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 10 of 10 for “"Annotation pipeline"”.
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Image annotation with discriminative model and annotation refinement by visual similarity matching
… and model-free approaches can provide quality annotation to images. In this thesis, I present a hybrid annotation pipeline that combines both approaches in hopes of increasing the accuracy of the resulting annotations. Given an unlabeled image, the first step is to suggest some words via a …
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Improving Dbnsfp
… goal of my project is to provide an automatic annotation pipeline to the WES based disease studies project by extending the dbNSFP with a tool for automated indel annotation and deleteriousness prediction. The current sequencing results typically include both SNVs and indels. Although there …
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Conservation and synteny of long non-coding RNAs invertebrate genomes and their identification in novel transcriptomes
… functional genomics dataset. I developed an annotation pipeline, which can effectively identify IncRNAs in entire transcriptomes. The pipeline is able to accurately annotate the coding genes while predicting a conservative estimate of the IncRNA population. It allowed me to show, for the …
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Drivable Area Segmentation on LiDAR Range View Images for Autonomous Driving
… this problem by implementing a segmentation pipeline to identify road regions that the vehicle can traverse, with the goal of providing a detailed representation of the road structure and its components. The central focus of this work is the segmentation of drivable areas and road markings …
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Improving the genome assembly and annotation of the white-tailed deer (Odocoileus virginianus borealis)
… Gene models were predicted with the BRAKER annotation pipeline using RNA and protein sequences as extrinsic evidence. The final assembly was highly contiguous, with 90% of the total length represented by 134 contigs. The largest contig was 108 million base pairs. Functional annotation was …
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Machine Learning Methods for Discovering Metabolite Structures from Mass Spectra
… computational methodologies for higher accuracy annotation of small molecule metabolites from mass spectrometry data that integrate chemistry-informed priors with modern deep learning advancements. I begin by decomposing and framing the metabolite annotation pipeline into four key tasks well-fit …
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GoPubMed: Ontology-based literature search for the life sciences
… Results: This work includes a novel annotation framework for free texts with ontological concepts. The framework allows to generate recognition patterns rules from the terminological and relational information in an ontology. Maximum entropy models can be trained to distinguish the …
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Establishing the feasibility of using ctDNA for molecular profiling in DLBCL
… validate a custom somatic variant calling and annotation pipeline for use on DLBCL FFPE biopsy and plasma ctDNA samples. This was conducted in the context of a prospective observational clinical trial, DIRECT. After establishing the variant calling pipeline, the next aim of the project was to …
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Gene misexpression in humans
… approaches. I created an extensive feature annotation pipeline that can label sORFs with 88 features spanning DNA, RNA, regulatory and peptide properties. Next, I trained different model architectures to identify functional sORFs among all sORFs types as well as models for specific sORF …
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Development of a comprehensive annotation and curation framework for analysis of Glossina Morsitans Morsitans expresses sequence tags
This study has successfully identified transcripts differentially expressed in the salivary gland and midgut and provides candidate genes that are critical to response to parasite invasion. Furthermore, an open-source Glossina resource (G-ESTMAP) was developed that provides interactive features and …