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Full-Text Articles in Life Sciences
The Nuances Of Statistically Analyzing Next-Generation Sequencing Data, Sanvesh Srivastava, R. W. Doerge
The Nuances Of Statistically Analyzing Next-Generation Sequencing Data, Sanvesh Srivastava, R. W. Doerge
Conference on Applied Statistics in Agriculture
High-throughput sequencing technologies, in particular next-generation sequencing (NGS) technologies, have emerged as the preferred approach for exploring both gene function and pathway organization. Data from NGS technologies pose new computational and statistical challenges because of their massive size, limited replicate information, large number of genes (high-dimensionality), and discrete form. They are more complex than data from previous high-throughput technologies such as microarrays. In this work we focus on the statistical issues in analyzing and modeling NGS data for selecting genes suitable for further exploration and present a brief review of the relevant statistical methods. We discuss visualization methods to assess …
A Hierarchical Bayesian Approach For Detecting Differential Gene Expression In Unreplicated Rna-Sequencing Data, Sanvesh Srivastava, R. W. Doerge
A Hierarchical Bayesian Approach For Detecting Differential Gene Expression In Unreplicated Rna-Sequencing Data, Sanvesh Srivastava, R. W. Doerge
Conference on Applied Statistics in Agriculture
Next-generation sequencing technologies have emerged as a promising technology in a variety of fields, including genomics, epigenomics, and transcriptomics. These technologies play an important role in understanding cell organization and functionality. Unlike data from earlier technologies (e.g., microarrays), data from next-generation sequencing technologies are highly replicable with little technical variation. One application of next-generation sequencing technologies is RNA-Sequencing (RNA-Seq). It is used for detecting differential gene expression between different biological conditions. While statistical methods for detecting differential expression in RNA-Seq data exist, one serious limitation to these methods is the absence of biological replication. At present, the high cost of …
Functional Divergence Of Duplicated Genes In The Soybean Genome, Paul L. Auer, R. W. Doerge
Functional Divergence Of Duplicated Genes In The Soybean Genome, Paul L. Auer, R. W. Doerge
Conference on Applied Statistics in Agriculture
The soybean genome has undergone many different evolutionary changes that are observable with modern technologies. Of particular interest to scientists and plant breeders is the fact that the soybean genome exhibits features of genome duplication from millions of years ago. Genes that were copied during the duplication event have since diverged functionally. Identifying functionally divergent duplicate genes may provide insight into the evolution of soybean. To investigate functional divergence, transcripts from seven different tissue samples of pooled soybean messenger RNA were sequenced using the Solexa next-generation sequencer and analyzed for gene expression. We tested differential expression of duplicated genes within …
Statistical Issues In Next-Generation Sequencing, Paul L. Auer, R. W. Doerge
Statistical Issues In Next-Generation Sequencing, Paul L. Auer, R. W. Doerge
Conference on Applied Statistics in Agriculture
High throughput deep-sequencing or next-generation sequencing has emerged as an exciting new tool in a great number of applications (e.g., variant discovery, profiling of histone modifications, identifying transcription factor binding sites, resequencing, and transcriptome characterization). Even though this technology has generated unprecedented amounts of data in the scientific community few studies have looked carefully at its inherent variability. Recent studies of mRNA expression levels found little appreciable technical variation in Illumina’s Solexa sequencing platform (a next-generation sequencing device). Although these results are encouraging, they are limited to a specific platform and application, and have been made without any attention to …