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Author:

Burgard, Anthony P.

Title:

OPTIMIZATION-BASED FRAMEWORKS FOR THE ANALYSIS AND REDESIGN OF METABOLIC NETWORKS

Graduate Program:

Chemical Engineering

Keywords:

metabolic network
stoichiometric modeling
microbial strain design

File:

Download Thesis_Complete.pdf

Committee Members:

Costas D Maranas, Committee Chair/Co-Chair
Andrew Zydney, Committee Member
Darrell Velegol, Committee Member
Reka Z Albert, Committee Member

Author:

On, Byung-Won

Title:

Data Cleaning Techniques by means of Entity Resolution

Graduate Program:

Computer Science and Engineering

Keywords:

Data Mining
Clustering Algorithms
Graph Algorithms

File:

Download dissertation.pdf

Committee Members:

Dongwon Lee, Committee Chair/Co-Chair
C Lee Giles, Committee Member
Sandeep Purao, Committee Member
Wang Chien Lee, Committee Member
Piotr Berman, Committee Member
Reka Z Albert, Committee Member

Author:

Carrino, Christopher N.

Title:

A Study of Repeat Collaboration in Social Affiliation Networks

Graduate Program:

Industrial Engineering

Keywords:

social network analysis
repeat collaboration
link prediction
link analysis
affiliation network
centrality
similarity
network data mining
pareto clique

File:

Download ChristopherCarrino-Dissertation.pdf

Committee Members:

Soundar Rajan Tirupatikumara, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Leah C Newman, Committee Member
Tao Yao, Committee Member

Author:

Christensen, Claire Petra

Title:

INFERENCE, SIMULATION, MODELING, AND ANALYSIS OF COMPLEX NETWORKS, WITH SPECIAL EMPHASIS ON COMPLEX NETWORKS IN SYSTEMS BIOLOGY

Graduate Program:

Physics

Keywords:

systems biology
gene regulatory networks
graph theory
networks
disease dynamics
computational modeling

File:

Download Christensen_thesis.pdf

Committee Members:

Reka Z Albert, Committee Chair/Co-Chair
Dezhe Jin, Committee Member
Peter E Schiffer, Committee Member
Costas D Maranas, Committee Member

Author:

Wolfe, Daniel N.

Title:

Interactions Between Endemic Bordetella Species and Host Immunity

Graduate Program:

Pathobiology

Keywords:

infectious disease
bacteria
parapertussis
Bordetella
whooping cough

File:

Download thesis__final_version_.pdf

Committee Members:

Eric Thomas Harvill, Committee Chair/Co-Chair
Avery August, Committee Member
Reka Z Albert, Committee Member
Biao He, Committee Member
Mary J Kennett, Committee Member

Author:

Mallapragada, Girish

Title:

Being Open in a Closed World: Essays on Innovation in Open Source Networks

Graduate Program:

Business Administration

Keywords:

new product development
innovation
collaboration
social networks
open source

File:

Download Girish_Mallapragada_Dissertation.pdf

Committee Members:

Gary L Lilien, Committee Chair/Co-Chair
Rajdeep Grewal, Committee Chair/Co-Chair
William T Ross, Committee Member
John C Liechty, Committee Member
Reka Z Albert, Committee Member

Author:

Thadakamalla, Hari Prasad

Title:

Decentralized algorithms for search and routing in large-scale networks

Graduate Program:

Industrial Engineering

Keywords:

decentralized search
localized algorithms
complex networks
networks
local search
algorithms

File:

Download Thadakamalla-Dissertation.pdf

Committee Members:

Soundar Rajan Tirupatikumara, Committee Chair/Co-Chair
Reka Z Albert, Committee Chair/Co-Chair
M Jeya Chandra, Committee Member
Arunachalam Ravindran, Committee Member
Arvind Rangaswamy, Committee Member
Leonid N Vaserstein, Committee Member

Author:

De Keyser, Joshua Gordon

Title:

ALTERNATIVE SPLICING OF THE HUMAN CONSTITUTIVE ANDROSTANE RECEPTOR GENE CREATES RECEPTORS WITH UNIQUE FUNCTION AND LIGAND SPECIFICITY

Graduate Program:

Molecular Toxicology

Keywords:

phthalates
alternative splicing
constitutive androstane receptor
drug and xenobiotic metabolism
meclizine
nuclear receptors
gene induction

File:

Download DeKeyser_dissertation_final.pdf

Committee Members:

Curtis John Omiecinski, Dissertation Advisor/Co-Advisor
Curtis John Omiecinski, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Adam Bleier Glick, Committee Member
John Patrick Vanden Heuvel, Committee Member

Author:

JEONG, JIEUN

Title:

Algorithms for classification and prediction of protein structure and function

Graduate Program:

Computer Science and Engineering

Keywords:

protein structure
protein folds
hairpin loops
folding rules
approximation algorithms
gene regulatory network

File:

Download mythesis.pdf

Committee Members:

Piotr Berman, Committee Chair/Co-Chair
Arthur Mallay Lesk, Committee Member
Webb Colby Miller, Committee Member
Reka Z Albert, Committee Member

Author:

Ko, Kyung Dae

Title:

QUANTITATIVE FUNCTIONAL MEASUREMENT OF A PROTEIN USING PHYLOGENETIC PROFILES

Graduate Program:

Integrative Biosciences

Keywords:

the function of protein
proteomics
bioinformatics
RNA binding protein

File:

Download dissertation_kkd_final.pdf

Committee Members:

Randen L Patterson, Dissertation Advisor/Co-Advisor
Randen L Patterson, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Anton Nekrutenko, Committee Member
Michael N Teng, Committee Member
Damian Van Rossum, Committee Member

Author:

Chen, Ke

Title:

GRANULAR MATERIALS UNDER VIBRATION AND THERMAL CYCLES

Graduate Program:

Physics

Keywords:

thermal cycles
Granular flow
vibration

File:

Download KeChenThesisFinal.pdf

Committee Members:

Peter E Schiffer, Committee Chair/Co-Chair
Julian Decatur Maynard Jr., Committee Member
Reka Z Albert, Committee Member

Author:

Pomeroy, Laura Warlow

Title:

Ecology and Evolution of the Paramyxoviridae

Graduate Program:

Biology

Keywords:

SIR models
harbor seals
wildlife diseases
phocine distemper virus
Paramyxoviruses
coalescent methods

File:

Download LauraPomeroyDissertation.pdf

Committee Members:

Ottar N Bjornstad, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Bryan Grenfell, Committee Member
Edward C Holmes, Committee Member
Peter John Hudson, Committee Member

Author:

Cui, Liying

Title:

Mathematical theory of service composition and service networks

Graduate Program:

Industrial Engineering

Keywords:

dynamic programming
service composition
complex networks
mathematical theory
concept service (CS) network matrix
goal programming
enterprise integration

File:

Download LiYingCui_DissertationApril1111_AdvisorRevised.pdf

Committee Members:

Soundar Kumara, Dissertation Advisor/Co-Advisor
Soundar Kumara, Committee Chair/Co-Chair
Arunachalam Ravindran, Committee Member
Tao Yao, Committee Member
Hong Xu, Committee Member
Reka Z Albert, Committee Member
Dongwon Lee, Committee Member

Author:

Nelson, Martha Irene

Title:

The Genomic Evolution of Human Influenza A Virus

Graduate Program:

Biology

Keywords:

influenza virus
phylogenetics

File:

Download Nelson_MI_Dissertation.pdf

Committee Members:

Andrew George Stephenson, Committee Chair/Co-Chair
Edward C Holmes, Committee Member
Reka Z Albert, Committee Member
Kateryna Dmytrivna Makova, Committee Member

Author:

Shuster, Mitchell

Title:

DEVELOPMENT AND CHARACTERIZATION OF SMALL-MOLECULE-FUNCTIONALIZED CAPTURE SURFACES

Graduate Program:

Physics

Keywords:

quartz crystal microgravimetry
infrared reflection absorption spectroscopy
oligo(ethylene glycol)
small molecule functionalization
microcontact insertion printing
alkanethiol
self-assembled monolayer

File:

Download MJS_thesis.pdf

Committee Members:

Paul S Weiss, Dissertation Advisor/Co-Advisor
Paul S Weiss, Committee Chair/Co-Chair
Anne M Andrews, Committee Member
Vincent Henry Crespi, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Jun Huang, Committee Member

Author:

Dasika, Madhukar S

Title:

SYSTEMS ENGINEERING BASED APPROACHES FOR BIOLOGICAL NETWORK INFERENCE, ANALYSIS AND REDESIGN

Graduate Program:

Chemical Engineering

Keywords:

gene regulatory networks
signaling networks
Optimization
synthetic biology

File:

Download Dasika_Thesis.pdf

Committee Members:

Costas D Maranas, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Patrick C Cirino, Committee Member
Antonios Armaou, Committee Member

Author:

Veeraraghavan, Narayanan

Title:

CATALYTIC AND STRUCTURAL ROLES OF NUCLEOBASES AND METAL IONS IN SMALL RIBOZYMES: NEW INSIGHTS FROM CALCULATIONS AND COMPARISON TO EXPERIMENTS

Graduate Program:

Integrative Biosciences

Keywords:

NLPB
reverse GU wobble
wobble
ribozyme
RNA
molecular dynamics
HDV

File:

Download NVeeraraghavan-eTD.pdf

Committee Members:

Prof Sharon Hammes Schiffer, Dissertation Advisor/Co-Advisor
Philip C. Bevilacqua, Committee Chair/Co-Chair
Sharon Hammes Schiffer, Committee Chair/Co-Chair
William George Noid, Committee Member
Andrey S Krasilnikov, Committee Member
Reka Z Albert, Committee Member

Author:

Zhang, Ranran

Title:

Understanding the long-term survival of cytotoxic T lymphocytes and its application in cancer immunotherapy through a modeling approach

Graduate Program:

Molecular Medicine

Keywords:

cytotoxic T lymphocytes
signaling network
large granular lymphocyte leukemia
cancer immunotherapy
dynamic model

File:

Download Thesis_ZhangR_Jul_3.pdf

Committee Members:

Andrew Paul Loughran, Dissertation Advisor/Co-Advisor
"Thomas P Loughran, Jr", Committee Chair/Co-Chair
Reka Z Albert, Committee Chair/Co-Chair
Istvan Albert, Committee Member
Avery August, Committee Member
Todd Schell, Committee Member

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:

Li, Song

Title:

Identification of Key Regulators of Guard Cell Functions Using Systems Biology Approaches

Graduate Program:

Integrative Biosciences

Keywords:

systems biology
guard cells

File:

Download SongLi_Dissertation.pdf

Committee Members:

Sarah Mary Assmann, Dissertation Advisor/Co-Advisor
Sarah Mary Assmann, Committee Chair/Co-Chair
Reka Z Albert, Committee Chair/Co-Chair
Andrew George Stephenson, Committee Member
Claude Walker Depamphilis, Committee Member
Debashis Ghosh, Committee Member