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 172 for “"Gene Ontology"”.
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GOGO: An Improved Algorithm to Measure the Semantic Similarity Between Gene Ontology Terms
<p>Measuring the semantic similarity between Gene Ontology (GO) terms is an essential step in functional bioinformatics research. We implemented a software named GOGO for calculating the semantic similarity between GO terms. GOGO has the advantages of both information-content-based and hybrid …
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The classification of gene products in the molecular biology domain: Realism, objectivity, and the limitations of the Gene Ontology
… across database resources. One such tool is the Gene Ontology (GO), a classification designed to act as a universal index for gene products from any species. The Gene Ontology is used extensively in annotating gene products and analysing gene expression data, yet very little research exists from …
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Evaluation of Annotation Performances between Automated and Curated Databases of <i>E.COLI</i> Using the Correlation Coefficient
… by drawing upon over 30 information sources. Gene ontology served as one basis of comparison between these databases because of the limited common terms in the ontology annotations. Translation libraries were used to extend the number of BASys terms that could be compared to the gene ontology …
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Genetic analysis of Ximenia Americana under natural conditions
… hybridization approaches have been used for genetic analysis of species that do not have complete genome arrays available. The study used the cross-species DNA-DNA hybridization approach to characterize Ximenia americana biological processes. Preliminary micro-array studies done in the …
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The control of the false discovery rate under structured hypotheses
… structure based on prior information such as Gene Ontology in gene expression data. However, few false discovery rate (FDR) controlling procedures take advantage of this inherent structure. In this dissertation, we develop FDR controlling methods which exploit the structural information of the …
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Proteomic Evaluation and Cytotoxicity of Red Maple (Acer rubrum) Leaves
… De Novo protein profiling by PEAKS Studio-X and Gene Ontology Bioinformatics. The red maple leaves were grounded, defatted in hexane and proteins extracted in 25 mM sodium phosphate buffer pH 6.5. The extracted crude proteins were recovered by precipitation in 80% ammonium sulfate. The …
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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
This is a study of gene regulation in soybean (Glycine max), specifically at the level of transcription. Analysis was performed on publicly available soybean EST data, deposited in the NCBI UniGene database, combined with the soybean genome sequence. EST libraries were grouped based on the tissue …
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Accurate Protein Function Prediction with Graph Transformer-Based Function Localization
… identification of functional regions within the Gene Ontology term prediction pipeline. The core of the model is a Region Proposal Network module that processes protein structure graphs (residues as nodes, contacts as edges) to identify potential functional regions, termed anchors. These anchors …
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Knowledge-based artificial neural network modeling assessment: integrating heterogeneous genomics data to uncover lifespan regulation
… learning continues to grow. More specifically, genetic modeling and neural network building are gaining interest as it becomes a fundamental piece of most model building we see today. We propose a Knowledge-Based Artificial Neural Network (KBANN) to predict phenotype while providing insight to …
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BRIDGE : a bioinformatics software platform for the integration of heterogeneous data from genomic explorations
… arise that often focus on the comparison of genes, genomes and their expression profiles. Inferring new knowledge by combining different kinds of "post genomics" data obviously necessitates the development of new approaches that allow the integration of variable data sources into a flexible …
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Integrating Functional Knowledge into Protein Design: A Novel Approach to Tokenization and Noise Injection for Function-Aware Protein Language Models
… encoding functional context during protein generation. In this work, we present a multimodal protein co-design framework that conditions sequence generation on fine-grained functional annotations, specifically leveraging residue-level Gene Ontology (GO) term labels on sequences from the …
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Structure, Function, and Interaction in Protein Language Models
… for predicting protein functions structured as Gene Ontology terms and predicting protein-protein interactions. Notably, we develop a novel method of modeling the hierarchy constraint in GO term prediction that improves training convergence and test performance while making the model …
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Leveraging expression and network data for protein function prediction
… without human supervision, this is the goal. The Gene Ontology (GO) is a collection of terms that are the standard for protein function annotations. Because of the structure of GO, protein function prediction is a hierarchical multi-label classification problem. The classification method used in …
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Multi-Modal Protein Function Prediction using a Joint Embedding Space from Two Graph Neural Networks
… including enzyme commission (EC) numbers and gene ontology (GO) terms. Experimental results on protein function prediction, as well as a qualitative visual analysis of the protein embedding space show that our framework is able to successfully capture both structure and biomedical context of …
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From Protein Folds to Chromatin: Topological Data Analysis and Deep Learning at Multiple Scales
… provides functional pocket annotations with Gene Ontology and Enzyme Commission terms and enables pocket similarity search for surface and interface comparison through the CASTpFold web server. At the chromatin scale, CHROME introduces a chromatin-structure–guided graph attention framework …
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Investigating gene expression differences in acute and organotypic mouse hippocampal brain slices as models for studying the brain
… I performed a comprehensive comparison of gene expression between OBSCs and acute brain slices prepared from postnatal day 7 mouse hippocampus. I identified significant differences in cellular composition, with OBSCs showing an overrepresentation of glial cells and a relative …
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Within the skin: Grape berries during the mature stages of ripening
… in the late stages of berry development. Gene set enrichment analysis of functional Gene Ontology terms provided evidence for a complex interplay of many gene ontology categories including those involved in the circadian clock, postembryonic development, photosynthesis, hormone signaling, …
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Gene expression patterns of encapsulated microbial cells
… matrices is vital. We analyze the gene expression patterns of stationary phase Saccharomyces cerevisiae (S. cerevisiae) cells encapsulated within three distinct nanostructured silica matrices and relate those patterns to known naturally occurring metabolic states. It was found that …
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Protein Function Prediction Using Graph Convolutional Network
… PLM, high-dimensional feature embeddings are generated from protein sequences. These are integrated with PPI network data and InterPro domains through a two-layer GCN, enabling the model to capture complex interdependencies. The model’s performance was evaluated using metrics such as Fmax and …
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Applications of Machine Learning in Source Attribution and Gene Function Prediction
… data, and (2) the functional annotation of genes using single- cell RNA sequencing data. This work proposes the development of a bioinformatics pipeline tailored for identifying genomic variants, including gene presence/absence and single nu- cleotide polymorphism. This methodology is …
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