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 46 for “"regulatory interactions"”.
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Investigation of the regulatory interactions and dynamics between the circadian clock and sigma factors in the cyanobacterium Synechococcus elongatus
… of different lengths we showed that the cis-regulatory elements of rpoD4 transcription are located within 100 bp upstream of its start codon. In addition, deletion of each alternative sigma factor or the known rpoD4 regulator NtcA did not abolish the rpoD4 pulsing dynamics. By analysing …
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Constructing Mathematical Models of Gene Regulatory Networks for the Yeast Cell Cycle and Other Periodic Processes
… work on constructing mathematical models of gene regulatory networks for periodic processes, such as the cell cycle in budding yeast, using biological data sets and applying or developing analysis methods in the areas of mathematics, statistics, and computer science. We identify genes with …
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Regulatory architecture of the Pax6 locus
… a large array of long-range tissue-specific cis-regulatory elements primarily identified through multispecies sequence conservation and reporter studies. I have set out to understand how the chromatin architecture of the locus contributes to the mechanism and specificity of cis-regulatory …
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Developing machine learning tools to understand transcriptional regulation in plants
… of mining gene associations and reconstructing regulatory interactions from large-scale data sets. In this dissertation, several computational tools were developed to address the challenges. In Chapter 2, ConSReg was developed to infer condition-specific regulatory interactions and prioritize …
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Integrating Epigenetic Priors For Improving Computational Identification of Transcription Factor Binding Sites
… binding sites is key in understanding the regulatory interactions of gene expression. Nave computational approaches uses solely DNA sequence data to construct models known as Position Weight Matrices. However, the various assumptions and the lack of background genomic information leads to a …
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CoryneRegNet : a reference database and analysis platform for corynebacterial gene regulatory networks
… of gene expression) and on transcriptional regulatory interactions of microorganisms deduced from literature-derived knowledge, computer predictions and global DNA microarray hybridization experiments, has opened the way for the genome-wide analysis of transcriptional regulatory networks. …
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Convergence of regulatory mutations into oncogenic pathways across multiple tumor types
… genes enriched for non-coding mutations in their regulatory neighborhood and evaluate these in a pan-cancer context. Taken together, we show that low-frequency alterations converge into high-frequency recurrent events on downstream targets through tissue-specific regulatory interactions.
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The Nucleosome Remodelling & Deacetylase complex: Genome folding & transcriptional regulation
… and to modulate the physical dynamics of regulatory genomic elements. In this thesis I will investigate the role of 3D chromatin organisation in NuRD-mediated transcriptional regulation in mouse embryonic stem cells. Specifically, I will make use of experimental data generated from a …
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Non-coding RNA networks regulating leaf vegetative desiccation tolerance in the resurrection plant Xerophyta humilis.
… very little is known with regards to the role of regulatory noncoding RNAs (ncRNAs). To investigate the presence and roles of possible ncRNA players, RNA-Seq was performed on desiccating Xerophyta humilis leaves and a bioinformatic pipeline assembled to identify the potential decoy lncRNAs and …
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Extracting transcriptional regulatory information from DNA microarray expression data
… We have developed networks of potential genetic regulatory interactions through time-series analysis based on the data from our studies. An algorithm for combining gene position information, clustering, and time-lagged correlations has been created to generate networks of hypothetical biological …
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Organizing morphogenesis: Mechanisms of actomyosin patterning by RhoGTPase signaling
… C-GAP are more than simple antagonists and their regulatory interactions provide essential components of myosin patterning and organization. In summary, this thesis provides insight into how a simple and common regulatory module organizes contractility in the ventral furrow across multiple scales, …
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Supervised Inference of Gene Regulatory Networks
A gene regulatory network (GRN) records the interactions among transcription factors and their target genes. GRNs are useful to study how transcription factors (TFs) control gene expression as cells transition between states during differentiation and development. Scientists usually construct GRNs …
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Expression and function of small RNAs in normal and psoriatic skin
… skin. microRNAs: miRNAs) are a class of short, regulatory RNAs that play critical roles in human development and disease. I hypothesized that differential expression of miRNAs might underlie some of the gene expression changes in psoriatic skin. Thus, I sought to characterize the global …
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In silico bacterial gene regulatory network reconstruction from sequence
… notorious example is in the area of gene regulatory networks. A molecular study of gene regulation proceeds one protein at a time, requiring bench scientists months of work purifying transcription factors and performing DNA footprinting studies. Massive scale options like ChIP-Seq and …
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Comparative analysis of BNP Paribas' approaches to energy sustainability, security, and costs in France and South Africa
… sustainability strategies across different regulatory and socio-economic contexts. The study aims to understand how BNP Paribas balances sustainability and profitability in these regions. The research employs a qualitative methodology, using a comparative case study approach. Data was …
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Identification of a Novel Link between the Motor Proteins Dynein and Kinesin-1
… expand our understanding of dynein physical and regulatory interactions, we employed genetic, molecular, and fluorescence microscopy techniques to isolate and analyze mutants affected in hyphal growth and in the localization of cytoplasmic dynein in the model organism Neurosporacrassa. Here we …
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Dissecting Transcriptional Regulatory Networks with Systems Biology Approaches
… using systems biology approaches. Transcription regulatory networks play an important role in mediating external stimuli and coordinating responses to changing environments. Different methods that infer regulatory interactions directly from microarray data have been developed in the recent past. …
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Mathematical modeling approaches for dynamical analysis of protein regulatory networks with applications to the budding yeast cell cycle and the circadian rhythm in cyanobacteria
… become increasingly popular as a tool to study regulatory interactions within gene-protein networks. From the modeler's perspective, two challenges arise in the process of building a mathematical model. First, the same regulatory network can be translated into different types of models at …
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Computational methods for integrating metabolomics data with metabolic engineering strain design
… structures, and explored the impact of regulatory structure on model behavior to determine its robustness and the viability of using a greedy search method to identify regulatory interactions. The work described has led to the development of a modeling framework that allows widely-used …
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Eukaryotic Transcriptional Activation Mechanism: Protein-Protein Interactions
… demonstrated to have physical and functional interactions with TBP and/or TFIIB. Given the central role of TBP in transcriptional regulation, I also identified distinct TBP domains (or residues) important for different regulatory interactions including those with acidic activators, TFIIB, Dr1 …
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