisados os procedimentos utilizados no desenho manual de sondas, desenvolveu-se um soflware de forma a automatizar o processo, reduzindo o tempo dispendido e aumentando a especificidade das sondas finais, ABSTRACT: Microarrays for genome rnutations analysis is one of the wide variety applications of this technology in molecular biology and rnedicine. Mutations are changes in genes nucleotides, and can be as srnall as a single base difference between two sequences, known, in this case, as Single Nucleotide Polymorphisrn (SNP). With microarrays technology it is possible to detect such mutations. However, it is a large time consuming work associated with the design of probesfor such propose, dueto the several properties that ali probes rnust have in common and, at sarne time, the uniqueness of each one. After evaluated several probes design software, it was evident the rnissing of bioinforrnatic tools for autornatic probes design for mutation detection. Analyzing the usual procedure of manual probes design, we developed software in order to automate the process, reducing the overall workflow time and increasing the accuracy of final probes.
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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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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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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 hardware, adding another layer of complexity. It may not be possible to say what the software should do, or what the results should be, as these may be connected to very scientific questions for which the software is being developed. Software development in this realm requires a deep understanding of the relevent scientific domain area. The present work describes applications resulting from a scientific software development process that builds upon detailed understanding of the scientific domain area. YODA is an application primarily for selecting microarray probe sequences for measuring gene expression. At the time of its development, none of the existing programs for this task satisfied the best-known requirements for microarray probe selection. The question of what makes a good microarray probe was a research area at the time, and YODA was developed to incorporate the latest understanding of these requirements, drawn from the research literature, into a tool that can be used by a research biologist. An appendix examines the response and use in the years since YODA was released. PEPR is a software system for inferring highly resolved whole-genome phylogenies for hundreds of genomes. It encodes a process developed through years of research and collaboration to produce some of the highest quality phylogenies available for large sets of bacterial genomes, with no manual intervention required. This process is described in detail, and results are compared with high quality results from the literature to show that the process is at least as successful as more labor-intensive manual efforts. An appendix presents additional results, including high quality phylogenies for many bacterial Orders.<br>Ph. D.
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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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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 serial circle amplification, which provides a highly precise tool for nucleic acid studies. Rolling circle products are digested to unit lengths, and each monomer converted to new circular oligonucleotides that can serve as templates in consecutive rounds of RCA. The final products are single-stranded DNA molecules, readily available for hybridization-based detection, for instance using molecular beacons or array hybridization.</p><p>Padlock probes have the potential to be combined in large numbers for parallel gene analysis. A significant improvement of the level of multiplexed genotyping is presented using padlock probes and a molecular inversion strategy. Padlock probes containing common primer sequences along with locus-specific tag sequences were combined in multiplexed ligation reactions. After exonucleolytic selection for circular molecules, the probes were cleaved at uracil residues situated between the primer sequences, which facilitated release from the genomic DNA. A single PCR primer pair amplified all molecularly inverted probes, and the products were finally sorted on microarrays for simultaneous readout. Up to 1,500 genotypes could be detected in parallel, with sufficient signal strength for further scale-up. Finally, an application of the same parallel genotyping strategy is described where a set of padlock probes was used to study tumor induced immune responses. The distribution of TCR Vβ transcripts in tumor infiltrating T-cells and in normal control tissues were investigated in a microarray format.</p>
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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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Kennedy, Richard Ellis. "Probe Level Analysis of Affymetrix Microarray Data." VCU Scholars Compass, 2008. http://hdl.handle.net/10156/1637.

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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. The larger contig sequences are then used for similarity search against known proteins in model organism such as Arabidopsis thaliana. We have designed three different methods to assign annotations to the contigs: bidirectional hits (BH), bidirectional best hits (BBH), and unidirectional best hits (UBH). We apply these methods to pine and potato EST sets. Results show that the UBH method assigns unambiguous annotations to a large fraction of contigs in an organism. Hence, we use UBH to assign annotations to ESTs in GeneSieve. To select a single EST from a contig, GeneSieve assigns a quality score to each EST based on its protein homology (PH), cross hybridization (CH), and relative length (RL). We use this quality score to rank ESTs according to seven different measures: length, 3' proximity, 5' proximity, protein homology, cross hybridization, relative length, and overall quality score. Results for pine and potato EST sets indicate that EST probes selected by quality score are relatively long and give better values for protein homology and cross hybridization. Results of the GeneSieve protocol are stored in a database and linked with sequence databases and known functional category schemes such as MIPS and GO. The database is made available via a web interface. A biologist is able to select large number of EST probes based on annotations or functional categories in a quick and easy way.<br>Master of Science
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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 several groups of genes that are transcribed in vivo with potential significance for virulence. The structural and thermodynamic properties of a set of 70mer oligonucleotide probes for a combined B. abortus, B. melitensis and B. suis microarray were modeled to help perform quantitative interpretation of the microarray data. Prediction and thermodynamic analysis of secondary structure formation in a genome-wide set of transcripts from Brucella suis 1330 demonstrated that properties of the target molecule have the potential to strongly influence the rate and extent of hybridization between transcript and an oligonucleotide probe in a microarray experiment. Despite relatively high hybridization temperatures used in the modeling process, parts of the target molecules are predicted to be inaccessible to intermolecular hybridization due to the formation of stable intramolecular secondary structure. Features in the Brucella genomes with potential diagnostic use were identified, and the extent to which target secondary structure, a molecular property which is not considered in the array design process, may influence the quality of results was characterized.<br>Master of Science
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Books on the topic "Microarray Probes"

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Microarray Biochip Technology. Eaton Publishing Company/Biotechniques Books, 2000.

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Zrazhevskiy, P., and X. Gao. Bioconjugated quantum dots for tumor molecular imaging and profiling. Edited by A. V. Narlikar and Y. Y. Fu. Oxford University Press, 2017. http://dx.doi.org/10.1093/oxfordhb/9780199533060.013.17.

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This article discusses the use of bioconjugated quantum dots (QDs) for tumor molecular imaging and profiling. The need for personalized diagnostics and therapy is becoming apparent in all areas of medicine, and especially urgent and sought after in treating cancer. Mechanisms of cancerogenesis and cancer response to therapy remain poorly understood, thus precluding accurate cancer diagnosis, prognosis, and effective treatment. Accurate molecular profiling of individual tumors is one key to effective treatment. This article first considers the photophysical properties of QDs before reviewing the most common methods for engineering QD-based probes for biomedical applications, including water solubilization and bioconjugation approaches. It also describes a number of techniques for molecular imagingand profiling of tumors, ranging from QD-based multicolor flow cytometry and applications of QDs in high-resolution correlated fluorescence/electron microscopy, QD bioprobes for molecular profiling of tumor-tissue sections and microarrays, and QD-oligonucleotide bioconjugates for in-situ hybridization.
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Eljaafari, Assia, and Pierre Miossec. Cellular side of acquired immunity (T cells). Oxford University Press, 2013. http://dx.doi.org/10.1093/med/9780199642489.003.0049.

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The adaptive T-cell response represents the most sophisticated component of the immune response. Foreign invaders are recognized first by cells of the innate immune system. This leads to a rapid and non-specific inflammatory response, followed by induction of the adaptive and specific immune response. Different adaptive responses can be promoted, depending on the predominant effector cells that are involved, which themselves depend on the microbial/antigen stimuli. As examples, Th1 cells contribute to cell-mediated immunity against intracellular pathogens, Th2 cells protect against parasites, and Th17 cells act against extracellular bacteria and fungi that are not cleared by Th1 and Th2 cells. Among the new subsets, Th22 cells protect against disruption of epithelial layers secondary to invading pathogens. Finally these effector subsets are regulated by regulatory T cells. These T helper subsets counteract each other to maintain the homeostasis of the immune system, but this balance can be easily disrupted, leading to chronic inflammation or autoimmune diseases. The challenge is to detect early changes in this balance, prior to its clinical expression. New molecular tools such as microarrays could be used to determine the predominant profile of the immune effector cells involved in a disease process. Such understanding should provide better therapeutic tools to counteract deregulated effector cells.
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D, Zanders Edward, ed. Chemical genomics: Reviews and protocols. Humana Press, 2005.

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(Editor), John Sterling, Ellyn Kerr (Editor), and Shannon Simons (Editor), eds. Methods and Technologies in Drug Discovery. Mary Ann Liebert, Inc., 2005.

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Chemical genomics: Reviews and protocols. Humana Press, 2004.

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Zanders, Edward D. Chemical Genomics: Reviews and Protocols (Methods in Molecular Biology). Humana Press, 2005.

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Book chapters on the topic "Microarray Probes"

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Foszner, Pawel, Aleksandra Gruca, Andrzej Polanski, Michal Marczyk, Roman Jaksik, and Joanna Polanska. "Efficient Algorithm for Microarray Probes Re-annotation." In Computational Collective Intelligence. Technologies and Applications. Springer Berlin Heidelberg, 2011. http://dx.doi.org/10.1007/978-3-642-23938-0_29.

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Foszner, Pawel, Aleksandra Gruca, Andrzej Polanski, Michal Marczyk, Roman Jaksik, and Joanna Polanska. "An Efficient Algorithm for Microarray Probes Re-annotation." In Transactions on Computational Intelligence XIII. Springer Berlin Heidelberg, 2014. http://dx.doi.org/10.1007/978-3-642-54455-2_9.

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Klebes, Ansgar, and Thomas B. Kornberg. "Linear RNA Amplification for the Production of Microarray Hybridization Probes." In Methods in Molecular Biology. Humana Press, 2008. http://dx.doi.org/10.1007/978-1-59745-583-1_19.

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Jobs, Magnus, Ronnie Eriksson, and Jonas Blomberg. "Multiplex and Quantifiable Detection of Infectious Fungi Using Padlock Probes, General qPCR, and Suspension Microarray Readout." In Laboratory Protocols in Fungal Biology. Springer New York, 2012. http://dx.doi.org/10.1007/978-1-4614-2356-0_33.

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Shi, Haibin, Mahesh Uttamchandani, and Shao Q. Yao. "A Method for Small Molecule Microarray-Based Screening for the Rapid Discovery of Affinity-Based Probes." In Methods in Molecular Biology. Humana Press, 2010. http://dx.doi.org/10.1007/978-1-60761-845-4_5.

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Matson, Robert S., and Jang B. Rampal. "Hybridization Analysis Using Oligonucleotide Probe Arrays." In Microarrays. Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-303-5_14.

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Ji, Hanlee, and Katrina Welch. "Molecular Inversion Probe Assay for Allelic Quantitation." In Microarray Analysis of the Physical Genome. Humana Press, 2009. http://dx.doi.org/10.1007/978-1-60327-192-9_6.

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Parisot, Nicolas, Eric Peyretaillade, Eric Dugat-Bony, Jérémie Denonfoux, Antoine Mahul, and Pierre Peyret. "Probe Design Strategies for Oligonucleotide Microarrays." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3136-1_6.

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Sebastiani, Paola, Jacqui Milton, and Ling Wang. "Designing Microarray Experiments." In Problem Solving Handbook in Computational Biology and Bioinformatics. Springer US, 2010. http://dx.doi.org/10.1007/978-0-387-09760-2_13.

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Desmet, C., and C. A. Marquette. "Surface Functionalization for Immobilization of Probes on Microarrays." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3136-1_2.

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Conference papers on the topic "Microarray Probes"

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Martins, Diogo, Xi Wei, Rastislav Levicky, and Yong-Ak Song. "Accelerating the Mass Transport of DNA Biomolecules Onto DNA Microarray for Enhanced Detection by Electrokinetic Concentration in a Microfluidic Chip." In ASME 2016 5th International Conference on Micro/Nanoscale Heat and Mass Transfer. American Society of Mechanical Engineers, 2016. http://dx.doi.org/10.1115/mnhmt2016-6562.

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Morpholinos (MOs) are synthetic nucleic acids analogues with a non-charged backbone of morpholine rings. To enhance the MO-DNA hybridization assay speed, we propose the integration of a MO microarray with an ion concentration polarization (ICP) based microfluidic concentrator. The ICP concentrator collects target biomolecules from a ∼μL fluidic DNA sample and concentrates them electrokinetically into a ∼nL plug located in the vicinity of the MO probes. ICP preconcentration not only reduces the analyte diffusion length but also increases the binding reaction rate, and as a result, ICP-enhanced MO microarrays allow much faster hybridization than standard diffusion-limited MO microarrays.
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Almeida, Pedro, Laura Carreto, and José Luís Oliveira. "Design of Microarray Probes for Detection of Mutations." In 2008 International Conference on Biocomputation, Bioinformatics, and Biomedical Technologies (BIOTECHNO). IEEE, 2008. http://dx.doi.org/10.1109/biotechno.2008.39.

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Langdon, W. B. "Correlation of microarray probes give evidence for mycoplasma contamination in human studies." In Proceeding of the fifteenth annual conference companion. ACM Press, 2013. http://dx.doi.org/10.1145/2464576.2482725.

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Ma, Jie, Sheng Ning, and Pengfeng Xiao. "Multiple SNPs genotyping by ligation of universal probes on 3D DNA microarray." In 2010 3rd International Conference on Biomedical Engineering and Informatics (BMEI). IEEE, 2010. http://dx.doi.org/10.1109/bmei.2010.5639397.

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Dilek, E., Guang Lan Zhang, Jae Young Lee, Tanya Zlateva, Lou Chitkushev, and Vladimir Brusic. "Probe design optimization of HLA microarray: Data cleaning of probe signals from cDNA tiling microarray: Outlier detection, noise reduction, and identification of uninformative probes in HLA typing application." In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW). IEEE, 2011. http://dx.doi.org/10.1109/bibmw.2011.6112452.

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Gasieniec, Leszek, Cindy Y. Li, Paul Sant, and Prudence W. H. Wong. "Efficient Probe Selection in Microarray Design." In 2006 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology. IEEE, 2006. http://dx.doi.org/10.1109/cibcb.2006.331018.

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Heller, Michael J., Dieter Dehlinger, Sadik Esener, and Benjamin Sullivan. "Electric Field Directed Fabrication of Biosensor Devices From Biomolecule Derivatized Nanoparticles." In ASME 2007 2nd Frontiers in Biomedical Devices Conference. ASMEDC, 2007. http://dx.doi.org/10.1115/biomed2007-38093.

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An electronic microarray has been used to carry out directed self-assembly of higher order 3D structures from Biotin/Streptavidin and DNA derivatized nanoparticles. Structures with more than forty layers of alternating biotin and streptavidin and DNA nanoparticles were fabricated using a 400 site CMOS microarray system. In this process, reconfigurable electric fields produced by the microarray device have been used to rapidly transport, concentrate and accelerate the binding of 40 and 200 nanometer biotin, streptavidin, DNA and peroxidase derivatized nanoparticles to selected sites on the microarray. The nanoparticle layering process takes less than one minute per layer (10–20 seconds for addressing and binding nanoparticles, 40 seconds for washing). The nanoparticle addressing/binding process can be monitored by changes in fluorescence intensity as each nanoparticle layer is deposited. The final multilayered 3-D structures are about two microns in thickness and 50 microns in diameter. Work is now focused on assembling “micron size” biosensor devices from bio-molecule derivatized luminescent and fluorescent nanoparticles. The proposed structure for a nanolayered glucose sensor device includes a base layer of biotin/streptavidin nanoparticles, a layer of glucose oxidase derivatized nanoparticles, a layer of peroxidase derivatized nanoparticles, a layer of quantum dots, and a final layer of biotin/streptavidin nanoparticles. Such a device will serve as a prototype for a wide variety of applications which includes other biosensor devices, lab-on a-chip devices, in-vivo drug delivery systems and “micron size” dispersible bio/chem sensors for environmental, military and homeland security applications.
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Roberts, S. "Microarray analysis - problems and potential solutions." In IET Seminar on Signal Processing for Genomics. IEE, 2006. http://dx.doi.org/10.1049/ic:20060373.

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Dai, Wei, Olgica Milenkovic, Mona A. Sheikh, and Richard G. Baraniuk. "Probe Design for Compressive Sensing DNA Microarrays." In 2008 IEEE International Conference on Bioinformatics and Biomedicine. IEEE, 2008. http://dx.doi.org/10.1109/bibm.2008.56.

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Fu, Chen-Ping, Catherine E. Welsh, Fernando Pardo-Manuel de Villena, and Leonard McMillan. "Inferring ancestry in admixed populations using microarray probe intensities." In the ACM Conference. ACM Press, 2012. http://dx.doi.org/10.1145/2382936.2382950.

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Reports on the topic "Microarray Probes"

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Gardner, S., and C. Jaing. Interim report on updated microarray probes for the LLNL Burkholderia pseudomallei SNP array. Office of Scientific and Technical Information (OSTI), 2012. http://dx.doi.org/10.2172/1047245.

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Jaing, C., and S. Gardner. Interim Report on SNP analysis and forensic microarray probe design for South American hemorrhagic fever viruses, tick-borne encephalitis virus, henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever viruses, Rift Valley fever. Office of Scientific and Technical Information (OSTI), 2012. http://dx.doi.org/10.2172/1044237.

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