Oligonucleotide array sequence analysis

Oligonucleotides are short sequences of nucleotides (RNA or DNA), typically with twenty or fewer bases. Automated synthesisers allow the synthesis of oligonucleotides up to 160 to 200 bases. The length of a synthesised base is usually denoted by 'mer' (from 'Greek' meros "part"). For example, a fragment of 25 bases would be called a 25-mer. Oligonucleotides are often used as probes for detecting complementary DNA or RNA because they bind readily to their complements. Examples of procedures that use oligonucleotides are DNA microarrays, Southern blots, fluorescent in situ hybridisation (FISH), and the synthesis of artificial genes. This book brings together leading research in the field from around the globe.

Yuichi Michikawa and Tomo Suga and Atsuko Ishikawa and Yoshimi Ohtsuka and Mayumi Iwakawa and Takashi ImaiHinanit Koltai and Carmiya Weingarten-BarorSergey V. AnisimovChristopher H. Woelk and Michael E. BurczynskiLuis Rueda and Ataul BariXiangfeng WangMeena R. Sharma and Mahesh C. Sharma and Amin A. NanjiHiromi SatoHua Li and Dongxiao ZhuDavid Honys and Nikoleta Dupl'akova and David RenakAngelica Rangel-Lopez and Alfonso Mendez-Tenorio and Rogelio Maldonado-Rodriguez and Kenneth L. BeattieShunpu ZhangRoberta Bosotti and Raffaele Calogero and Vanessa MarchesiNatalia V. Zakharova and Alexei L. Drobyshev and Dmitry A. Khodakov and Anna I. Myznikova and Irina A. GorbanMichael J. Allen and Andrew R. Cossins and Neil Hall and Mark Blaxter and Terry Burke and Dawn FieldYoulian Pan and Sieu PhanManuel Nieto-Diaz and Wolfgang Pita-Thomas and Rodrigo Martinez-Maza and Manuel Nieto-SampedroJohn BrunsteinRossana Scavelli and Sergio Abrignani and Marco CrimiJason R.E. Shepard

Preface	p. ix
Expert Commentaries	p. 1
Visible Haplotype-tagSNP Typing Array Device for Human Radiation Sensitivity-Associated Genes	p. 3
Specificity of Oligonucleotide Microarray Hybridization: Effectors and Their Effects	p. 15
Research and Review Studies	p. 25
Chapter 1 Selecting a Proper Platform for Microarray Experiment	p. 27
Chapter 2 The Clinical Relevance of Gene Expression Profiles in Peripheral Blood Mononuclear Cells	p. 37
Chapter 3 Clustering Time-Series Gene Expression Data	p. 83
Chapter 4 Recent Advances in Microbial Discovery Using Metagenomics, DNA Microarray, Biosensors, Molecular Subtyping, and Phage Recombinant ProbesSufian F. Al-Khaldi and Magdi M. Mossoba and Betsy Jean Yakes and Eric Brown and Devang Sharma and Santina Carnazza\|p123
Chapter 5 Statistical Analysis of Tiling-Path Microarrays	p. 149
Chapter 6 Application of Microarray in Rat Model of Alcoholic and Nonalcoholic Liver Disease	p. 175
Chapter 7 Biological Interpretation in Oligonucleotide Array Sequence Analysis Based on Molecular Networks	p. 209
Chapter 8 Generalized Analysis of Variance (ANOVA) Models for Oligonucleotide Microarray Data Analysis	p. 245
Chapter 9 Online Tools for Presentation and Analysis of Plant Microarray Data	p. 265
Chapter 10 Methods, Strategies and Facts for Improving the Analysis of Genetic Variations Using DNA Arrays	p. 297
Chapter 11 Improving Detection of Differentially Expressed Genes in Microarrays Using More Efficient Statistics, the Local Optimal Fudge Factor and a Two-Stage FDR Correction	p. 323
Chapter 12 Basic Approaches to Gene/Exon Level Data Analysis: 3' IVT and Exon 1.0 ST Microarray Platforms	p. 347
Chapter 13 Simultaneous Qualitative and Quantitative Identification of Multiple Targets by Polymerase Chain Reaction on Microarray	p. 367
Chapter 14 Use of Arrays with Non-model Organisms: A UK Perspective	p. 387
Chapter 15 Positional Weight Matrix as a Sequence Motif Detector	p. 403
Chapter 16 Quality Control Methods for Oligonucleotide Microarrays	p. 423
Chapter 17 Applications of Qiagen QIAplex Technology in Clinical Multiplex Assays	p. 443
Chapter 18 Oncology Applications of Microarray Technology Detecting Small Genomes Variability	p. 457
Chapter 19 Oligonucleotide Arrays in Forensic DNA Testing	p. 469
Index	p. 491

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