Genome Assemblies, Analyses, and Comparisons

DNA测序的技术进步正在使基因组研究的新领域成为可能，从而使基因组变体和表型之间建立良好的联系。我们正在研究各种真核和原核非模式生物的转录组和基因组，并有助于获得生物学的见解。目前，我们正在与哥伦比亚Corpoica的研究人员合作，继续利用下一代测序技术生成的额外数据对Cape gooseberry转录组进行表征，并计划使用NCBI工具构建一个数据库，以显示新组装的Cape gooseberry转录组。此外，我们正在使用NCBI Proximity Genomes Annotation Pipeline组装和注释来自哥伦比亚的本地沙门氏菌分离株。这是与Richa Agarwala和Roberto Vera Alvarez合作完成的。 在与John Spouge和Sergey Sheetlin的合作中，我们使用了广义Ruzzo-Tompa算法来查找基因组序列中的重复序列，并实现了一个名为RepWords的算法，该算法允许惩罚删除不利的字母，因此算法泛化包括间隙。RepWords程序在DNA中发现了不精确的简单重复序列，它通过超越先前描述的类似特设工具来简化一般概念。在另一项与I.我们测试了全麦散布重复序列（MIRs）为人类基因组提供功能增强子的可能性。我们发现MIRs高度集中在K562和HeLa人类细胞类型的增强子中，并且发现MIRs衍生的增强子是转录因子结合位点的丰富来源。因此，MIRs可以在人类基因组中发挥调节功能，这项研究有助于解释为什么它们作为最古老的转座因子家族的作用。 我们对从临床和环境来源获得的三种纳瓦弧菌菌株的第一个基因组序列的基因组组装和注释做出了贡献。使用Pacific Biosciences和Illumina技术构建杂交组装体，并用NCBI Proximity Genome Automatic Annotation Pipeline（PGAAP）注释基因组。这项研究是与I。约旦国王和谢丽尔塔尔（CDC）。在与卡洛斯Y.索托我们确定了新的基因的糖肽脂生物合成的分枝杆菌cologlobulense，有助于了解滑动运动，生物膜的形成，和糖肽脂生产在这些分枝杆菌。

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 plans to construct a database using NCBI tools to display the newly assembled Cape gooseberry transcriptome. Additionally, we are in the process of assembling and annotating native Salmonella enterica isolates from Colombia using the NCBIs Prokaryotic Genomes Annotation Pipeline. This is done in collaboration with Richa Agarwala and Roberto Vera Alvarez. In collaboration with John Spouge and Sergey Sheetlin, we have used the generalized Ruzzo-Tompa algorithm to find repeats in genomic sequences and made an implementation of the algorithm called RepWords, the implementation allows the penalized deletion of unfavorable letters, the algorithmic generalization therefore includes gaps. The program RepWords, which finds inexact simple repeats in DNA, exemplifies the general concepts by out-performing similar ad hoc previously described tools. In another study related to the investigation of repeated sequences in genomes in collaboration with I. King Jordan we tested the possibility that mammalian-wide interspersed repeats (MIRs) contribute functional enhancers to the human genome. We found that MIRs are highly concentrated in enhancers of the K562 and HeLa human cell-types and MIR-derived enhancers were found to be a rich source of transcription factor binding sites. Therefore, MIRs can exercise a regulatory function in the human genome and this study contributes to explain why their role as the most ancient family of transposable elements. We contributed to the genome assembly and annotation of the first genome sequences of three Vibrio navarrensis strains obtained from clinical and environmental sources. Hybrid assembly were constructed using Pacific Biosciences and Illumina technologies 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 Cheryl Tarr (CDC). In a different study in collaboration with Carlos Y. Soto we identified novel genes for glycopeptidolipids biosynthesis in Mycobacterium colombiense, contributing to the understanding of sliding motility, biofilm formation, and glycopeptidolipid production in these mycobacteria.