Physical Sciences and Mathematics Commons^™

Comparative Analyses Of De Novo Transcriptome Assembly Pipelines For Diploid Wheat, Natasha Pavlovikj

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Gene expression and transcriptome analysis are currently one of the main focuses of research for a great number of scientists. However, the assembly of raw sequence data to obtain a draft transcriptome of an organism is a complex multi-stage process usually composed of pre-processing, assembling, and post-processing. Each of these stages includes multiple steps such as data cleaning, error correction and assembly validation. Different combinations of steps, as well as different computational methods for the same step, generate transcriptome assemblies with different accuracy. Thus, using a combination that generates more accurate assemblies is crucial for any novel biological discoveries. Implementing …

Formal Concept Analysis Applications In Bioinformatics, Sarah Roscoe

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Bioinformatics is an important field that seeks to solve biological problems with the help of computation. One specific field in bioinformatics is that of genomics, the study of genes and their functions. Genomics can provide valuable analysis as to the interaction between how genes interact with their environment. One such way to measure the interaction is through gene expression data, which determines whether (and how much) a certain gene activates in a situation. Analyzing this data can be critical for predicting diseases or other biological reactions. One method used for analysis is Formal Concept Analysis (FCA), a computing technique based …

Application Of Cosine Similarity In Bioinformatics, Srikanth Maturu

Department of Computer Science and Engineering: Dissertations, Theses, and Student Research

Finding similar sequences to an input query sequence (DNA or proteins) from a sequence data set is an important problem in bioinformatics. It provides researchers an intuition of what could be related or how the search space can be reduced for further tasks. An exact brute-force nearest-neighbor algorithm used for this task has complexity O(m * n) where n is the database size and m is the query size. Such an algorithm faces time-complexity issues as the database and query sizes increase. Furthermore, the use of alignment-based similarity measures such as minimum edit distance adds an additional complexity to the …

Chemometric And Bioinformatic Analyses Of Cellular Biochemistry, Bradley Worley

Department of Chemistry: Dissertations, Theses, and Student Research

The amount of information collected and analyzed in biochemical and bioanalytical research has exploded over the last few decades, due in large part to the increasing availability of analytical instrumentation that yields information-rich spectra. Datasets from Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), infrared (IR) or Raman spectroscopy may easily carry tens to hundreds of thousands of potentially correlated variables observed from only a few samples, making the application of classical statistical methods inappropriate, if not impossible. Drawing useful biochemical conclusions from these unique sources of data requires the use of specialized multivariate data handling techniques.

Unfortunately, proper implementation of …