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 50 for “"Gene Ontology (GO)"”.
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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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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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Leveraging expression and network data for protein function prediction
… be used 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 …
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Multi-Modal Protein Function Prediction using a Joint Embedding Space from Two Graph Neural Networks
… an influx of deep-learning protein folding algorithms used for predicting function by transfer learning. Protein function is only partially captured by each of a large number of modalities including structure, however, in isolation they only give us a partial understanding of function. Uniting …
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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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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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Detecting Phenotype-Specific Interactions Between Biological Processes From Microarray Data And Annotations
… biological interpretation of the voluminous data generated by these technologies, however, remains a challenging problem. A commonly used approach in interpreting the results of such high throughput experiments is to map the list of differentially expressed (DE) genes to gene ontology (GO) terms, …
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Investigating the effect of paralogs on microarray gene-set analysis
… analysis of individual differentially expressed genes to analyses of sets of genes. These gene-set analysis (GSA) methods use previously accumulated biological knowledge from databases such as the Gene Ontology (GO) or KEGG to group genes into sets based on their annotations. They aim to rank …
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Development of an ontology of animals in context within the OBO Foundry framework from a SNOMED-CT extension and subset
… sharing of information. This work develops an ontology of animal classes that form the basis for communication of animal identifying information among animal managers, medical professionals caring for animals and biomedical researchers involved in disciplines as diverse as wildlife ecology and …
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Computational Labeling, Partitioning, and Balancing of Molecular Networks
… prediction on bilayer networks. By integrating Gene Ontology (GO) hierarchy with protein-protein interaction network, our AptRank outperforms four state-of-the-art methods in a comprehensive evaluation using benchmark datasets. (2) We next extend our AptRank into a network partitioning method, …
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Proteomic Identification of Hemp (Cannabis sativa) Seeds by Tandem Mass Spectrometry and Evaluation of Cytotoxic Activity
… 154 µg/ml, suggesting relatively mild effects. Gene Ontology (GO) analysis was employed to elucidate the biological processes, molecular functions, and cellular components associated with trypsin-digested bound Blue Sepharose hemp seed proteins.</p>
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Co-regulation of the Smooth Muscle Cell Alternative Splicing Programme by the RNA-Binding Proteins RBPMS, RBFOX2, MBNL1, and QKI
… et al., 2019). However, the cooperative and antagonistic relationships between RBPMS and other RNAbinding proteins (RBPs) in this regulatory network remain unclear. In this study, I investigated RBFOX2, MBNL1, and QKI as potential co-regulators of RBPMS in VSMC AS regulation. RBFOX2 was …
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Computational Dissection of Composite Molecular Signatures and Transcriptional Modules
… modeling framework with which to analyze gene expression profiling data for computational dissection of molecular signatures and transcriptional modules. The first part of the dissertation is focused on extracting pure gene expression signals from tissue or cell mixtures. The main goal of …
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Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissues as Revealed by Deep Sequencing
… junctions - splice variants of previously known gene models and potential novel transcription units. An attempt was also made to exploit the data to understand the drought mediated transcriptional events (e.g. alternative splicing). Gene Ontology (GO) enrichment analysis revealed massive …
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The Secretory Pathway Calcium ATPase 2C promotes increased cytosolic calcium levels
… influx involving Orai1 in breast cancer. The goal of this study was to determine the effects of SPCA2C on Ca2+ homeostasis. Here, epitope-tagged SPCA2C was expressed in HEK293A cells. Co-immunofluorescence (Co-IF) determined subcellular localization. Using Fura2 imaging, cytosolic Ca2+ …
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Unveiling Global Roles of G-Quadruplexes and G4-22 In Human Genetics
… previous studies showed the impact of G4 in gene expression, none of them summarized the location-specific effect of G4. Also, there is no broad understanding about the most common G4 repeat in the human genome, named here as G4-22, and how it links to the evolution of mammals and their …
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Stem cell differentiation study: Statistical analysis and application to microarray data
… data mining procedures for modeling stem cell genes during the differentiation process, (2) To present biological interpretations of "sternness" genes based on time-course expression patterns and genetic networks. Stem cells have been of much interest over the past few years. Up to now, …
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ING1 Impacts Ovarian Cancer by Altering EMT
… are type II tumour suppressors that regulate epigenetic state and transcription by recruiting various chromatin-modifying complexes to chromatin. INGs are involved in multiple cellular processes such as DNA repair, apoptosis and cellular senescence. In this study, we investigated the potential …
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Analisi dei profili di espressione dei microRNA: identificazione di biomarker nel suicidio
… role as post-transcriptional regulators of gene expression. A growing body of evidence has shown that alterations in miRNA expression pattern are associated with several pathological processes. In particular, post-mortem brain studies support miRNA involvement in the pathophysiology of …
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Large-scale studies and biophysical analysis of systems involved in plant immunity.
… driven primarily by both forward and reverse genetics and to a lesser extent by molecular biology techniques. However, many unknowns still remain before a more complete picture of this system can be achieved, which hinders our capacity to develop biotechnological solutions to ensure food …
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