Pt. One: Tag-based nucleic acid analysis -- DeepSuperSAGE: high-throughput transcriptome sequencing with now- and next-generation sequencing technologies -- DeepCAGE: genome-wide mapping of transcription start sites -- Definition of promotome-transcriptome architecture using CAGEscan -- RACE: new applications of an old method to connect exons -- RNA-PET: full-length transcript analysis using 50-and 30-paired-end tag next-generation sequencing -- Stranded RNA-seq: strand-specific shotgun sequencing of RNA -- Differential RNA sequencing (dRNA-Seq): deep-sequencing-based analysis of primary transcriptomes -- Identification and expression profiling of small RNA populations using high-throughput sequencing -- Genome-wide mapping of protein-DNA interactions by ChIP-Seq -- Analysis of protein-RNA interactions with single-nucleotide resolution using iCLIP and next-generation sequencing -- Massively parallel tag sequencing unveils the complexity of marine protistan communities in oxygen-depleted habitats -- Chromatin interaction analysis using paired-end tag sequencing (ChIA-PET) -- Tag-Seq: next-generation tag sequencing for gene expression profiling -- Isolation of active regulatory elements from eukaryotic chromatin using FAIRE (Formaldehyde-ssisted isolation of regulatory elements) -- Identification of nucleotide variation in genomes using next-generation sequencing -- DGS (Ditag genome scanning) - A restriction-based paired-end sequencing approach for genome structural analysis -- Next-generation sequencing of bacterial artificial chromosome clones for next-generation physical mapping -- HELP-tagging: tag-based genome-wide cytosine methylation profiling -- Second-generation sequencing library preparation: in vitro tagmentation via transposome insertion -- Pt. Two: next-generation tag-based sequencing -- Moving towards third-generation sequencing technologies -- Beyond tags to full-length transcripts -- Helicos single-molecule sequencing for accurate tag-based RNA quantitation -- Total RNA-seq: complete analysis of the transcriptome using illumina sequencing-by-synthesis sequencing -- Pt. Three: bioinformatics for tag-based technologies -- Computational infrastructure and basic data analysis for next-generation sequencing -- CLC bio integrated platform for handling and analysis of tag sequencing data -- Multidimensional context of sequence tags: biological data integration -- Experimental design and quality control of next-generation sequencing experiments -- UTGB toolkit for personalized genome browsers -- Beyond the pipelines: cloud computing facilitates management, distribution, security, and analysis of high-speed sequencer data -- Computational methods for the identification of microRNAs from small RNA sequencing data

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