Combinatorial models and algorithms for comparative genomics

我提出的研究计划侧重于开发用于基因组数据比较和分析的非平凡组合模型和有效算法。这个项目的主要方面是比较，在基因顺序方面，全基因组。特别是，我将研究两个方面：(1)利用组合结构守恒所提供的信息，(2)将现有模型扩展到具有多基因家族的基因组的情况。在这两个问题中，我将把精力集中在公共区间的概念上。将首次研究的精确问题是重排基因簇的检测，多基因家族中合理进化关系的分配以及进化情景的计算。由此产生的算法将被实施并用于分析几个基因组数据集，包括原核基因组——本质上是细菌基因组，从生物医学的角度来看是最重要的——和真核基因组——酵母和脊椎动物。我还计划研究生物网络，特别是基因调控网络。我将研究几个网络之间的保守结构的概念和可能的祖先网络的重建。最后，我对非编码RNA基因分析算法的发展很感兴趣。特别是，我将研究如何通过将它们分解成简单的茎环子结构来比较这些结构。

The research program I propose focuses on the development of  non-trivial combinatorial  models and efficient algorithms for genomic data comparison and analysis. The main aspect of this project deals with the comparison, in terms of gene order, of whole genomes. In particular, I will study two aspects: (1) using the information given by the conservation of combinatorial structures, (2) extending the existing models to the case of genomes with multigenes families. In both problems, I will concentrate my efforts on the notion of common intervals. The precise problems that will be studied in a first time are the detection of rearranged gene clusters, the assignment of plausible evolutionary relations in multigenes families, and the computation of evolution scenarios. The resulting algorithms will be implemented and used to analyse several datasets of genomes, including prokaryotic genomes - essentially bacterial genomes, that are of primary importance from a biomedical point of view - and eukaryotic genomes - yeasts and vertebrates. I also plan to work on biological networks, in particuliar gene regulation networks. I will study the notion of conserved structures among a set of several networks and the reconstruction of possible ancestral networks. Finally, I am interested in the developement of algorithms for the analysis of noncoding RNA genes. In particular, I will study how to compare such structures by decomposing them into simple stem-loops substructures.