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Author:

Chen, Xiangyun

Title:

Novel Self-assemble nanoparticles to inhibit cancer growth -effects on ER stress, autophagy, and multidrug resistance by a small molecule

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

Nanomedicine
Multi-drug resistance
cancer

File:

Download XAC-Thesis-20151209-2.pdf

Committee Members:

Yanming Wang, Dissertation Advisor/Co-Advisor
Douglas Cavener, Committee Chair/Co-Chair
Zhi Chun Lai, Committee Member
Lu Bai, Committee Member
Gavin Peter Robertson, Special Member

Author:

Gomez Tejeda Zanudo, Jorge

Title:

Network-based dynamic modeling and control strategies in complex diseases

Graduate Program:

Physics

Keywords:

Systems Biology
Complex Networks
Network models
Cancer

File:

Download Dissertation-JGTZanudo-Final.pdf

Committee Members:

Reka Z Albert, Dissertation Advisor/Co-Advisor
Reka Z Albert, Committee Chair/Co-Chair
Dezhe Jin, Committee Member
Lu Bai, Committee Member
Timothy Reluga, Committee Member
Richard Wallace Robinett, Special Member

Author:

Surendra Lal, Sumithra

Title:

Statistical inference of syntax from vocal sequences and implications for neural mechanisms

Graduate Program:

Physics

Keywords:

vocal sequences
syntax
Partially Observable Markov Model
songbird
Bengalese finch
syllable repetition
canary
swamp sparrow
neural circuits

File:

Download SSurendralal-Dissertation.pdf

Committee Members:

Dezhe Z Jin, Dissertation Advisor/Co-Advisor
Dezhe Z Jin, Committee Chair/Co-Chair
John C Collins, Committee Member
Lu Bai, Committee Member
Patrick James Drew, Outside Member

Author:

sun, jinquan

Title:

A NOVEL SMALL MOLECULE DNA INTERCALATOR PZ1225 IN CANCER CELL APOPTOSIS AND A HISTONE MODIFIER PAD4 IN MACROPHAGE EXTRACELLULAR TRAP FORMATION

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

DNA damage
DNA intercalator
small molecule
MAPK
mTOR
apoptosis
macrophage
extracellular traps
PAD4
citrullination
stroke

File:

Download Graduation_Thesis-Jinquan-20161201.pdf

Committee Members:

Yanming Wang, Dissertation Advisor/Co-Advisor
Zhi-Chun Lai, Committee Chair/Co-Chair
Douglas Cavener, Committee Member
Lu Bai, Committee Member
Robert Paulson, Outside Member

Author:

Kim, Sang-Ah

Title:

STRUCTURAL AND BIOCHEMICAL CHARACTERIZATION OF LSD1/COREST HISTONE DEMETHYLASE COMPLEX ON THE NUCLEOSOME

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

nucleosome
chromatin
structural biology
gene regulation
histone demethylase
lsd1

File:

Download PhD_Dissertation__Sang-Ah_Kim__-_Final_Draft_2016_12_08.pdf

Committee Members:

Song Tan, Dissertation Advisor/Co-Advisor
Andrey S. Krasilnikov, Committee Chair/Co-Chair
Lu Bai, Committee Member
David S. Gilmour, Committee Member
Scott Showalter, Outside Member

Author:

Browder, Kristen Cherie

Title:

THE ROLE AND REGULATION OF APICAL SPECTRINS IN CELL POLARITY, TRAFFICKING, GROWTH, AND CORTICAL TENSION IN DROSOPHILA MELANOGASTER

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Crumbs
Protein Phosphatase 2A (PP2A)
Tension
Beta Heavy-Spectrin
Alpha Spectrin
Polarity
Par6
Sdt
aPKC
Strain Sensor
Endocytosis
Hippo/Warts Pathway
cpstFRET
Drosophila

File:

Download Kristen_C_Browder_Dissertation.pdf

Committee Members:

Graham H. Thomas, Dissertation Advisor/Co-Advisor
Graham H. Thomas, Committee Chair/Co-Chair
Melissa Rolls, Committee Member
Lorraine Santy, Committee Member
William Hancock, Outside Member
Lu Bai, Committee Member

Author:

Liu, Jingrui

Title:

Identification and characterization of DUF288 (Domain of Unknown Function 288) proteins required for cell wall synthesis

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

glycosyltransferase
polysaccharides
cell wall synthesis
Arabidopsis
plants

File:

Download master_thesis_Jingrui_Liu.pdf

Committee Members:

Ying Gu, Thesis Advisor/Co-Advisor
Xin Zhang, Committee Member
Lu Bai, Committee Member

Author:

Foley, Thomas Thomassen

Title:

Statistical Mechanics of Coarse-Graining

Graduate Program:

Physics

Keywords:

Coarse-graining
Modeling
Renormalization
Statistical Mechanics
Gaussian Network Model
Complex Networks
Community Detection
Model Selection
Phase Transitions

File:

Download ThomasFoley.pdf

Committee Members:

William George Noid, Dissertation Advisor/Co-Advisor
Jorge Osvaldo Sofo, Committee Chair/Co-Chair
Reka Z Albert, Committee Member
Lu Bai, Committee Member
Lu Bai, Outside Member

Author:

Baumann, Douglas G

Title:

CORE PROMOTER FUNCTION IN TRANSCRIPTIONAL REGULATION OF CONSTITUTIVELY EXPRESSED GENES IN DROSOPHILA

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Promoter
Transcription
Drosophila
Initiation
Glutathione
Motif 1
Pausing
GST
Housekeeping
TRF2
TBP-related factors
TBP
TFIID
DREF
M1BP
DRE
Motif 6
TADs
GFZF

File:

Download Dissertation_Baumann__Final.pdf

Committee Members:

David Scott Gilmour, Dissertation Advisor/Co-Advisor
David Scott Gilmour, Committee Chair/Co-Chair
Joseph C. Reese, Committee Member
Lu Bai, Committee Member
Tae-Hee Lee, Outside Member
Shaun A Mahony, Committee Member

Author:

Yan, Chao

Title:

Gene Regulation By Divergent Gene Pairs and Nucleosome Depleting Factors

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Nucleosome depleting factors
divergent gene pairs
divergent transcription
transcription
gene regulation

File:

Download 1810_Thesis_Draft_Chao_final.pdf

Committee Members:

Lu Bai, Dissertation Advisor/Co-Advisor
Lu Bai, Committee Chair/Co-Chair
Joseph C. Reese, Committee Member
Benjamin Franklin Pugh, Committee Member
William O Hancock, Outside Member
Shaun A Mahony, Committee Member

Author:

Du, Manyu

Title:

MECHANISTIC STUDIES OF LONG-DISTANCE GENE REGULATION IN BUDDING YEAST

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

gene expression
3D genome organization
long-distance chromosomal interactions
3D gene clustering

File:

Download Thesis_ManyuDu_final.pdf

Committee Members:

Lu Bai, Dissertation Advisor/Co-Advisor
Lu Bai, Committee Chair/Co-Chair
Manuel Llinas, Committee Member
Benjamin Franklin Pugh, Committee Member
Qunhua Li, Outside Member
Ken Keiler, Program Head/Chair
David Scott Gilmour, Committee Member

Author:

Singh, Suprita

Title:

Characterizing the functional role of the transcriptional regulator PfAP2-G2 in Plasmodium falciparum gametocytogenesis

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Plasmodium falciparum
AP2-G2

File:

Download Suprita_Singh_Thesis_FINAL_DRAFT.pdf

Committee Members:

Manuel Llinas, Dissertation Advisor/Co-Advisor
Manuel Llinas, Committee Chair/Co-Chair
Scott Eugene Lindner, Committee Member
Shaun Mahony, Committee Member
Andrew Fraser Read, Outside Member
Lu Bai, Committee Member
Wendy Hanna-Rose, Program Head/Chair

Author:

Shin, Yeonoh

Title:

Structural Basis of Bacterial Transcription: Investigation of Mechanisms of Reiterative Transcription and Ribosomal RNA Transcription by X-ray Crystallography and Cryo-Electron Microscopy

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology

Keywords:

Transcription
RNA polymerase
X-ray crystallography
Cryo-electron microscopy
Ribosomal RNA
Reiterative transcription

File:

Download YeonohShin_DissertationFinal.pdf

Committee Members:

Katsuhiko Murakami, Dissertation Advisor/Co-Advisor
Katsuhiko Murakami, Committee Chair/Co-Chair
Paul Babitzke, Committee Member
David Scott Gilmour, Committee Member
Philip C Bevilacqua, Outside Member
Lu Bai, Committee Member
Wendy Hanna-Rose, Program Head/Chair

Author:

Feng, Qingzhou

Title:

Motor dynamics underling bidirectional cargo transport by kinesin and dynein

Graduate Program:

Molecular, Cellular and Integrative Biosciences

Keywords:

kinesin
dynein
microtubule
bidirectional transport

File:

Download Thesis_May2020QF.pdf

Committee Members:

William O Hancock, Dissertation Advisor/Co-Advisor
Melissa Rolls, Committee Member
Lu Bai, Committee Member
Charles T Anderson, Committee Member
Christopher Martin Yengo, Outside Member
Melissa Rolls, Program Head/Chair
William O. Hancock, Committee Chair/Co-Chair

Author:

Bonnell, Victoria

Title:

DNA sequence context and the chromatin landscape differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology (PHD)

Keywords:

Molecular Parasitology
Gene Regulation
Transcription Factor Binding
Malaria
Sequence-specific Transcription Factors

File:

Download BONNELL_Dissertation_HighResVersion_FINAL_March2023_FormatFixed.pdf

Committee Members:

Elizabeth Mcgraw, Outside Unit & Field Member
Shaun Mahony, Major Field Member
Scott Lindner, Major Field Member
Manuel Llinas, Chair & Dissertation Advisor
Wendy Hanna-Rose, Program Head/Chair
Lu Bai, Major Field Member
B. Franklin Pugh, Special Member

Author:

Huynh, Mai

Title:

The structure and dynamics of the nucleosome at a single molecule level

Graduate Program:

Chemistry (PHD)

Keywords:

transcription
nucleosome
histone post-translational modifications
histone acetylation
histone methylation
histone ubiquitylation

File:

Download PhD_Dissertation_MH_v4.pdf

Committee Members:

Mark Hedglin, Major Field Member
Lu Bai, Outside Unit & Field Member
Tae-Hee Lee, Chair & Dissertation Advisor
Philip Bevilacqua, Program Head/Chair
Ruobo Zhou, Major Field Member

Author:

Rozum, Jordan

Title:

Attractor identification and control of Boolean and ODE network models in systems biology

Graduate Program:

Physics (PHD)

Keywords:

systems biology
network science
discrete dynamics
Boolean networks
gene regulatory networks
ordinary differential equations
control theory
stable motifs

File:

Download Rozum_Dissertation_format-revision.pdf

Committee Members:

Dezhe Jin, Major Field Member
Lu Bai, Major Field Member
Reka Albert, Chair & Dissertation Advisor
Timothy Reluga, Outside Unit & Field Member
Nitin Samarth, Program Head/Chair

Author:

Zou, Fan

Title:

Long Range Chromosomal Interactions and First Passage Process in Budding Yeast

Graduate Program:

Physics (PHD)

Keywords:

Chromosome organization
Chromosomal interaction
chromosomal diffusion
first passage time
Rouse polymer model

File:

Login to Download

Committee Members:

Qunhua Li, Outside Unit Member
Dezhe Jin, Major Field Member
David Gilmour, Outside Field Member
Lu Bai, Chair & Dissertation Advisor
Reka Albert, Major Field Member
Nitin Samarth, Program Head/Chair

Author:

Chen, Hengye

Title:

Investigation of the mechanism underlying nucleosome invasion by nucleosome-displacing factors

Graduate Program:

Biochemistry, Microbiology, and Molecular Biology (PHD)

Keywords:

gene regulation
pioneer factor
nucleosome positioning
chromatin remodeler
nucleosome-displacing factor
nucleosome-depleted region
TF binding
nucleosome mapping

File:

Download 202208_Hengye_Chen_thesis_v5.pdf

Committee Members:

Joseph Reese, Major Field Member
David Gilmour, Major Field Member
Xiaojun Lian, Outside Unit & Field Member
Shaun Mahony, Major Field Member
Lu Bai, Chair & Dissertation Advisor
Ken Keiler, Professor in Charge/Director of Graduate Studies

Author:

Lu, Jiali

Title:

Modelling Birdsong Syntax with Partially Observed Markov Models

Graduate Program:

Physics (PHD)

Keywords:

birdsong
neuroscience
probabilistic modelling
complex system

File:

Login to Download

Committee Members:

Yingwei Mao, Outside Unit & Field Member
Dezhe Jin, Chair & Dissertation Advisor
Lu Bai, Major Field Member
Reka Albert, Major Field Member
Mauricio Terrones, Program Head/Chair