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.
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Showing 1 to 20 of 28 for “"regulatory motifs"”.
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Exploring transcription patterns and regulatory motifs in Arabidopsis thaliana
… be useful in the process of constructing gene regulatory networks. Furthermore, analysis of the intergenic regions corresponding to bidirectional genes can help to identify regulatory elements, such as transcription factor binding sites. Approximately 2500 bidirectional gene pairs have been …
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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… (KMAC) method which discovers DNA-binding motifs from ChIP-Seq derived sequences. I demonstrate that the KSM model is more predictive than the widely used position weight matrix model, and that KMAC outperforms other existing motif discovery programs in recovering known motifs from a large …
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Identification of potential constitutive and tissue-specific promoters and regulatory motifs in Glycine max through datamining of publicly available sequence data
… promoters, as well as several over-represented motifs.
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Computational comparative genomics : genes, regulation, evolution
… blueprint of all protein-coding genes and the regulatory motifs used to coordinate the expression of these genes. Comparative genome analysis of related species provides a general approach for identifying these functional elements, by virtue of their stronger conservation across evolutionary …
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Extracting regulatory signals from DNA sequences using syntactic pattern discovery
… in Escherichia Coli, with known instances of regulatory motifs collected from biological literature, the algorithm showed, in 14 cases, a high sensitivity and specificity of 70% and 80%, respectively. TABS was shown to perform better than two other popular state-of-the-art motif-finding …
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Characterization of six Arabidopsis AROGENATE DEHYDRATASE promoters
… specialized role of each ADT, unique patterns of regulatory motifs were identified for all six ADT promoters, as well as corresponding transcription factors with similar expression profiles to each enzyme. Seven stable transgenic Arabidopsis lines were also generated using ADT promoter-eGFP/GUS …
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A Combined Motif Discovery Method
… bioinformatics is to find the binding sites for regulatory motifs. This is a challenging problem that leads us to a platform to apply a variety of data mining methods. In the efforts described here, a combined motif discovery method that uses mutual information and Gibbs sampling was developed. A …
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Using machine learning to predict gene expression and discover sequence motifs
… a novel algorithm to discover gene sequence motifs associated with temporal expression patterns of genes. Our algorithm, which is based on partial least squares (PLS) regression, is able to directly model the flow of information, from gene sequence to gene expression, to learn cis regulatory …
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QUANTITATIVE MODELING OF SCALING OF PATTERNS AND RECEPTOR SIGNALING IN MORPHOGENESIS
… in the presence of perturbations, and what regulatory mechanisms act to ensure robust and reproducible patterning are two longstanding questions that need unraveling. Moreover, determining the mechanisms by which BMP heterodimers dominate signaling in developing zebrafish embryos and other …
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The identification of potential cis- and trans-acting factors in the regulation of DARK INDUCIBLE 3 (DIN3) expression during darkness and chilling in Arabidopsis thaliana
… could be repressed by low temperature. Specific motifs within the crucial 50bp of the DIN3 promoter were found to be necessary for dark-induced expression, which together was hypothesised to constitute a sugar-responsive sequence. No cis-acting regulatory motifs were found to contribute …
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Models and analysis of yeast mating response : tools for model building, from documentation to time-dependent stimulation
… have revealed many protein families and regulatory motifs also found in higher eukaryotes. This thesis develops several computational and experimental approaches that facilitate characterization of cellular signaling systems, and tests these approaches using yeast mating response as a …
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Whole-organism integrative expressome for C. elegans enables in silico study of developmental regulation
… types is this specific gene most active?"; "Do regulatory motifs exist that switch on or off genes in whole subtrees of the cell pedigree?"; "Which genes are most strongly implicated in apoptosis?", etc. This whole-organism expressome enables direct and powerful in silico analysis of development.
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Mammalian gene regulation through the 3' UTR
… end of a mammalian mRNA is typically rich with regulatory motifs that influence the stability, localization, translation and other properties of the message. We explored two classes of motifs, microRNA (miRNA) complementary sites and cleavage and polyadenylation (poly(A)) signals, and provide …
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A general framework for genome interpretation using evolutionary signatures
… genes [11], RNA genes [17], microRNA genes [16], regulatory motifs and individual binding sites for transcription factors and microRNAs [10]. This work has benefited from the use of evolutionary signatures obtained by observing the genomics changes across the sequence data of related species. We …
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Elucidation of Transcriptional Regulatory Relationships Via Information Theoretic Clustering and Consensus Nucleotide Motif Extraction
… begins with clustering genes based on their co-regulatory expression patterns over the course of a given experiment. An examination of the proposal that clustering genes exhibiting both positively- and negatively-correlated expression provides insight into functional relationships not extracted …
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Cooperative assembly confers regulatory specificity and promotes evolution
… transcriptional regulators (TRs) and DNA cis-regulatory motifs (CRMs) coordinates precise gene expression in eukaryotes. Complexes of multivalent TRs enable the formation of highly specific regulatory connections between otherwise weakly-interacting, low-specificity molecular components and …
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Identifying protein-coding genes and synonymous constraint elements using phylogenetic codon models
… including splicing- and translation-associated regulatory motifs, microRNA target sites, RNA secondary structures, dual-coding genes, and developmental enhancers. We also develop a lineage-specific test which we use to study the evolutionary history of SCEs, and a Bayesian framework that further …
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Interpreting the role of non-coding genetic variation in human disease
… diverse data types: epigenomic profiles, gene regulatory circuitry, and biological pathways. We first develop a method to simultaneously select relevant genomic regions not yet associated with disease as well as select relevant functional annotations enriched in those regions. We show that both …
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Computational Analysis of Gene Expression Regulation from Cross Species Comparison to Single Cell Resolution
… hundreds of common gene families and conserved regulatory motifs between monocots and dicots. We also presented a BLS-based clustering method which takes into account evolutionary relationships among species to identify conserved co-expression genes. Last, we analyzed single-cell RNA-seq data …
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