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Understanding microbial metabolism using computational methods at different levels of abstraction

dc.contributor.authorGhadermazi, Parsa, author
dc.contributor.authorChan, Siu Hung Joshua, advisor
dc.contributor.authorMunsky, Brian, committee member
dc.contributor.authorPrasad, Ashok, committee member
dc.contributor.authorWrighton, Kelly, committee member
dc.date.accessioned2025-06-02T15:21:06Z
dc.date.available2027-05-28
dc.date.issued2025
dc.descriptionZip file contains supplementary tables 1 and 2 spreadsheets.
dc.description.abstractUnderstanding microbial metabolism and its effect on the surrounding environment represents a critical challenge in microbial ecology, requiring sophisticated computational approaches that can bridge molecular-level interactions with complex ecosystem dynamics. This research presents a comprehensive suite of computational methods that advance our ability to model and predict microbial system behaviors at multiple levels of complexity. This work introduces four computational distinct approaches that address key limitations in existing microbiome modeling techniques: • A bottom-up cellular metabolism model that enables predicting cellular phenotype using a simplified kinetic model for a replicating bacterial cell • SPAM-DFBA, a novel approach integrating dynamic flux balance analysis with reinforcement learning • ADToolbox, a metagenome-informed tool for modeling anaerobic digestion processes • A bioinformatics approach for analyzing complex host-microbiota interactions in mice with colorectal cancer By systematically exploring the trade-offs between model complexity and predictive power, this research expands the analytical toolkit available to microbiome researchers. The methodological progression demonstrates how computational techniques can overcome significant challenges in metabolic modeling, including limited kinetic parameters and biochemical knowledge gaps. Key contributions include: • Novel optimization techniques for simulating cellular metabolism • Enhanced modeling approaches for heterogeneous bacterial communities • Integration of metagenomic data into predictive computational frameworks These advances represent a significant step forward in our ability to understand, predict, and potentially manipulate microbial systems across diverse contexts, from industrial biotechnology to human health applications.
dc.format.mediumborn digital
dc.format.mediumdoctoral dissertations
dc.format.mediumZIP
dc.format.mediumXLSX
dc.identifierGhadermazi_colostate_0053A_18795.pdf
dc.identifier.urihttps://hdl.handle.net/10217/241017
dc.languageEnglish
dc.language.isoeng
dc.publisherColorado State University. Libraries
dc.relation.ispartof2020-
dc.rightsCopyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright.
dc.rights.accessEmbargo expires: 05/28/2027.
dc.titleUnderstanding microbial metabolism using computational methods at different levels of abstraction
dc.typeText
dcterms.embargo.expires2027-05-28
dcterms.embargo.terms2027-05-28
dcterms.rights.dplaThis Item is protected by copyright and/or related rights (https://rightsstatements.org/vocab/InC/1.0/). You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s).
thesis.degree.disciplineChemical and Biological Engineering
thesis.degree.grantorColorado State University
thesis.degree.levelDoctoral
thesis.degree.nameDoctor of Philosophy (Ph.D.)

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