Postdoctoral Research Fellowship in Biological Informatics FY 2006

该项目是根据2006年生物信息学博士后研究奖学金项目授予的。众所周知，随着微生物的进化，它们会定期相互交换遗传物质。这种交流有助于成功地适应新的环境，而且似乎在同一物种的成员之间相对频繁，但在远亲微生物之间不太频繁。这项研究项目将开发和应用计算工具来研究同源重组和横向遗传转移在微生物物种形成过程中的作用。DNA测序技术的进步为大量密切相关的微生物提供了全基因组频率，而基因组比对的相应进展使准确识别多个基因组之间的保守区域成为可能。具体地说，将分析密切相关的肠杆菌和链球菌的基因组，以更好地了解在物种形成过程中重组和遗传交换的速度如何衰退。为此，将发展马尔可夫链蒙特卡罗抽样方法，将系谱建模为具有不同的重组速率参数的跨物种横向转移和种内重组的合并过程。当地的系统发育信号将被结合起来，以推断物种系统发育和分化时间的可靠估计。将这些分析方法应用于已测序的微生物基因组将阐明重组在物种形成中的作用，此外还将提供关于微生物基因组自然选择和适应的历史信息。科学培训目标分为两大类：信息学和生物学。信息学培训将在昆士兰大学分子生物科学研究所进行。信息学培训将促进研究员对种群遗传学、系统发育的统计模型和计算方法(如马尔科夫链蒙特卡罗)的理解。生物培训将在加州大学戴维斯分校乔纳森·艾森博士的实验室进行，包括DNA修复和重组的分子机制等主题。专业培训目标将在研究金期间在两个学习地点进行，如培养指导研究生的能力，撰写可资助的补助金，以及提供内容丰富、愉快的科学演讲。这位研究员在昆士兰大学的研究将提供与系统发育和分子进化领域的领先国际研究人员建立网络的机会。在加州大学戴维斯分校学习将通过与加州大学戴维斯分校和邻近机构(如加州大学伯克利分校、伦敦帝国理工学院和美国能源部联合基因组研究所)的研究人员互动，为未来的职业机会做好准备。

This project is awarded under the Postdoctoral Research Fellowships in Biological Informatics Program for 2006. As microbes evolve they are known to periodically exchange genetic material with each other. Such exchange can contribute to successful adaptation to new environments and appears to be relatively frequent between members of the same species but less frequent between distantly related microbes. This research project will develop and apply computational tools to investigate the role of homologous recombination and lateral genetic transfer during the process of microbial speciation. Advances in DNA sequencing technology have provided whole genome fequences for a large number of closely-related microbes, while corresponding advances in genome alignment enable accurate identification of regions conserved among multiple genomes. Specifically, genomes of closely-related /Enterobacteriacae/ and /Streptococci/ will be analyzed to better understand how the rate of recombination and genetic exchange decayed during the process of speciation. Towards this end, Markov-chain Monte-Carlo sampling methods will be developed to model genealogies as a coalescent process with separate recombination rate parameters for cross-species lateral transfer and intraspecific recombination. Local phylogenetic signals will be combined to infer robust estimates of species phylogenies and divergence times. Application of these analytic methods to sequenced microbial genomes will illuminate the role of recombination during speciation, in addition to providing historical information about natural selection and adaptation of microbial genomes.The scientific training objectives fall into two general categories: informatic and biological. Informatic training will be carried out at the Institute for Molecular Bioscience at the University of Queensland. The informatic training will foster growth in the Fellow's understanding of population genetics, statistical models for phylogenetics, and computational methods such as Markov-chain Monte-Carlo. Biological training will take place in the lab of Dr. Jonathan Eisen at UC-Davis and includes topics such as molecular mechanisms of DNA repair and recombination. Professional training goals such as developing the abilities to mentor graduate students, write fundable grants, and deliver informative, enjoyable scientific talks will take place at both locations of study over the duration of the fellowship period. The Fellow's research at the University of Queensland will provide the opportunity to network with leading international researchers in phylogenetics and molecular evolution. Study at UC-Davis will prepare the Fellow for future career opportunities through interaction with researchers at both UC-Davis and neighboring institutions such as UC-Berkeley, LBL, and the DOE Joint Genome Institute.