New computational and biological protocols to better understand fungi using synthetic and systems biology

Abstract

Genetic engineering through synthetic biology, and systems biology through omics data analysis, are two areas of research which have potential applications in all domains of life. These fields encompass the entire search space of biological life, where genotypic possibilities and combinatorial molecular interactions are greater in number than there are humans on this planet. This work examines novel frontiers in both technologies in the scope of fungal host-cell platforms, with the hope of developing new knowledge and protocols which have potential applications in all of biology. Chapters 2 and 3 are studies in synthetic biology in Y. lipolytica, where chapters 4 and 5 are studies involving systems biology in A. nidulans. Chapters 2 and 4 are computationally focused, whereas chapters 3 and 5 focus on biological phenomena. Together, these chapters will introduce you to the research development cycle of synthetic and systems biology, from synthetic gene network simulation and genetic pathway manipulation to systems scale data analysis used for data driven hypotheses in fungal systems biology.