Network Structure and Dynamics, and Emergence of Robustness by Stabilizing Selection in an Artificial Genome

Emergent Network Structure, evolvable Robustness and non-linear Effects of Point Mutations in an Artificial Genome Model

Genetic regulation is a key component in development, but a clear understanding of the structure and dynamics of genetic networks is not yet at hand. In this paper we investigate these properties within an artificial genome model originally introduced by Reil (1999). We analyze statistical properties of randomly generated genomes both on the sequence- and network level, and show that this model correctly predicts the frequency of genes in genomes as found in experimental data. Using an evolutionary algorithm based on stabilizing selection for a phenotype, we show that dynamical robustness agai…

Primate specific retrotransposons, SVAs, in the evolution of networks that alter brain function

The hominid-specific non-LTR retrotransposon termed SINE VNTR Alu (SVA) is the youngest of the transposable elements in the human genome. The propagation of the most ancient SVA type A took place about thirteen millions years ago ago, and the youngest SVA types appeared in the human genome after the chimpanzee divergence. Functional enrichment analysis of genes associated with SVA insertions demonstrated their strong link to multiple ontological categories attributed to brain function and the disorders. SVA types that expanded their presence in the human genome at different stages of hominoid …

高度保守的序列特异性双链DNA结合网络对人类和黑猩猩大脑发育的分歧基因组进化起作用

Highly conserved sequence-specific double-stranded DNA binding networks contributing to divergent genomic evolution of human and chimpanzee brain development

本研究发现人类和黑猩猩大脑发育的分歧基因组进化与高度保守的序列特异性双链DNA结合网络有关，这些网络通过转座子提供的基因组调控种子模板起关键作用。

代谢过程中的手性涌现

The Emergence of Chirality from Metabolism

本研究通过模拟生物圈规模代谢网络演化，揭示了非手性分子如何产生手性分子并形成手性富集规律，为理解生命起源中的手性选择及寻找生物特征提供了新途径。

Stress induces remodelling of yeast interaction and co-expression networks

Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks under different conditions. In this work, we study the effect of stress on cellular networks in fission yeast. Stress elicits a sophisticated and large scale cellular response, involving a shift of resources from cell growth and metabolism towards protection and maintenance. Previous work has suggested that these changes can be appreciated at the network level. …