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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:

Zuroff, Trevor Roman

Title:

Engineering a microbial consortium for lignocellulosic biofuel production

Graduate Program:

Chemical Engineering

Keywords:

Lignocellulose
biofuels
Clostridium phytofermentans
cellulose
microbial consortia

File:

Download TRZ_Thesis_7.15.14.pdf

Committee Members:

Wayne Roger Curtis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Member
Thomas Keith Wood, Committee Member
Katriona Shea, Committee Member
Manish Kumar, 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:

Kwan, Brian Wai

Title:

Genetic Basis for Persister Cell Formation

Graduate Program:

Chemical Engineering

Keywords:

persister cells
antibiotic tolerance
toxin/antitoxin system

File:

Download Dissertation_-_Genetic_Basis_for_Persister_Cell_Formation__Brian_Kwan_Final_.pdf

Committee Members:

Thomas Keith Wood, Dissertation Advisor/Co-Advisor
Manish Kumar, Committee Member
Howard M Salis, Committee Member
Stephen John Knabel, 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:

Espah Borujeni, Amin

Title:

The Development of Equilibrium and Non-equilibrium Models of Translation and Riboswitch Regulation: Towards the Automated Design of Cellular Sensors

Graduate Program:

Chemical Engineering

Keywords:

Biophysical Modelling
Translation Initiation
Riboswitch function
RNA folding thermodynamics
RNA folding Kinetics

File:

Download PhD_dissertation_--_Amin_Espah_Borujeni.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Manish Kumar, Committee Member
Kyle Jeffrey Magnuson Bishop, Committee Member
Philip C. Bevilacqua, Committee 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:

Halper, Sean

Title:

Design Optimization Algorithms for Synthetic Biology Applications

Graduate Program:

Chemical Engineering

Keywords:

Synthetic Biology
Metabolic Engineering
CRISPR
Design Optimization
Gene Synthesis

File:

Download Halper_Dissertation_Design_Optimization.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Phillip E Savage, Committee Member
Reka Z Albert, Outside Member
Phillip E Savage, Program Head/Chair

Author:

Reis, Alexander

Title:

Sequence-Level Design of Evolutionary-Robust Genetic Systems

Graduate Program:

Chemical Engineering

Keywords:

synthetic biology
biophysics
CRISPR
genetic circuits
translation initiation

File:

Download Alex_Reis_Dissertation.pdf

Committee Members:

Howard M Salis, Dissertation Advisor/Co-Advisor
Howard M Salis, Committee Chair/Co-Chair
Phillip E Savage, Committee Member
Kristen Fichthorn, Committee Member
Philip C Bevilacqua, Outside Member
Phillip E Savage, Program Head/Chair