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 18 of 18 for “"manual curation"”.
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A robust pathfinding algorithm using chemical composition
… networks using the degree of nodes or the manual curation of edges in the metabolic network. The former method wrongfully penalizes some primary metabolites central to metabolism, while the latter requires someone to complete manual curation. KEGG RPAIR database is an annotation to describe …
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Benchmarking Methods For Predicting Phenotype Gene Associations
… posed by traditional approaches such as manual curation to link genes to phenotypes in the HPO. It is only in recent years that computational methods have been applied in a network-based approach for predicting genes to disease-related phenotypes. In this thesis, we present an extensive …
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Applying deep learning technologies to discovery and characterization of genetic variants in animal genomes
… that the resulting variants required less manual curation for selecting reliable consensus calls. This research builds the foundation for the animal genomics community to adopt new technologies that will rapidly accelerate our comparative knowledge of the genome.
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Automation of Drosophila gene expression pattern image annotation : development of web-based image annotation tool and application of machine learning methods
… with their downstream targets. However, the manual curation has become a bottleneck in the process of analyzing the rapidly generated data therefore it is necessary to explore computational methods for the curation of gene expression pattern images. This thesis addresses improving the manual …
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Exploring the TE landscape of elephant and CR1 accumulation, evolution and effects of selection in the class Chondrichthyes
… using a combination of sequence-homology and manual curation. We discovered that much of the genome (29%) was composed of non-LTR retrotransposons such as SINE and LINES. Interestingly the LINE CR1 showed peaks of accumulation in the distant past. We estimated that these insertions occurred ~ …
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Enabling the in vitro study of long noncoding RNAs to understand their role in Plasmodium falciparum
… generated a high-quality lncRNA annotation using manual curation of sequencing data generated at the Sanger Institute, along with supportive datasets from the literature. I evaluated CRISPR-based approaches for *in vitro* disruption of lncRNAs including gene knockout, knockdown, and interference. …
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Metabolic network reconstruction and genome-scale model of butanol-producing strain clostridium beijerinckii ncimb 8052
… utilized computational algorithms and extensive manual curation to improve model completeness. Interestingly, we found only a 34% overlap in annotation information between the three databases—highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To …
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Interplay between interkinetic nuclear migration and cell fate determination in the developing zebrafish retina
… nuclei, using automated tracking software and manual curation. Subsequently, these tracks were used to create a model of retinal IKNM as a diffusive process across a nuclear concentration gradient generated by the addition of new nuclei at the apical surface. This analytical model is based on …
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Approaches to understanding diversity in rubber and carotenoid synthesis in <i>Hevea brasiliensis </i>latex
… transcript variants were also discovered. Manual curation of gene models for key steps associated with rubber and carotenoids resulted in a repertoire of 115 genes, with 151 corresponding transcript variants. Subsequently, differential expression analysis on the basis of mapping RRIM600 and …
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Modeling problem solving in Massive Open Online Courses
… offering, a large scale, mixed automated and manual process that starts with the re-organization of MOOCdb source data into relevant and retrieval-efficient abstractions we call student resource trajectories and answer type transition matrices. This step must be interleaved with meticulous and …
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Intelligent Event Focused Crawling
… that link to other relevant webpages). Although manual curation of seed URLs guarantees quality, it requires exhaustive manual labor. We proposed an automated approach for curating seed URLs using social media content. We leveraged the richness of social media content about events to extract URLs …
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Viral metagenomics and phylogenomics for One Health
… assembled from human microbiomes and viromes by manual curation and comparative genomics and developed a new approach to study their evolution in relation to their bacterial hosts. I found that the strength of co-phylogenetic patterns between viruses and their hosts is generally weak, suggesting …
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PathMeld: A Methodology for The Unification of Metabolic Pathway Databases
… 17% substrates require approximate matching and manual curation by a biochemist. We presented several di®erent techniques for substrate matching and showed that about 10% of the MetaCyc substrates do not match and hence are absent from KEGG.
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Biosynthetic and bioinformatic investigation of RiPPs with radical SAM-installed crosslinks
… analyses have been limited, requiring extensive manual curation to identify cyclophane precursors. In Chapter 3 I discuss the generation of a RODEO module (a genome mining tool) to enable automatic scoring and classification of rSAM cyclophane RiPP precursor peptides. Focusing on enzyme- and …
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From Hidden Data and Information towards Data-Driven Research in the Biomedical Domain
… results on available corpora. However, as manual curation of data sets is a complex and time-consuming task often resulting in very small data sets, it remains questionable how robust the methods are on new data and whether they are ready to be used in digital services to support …
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Interaktivní databáze pro úschovu a údržbu biologických dat
Cieľom tejto práce je vytvorenie novej databázy dát pre proteínovú stabilitu, ktorá bude udržiavať a poskytovať experimentálne dáta. Výsledkom práce je databáza FireProtDB, ktorá poskytuje manuálne overené experimentálne dáta z dostupných zdrojov a implementuje grafické užívateľské rozhranie, ktoré …
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Integrating manual and automated metabolic engineering methods
Made available in DSpace on 2016-07-07T20:27:15Z (GMT). No. of bitstreams: 4 RICHARDS-DISSERTATION-2016.pdf: 3860821 bytes, checksum: cbaf30718ce7594d7f76859b49a220de (MD5) Richards_Matthew.docx: 2576729 bytes, checksum: e2a1076a288d7d31c646df244282d03a (MD5) LICENSE.txt: 4213 bytes, checksum: …
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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 …