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 12 of 12 for “"cis-regulatory modules"”.
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Identification of Drosophila heart-specific Cis-Regulatory Modules under Hox control
… aim of our work is to isolate the heart-specific cisregulatory sequences of abd-A direct target genes, the realizator genes granting heart identity. In each segment of the heart, four pairs of cardiomyocytes (CMs) express tinman (tin), homologous to NKX2-5, and acquire strong contractile and …
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ModuleFinder : a computational model for the identification of Cis regulatory modules
… the likelihood that a given genomic region is a cis regulatory module (CRM) for an input set of TFs according to its degree of: (1) homotypic site clustering; (2) heterotypic site clustering; and (3) evolutionary conservation across multiple genomes. Importantly, ModuleFinder obtains all …
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Discovering Conserved cis-Regulatory Elements That Regulate Expression in Caenorhabditis elegans
… is two-fold:: 1) To catalog all <italic>cis</italic>-regulatory elements within the intergenic and intronic regions surrounding every gene in <italic>C.elegans</italic>: i.e. the regulome) and: 2) to determine which cis-regulatory elements are associated with expression under specific …
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Computational Models of Function and Evolution of cis-Regulatory Sequences
Gene expression is controlled by regulatory DNA sequences, often called cis-regulatory modules or CRMs in higher organisms. Even though complete genomes are available in many species, a catalog of CRMs is far from complete. Meanwhile, how basic building blocks of CRMs, called transcription factor …
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Exploiting rice diversity to uncover durable and broad-spectrum resistance
… presence and polymorphisms in defense-responsive cis-regulatory modules (CRMs) in gene promoters, (2) predicting gene promoters targeted by multiple X. oryzae strains, and (3) assessing the presence of SNP markers associated with resistance to X. oryzae strains. We also analyzed a cluster of …
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In silico approaches to investigating mechanisms of gene regulation
… characterization of regions influencing the precise spatial and temporal expression of genes is critical to our understanding of gene regulatory networks. Connecting transcription factors to the cis-regulatory elements that they bind and regulate remains a challenging problem in computational …
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Computational discovery of Cis-regulatory elements in multiple drosophila species
… factors control gene expression by binding regulatory DNA segments called cis-regulatory modules (CRMs). The increasing number of sequenced genomes of multicellular eukaryotes along with high-throughput methods such as whole genome microarray expression data allows for systematic …
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Computational Prediction of Functional Elements through Comparative Genomics
… such as protein coding genes, transcriptional regulatory sequences, and non-coding RNA genes. This dissertation research has been focused on two grand challenges of genomics: (i) to decode cis-regulatory modules (CRMs), non-coding DNA sequences controlling gene expression; and (ii) to discover …
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Bayesian Integration and Modeling for Next-generation Sequencing Data Analysis
… on weak binding signal detection. To infer cis-regulatory modules (CRMs) of multiple TFs, we propose to develop a Bayesian integration approach, namely BICORN, to integrate ChIP-seq and RNA-seq data of the same tissue. Each TFBS identified from ChIP-seq data can be either a functional …
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Cis-regulatory module analysis: inferring regulatory networks and underlying mechanisms
… and annotate the regions that control the precise spatial and temporal expression of the genes. Cis- regulatory modules (CRMs/enhancers), main players of this regulatory process, are typically short (<1kb) sequences that are embedded in non-coding regions of the genome. They harbor …
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Computationally-guided inference of cis-regulatory codes in metazoans
… Deciphering the networks of genes, their regulatory proteins (transcription factors (TFs)) and their regulatory DNA elements (cis-regulatory modules (CRMs)) is fundamental to the understanding of the biological processes they underlie. These processes include the formation and maintenance …
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Computational modeling of gene expression from regulatory sequences
… regulation of gene expression is dictated by regulatory DNA sequences, often called cis-regulatory modules (CRM; also known as “enhancer”), that contain specific binding sites for regulatory proteins (transcription factors, TF). The assembly of TFs bound on a CRM drives the desired expression …