Finding New Cell Wall Regulatory Genes in Using Multiple Lines of Evidence.

Understanding the regulatory network controlling cell wall biosynthesis is of great interest in , both because of its status as a model woody perennial and its importance for lignocellulosic products. We searched for genes with putatively unknown roles in regulating cell wall biosynthesis using an extended network-based Lines of Evidence (LOE) pipeline to combine multiple omics data sets in , including gene coexpression, gene comethylation, population level pairwise SNP correlations, and two distinct SNP-metabolite Genome Wide Association Study (GWAS) layers. By incorporating validation, ranking, and filtering approaches we produced a list of nine high priority gene candidates for involvement in the regulation of cell wall biosynthesis.

Wavelet-Based Genomic Signal Processing for Centromere Identification and Hypothesis Generation.

Various 'omics data types have been generated for , each providing a layer of information which can be represented as a density signal across a chromosome. We make use of genome sequence data, variants data across a population as well as methylation data across 10 different tissues, combined with wavelet-based signal processing to perform a comprehensive analysis of the signature of the centromere in these different data signals, and successfully identify putative centromeric regions in from these signals. Furthermore, using SNP (single nucleotide polymorphism) correlations across a natural population of , we find evidence for the co-evolution of the centromeric histone CENH3 with the sequence of the newly identified centromeric regions, and identify a new CENH3 candidate in .