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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:

Sysoeva, Tatyana A

Title:

ASYMMETRY IN THE OLIGOMERIC NTRC1 AAA+ MOTOR: NEW IMPLICATIONS FOR THE MECHANISM

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

sigma54-dependent transcription
transcription activator
SAXS
NtrC1
AAA+ ATPase
protein motor

File:

Download Sysoeva_TA_thesis.pdf

Committee Members:

B Tracy Nixon, Dissertation Advisor/Co-Advisor
B Tracy Nixon, Committee Chair/Co-Chair
Kathleen Postle, Committee Member
Ming Tien, Committee Member
Hemant P Yennawar, Committee Member
Howard M Salis, Committee Member

Author:

Speer, Michael Arthur

Title:

Development of a Genetically Modified Silage Inoculant for the Biological Pretreatment of Lignocellulosic Biomass

Graduate Program:

Agricultural and Biological Engineering

Keywords:

Silage
Lactobacillus
Biomass
Bioenergy
Digestibility

File:

Download Mike_Speer_Dissertation.pdf

Committee Members:

Thomas Lehman Richard, Dissertation Advisor/Co-Advisor
Thomas Lehman Richard, Committee Chair/Co-Chair
Howard M Salis, Committee Member
Ming Tien, Committee Member
Maryann Victoria Bruns, Committee Member
Patrick C Cirino, Special 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:

Tian, Tian

Title:

development of a biophysical model of translational coupling to coordinate protein expression

Graduate Program:

Agricultural and Biological Engineering

Keywords:

Translational coupling
Biophysical model
Protein expression
Synthetic biology
Escherichia coli

File:

Download LastThesisFinal.pdf

Committee Members:

Howard M Salis, Thesis Advisor/Co-Advisor

Author:

Chen, Long

Title:

engineering a synthetic replication system to securely store recombinant Dna

Graduate Program:

Agricultural and Biological Engineering

Keywords:

synthetic biology
recombinant DNA
plasmid replication

File:

Download Final_Thesis_Long_2012.pdf

Committee Members:

Howard M Salis, Thesis Advisor/Co-Advisor

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:

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:

Dunham, Noah Paul

Title:

MECHANISTIC INVESTIGATION OF THE DIVERSE IRON AND 2-OXOGLUTARATE-DEPENDENT OXYGENASE SUPERFAMILY

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

enzymology
metalloenzymes
oxygenase
crystallography
structural biology
C-H activation

File:

Download dunham_dissertation_2018.pdf

Committee Members:

Amie Kathleen Boal, Dissertation Advisor/Co-Advisor
Joseph M Bollinger Jr., Committee Chair/Co-Chair
Carsten Krebs, Committee Member
Squire J Booker, Committee Member
Howard M Salis, Outside Member

Author:

Mc Carthy, Erin Lynn

Title:

Destruction and Reformation of an Iron-Sulfur Cluster During Catalysis by Lipoyl Synthase

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Lipoyl Synthase
Lipoic Acid
Radical SAM
NfuA
Iron-sulfur cluster
S-adenosylmethionine

File:

Download McCarthy_thesis_FINAL.pdf

Committee Members:

Squire J Booker, Dissertation Advisor/Co-Advisor
Squire J Booker, Committee Chair/Co-Chair
Carsten Krebs, Committee Member
Amie Kathleen Boal, Committee Member
Howard M Salis, Outside Member
Xin Zhang, Committee Member
Wendy Hanna-Rose, Program Head/Chair

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

Author:

Roggenbaum, Morgan

Title:

Engineering transcriptional logic within bacteria using complex, modular CRISPRi circuit arrays

Graduate Program:

Agricultural and Biological Engineering (MS)

Keywords:

synthetic biology
genetic circuits
CRISPRi
transcriptional read-through

File:

Login to Download

Committee Members:

Jeffrey Catchmark, Professor in Charge/Director of Graduate Studies
Howard M Salis, Thesis Advisor/Co-Advisor
Justin R Pritchard, Committee Member
Esther Gomez, Committee Member

Author:

Essington, Erin

Title:

Rational Engineering of Explosive-Sensing Soil Bacteria

Graduate Program:

Chemical Engineering (MS)

Keywords:

buried explosives
Bacillus subtilis
genetic circuits

File:

Login to Download

Committee Members:

Howard M Salis, Thesis Advisor/Co-Advisor
Esther Gomez, Committee Member
Phillip Savage, Program Head/Chair
Amir Sheikhi, Committee Member