Computational Tools for Metabolic Modeling and Gene Duplication Analysis ...

• Main Author: Spivakovsky-Gonzalez, Pablo
• Format: Thesis
• Language: English
• Published: Apollo - University of Cambridge Repository 2021
• Subjects: Bioinformatics; FOS Computer and information sciences; Antarctic; Antarc*
• Online Access: https://dx.doi.org/10.17863/cam.86478; https://www.repository.cam.ac.uk/handle/1810/339067

This thesis presents new computational methods to analyse both short and long-term effects of temperature increase on biological systems. First, we consider the problem of acclimation of an organism to increased temperatures on short timescales. We develop a novel method of network regression, AccliNet, based on the acclimation times, which takes into account prior knowledge of functional links between genes to improve the performance of the algorithm. The results obtained by AccliNet are compared with the performance of existing algorithms and are shown to be an improvement in this area. Next, we delve deeper into the metabolic response of the organism to changing temperatures, and develop methods to model and simulate the fluxes of metabolites occurring through a metabolic network. In particular, we construct a simplified model of aerobic respiration for an Antarctic species, and, given a gene expression dataset across different temperatures, we develop two different machine learning approaches to model ...