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Systems biology approaches to corticosteroid pharmacogenomics and systemic inflammation

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TitleInfo
Title
Systems biology approaches to corticosteroid pharmacogenomics and systemic inflammation
Name (type = personal)
NamePart (type = family)
Nguyen
NamePart (type = given)
Tung Thanh
NamePart (type = date)
1979-
DisplayForm
Tung Nguyen
Role
RoleTerm (authority = RULIB)
author
Name (type = personal)
NamePart (type = family)
Androulakis
NamePart (type = given)
Ioannis P
DisplayForm
Ioannis P Androulakis
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
chair
Name (type = personal)
NamePart (type = family)
Bhanot
NamePart (type = given)
Gyan
DisplayForm
Gyan Bhanot
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Shinbrot
NamePart (type = given)
Troy
DisplayForm
Troy Shinbrot
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
internal member
Name (type = personal)
NamePart (type = family)
Calvano
NamePart (type = given)
Steven E
DisplayForm
Steven E Calvano
Affiliation
Advisory Committee
Role
RoleTerm (authority = RULIB)
outside member
Name (type = corporate)
NamePart
Rutgers University
Role
RoleTerm (authority = RULIB)
degree grantor
Name (type = corporate)
NamePart
Graduate School - New Brunswick
Role
RoleTerm (authority = RULIB)
school
TypeOfResource
Text
Genre (authority = marcgt)
theses
OriginInfo
DateCreated (qualifier = exact)
2012
DateOther (qualifier = exact); (type = degree)
2012-01
CopyrightDate (qualifier = exact)
2012
Place
PlaceTerm (type = code)
xx
Language
LanguageTerm (authority = ISO639-2b); (type = code)
eng
Abstract (type = abstract)
Despite increasing knowledge about pathophysiological pathways and cellular processes involved in diseases, the molecular mechanisms and physiological significance are not fully understood. Consequently, within this exploratory research we wish to lay the foundations for developing bioinformatics tools and systems biology approaches towards the analysis and modeling of transcriptional dynamics and the understanding of gene transcriptional regulatory program. Two in vivo models, namely corticosteroid pharmacogenomics in rat and human endotoxemia in human, have been investigated to gain insights into (1) adverse-effects, tissue-specificity, and circadian effects under corticosteroid treatment, (2) temporal regulatory programs in acute inflammation, and (3) cellular variability and synchronization as well as time-dependent systemic responses under acute stress. In order to pursue these goals, the hypothesis that informative components of the genome-wide transcriptional dynamics are composed of genes which are either co-expressed and co-functional or co-expressed across multiple conditions has been pursued to identify significant genome-wide transcriptional signatures. Concepts from consensus clustering and meta-analysis have been explored to avoid the bias and assumption of each single clustering method/metric and handle challenges in the analysis of microarray data from heterogeneous sources. Subsequently, the mysteries and complexities of transcriptional regulation have been explored by using two main strategies, namely phylogenetic foot-printing and context-specific CRM search, to identify relevant transcriptional regulators and examine the putative temporal transcriptional regulatory program. Additionally, an in silico multi-level agent-based model of human endotoxemia has been constructed to gain insights into cellular behaviors and circadian effects under acute stress. The model captures stochastic transcriptional dynamics and critical aspects of the in vivo physiological human endotoxemia model. By defining novel hypothetical quantities such as the variability-based fitness and the synchronization level, we provided a step forward to the exploration of cell-to-cell variability and stochastic dynamics of cellular behaviors as well as predictive implications inferred from cellular variability. In summary, our work aims at (i) identification of critical transcriptional signatures and regulatory controls to provide a better understanding of system behaviors and (ii) simulation to understand the cellular behaviors and circadian effects within specific contexts.
Subject (authority = RUETD)
Topic
Computational Biology and Molecular Biophysics
RelatedItem (type = host)
TitleInfo
Title
Rutgers University Electronic Theses and Dissertations
Identifier (type = RULIB)
ETD
Identifier
ETD_3780
PhysicalDescription
Form (authority = gmd)
electronic resource
InternetMediaType
application/pdf
InternetMediaType
text/xml
Extent
xiv, 200 p. : ill.
Note (type = degree)
Ph.D.
Note (type = bibliography)
Includes bibliographical references
Note (type = vita)
Includes vita
Note (type = statement of responsibility)
by Tung Thanh Nguyen
Subject (authority = ETD-LCSH)
Topic
Computational biology
Subject (authority = ETD-LCSH)
Topic
Bioinformatics
Subject (authority = ETD-LCSH)
Topic
Systems biology
Identifier (type = hdl)
http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000064152
RelatedItem (type = host)
TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
Identifier (type = local)
rucore19991600001
Location
PhysicalLocation (authority = marcorg); (displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier (type = doi)
doi:10.7282/T34B30BD
Genre (authority = ExL-Esploro)
ETD doctoral
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Rights

RightsDeclaration (ID = rulibRdec0006)
The author owns the copyright to this work.
RightsHolder (type = personal)
Name
FamilyName
Nguyen
GivenName
Tung
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime (encoding = w3cdtf); (qualifier = exact); (point = start)
2012-01-04 17:44:36
AssociatedEntity
Name
Tung Nguyen
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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