Browsing by Author "Delaney, Nigel Francis"
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The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum
Harcombe, William R.; Delaney, Nigel F.; Leiby, Nicholas; Klitgord, Niels; Marx, Christopher J. (Public Library of Science, 2013)The most powerful genome-scale framework to model metabolism, flux balance analysis (FBA), is an evolutionary optimality model. It hypothesizes selection upon a proposed optimality criterion in order to predict the set of ... -
Development of an Optimized Medium, Strain and High-Throughput Culturing Methods for Methylobacterium extorquens
Delaney, Nigel Francis; Kaczmarek, Maria E.; Ward, Lewis M.; Swanson, Paige Kathleen; Lee, Ming-Chun; Marx, Christopher J (Public Library of Science, 2013)Methylobacterium extorquens strains are the best-studied methylotrophic model system, and their metabolism of single carbon compounds has been studied for over 50 years. Here we develop a new system for high-throughput ... -
FREQ-Seq: A Rapid, Cost-Effective, Sequencing-Based Method to Determine Allele Frequencies Directly from Mixed Populations
Chubiz, Lon M; Lee, Ming-Chun; Delaney, Nigel Francis; Marx, Christopher J (Public Library of Science, 2012)Understanding evolutionary dynamics within microbial populations requires the ability to accurately follow allele frequencies through time. Here we present a rapid, cost-effective method (FREQ-Seq) that leverages Illumina ... -
Mapping the Fitness Landscape of Gene Expression Uncovers the Cause of Antagonism and Sign Epistasis between Adaptive Mutations
Chou, Hsin-Hung; Delaney, Nigel F.; Draghi, Jeremy A.; Marx, Christopher J. (Public Library of Science, 2014)How do adapting populations navigate the tensions between the costs of gene expression and the benefits of gene products to optimize the levels of many genes at once? Here we combined independently-arising beneficial ... -
Processes and Rates of Bacterial Evolution
Delaney, Nigel Francis (2013-10-08)A long-standing question in evolutionary biology is whether adaptation will typically proceed through a few mutations with large selective effects or many mutations with small effects. Many studies have implicated few ...