Computational methods in methaphlogenomics

随着快速和廉价测序技术的出现，有可能从不同环境中采样的大量生物体中获得完整的基因组。虽然这些宏基因组的功能分析最近取得了一些进展，但它们的进化分析仍然受到方法和计算问题的阻碍，特别是能够分析包含数千个序列的基因组学数据集。在这个建议中，我提出了一个新领域的发展，即metaphyrogenomics，通过（i）评估metaphyrogenomics方法的性能，以重建过去的进化模式，并将结果设置在生态环境中;（ii）开发方法，将预测未来或新兴的宏基因组;（iii）调查人口宏基因组学的新方向。除了培养至少四名研究生外，拟议的研究计划预计将推动metaphylogenomics领域的发展，通过改进针对病毒宏基因组的疫苗设计来造福公共卫生，并为这一新领域提供坚实的理论基础。

With the advent of rapid and cheap sequencing technologies comes the possibility to obtain complete genomes from a large range of organisms sampled across diverse environments. While the functional analysis of such metagenomes has made some recent headway, their evolutionary analysis is still hampered by methodological and computational issues, in particular to be able to analyze genomics data sets containing thousands of sequences. In this proposal I put forward the development of a new field, that of metaphylogenomics, by (i) assessing the performance of metaphylogenomics methods to reconstruct past evolutionary patterns and setting the results in an ecological context; (ii) developing methods that will predict future or emerging metagenomes; and (iii) investigating new directions in population metagenomics. In addition to training at least four graduate students, the proposed research program is expected to advance the field of metaphylogenomics, to benefit public health by improving vaccine design against viral metagenomes, and to provide this new field with a solid theoretical foundation.