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Full-Text Articles in Life Sciences

Decoding Heterogeneous Big Data In An Integrative Way, Xia Zhang Jan 2013

Decoding Heterogeneous Big Data In An Integrative Way, Xia Zhang

Graduate Theses and Dissertations

Biotechnologies in post-genomic era, especially those that generate data in high-throughput, bring opportunities and challenges that are never faced before. And one of them is how to decode big heterogeneous data for clues that are useful for biological questions. With the exponential growth of a variety of data, comes with more and more applications of systematic approaches that investigate biological questions in an integrative way. Systematic approaches inherently require integration of heterogeneous information, which is urgently calling for a lot more efforts.

In this thesis, the effort is mainly devoted to the development of methods and tools that help to ...


Molecular Regulation Of Il-2 Inducible T-Cell Kinase (Itk) And The Tec Kinases: A Combined Experimental And Computational Study, With Emphasis On The N-Terminal Pleckstrin Homology Domain, Scott Edward Boyken Jan 2013

Molecular Regulation Of Il-2 Inducible T-Cell Kinase (Itk) And The Tec Kinases: A Combined Experimental And Computational Study, With Emphasis On The N-Terminal Pleckstrin Homology Domain, Scott Edward Boyken

Graduate Theses and Dissertations

This dissertation investigates the complex regulation of IL-2 inducible T-cell kinase (Itk) and its related Tec family kinase members, using a combination of experimental and computational approaches. Tec kinases are expressed primarily in hematopoietic cells and regulate key signaling events in lymphocyte activation, differentiation, and development. Itk functions in immune response, fine-tuning signaling downstream of the T-cell Receptor (TCR), and is a putative drug target for allergies and autoimmune disease. Btk, a Tec kinase found in B-cells, carries out a similar role to that of Itk, only downstream of B-cell Receptor (BCR) signaling. The chapters of this dissertation focus on ...


Computational Prediction Of Rna-Protein Interaction Partners And Interfaces, Usha Muppirala Jan 2013

Computational Prediction Of Rna-Protein Interaction Partners And Interfaces, Usha Muppirala

Graduate Theses and Dissertations

RNA-protein interactions play important roles in fundamental cellular processes involved in human diseases, viral replication and defense against pathogens in plants, animals and microbes. However, the detailed recognition mechanisms underlying these interactions are poorly understood. To gain a better understanding of the molecular recognition code for RNA-protein interactions, this dissertation has three related goals: i) to develop methods for predicting RNA-protein interaction partners; ii) to develop an approach for predicting interfacial residues in both the RNA and protein components of RNA-protein complexes; and iii) to develop computational tools and resources for investigating RNA-protein interactions.

First, we present machine learning classifiers ...


On Inferring And Interpreting Genetic Population Structure - Applications To Conservation, And The Estimation Of Pairwise Genetic Relatedness, Arun Sethuraman Jan 2013

On Inferring And Interpreting Genetic Population Structure - Applications To Conservation, And The Estimation Of Pairwise Genetic Relatedness, Arun Sethuraman

Graduate Theses and Dissertations

The presence of population structure is ubiquitous in most wild populations of species. Detecting genetic population structure and understanding its consequences for the evolutionary trajectories of species has shaped a lot of our understanding of the process of evolution. This delineation of subdivision within a population plays an important role in several allied fields, including conservation genetics, association studies, phylogeography, and quantitative genetics. This dissertation addresses methods to infer and interpret subpopulation structure. In this regards, I discuss the standing motivation for developing new analytic tools, a classic population

genetics study of the imperiled freshwater turtle, Emys blandingii, the development ...


Statistical Summary Of Protein Structures, Yuanyuan Huang Jan 2013

Statistical Summary Of Protein Structures, Yuanyuan Huang

Graduate Theses and Dissertations

Every biological system has proteins, and almost all biological activities require the participation or support of a specific set of proteins. Therefore, understanding the functions of the proteins is essential to research in all biological and medical fields. To fully understand their functions, however, it is critical to know their structures and related dynamic behaviours.

There is no unique way of modelling protein structure and dynamics. Experimental techniques have been employed to collect some indirect structural data from which the structures can be deduced. These techniques are costly and time consuming and limited to certain types or sizes of proteins ...


Building And Simulating Protein Machines, Ataur Rahim Katebi Jan 2013

Building And Simulating Protein Machines, Ataur Rahim Katebi

Graduate Theses and Dissertations

Glycolysis is a central metabolic pathway, present in almost all organisms, that produces energy. The pathway has been extensively investigated by biochemists. There is a significant body of structural and biochemical information about this pathway. The complete pathway is a ten step process. At each step, a specific chemical reaction is catalyzed by a specific enzyme. Fructose bisphosphate aldolase (FBA) and triosephosphate isomerase (TIM) catalyze the fourth and the fifth steps on the pathway.

This thesis investigates the possible substrate transfer mechanism between FBA and TIM. FBA cleaves its substrate, the six-carbon fructose-1,6-bisphosphate (FBP), into two three-carbon products - glyceraldehydes ...


Fatty Acid And Polyketide Synthesis Enzymes: Sequences, Structures, And Mechanisms, David Cantu Jan 2013

Fatty Acid And Polyketide Synthesis Enzymes: Sequences, Structures, And Mechanisms, David Cantu

Graduate Theses and Dissertations

The fatty acid and polyketide synthesis enzymes were studied, and findings compose this dissertation. The thioester-active enzyme database (ThYme) was constructed, which provides almost all known sequences of fatty acid and polyketide synthesis enzymes classified and organized into families based on amino acid sequence similarity. ThYme aids in predicting active sites, catalytic residues, and mechanisms of individual sequences, as well as providing a standardized nomenclature. Detailed and timely reviews on thioesterases, ketoacyl reductases, hydroxyacyl dehydratases, enoyl reductases, and acyl carrier proteins, as well as their products and pathways, were also done.

Normal vibrational mode analysis showed that the dynamic behavior ...


Workflow Tools For Biological Applications, Marie C. Vendettuoli Jan 2013

Workflow Tools For Biological Applications, Marie C. Vendettuoli

Graduate Theses and Dissertations

When identifying best practices for multistep processes involving data analysis, it is fre- quently the case that the data scientist is asked to wear many hats simultaneouly: developer, programmer, statistician, graphic designer, writer, administrator. Although many scientists address these roles with great success, it is often at the expense of reproducibility, scalability, and organizational knowledge. The process of formalizing each step of the process creates op- portunity to apply lessons learned and proven tools from multiple disciplines to optimize each step of the transformation from raw data to usable output. This modular approach allows organizations to mix off the shelf ...


Integration Of Large Datasets For Plant Model Organisms, Yves Sucaet Jan 2013

Integration Of Large Datasets For Plant Model Organisms, Yves Sucaet

Graduate Theses and Dissertations

This dissertation is concerned with bioinformatics data integration. The first chapter illustrates the current state of biological pathway databases in general, and in particular, plant pathway databases. Key studies are cited to illustrate the potential benefits that may come from further research into integration methods.

Different models are explored to interface with the various stakeholders of biological data repositories. A public website (http://www.metnetonline.org) was built to address the role of a bioinformatics data warehouse as a server for external third parties. A dedicated API (MetNetAPI: http://www.metnetonline.org/api) accommodates bioinformaticians (and software developers in general ...


Computational And Experimental Analysis Of Tal Effector-Dna Binding, Erin Lynn Doyle Jan 2013

Computational And Experimental Analysis Of Tal Effector-Dna Binding, Erin Lynn Doyle

Graduate Theses and Dissertations

TAL effectors, from the plant-pathogenic bacterial genus Xanthomonas, are DNA binding proteins that can be engineered to bind to almost any sequence of interest. The DNA target of the TAL effector is encoded by a modular central repeat region, with each repeat specifying a single binding site nucleotide. TAL effectors can be targeted to novel DNA sequences by assembling the corresponding repeat sequence. Therefore, custom TAL effectors have become important tools for manipulating gene expression and creating site-specific DNA modifications. This dissertation explores TAL effector-DNA binding through computational and experimental analyses.

I identified positional and composition biases in known TAL ...


Visualization Of Biological Data: Infrastructure, Design And Application, Tengfei Yin Jan 2013

Visualization Of Biological Data: Infrastructure, Design And Application, Tengfei Yin

Graduate Theses and Dissertations

Visualization is an important component of biological data analysis. Ideally, visual methods are tightly integrated with analysis methods, so that it is seamless to plot data from different intermediate stages of the analysis. Bioconductor provides a substantial analysis platform, but limited tools for genomic data visualization. Visual tools for genomic data, eg GenomeView, IGV, IGB, primarily are detached from the analysis engine. This research fills this gap, by developing visualization methods that are integrated into the Bioconductor suite. There are three main components of the research:

* New visual tools for genomic data that utilize the latest research in visualization.

* Infrastructure ...


Understand Biological Regulatory Systems Using Computational Models: Reconstruction, Analysis And Integration, Yao Fu Jan 2013

Understand Biological Regulatory Systems Using Computational Models: Reconstruction, Analysis And Integration, Yao Fu

Graduate Theses and Dissertations

Biological regulatory system is complex and involves many types of interactions, including transcriptional regulations, protein interactions, metabolic reactions and etc., to ensure the regulations of biological organisms. These regulations forms complex networks and play important roles in living organisms to adapt to the environment, control the rate of growth, and develop different phenotypes accordingly to its life cycle and the surrounding environment. Many of mechanisms and interactions of these networks are still not clear. Although better understanding of the regulatory systems is very important for biological research and engineering, to systematically reconstruct, analyze and integrate the complex regulatory systems is ...


Fpga-Based Acceleration Of The Rmap Short Read Mapping Tool, Pooja N. Mhapsekar Jan 2013

Fpga-Based Acceleration Of The Rmap Short Read Mapping Tool, Pooja N. Mhapsekar

Graduate Theses and Dissertations

Bioinformatics is a quickly emerging field. Next generation sequencing technologies are producing data up to several gigabytes per day, making bioinformatics applications increasingly computationally intensive. In order to achieve greater speeds for processing this data, various techniques have been developed. These techniques involve parallelizing algorithms and/or spreading data across many computing nodes composed of devices such as Microprocessors, Graphics Processing Units (GPUs), and Field Programmable Gate Arrays (FPGAs).

In this thesis, an FPGA is used to accelerate a bioinformatics application called RMAP, which is used for Short-Read Mapping. The most computationally intensive function in RMAP, the read mapping function ...


Discovering Meaning From Biological Sequences: Focus On Predicting Misannotated Proteins, Binding Patterns, And G4-Quadruplex Secondary, Carson Michael Andorf Jan 2013

Discovering Meaning From Biological Sequences: Focus On Predicting Misannotated Proteins, Binding Patterns, And G4-Quadruplex Secondary, Carson Michael Andorf

Graduate Theses and Dissertations

Proteins are the principal catalytic agents, structural elements, signal transmitters, transporters, and molecular machines in cells. Experimental determination of protein function is expensive in time and resources compared to computational methods. Hence, assigning proteins function, predicting protein binding patterns, and understanding protein regulation are important problems in functional genomics and key challenges in bioinformatics. This dissertation comprises of three studies. In the first two papers, we apply machine-learning methods to (1) identify misannotated sequences and (2) predict the binding patterns of proteins. The third paper is (3) a genome-wide analysis of G4-quadruplex sequences in the maize genome. The first two ...