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"Applied Biosystems SOLiD^TM System: Ligation-Based Sequencing," Next Generation Genome Sequencing: Towards Personalized Medicine , Pandey V, Nutter RC, Prediger E (2008), Wiley, pages 29-41

"New Frontiers in Plant Functional Genomics Using Next Generation Sequencing Technologies," The Handbook of Plant Functional Genomics, Concepts and Protocols. R. Nutter, G. Kahl et. al. (2008) Wiley, pages 431-444

Local alignment of two-base encoded DNA sequence Homer et al. BMC Bioinformatics 2009, 10:175 doi:10.1186/1471-2105-10-175

Efficient mapping of Applied Biosystems SOLiD sequence data to a reference genome for functional genomic applications . Ondov et.al., Bioinformatics 2008 24(23):2776-2777

Sequence and structural variation in a human genome uncovered by short-read, massively parallel ligation sequencing using two base encoding . McKernan, K. J., et al. Genome Research online. 2009.

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses . Fullwood et al. Genome Res. 2009 19: 521-532

The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse Durfee, T., et al. J. of Bacteriology Online 190(7): 2597-2606.

Rapid whole-genome mutational profiling using next-generation sequencing technologies . Smith et al., Genome Res. 2008. 18: 1638-1642

Comparing Platforms for C. elegans Mutant Identification Using High-Throughput Whole-Genome Sequencing . Shen et al. I (2008) PLoS ONE 3(12): e4012. doi:10.1371/journal.pone.0004012

Limitations and possibilities of small RNA digital gene expression profiling . Linsen et al. Nature Methods 6, 474-476 (30 June 2009)

Chromatin immunoprecipitation sequencing (ChIP-Seq) on the SOLiD^TM System . Shah, et al. Published online: Nature Methods 6, (2009)

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning . Valoeuv, A., et al., Genome Research. 2008 Jul;18(7):1051-63.

RNA-MATES: A recursive mapping strategy for high-thoughput RNA-sequencing data . Cloonan, N., et al. Bioinformatics Published online: 30 July 2009

mRNA-Seq whole-transcriptome analysis of a single cell . Tang, et al. Nature Methods Published online: 6 April 2009

The Structure and Complexity of a Bacterial Transcriptome . Passalacqua, K., et al. Bacteriol. 2009 : JB.00122-09v1

Stem cell transcriptome profiling via massive-scale mRNA sequencing . Cloonan, N., et al. Nature Methods Online. 2008 Jul;5(7):613-9.

High-Resolution Analysis of the 5-End Transcriptome Using a Next Generation DNA Sequencer . Hashimoto, S., et al. PLoS ONE. 2009;4(1):e4108. Epub 2009 Jan 1

Preparation of genome-wide DNA fragment libraries using bisulfite in polyacrylamide gel electrophoresis slices with formamide denaturation and quality control for massively parallel sequencing by oligonucleotide ligation and detection . Ranade, S., et al. Analytical Biochemistry (July 2009) 390, (2): 126-135.