Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
Results
Showing 1 to 20 of 64 for “"Computational and Systems Biology Program."”.
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Genomic signatures of sex, selection and speciation in the microbial world
Understanding the microbial world is key to understanding global biogeochemistry, human health and disease, yet this world is largely inaccessible. Microbial genomes, an increasingly accessible data source, provide an ideal entry point. The genome sequences of different microbes may be compared …
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Modeling and designing Bc1-2 family protein interactions using high-throughput interaction data
… cellular function, mediating signal processing and regulating enzymatic activity. Understanding how proteins interact is essential for predicting new binding partners and engineering new functions. Mutational analysis is one way to study the determinants of protein interaction. Traditionally, …
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Web servers, databases, and algorithms for the analysis of protein interaction networks
Understanding the cell as a system has become one of the foremost challenges in the post-genomic era. As a result of advances in high-throughput (HTP) methodologies, we have seen a rapid growth in new types of data at the whole-genome scale. Over the last decade, HTP experimental techniques such as …
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Molecular systems analysis of a cis-encoded epigenetic switch
… for cell populations to survive uncertain and ever-changing environments or make cell-fate decisions in response to external stimuli. Cells may control the degree of gene expression heterogeneity and ultimately levels of phenotypic heterogeneity by modulating promoter switching dynamics. In …
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A constraint optimization framework for discovery of cellular signaling and regulatory networks
Cellular signaling and regulatory networks underlie fundamental biological processes such as growth, differentiation, and response to the environment. Although there are now various high-throughput methods for studying these processes, knowledge of them remains fragmentary. Typically, the majority …
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Protein structure and interaction under environmental stress : from quality control recognition to evolution of collective behavior
… interact with each other, protein misfolding and cellular stress response must be examined both on the scale of individual protein conformational changes and on a more global level, where interaction patterns can reveal larger-scale protein responses to cellular stress. On the individual …
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Biochemical and functional characterization of human RNA binding proteins
RNA not only shuttles information between DNA and proteins but also carries out many other essential cellular functions. Nearly all steps of an RNA's life cycle are controlled by approximately one thousand RNA binding proteins (RBPs) that direct RNA splicing, cleavage and polyadenylation, …
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Measuring the effects of drugs on single cancer cell growth
Understanding the effectiveness of a drug therapy on halting disease progression is an essential aspect of cancer biology. Conventional assays that study cell behavior after a drug intervention report the average response of a cell population which can mask the heterogeneity and dynamics of …
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Dynamics of DNA methylation and genomic imprinting in arabidopsis
… is an epigenetic mark that is highly conserved and important in diverse cellular processes, ranging from transposon silencing to genomic imprinting. In plants, DNA methylation is both mitotically and meiotically heritable, and changes in DNA methylation can be generationally stable and have …
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Experimental and computational analysis of epidermal growth factor receptor pathway phosphorylation dynamics
… processes, including proliferation, migration and differentiation. ErbB 1 heterooligomerizes with three close homologues: ErbB2, ErbB3 and ErbB4. ErbB1-3 receptors are frequently mutated, overexpressed or activated by autocrine or paracrine ligand production in solid tumors and have been the …
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The mechanism and function of pervasive noncoding transcription in the mammalian genome
… RNAs (ncRNAs). We are starting to understand the biogenesis and mechanisms regulating the noncoding transcription. However, it is still unclear what's the functional impact of pervasive transcription and the ncRNAs at the level of the'genome, the cell, and the organism. A large fraction of …
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Microbial community structure and dynamics on patchy landscapes
… effects on industry, the environment, and human health. Understanding how the micron-scale actions (and interactions) of individual microbes give rise to macro-scale consequences remains a major challenge in microbial ecology. However, for the most part, studies employ coarsegrained …
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Computational design of orthogonal antiparallel homodimeric coiled coils
… to biosynthesis, nanostructural assembly, and in processing environmental stimuli through cell-signaling pathways. As fields such as synthetic biology and protein engineering mature they seek to mimic and expand the functions found in living systems that integrate PPIs. A critical feature …
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Mechanistic analysis of polymer-attached inhibitors of influenza virus and their effect on minimizing drug resistance
With the emergence of the 2009 A(H1N1) pandemic influenza virus and the rapid spread of drug resistance in recent years, the need to develop new anti-influenza drugs that can reduce the emergence of new resistant viruses is both urgent and important. This thesis explores the use of polymer-attached …
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Cell-type specific cholinergic modulation of the cortex
… processing, cortical plasticity, arousal and attention. To understand the physiological basis of these brain functions during cholinergic modulation, it is critical to identify the cortical circuit elements involved and define how their interactions contribute to cortical network dynamics. …
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Genetic networks controlled by the bacterial replication initiator and transcription factor DnaA in Bacillus subtilis
… been shown to repress its own transcription and has also been implicated in directing part of the transcriptional response to replication stress. Because dnaA is essential, most of DnaA's potential effects on gene expression have been determined through indirect methods, which have …
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Integrating Omics data : a new software tool and its use in implicating therapeutic targets in Huntington's disease
… are becoming commonplace in biological research and can provide important translational insights, but there is a need for well-crafted user-friendly tools for integrating and analyzing these data. In this thesis, I present versions 1 and 2 of Omics Integrator, a software tool designed to take …
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Integrative approaches for systematic reconstruction of regulatory circuits in mammals
… networks is one of the most challenging tasks in systems biology. Although some models for inferring regulatory networks can make useful predictions about the wiring and mechanisms of molecular interactions, these approaches are still limited and there is a strong need to develop increasingly …
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Rational drug combinations design against intratumoral heterogeneity and clonal evolution
… This results in complex clonal architecture and intratumoral heterogeneity in each patient. This also presents challenges for effective therapeutic intervention - with constant selective pressure to induce or select pre-existing resistant subclones toward drug resistance. …
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Order, disorder, and protein aggregation
… diseases, including Alzheimer's and Parkinson's. At the molecular level, neurotoxicity is thought to originate from toxic gains of function in multimeric aggregates of proteins that are otherwise predominantly monomeric and disordered, fluctuating between a very large number of …
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