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Articles 1 - 5 of 5
Full-Text Articles in Bioinformatics
Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben
Electronic Theses and Dissertations
Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …
Small Rnas: Big Roles In White Mold Infecting Crop Plants, Achal Neupane
Small Rnas: Big Roles In White Mold Infecting Crop Plants, Achal Neupane
Electronic Theses and Dissertations
In eukaryotes, small RNAs (sRNAs) are key regulators of RNA silencing which is also known as RNA interference (RNAi). RNAi is an essential mechanism known in plants, animals and fungi that regulates various biological activities, including defense against foreign nucleic acids and viruses. Fungal pathogens, such as Sclerotinia sclerotiorum, severely limit crop production in all parts of the world. Sclerotinia sclerotiorum cause white mold infection, affecting all dicotyledonous plants including many economically important field crops, vegetables, and floriculture. There does not exist known host resistance, and only limited chemical control can be achieved. Given the growing cost and environmental impacts …
Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang
Development Of Computational Techniques For Identification Of Regulatory Dna Motif, Cankun Wang
Electronic Theses and Dissertations
Identifying precise transcription factor binding sites (TFBS) or regulatory DNA motif (motif) plays a fundamental role in researching transcriptional regulatory mechanism in cells and helping construct regulatory networks for biological investigation. Chromatin immunoprecipitation combined with sequencing (ChIP-seq) and lambda exonuclease digestion followed by high-throughput sequencing (ChIP-exo) enables researchers to identify TFBS on a genome-scale with improved resolution. Several algorithms have been developed to perform motif identification, employing widely different methods and often giving divergent results. In addition, these existing methods still suffer from prediction accuracy. Thesis focuses on the development of improved regulatory DNA motif identification techniques. We designed an …
Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu
Applying Machine Learning Algorithms For The Analysis Of Biological Sequences And Medical Records, Shaopeng Gu
Electronic Theses and Dissertations
The modern sequencing technology revolutionizes the genomic research and triggers explosive growth of DNA, RNA, and protein sequences. How to infer the structure and function from biological sequences is a fundamentally important task in genomics and proteomics fields. With the development of statistical and machine learning methods, an integrated and user-friendly tool containing the state-of-the-art data mining methods are needed. Here, we propose SeqFea-Learn, a comprehensive Python pipeline that integrating multiple steps: feature extraction, dimensionality reduction, feature selection, predicting model constructions based on machine learning and deep learning approaches to analyze sequences. We used enhancers, RNA N6- methyladenosine sites and …
Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa
Transcriptome Analysis Of Root Development In Wheat Triticum Aestivum Using High Throughtput Sequencing Technologies, Ghana Challa
Electronic Theses and Dissertations
Root provides plant water, nutrients and anchorage from soil. Most our knowledge of molecular mechanisms of root development is from the dicot model plant Arabidopsis, but very few studies have done in monocot crop systems like rice, maize, and wheat. We are studying very short root (VSR) phenotype in wheat, and lack of a sequenced reference genome in wheat prompted us to sequence and assemble the root transcriptome of the reference cultivar Chinese Spring (CS). A root transcriptome was assembled from the sequenced reads generated from root tip and the mature root tissues of CS. Approximately 169 million reads were …