Dissertation/Thesis Abstract

Evaluating Transcriptional Regulation Through Multiple Lenses
by Grubisic, Ivan, Ph.D., University of California, Berkeley, 2014, 129; 3640448
Abstract (Summary)

Scientific research, especially within the space of translational research is becoming increasingly multidisciplinary. With the development of each new method there is not only a need for a broad fundamental understanding of all the sciences and mathematics, but also an acute awareness of how errors propagate across methods, the limitation of the methods and what contextual frameworks need to be used for the interpretation. The ability to understand transcriptional mechanisms and the affect that subtle changes in equilibrium may have on cell fate decisions has been greatly advanced by next generation sequencing and subsequent tools that have been developed. Bioinformatic techniques can serve multiple roles. They fundamentally provide a global picture of what is happening within an experimental condition which can then be used to either confirm individual experimental findings as globally relevant, or to discover new insights to inform the next iteration of experiments. Many of the experiments are done in in vitro conditions and therefore I have also focused energy on trying to understand how the mechanical inputs, largely not representative of what is occurring in vivo, from these methods affect transcriptional regulation. Much of this research requires the switching of frameworks to understand how results from disparate data sources can be correlated. I then applied a similar thought process to the development of Lens. Without an effective means of communicating research findings in an elegant and streamline mannered, we are slowing down the ability for researchers to learn new frame- works to efficiently approach the next research questions. In addition to better methods of communicating, we also need more modular and simplified tools that can be applied to various experimental systems to increase the speed and efficiency of translational research.

Indexing (document details)
Advisor: Tjian, Robert, Fletcher, Daniel
Commitee: Alliston, Tamara, Eisen, Michael
School: University of California, Berkeley
Department: Bioengineering
School Location: United States -- California
Source: DAI-B 76/02(E), Dissertation Abstracts International
Subjects: Biomedical engineering, Bioinformatics
Keywords: Bioinformatics, Mechanotransduction, Multiply-aligned sequences, Next-generation sequencing, Open access publishing
Publication Number: 3640448
ISBN: 9781321259100
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