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Journal articles on the topic 'Microarray Probes'

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Published: 4 June 2021
Last updated: 1 February 2022

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1

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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2

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
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3

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
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4

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 mic
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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 analyz
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7

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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8

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 intensiti
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9

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 th
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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.t
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11

Kingsley, Mark T., Timothy M. Straub, Douglas R. Call, Don S. Daly, Sharon C. Wunschel, and Darrell P. Chandler. "Fingerprinting Closely Related Xanthomonas Pathovars with Random Nonamer Oligonucleotide Microarrays." Applied and Environmental Microbiology 68, no. 12 (2002): 6361–70. http://dx.doi.org/10.1128/aem.68.12.6361-6370.2002.

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ABSTRACT Current bacterial DNA-typing methods are typically based on gel-based fingerprinting methods. As such, they access a limited complement of genetic information and many independent restriction enzymes or probes are required to achieve statistical rigor and confidence in the resulting pattern of DNA fragments. Furthermore, statistical comparison of gel-based fingerprints is complex and nonstandardized. To overcome these limitations of gel-based microbial DNA fingerprinting, we developed a prototype, 47-probe microarray consisting of randomly selected nonamer oligonucleotides. Custom ima
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12

Ahn, Soohyoun, David M. Kulis, Deana L. Erdner, Donald M. Anderson, and David R. Walt. "Fiber-Optic Microarray for Simultaneous Detection of Multiple Harmful Algal Bloom Species." Applied and Environmental Microbiology 72, no. 9 (2006): 5742–49. http://dx.doi.org/10.1128/aem.00332-06.

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ABSTRACT Harmful algal blooms (HABs) are a serious threat to coastal resources, causing a variety of impacts on public health, regional economies, and ecosystems. Plankton analysis is a valuable component of many HAB monitoring and research programs, but the diversity of plankton poses a problem in discriminating toxic from nontoxic species using conventional detection methods. Here we describe a sensitive and specific sandwich hybridization assay that combines fiber-optic microarrays with oligonucleotide probes to detect and enumerate the HAB species Alexandrium fundyense, Alexandrium ostenfe
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Barth, Stefanie A., Christian Menge, Inga Eichhorn, Torsten Semmler, Derek Pickard, and Lutz Geue. "Evaluation of applicability of DNA microarray–based characterization of bovine Shiga toxin–producing Escherichia coli isolates using whole genome sequence analysis." Journal of Veterinary Diagnostic Investigation 29, no. 5 (2017): 721–24. http://dx.doi.org/10.1177/1040638717700689.

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We assessed the ability of a commercial DNA microarray to characterize bovine Shiga toxin–producing Escherichia coli (STEC) isolates and evaluated the results using in silico hybridization of the microarray probes within whole genome sequencing scaffolds. From a total of 69,954 reactions (393 probes with 178 isolates), 68,706 (98.2%) gave identical results by DNA microarray and in silico probe hybridization. Results were more congruent when detecting the genoserotype (209 differing results from 19,758 in total; 1.1%) or antimicrobial resistance genes (AMRGs; 141 of 26,878; 0.5%) than when dete
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14

Gescher, Christine, Katja Metfies, Stephan Frickenhaus, Britta Knefelkamp, Karen H. Wiltshire, and Linda K. Medlin. "Feasibility of Assessing the Community Composition of Prasinophytes at the Helgoland Roads Sampling Site with a DNA Microarray." Applied and Environmental Microbiology 74, no. 17 (2008): 5305–16. http://dx.doi.org/10.1128/aem.01271-08.

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ABSTRACT The microalgal class Prasinophyceae (Chlorophyta) contains several picoeukaryotic species, which are known to be common in temperate and cold waters and have been observed to constitute major fractions of marine picoplankton. However, reliable detection and classification of prasinophytes are mainly hampered by their small size and few morphological markers. Consequently, very little is known about the abundance and ecology of the members of this class. In order to facilitate the assessment of the abundance of the Prasinophyceae, we have designed and evaluated an 18S rRNA gene-targete
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15

Urakawa, Hidetoshi, Said El Fantroussi, Hauke Smidt, et al. "Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays." Applied and Environmental Microbiology 69, no. 5 (2003): 2848–56. http://dx.doi.org/10.1128/aem.69.5.2848-2856.2003.

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ABSTRACT The discrimination between perfect-match and single-base-pair-mismatched nucleic acid duplexes was investigated by using oligonucleotide DNA microarrays and nonequilibrium dissociation rates (melting profiles). DNA and RNA versions of two synthetic targets corresponding to the 16S rRNA sequences of Staphylococcus epidermidis (38 nucleotides) and Nitrosomonas eutropha (39 nucleotides) were hybridized to perfect-match probes (18-mer and 19-mer) and to a set of probes having all possible single-base-pair mismatches. The melting profiles of all probe-target duplexes were determined in par
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16

Chim, Wilson, Abootaleb Sedighi, Christopher L. Brown, Ralph Pantophlet, and Paul C. H. Li. "Effect of buffer composition on PNA–RNA hybridization studied in the microfluidic microarray chip." Canadian Journal of Chemistry 96, no. 2 (2018): 241–47. http://dx.doi.org/10.1139/cjc-2017-0319.

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Herein, we report that peptide nucleic acid sequences (PNAs) have been used as the probe species for detection of RNA and that a microfluidic microarray (MMA) chip is used as the platform for detection of hybridizations between immobilized PNA probes and RNA targets. The RNA targets used are derived from influenza A sequences. This paper discusses the optimization of two probe technologies used for RNA detection and investigates how the composition of the probe buffer and the content of the hybridization solution can influence the overall results. Our data show that the PNA probe is a better c
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17

Kahlke, Tim, Paavo Jumppanen, Ralf Westram, Guy C. G. Abell, and Levente Bodrossy. "ProbeSpec: batch specificity testing and visualization of oligonucleotide probe sets implemented in ARB." F1000Research 7 (December 6, 2018): 1901. http://dx.doi.org/10.12688/f1000research.16905.1.

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High-throughput molecular methods such as quantitative polymerase chain reaction (qPCR) and environmental microarrays are cost-effective methods for semi-quantitative assessment of bacterial community structure and the identification of specific target organisms. Both techniques rely on short nucleotide sequences, so-called oligonucleotide probes, which require high specificity to the organisms in question to avoid cross-hybridization with non-target taxa. However, designing oligonucleotide probes for novel taxa or marker genes that show sufficient phylogenetic sensitivity and specificity is o
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18

Call, Douglas R., Marlene K. Bakko, Melissa J. Krug, and Marilyn C. Roberts. "Identifying Antimicrobial Resistance Genes with DNA Microarrays." Antimicrobial Agents and Chemotherapy 47, no. 10 (2003): 3290–95. http://dx.doi.org/10.1128/aac.47.10.3290-3295.2003.

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ABSTRACT We developed and tested a glass-based microarray suitable for detecting multiple tetracycline (tet) resistance genes. Microarray probes for 17 tet genes, the β-lactamase bla TEM-1 gene, and a 16S ribosomal DNA gene (Escherichia coli) were generated from known controls by PCR. The resulting products (ca. 550 bp) were applied as spots onto epoxy-silane-derivatized, Teflon-masked slides by using a robotic spotter. DNA was extracted from test strains, biotinylated, hybridized overnight to individual microarrays at 65°C, and detected with Tyramide Signal Amplification, Alexa Fluor 546, and
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19

Quiñones, Beatriz, Craig T. Parker, John M. Janda, William G. Miller, and Robert E. Mandrell. "Detection and Genotyping of Arcobacter and Campylobacter Isolates from Retail Chicken Samples by Use of DNA Oligonucleotide Arrays." Applied and Environmental Microbiology 73, no. 11 (2007): 3645–55. http://dx.doi.org/10.1128/aem.02984-06.

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ABSTRACT To explore the use of DNA microarrays for pathogen detection in food, we produced DNA oligonucleotide arrays to simultaneously determine the presence of Arcobacter and the presence of Campylobacter in retail chicken samples. Probes were selected that target housekeeping and virulence-associated genes in both Arcobacter butzleri and thermotolerant Campylobacter jejuni and Campylobacter coli. These microarrays showed a high level of probe specificity; the signal intensities detected for A. butzleri, C. coli, or C. jejuni probes were at least 10-fold higher than the background levels. Sp
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20

DE CARVALHO, SÉRGIO A., and SVEN RAHMANN. "BETTER GENECHIP MICROARRAY LAYOUTS BY COMBINING PROBE PLACEMENT AND EMBEDDING." Journal of Bioinformatics and Computational Biology 06, no. 03 (2008): 623–41. http://dx.doi.org/10.1142/s0219720008003576.

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The microarray layout problem is a generalization of the border length minimization problem, and asks to distribute oligonucleotide probes on a microarray and to determine their embeddings in the deposition sequence in such a way that the overall quality of the resulting synthesized probes is maximized. Because of its inherent computational complexity, it is traditionally attacked in several phases: partitioning, placement, and re-embedding. We present the first algorithm, Greedy+, that combines placement and embedding and that results in improved layouts in terms of border length and conflict
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21

Jia, Kun, Miao Yu, Gui-Hong Zhang, et al. "Detection and identification of Mycobacterium tuberculosis and Mycobacterium bovis from clinical species using DNA microarrays." Journal of Veterinary Diagnostic Investigation 24, no. 1 (2011): 156–60. http://dx.doi.org/10.1177/1040638711417141.

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The objectives of the current study were to evaluate the use of DNA microarray for the rapid and direct detection of Mycobacterium tuberculosis and Mycobacterium bovis in bovine milk, blood, and pharyngeal swab samples, and to compare the use of DNA microarrays with current molecular detection techniques. The present study describes a microarray assay based on mtp40 and pncA gene sequences, which can be used to detect M. tuberculosis and M. bovis species. Each probe was spotted onto a silylated glass slide with an arrayer and used for hybridization with fluorescently labeled DNA derived from a
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22

Letowski, Jaroslaw, Alejandra Bravo, Roland Brousseau, and Luke Masson. "Assessment of cry1 Gene Contents of Bacillus thuringiensis Strains by Use of DNA Microarrays." Applied and Environmental Microbiology 71, no. 9 (2005): 5391–98. http://dx.doi.org/10.1128/aem.71.9.5391-5398.2005.

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ABSTRACT A single Bacillus thuringiensis strain can harbor numerous different insecticidal crystal protein (cry) genes from 46 known classes or primary ranks. The cry1 primary rank is the best known and contains the highest number of cry genes which currently totals over 130. We have designed an oligonucleotide-based DNA microarray (cryArray) to test the feasibility of using microarrays to identify the cry gene content of B. thuringiensis strains. Specific 50-mer oligonucleotide probes representing the cry1 primary and tertiary ranks were designed based on multiple cry gene sequence alignments
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Rowsell, Joanna, Renata da Silva Camargo, William B. Langdon, Maria A. Stalteri, and Andrew P. Harrison. "Uncovering the expression patterns of chimeric transcripts using surveys of Affymetrix GeneChips." Journal of Integrative Bioinformatics 7, no. 3 (2010): 300–330. http://dx.doi.org/10.1515/jib-2010-137.

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Summary Background: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras.Results: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression
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24

Kappel, Kristina, Joanna Fafińska, Markus Fischer, and Jan Fritsche. "A DNA microarray for the authentication of giant tiger prawn (Penaeus monodon) and whiteleg shrimp (Penaeus (Litopenaeus) vannamei): a proof-of-principle." Analytical and Bioanalytical Chemistry 413, no. 19 (2021): 4837–46. http://dx.doi.org/10.1007/s00216-021-03440-2.

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AbstractThis proof-of-principle study describes the development of a rapid and easy-to-use DNA microarray assay for the authentication of giant tiger prawns and whiteleg shrimp. Following DNA extraction and conventional end-point PCR of a 16S rDNA segment, the PCR products are hybridised to species-specific oligonucleotide probes on DNA microarrays located at the bottom of centrifuge tubes (ArrayTubes) and the resulting signal patterns are compared to those of reference specimens. A total of 21 species-specific probes were designed and signal patterns were recorded for 47 crustacean specimens
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Sanguin, Herv�, Beno�t Remenant, Arnaud Dechesne, et al. "Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities." Applied and Environmental Microbiology 72, no. 6 (2006): 4302–12. http://dx.doi.org/10.1128/aem.02686-05.

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ABSTRACT Bacterial diversity is central to ecosystem sustainability and soil biological function, for which the role of roots is important. The high-throughput analysis potential of taxonomic microarray should match the breadth of bacterial diversity. Here, the power of this technology was evidenced through methodological verifications and analysis of maize rhizosphere effect based on a 16S rRNA-based microarray developed from the prototype of H. Sanguin et al. (Environ. Microbiol. 8:289-307, 2006). The current probe set was composed of 170 probes (41 new probes in this work) that targeted ess
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Kostina, Elena V., Alexander N. Sinyakov, and Vladimir A. Ryabinin. "A many probes-one spot hybridization oligonucleotide microarray." Analytical and Bioanalytical Chemistry 410, no. 23 (2018): 5817–23. http://dx.doi.org/10.1007/s00216-018-1190-8.

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27

Goji, Noriko, Trevor MacMillan, and Kingsley Kwaku Amoako. "A New Generation Microarray for the Simultaneous Detection and Identification ofYersinia pestisandBacillus anthracisin Food." Journal of Pathogens 2012 (2012): 1–8. http://dx.doi.org/10.1155/2012/627036.

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The use of microarrays as a multiple analytic system has generated increased interest and provided a powerful analytical tool for the simultaneous detection of pathogens in a single experiment. A wide array of applications for this technology has been reported. A low density oligonucleotide microarray was generated from the genetic sequences ofY. pestisandB. anthracisand used to fabricate a microarray chip. The new generation chip, consisting of 2,240 spots in 4 quadrants with the capability of stripping/rehybridization, was designated as “Y-PESTIS/B-ANTHRACIS 4x2K Array.” The chip was tested
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Liu, Wen-Tso, Huiling Guo, and Jer-Horng Wu. "Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays." Applied and Environmental Microbiology 73, no. 1 (2006): 73–82. http://dx.doi.org/10.1128/aem.01468-06.

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ABSTRACT The effect of target size on microarray hybridization efficiencies and specificity was investigated using a set of 166 oligonucleotide probes targeting the 16S rRNA gene of Escherichia coli. The targets included unfragmented native rRNA, fragmented rRNA (∼20 to 100 bp), PCR amplicons (93 to 1,480 bp), and three synthetic single-stranded DNA oligonucleotides (45 to 56 bp). Fluorescence intensities of probes hybridized with targets were categorized into classes I (81 to 100% relative to the control probe), II (61 to 80%), III (41 to 60%), IV (21 to 40%), V (6 to 20%), and VI (0 to 5%).
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Chizhikov, Vladimir, Avraham Rasooly, Konstantin Chumakov, and Dan D. Levy. "Microarray Analysis of Microbial Virulence Factors." Applied and Environmental Microbiology 67, no. 7 (2001): 3258–63. http://dx.doi.org/10.1128/aem.67.7.3258-3263.2001.

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ABSTRACT Hybridization with oligonucleotide microchips (microarrays) was used for discrimination among strains of Escherichia coli and other pathogenic enteric bacteria harboring various virulence factors. Oligonucleotide microchips are miniature arrays of gene-specific oligonucleotide probes immobilized on a glass surface. The combination of this technique with the amplification of genetic material by PCR is a powerful tool for the detection of and simultaneous discrimination among food-borne human pathogens. The presence of six genes (eaeA, slt-I,slt-II, fliC, rfbE, andipaH) encoding bacteri
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Kikuchi, Shoshi. "Rice Microarray Project in Japan." Asia-Pacific Biotech News 06, no. 24 (2002): 920–26. http://dx.doi.org/10.1142/s021903030200191x.

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Trost, Brett, Catherine A. Moir, Zoe E. Gillespie, Anthony Kusalik, Jennifer A. Mitchell, and Christopher H. Eskiw. "Concordance between RNA-sequencing data and DNA microarray data in transcriptome analysis of proliferative and quiescent fibroblasts." Royal Society Open Science 2, no. 9 (2015): 150402. http://dx.doi.org/10.1098/rsos.150402.

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DNA microarrays and RNA sequencing (RNA-seq) are major technologies for performing high-throughput analysis of transcript abundance. Recently, concerns have been raised regarding the concordance of data derived from the two techniques. Using cDNA libraries derived from normal human foreskin fibroblasts, we measured changes in transcript abundance as cells transitioned from proliferative growth to quiescence using both DNA microarrays and RNA-seq. The internal reproducibility of the RNA-seq data was greater than that of the microarray data. Correlations between the RNA-seq data and the individu
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Baaj, Yasser, Corinne Magdelaine, Virginie Ubertelli, et al. "Multiplex Detection and Genotyping of Point Mutations Involved in Charcot-Marie-Tooth Disease Using a Hairpin Microarray-Based Assay." Research Letters in Biochemistry 2009 (2009): 1–5. http://dx.doi.org/10.1155/2009/960560.

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We previously developed a highly specific method for detecting SNPs with a microarray-based system using stem-loop probes. In this paper we demonstrate that coupling a multiplexing procedure with our microarray method is possible for the simultaneous detection and genotyping of four point mutations, in three different genes, involved in Charcot-Marie-Tooth disease. DNA from healthy individuals and patients was amplified, labeled with Cy3 by multiplex PCR; and hybridized to microarrays. Spot signal intensities were 18 to 74 times greater for perfect matches than for mismatched target sequences
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Son, Ahjeong, Mikaela Nichkova, Dosi Dosev, Ian M. Kennedy, and Krassimira R. Hristova. "Luminescent Lanthanide Nanoparticles as Labels in DNA Microarrays for Quantification of Methyl Tertiary Butyl Ether Degrading Bacteria." Journal of Nanoscience and Nanotechnology 8, no. 5 (2008): 2463–67. http://dx.doi.org/10.1166/jnn.2008.18279.

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We report application of lanthanide nanoparticles for DNA quantification in a microarray platform as a substitute for conventional organic fluorophores. A non-PCR based DNA microarray assay for quantifying bacteria capable of biodegrading methyl tertiary-butyl ether (MTBE) was demonstrated. Probe DNA was immobilized on a glass surface, hybridized with biotinylated target DNA and subsequently incubated with Neutravidin-biofunctionalized nanoparticles. The fluorescence spot intensities, measured by a commercial laser scanner, show a linear relationship (R2 = 0.98) with bacterial 16S rDNA over a
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Thormar, Hans G., Bjarki Gudmundsson, Freyja Eiriksdottir, et al. "Importance of the Efficiency of Double-Stranded DNA Formation in cDNA Synthesis for the Imprecision of Microarray Expression Analysis." Clinical Chemistry 59, no. 4 (2013): 667–74. http://dx.doi.org/10.1373/clinchem.2012.193839.

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BACKGROUND The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. METHODS We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription–based microarray expression analysis. RESULTS The relative amount of double-stranded cDNA
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Burden, Conrad J., Yvonne E. Pittelkow, and Susan R. Wilson. "Statistical Analysis of Adsorption Models for Oligonucleotide Microarrays." Statistical Applications in Genetics and Molecular Biology 3, no. 1 (2004): 1–27. http://dx.doi.org/10.2202/1544-6115.1095.

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Recent analyses have shown that the relationship between intensity measurements from high density oligonucleotide microarrays and known concentration is non linear. Thus many measurements of so-called gene expression are neither measures of transcript nor mRNA concentration as might be expected.Intensity as measured in such microarrays is a measurement of fluorescent dye attached to probe-target duplexes formed during hybridization of a sample to the probes on the microarray. We develop several dynamic adsorption models relating fluorescent dye intensity to target RNA concentration, the simple
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Brors, B. "Microarray Annotation and Biological Information on Function." Methods of Information in Medicine 44, no. 03 (2005): 468–72. http://dx.doi.org/10.1055/s-0038-1633995.

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Summary Objectives: Many methods for statistical analysis of gene expression studies by DNA microarrays produce lists of genes as output. To understand gene lists in terms of traditional biology, e.g. which pathways may be affected, it is necessary to get appropriate annotations for the probes on an array. Methods: Problems arise with the different sources that have been used by manufacturers to design microarray probes, and their association to biological entities like genes, transcripts and proteins. Function annotation is of crucial importance, and systems like Gene Ontology can be used for
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Chen, Bao-An, Fan Zhang, Yan Wang, et al. "Microarray-Based Method for Quantificationally Detecting Methylation Changes of E-Cadherin Gene in Acute Leukemia." Blood 108, no. 11 (2006): 4406. http://dx.doi.org/10.1182/blood.v108.11.4406.4406.

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Abstract Aberrant DNA methylation of CpG sites is among the earliest and most frequent alterations in cancer. Several studies suggest that aberrant methylation of the CpG sites of the tumor suppressor gene is closely associated with carcinogenesis. So methylation detection is very important. The aim of this study was to describe a microarray-based method for quantificationally detecting changes of E-cadherin methylation in acute leukemia and to simply discuss the effect of microarray on detecting tumor methylation. This method used bisulfite-modified DNA as a template for PCR amplification, re
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Skreka, Konstantinia, Marek Zywicki, Michael Karbiener, Alexander Hüttenhofer, Marcel Scheideler, and Mathieu Rederstorff. "Expression Profiling of a Heterogeneous Population of ncRNAs Employing a Mixed DNA/LNA Microarray." Journal of Nucleic Acids 2012 (2012): 1–10. http://dx.doi.org/10.1155/2012/283560.

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Mammalian transcriptomes mainly consist of non protein coding RNAs. These ncRNAs play various roles in all cells and are involved in multiple regulation pathways. More recently, ncRNAs have also been described as valuable diagnostic tools. While RNA-seq approaches progressively replace microarray-based technologies for high-throughput expression profiling, they are still not routinely used in diagnostic. Microarrays, on the other hand, are more widely used for diagnostic profiling, especially for very small ncRNA (e.g., miRNAs), employing locked nucleic acid (LNA) arrays. However, LNA microarr
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Chiodi, Elisa, Francesco Damin, Laura Sola, et al. "A Reliable, Label Free Quality Control Method for the Production of DNA Microarrays with Clinical Applications." Polymers 13, no. 3 (2021): 340. http://dx.doi.org/10.3390/polym13030340.

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The manufacture of a very high-quality microarray support is essential for the adoption of this assay format in clinical routine. In fact, poorly surface-bound probes can affect the diagnostic sensitivity or, in worst cases, lead to false negative results. Here we report on a reliable and easy quality control method for the evaluation of spotted probe properties in a microarray test, based on the Interferometric Reflectance Imaging Sensor (IRIS) system, a high-resolution label free technique able to evaluate the variation of the mass bound to a surface. In particular, we demonstrated that the
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Ki, Jang-Seu, Dae-Sik Hwang, and Jae-Seong Lee. "Simultaneous detection ofAureliaandChrysaorascyphozoan jellyfish on a DNA microarray." Journal of the Marine Biological Association of the United Kingdom 90, no. 6 (2009): 1111–17. http://dx.doi.org/10.1017/s0025315409990373.

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To demonstrate the effectiveness of microarrays for the detection of jellyfish, we developed a low density DNA chip based on the mitochondrial COI gene sequences of scyphozoans (jellyfish). We designed species-specific oligonucleotide probes by sequence comparisons between scyphozoans and other cnidarians such as hydrozoans and anthozoans. Each amine-labelled capture probe was arrayed onto a silylated slide. PCR products of the COI gene were hybridized to the DNA microarray that contained COI consensus sequences. We tested the ability of the DNA chip to discriminate between species from the ge
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Young, Anna Rachel, Jessica Da Gama Duarte, Rhiannon Coulson, et al. "Immunoprofiling of Breast Cancer Antigens Using Antibodies Derived from Local Lymph Nodes." Cancers 11, no. 5 (2019): 682. http://dx.doi.org/10.3390/cancers11050682.

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Tumor antigens are responsible for initiating an immune response in cancer patients, and their identification may provide new biomarkers for cancer diagnosis and targets for immunotherapy. The general use of serum antibodies to identify tumor antigens has several drawbacks, including dilution, complex formation, and background reactivity. In this study, antibodies were generated from antibody-secreting cells (ASC) present in tumor-draining lymph nodes of 20 breast cancer patients (ASC-probes) and were used to screen breast cancer cell lines and protein microarrays. Half of the ASC-probes react
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Koizumi, Yoshikazu, John J. Kelly, Tatsunori Nakagawa, et al. "Parallel Characterization of Anaerobic Toluene- and Ethylbenzene-Degrading Microbial Consortia by PCR-Denaturing Gradient Gel Electrophoresis, RNA-DNA Membrane Hybridization, and DNA Microarray Technology." Applied and Environmental Microbiology 68, no. 7 (2002): 3215–25. http://dx.doi.org/10.1128/aem.68.7.3215-3225.2002.

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ABSTRACT A mesophilic toluene-degrading consortium (TDC) and an ethylbenzene-degrading consortium (EDC) were established under sulfate-reducing conditions. These consortia were first characterized by denaturing gradient gel electrophoresis (DGGE) fingerprinting of PCR-amplified 16S rRNA gene fragments, followed by sequencing. The sequences of the major bands (T-1 and E-2) belonging to TDC and EDC, respectively, were affiliated with the family Desulfobacteriaceae. Another major band from EDC (E-1) was related to an uncultured non-sulfate-reducing soil bacterium. Oligonucleotide probes specific
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Sun, Linlin, Dianjun Liu, and Zhenxin Wang. "Microarray-Based Kinase Inhibition Assay by Gold Nanoparticle Probes." Analytical Chemistry 79, no. 2 (2007): 773–77. http://dx.doi.org/10.1021/ac061687u.

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Deng, Ping, My T. Thai, Qingkai Ma, and Weili Wu. "Efficient non-unique probes selection algorithms for DNA microarray." BMC Genomics 9, Suppl 1 (2008): S22. http://dx.doi.org/10.1186/1471-2164-9-s1-s22.

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Hollingshead, Deborah, Željka Korade, David A. Lewis, Pat Levitt, and Károly Mirnics. "DNA self-polymers as microarray probes improve assay sensitivity." Journal of Neuroscience Methods 151, no. 2 (2006): 216–23. http://dx.doi.org/10.1016/j.jneumeth.2005.07.006.

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Wilson, Kenneth H., Wendy J. Wilson, Jennifer L. Radosevich, et al. "High-Density Microarray of Small-Subunit Ribosomal DNA Probes." Applied and Environmental Microbiology 68, no. 5 (2002): 2535–41. http://dx.doi.org/10.1128/aem.68.5.2535-2541.2002.

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ABSTRACT Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. Some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignme
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Li, Tao, Liping Guo, and Zhenxin Wang. "Microarray based Raman spectroscopic detection with gold nanoparticle probes." Biosensors and Bioelectronics 23, no. 7 (2008): 1125–30. http://dx.doi.org/10.1016/j.bios.2007.11.002.

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Huang, Chengzhi, Yuanfang Li, Xinhua Huang, and Meikun Fan. "Microarray of DNA probes on carboxylate functional beads surface." Science in China Series B: Chemistry 43, no. 4 (2000): 435–42. http://dx.doi.org/10.1007/bf02969450.

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Bates, Steven R., Donald A. Baldwin, Alexandra Channing, Lida K. Gifford, Angela Hsu, and Ponzy Lu. "Cooperativity of paired oligonucleotide probes for microarray hybridization assays." Analytical Biochemistry 342, no. 1 (2005): 59–68. http://dx.doi.org/10.1016/j.ab.2005.03.030.

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Tao, Qimeng, Xiurong Wang, Hongmei Bao, et al. "Detection and Differentiation of Four Poultry Diseases Using Asymmetric Reverse Transcription Polymerase Chain Reaction in Combination with Oligonucleotide Microarrays." Journal of Veterinary Diagnostic Investigation 21, no. 5 (2009): 623–32. http://dx.doi.org/10.1177/104063870902100506.

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Asymmetric reverse transcription polymerase chain reaction (RT-PCR) and microarrays were combined to distinguish 4 viruses, including Avian influenza virus (AIV), Newcastle disease virus (NDV), Infectious bronchitis virus (IBV), and Infectious bursal disease virus (IBDV), and hemagglutinin (HA) subtypes H5, H7, and H9, and neuraminidase (NA) subtypes N1 and N2 of AIV. The AIV matrix protein (M), and HA and NA genes, IBV nucleoprotein (NP) gene, NDV NP gene, and IBDV A fragment gene were cloned into plasmids. These genes were amplified from these positive recombinant plasmids, which included th
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