Relevant bibliographies by topics / Microarray Probes

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

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
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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
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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 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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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 intensiti
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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 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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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 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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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 h
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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 ser
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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.
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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 sever
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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 th
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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,
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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
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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 micr
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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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