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 15 of 15 for “"gene prediction"”.
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Gene prediction with conditional random fields
… annotation of an organism's protein-coding genes is crucial for subsequent genomic analysis. The rapid advance of sequencing technology has created a gap between genomic sequences and their annotations. Automated annotation methods are needed to bridge this gap, but existing solutions based …
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Two new approaches for learning Hidden Markov Models
… in applications such as speech recognition and gene prediction that involve inferring latent variables given observations. For the past few decades, the predominant technique used to infer these hidden variables has been the Baum-Welch algorithm. This thesis utilizes insights from two related …
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Gene identification using phylogenetic metrics with conditional random fields
… a comprehensive and accurate annotation of all genes encoded in the genome, providing the basis for understanding human variation, gene regulation, health and disease. Traditionally, the problem of computational gene prediction has been addressed using graphical probabilistic models of genomic …
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Computational methods for splice site prediction
… to the documentation of the coding exons of each gene, as well as non-coding and regulatory sequences. In spite of the extensive research done in the area, the production of genomic data remains far ahead of the ability to reliably predict such features computationally. Eukaryotic genes consist …
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Identification of novel components that connect cellulose synthases to the cytoskeleton
… approach, including forward and reverse genetics together with advanced co-expression analysis, we identified pom2 as a cellulose deficient mutant. Map- based cloning revealed that the gene locus of POM2 corresponded to CELLULOSE SYNTHASE INTERACTING 1 (CSI1). Intriguingly, we previously …
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Improving genome assembly by identifying reliable sequencing data
… that using partial reads for assembly ii and gene prediction recovers a significant proportion of genes and propose to use this approach for rapid pathogen detection in combination with Single Cell Genomics (SCG). Thanks to SCG, it is now possible to isolate one single cell from environmental …
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Part I characterization of MyoR in C2C12 mouse fibroblasts. Part II isolation and characterization of a novel class II bHLH transcription factor from the black widow spider, latrodectus hesperus
… in the MyoR DNA-binding activity during myogenesis we performed EMSA. Results suggest that changes in MyoR expression fail to account for differences in the DNAbinding complexes to an E-box site.</p> <p>Part II</p> <p>Members of the basic helix-loop-helix (bHLH) family are required for a …
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Data Mining for Selected Genes of Agronomic Interest from the Oil Palm Genome Using a Comparative Genomics Approach
Data mining of genes related to agronomic traits and transcription factors in plant genomes is essential to provide information on target genes for breeders. Taking advantage of the availability of completed genome sequences and the gene model available in a public database, the comparative genomic …
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Nicotine Alters Gene Regulatory Networks in Dopaminergic Neurons in the Ventral Tegmental Area
… and psychoactive component of tobacco, modulates gene expression in many brain regions implicated in the reward pathway. Dopaminergic (DA) neurons originating from the ventral tegmental area (VTA) of the brain are activated by nicotine and form the natural reward pathway that is known to …
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Integrative analysis of heterogeneous genomic datasets to discover genetic etiology of autism spectrum disorders
Understanding the genetic background of complex diseases is crucial to medical research, with implications to diagnosis, treatment and drug development. As molecular approaches to this challenge are time consuming and costly, computational approaches offer an efficient alternative. Such approaches …
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Annotating and characterizing orphan gene in Zea mays via diverse RNA-Seq data
… I refer to "dark transcriptome". Some functional genes have been identified from this dark transcriptome. Most genes in the dark transcriptome are orphan genes. Orphan genes are the recently emerged young genes, which share no sequence similarity with proteins in any other species. In the last 20 …
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Learning on the Graph: Link Prediction, Multi-label Learning, and Applications to Integrative Complex Disease Studies
… Issues of representing and integrating heterogeneous data are complicated by the ongoing growth of large-scale data. In this thesis, we focus on developing enabling network-based approaches for effectively integrating biological data characterized by inherent heterogeneity and …
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Meta State Generalized Hidden Markov Model for Eukaryotic Gene Structure Identification
Using a generalized-clique hidden Markov model (HMM) as the starting point for a eukaryotic gene finder, the objective here is to strengthen the signal information at the transitions between coding and non-coding (c/nc) regions. This is done by enlarging the primitive hidden states associated with …
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A Multimodal Graph Convolutional Approach to Predict Genes Associated with Rare Genetic Diseases
There exist a large number of rare genetic diseases in humans. Our knowledge of the specific gene variants whose presence in the genome of a person predisposes them towards developing a disease, called gene associations, is incomplete. Computational tools which can predict genes which may be …
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Detektion funktioneller RNAs in Genomsequenzen
… mit dem Ziel das Vorkommen von fRNA-kodierenden Genen und regulatorischen Elementen vorherzusagen. Die Pipeline ist nicht nur in der Lage komplette Genome zu untersuchen, sondern kann ebenfalls eine Auswahl einzelner Sequenzen behandeln. Sie wurde daher für die Suche nach möglichen …