1 research outputs found
Tools from statistical physics for systems biology and for genomics
My graduate studies involved three broad classes of problems, each of which are presented in diļ¬erent chapters of this thesis. The ļ¬rst two parts of my work were related to studying dynamics of biochemical networks. I studied a mean-ļ¬eld/stochastic model of epigenetic chromatin silencing in yeast. The model gives rise to diļ¬erent dynamical behaviors possible within the same molecular model and provides qualitative predictions that are being investigated experimentally. In another part of my work, I studied a model of segment polarity network in Drosophila and analyzed the parameter space of the system. I particularly studied the relation between the geometry of parameter space and the robustness of the network. I will show that, in addition to the volume, the geometry of this region has important consequences for the robustness and the fragility of a network. A major part of my PhD work involved applications of high-throughput sequencing technologies for extracting information at the genomic level. I present SOPRA, a new algorithm for exploiting the mate pair information for assembly of short reads. I have successfully applied SOPRA to real data and were able to assemble scaļ¬olds of signiļ¬cant length with very few errors introduced in the process.Ph.D.Includes bibliographical referencesIncludes vitaby Adel Dayaria