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Author:

Ranganathan, Sridhar

Title:

Using Computations to Analyze and Redesign Metabolism

Graduate Program:

Integrative Biosciences

Keywords:

Metabolic Engineering
Optimization

File:

Download Thesis_sridhar_04_18.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Eric Thomas Harvill, Committee Member
Howard M Salis, Committee Member
Cooduvalli S Shashikant, Committee Member

Author:

Zomorrodi, Ali Reza

Title:

Computational tools for genome-scale synthetic lethality analysis and metabolic modeling of microbial communities

Graduate Program:

Chemical Engineering

Keywords:

Metabolic networks
Flux balance analysis
Metabolic Enginnering
Optimization
Systems biology

File:

Download AliRZomorrodi_PhD_Dissertation_Final_2012.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Ali Borhan, Committee Member
Howard M Salis, Committee Member
Reka Z Albert, Committee Member

Author:

Pantazes, Robert Jeffrey

Title:

The development of computational methods for designing antibodies and other proteins

Graduate Program:

Chemical Engineering

Keywords:

protein
antibody
complementarity determining regions
IPRO
MAPs
de novo protein design

File:

Download RPantazesThesisFinal.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Arthur Mallay Lesk, Special Member
Themis Matsoukas, Committee Member
Howard M Salis, Committee Member

Author:

Saha, Rajib

Title:

Reconstruction and analysis of genome-scale metabolic models of photosynthetic organisms

Graduate Program:

Chemical Engineering

Keywords:

Genome-scale model
Cyanobacteria
Zea mays
Cyanothece sp. ATCC51142
Synechocystis sp. PCC6803

File:

Download Saha_dissertation_0728_final.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Howard M Salis, Committee Member
Reka Z Albert, Committee Member

Author:

Farasat, Iman

Title:

Sequence-to-function models for efficient optimization of metabolic pathways and genetic circuits

Graduate Program:

Chemical Engineering

Keywords:

metabolic pathway
genetic circuit
CRISPR
Cas9
modeling
combinatorial optimization
protein expression
optimization

File:

Download Farasat_PhD_dissertation.pdfDownload 1-Farasat_PhD_dissertation.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Ali Borhan, Committee Member
Timothy Charles Meredith, Committee Member
Costas D Maranas, Committee Member

Author:

Tian, Tian

Title:

Coordination of Protein Expression and Autonomous Control of Biosynthesis Pathways

Graduate Program:

Agricultural and Biological Engineering

Keywords:

Protein expression optimization
Dynamic pathway control
Translational coupling
Bio-sensor identification

File:

Download eTD_Tian_final.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Jeffrey M Catchmark, Committee Member
Nicole Robitaille Brown, Committee Member
Costas D Maranas, Outside Member
Thomas Keith Wood, Outside Member

Author:

Grisewood, Matthew Jeffery

Title:

Development and Applications of Computational Enzyme Engineering Tools

Graduate Program:

Chemical Engineering

Keywords:

Iterative Protein Redesign and Optimization
IPRO
Computational
Enzyme
Redesign
Methyl-coenzyme M reductase
acyl-ACP thioesterase
Mcr
'TesA
OptZyme
Optimization
beta-glucuronidase
Protein engineering
Specificity
Activity

File:

Download MGrisewood_Dissertation.pdf

Committee Members:

Costas D Maranas, Dissertation Advisor/Co-Advisor
Costas D Maranas, Committee Chair/Co-Chair
Michael John Janik, Committee Member
Howard M Salis, Committee Member
James Gregory Ferry, Outside Member

Author:

Mc Lellan, James

Title:

Engineering a Neural Network-Like Genetic Circuit In Escherichia coli

Graduate Program:

Chemical Engineering (MS)

Keywords:

CRISPRi
Genetic Circuits
Synthetic Biology

File:

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Committee Members:

Phillip Savage, Program Head/Chair
Howard M Salis, Thesis Advisor/Co-Advisor
Costas D Maranas, Committee Member
Esther Gomez, Committee Member