Probing statistical patterns across the tree of life: Comparative methods for microbial genomes and traits
Li, Zeqian
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https://hdl.handle.net/2142/122088
Description
Title
Probing statistical patterns across the tree of life: Comparative methods for microbial genomes and traits
Author(s)
Li, Zeqian
Issue Date
2023-07-31
Director of Research (if dissertation) or Advisor (if thesis)
Kuehn, Seppe
Doctoral Committee Chair(s)
Song, Jun
Committee Member(s)
Maslov, Sergei
Coleman, Maureen
Department of Study
Physics
Discipline
Physics
Degree Granting Institution
University of Illinois at Urbana-Champaign
Degree Name
Ph.D.
Degree Level
Dissertation
Keyword(s)
Microbial ecology
Abstract
Microbes are essential to the global ecosystem and constitute most biodiversity observed in the tree of life. In understanding microbes from natural environments, the central problem is to predict microbial community functions (phenotypes) from structures (composition and genetic content). While community structure measure- ment became accessible through next-generation sequencing, mapping the structure to function remains challenging due to difficulties in each level of the sequence-protein-metabolism-community hierarchy for diverse microbes. To address this challenge, comparative methods serve as a powerful data-driven tool, by identifying dominant statistical patterns in biological data, linking these patterns to biological phenomena, and ultimately accurately predicting functions from structures.
In this dissertation, I present my contributions to five projects that employ comparative methods to address the structure-function mapping problem in microbial communities within the sequence-protein-metabolism-community hierarchy. These projects include the statistical prediction of microbial metabolic traits from genomes, the discovery of novel constraints in the genome organization of closely related microbial strains, the investigation of co-evolution patterns within the denitrification pathway, and the measurement of two novel microbial traits using a theoretical framework of chemical equilibria.
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