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Articles 1 - 4 of 4
Full-Text Articles in Computational Biology
Computational Identification Of Terpene Synthase Genes And Their Evolutionary Analysis, Qidong Jia
Computational Identification Of Terpene Synthase Genes And Their Evolutionary Analysis, Qidong Jia
Doctoral Dissertations
Terpenoids, the largest and most structurally and functionally diverse class of natural compounds on earth, are mostly synthesized by plants to be involved in various plant environment interactions. Some terpenoids are classified as primary metabolites essential for plant growth and development. Terpene synthases (TPSs), the key enzymes for terpenoid biosynthesis, are the major determinant of the tremendous diversity of terpenoid carbon skeletons. The TPS genes represent a mid-size family of about 30-100 functional genes in almost all major sequenced plant genomes. TPSs are also found in fungi and bacteria, but microbial TPS genes share low levels of sequence similarity and …
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Comparative Genomics Of Microbial Chemoreceptor Sequence, Structure, And Function, Aaron Daniel Fleetwood
Doctoral Dissertations
Microbial chemotaxis receptors (chemoreceptors) are complex proteins that sense the external environment and signal for flagella-mediated motility, serving as the GPS of the cell. In order to sense a myriad of physicochemical signals and adapt to diverse environmental niches, sensory regions of chemoreceptors are frenetically duplicated, mutated, or lost. Conversely, the chemoreceptor signaling region is a highly conserved protein domain. Extreme conservation of this domain is necessary because it determines very specific helical secondary, tertiary, and quaternary structures of the protein while simultaneously choreographing a network of interactions with the adaptor protein CheW and the histidine kinase CheA. This dichotomous …
Development And Integration Of Informatic Tools For Qualitative And Quantitative Characterization Of Proteomic Datasets Generated By Tandem Mass Spectrometry, Rachel Michelle Adams
Development And Integration Of Informatic Tools For Qualitative And Quantitative Characterization Of Proteomic Datasets Generated By Tandem Mass Spectrometry, Rachel Michelle Adams
Doctoral Dissertations
Shotgun proteomic experiments provide qualitative and quantitative analytical information from biological samples ranging in complexity from simple bacterial isolates to higher eukaryotes such as plants and humans and even to communities of microbial organisms. Improvements to instrument performance, sample preparation, and informatic tools are increasing the scope and volume of data that can be analyzed by mass spectrometry (MS). To accommodate for these advances, it is becoming increasingly essential to choose and/or create tools that can not only scale well but also those that make more informed decisions using additional features within the data. Incorporating novel and existing tools into …
The Maximum Clique Problem: Algorithms, Applications, And Implementations, John David Eblen
The Maximum Clique Problem: Algorithms, Applications, And Implementations, John David Eblen
Doctoral Dissertations
Computationally hard problems are routinely encountered during the course of solving practical problems. This is commonly dealt with by settling for less than optimal solutions, through the use of heuristics or approximation algorithms. This dissertation examines the alternate possibility of solving such problems exactly, through a detailed study of one particular problem, the maximum clique problem. It discusses algorithms, implementations, and the application of maximum clique results to real-world problems. First, the theoretical roots of the algorithmic method employed are discussed. Then a practical approach is described, which separates out important algorithmic decisions so that the algorithm can be easily …