Genome Assemblies, Analyses, and Comparisons

DNA测序技术的进步使基因组研究的新领域成为可能，使基因组变异和表型之间有了很好的联系。我们正在研究各种真核和原核非模式生物的转录本和基因组，并为获得生物学见解做出了贡献。目前，我们正在与哥伦比亚科波伊卡的研究人员合作，继续利用下一代测序技术产生的更多数据来描述海角猕猴桃转录组的特征，并已使用NCBI工具完成了数据库的建设，以显示新组装的海角醋栗转录组。此外，我们正在分析植物生长促进菌与香蕉植物之间的相互作用。这是与里查·阿加瓦拉和罗伯托·维拉·阿尔瓦雷斯合作完成的。 与John Spouge合作，我们研究了转录因子结合位点(TFBS)在调控模块(RMS)中的共定位，发现它们的紧密位置保守解释了TFBS在转录起始位点(TSS)附近的大部分位置偏好。在另一项与I.King Jordan合作研究基因组中重复序列的研究中，我们研究了人类群体特有的基因表达和具有多态转座元件的转录网络修饰。我们系统地分析了由最近的转位活动产生的Polyte基因座的调节作用，因此个体之间存在差异。我们发现，人类TE活动的表型影响不仅限于有害影响；它还包括调节差异的产生，这些差异属于自然发生的人类变异的范围，涉及种群特异性的基因调节以及转录网络修饰。 我们参与了从临床和环境来源获得的26株霍乱弧菌基因组序列的组装和注释。使用Illumina构建组件，并使用NCBI原核基因组自动注释管道(PGAAP)注释基因组。这项研究是与I.King Jordan和布赖恩·K·哈默(佐治亚理工学院)合作完成的。

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).