Technological advances in DNA sequencing are enabling new areas of genomic research allowing fine connections between genomic variants and phenotype. We are studying transcriptomes and genomes from a variety of eukaryotic and prokaryotic non model organisms and have contributed to gain biological insights. At the moment we are collaborating with researchers in Corpoica, Colombia to continue the characterization of the Cape gooseberry transcriptome with additional data generated by next-generation sequencing technologies and have finalized the construction of a database using NCBI tools to display the newly assembled Cape gooseberry transcriptome. Additionally, we are in the process of analyzing interactions between plant growth promoting bacteria and banana plants. This is done in collaboration with Richa Agarwala and Roberto Vera Alvarez. In collaboration with John Spouge, we have studied the co-localization of transcription factor binding sites (TFBSs) within regulatory modules (RMs) and found that their tight positional conservation explains much of the TFBS positional preferences near the transcription start site (TSS). In another study related to the investigation of repeated sequences in genomes in collaboration with I. King Jordan we studied the human population-specific gene expression and transcriptional network modification with polymorphic transposable elements. We presented a systematic analysis of the regulatory contributions of polyTE loci that were generated by recent transpositional activity and thereby differ between individuals. We found that the phenotypic impact of human TE activity is not limited to deleterious effects; it also includes the generation of regulatory differences that fall within the scope of naturally occurring human variation and are involved in population-specific gene regulation as well as transcriptional network modification. We contributed to the genome assembly and annotation of 26 genome sequences of Vibrio cholerae strains obtained from clinical and environmental sources. Assemblies were constructed using Illumina and the genomes were annotated with the NCBI Prokaryotic Genome Automatic Annotation Pipeline (PGAAP). This research was done in collaboration with I. King Jordan and Brian K. Hammer (Georgia Tech).
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