Engineering Commons^™

Quasinovo: Algorithms For De Novo Peptide Sequencing, James Paul Cleveland

Theses and Dissertations

High-throughput proteomics analysis involves the rapid identification and characterization of large sets of proteins in complex biological samples. Tandem mass spectrometry (MS/MS) has become the leading approach for the experimental identification of proteins. Accurate analysis of the data produced is a computationally challenging process that relies on a complex understanding of molecular dynamics, signal processing, and pattern classification. In this work we address these modeling and classification problems, and introduce an additional data-driven evolutionary information source into the analysis pipeline.

The particular problem being solved is peptide sequencing via MS/MS. The objective in solving this problem is to decipher the …

Computational Methods For Comparative Non-Coding Rna Analysis: From Structural Motif Identification To Genome-Wide Functional Classification, Cuncong Zhong

Electronic Theses and Dissertations

Recent advances in biological research point out that many ribonucleic acids (RNAs) are transcribed from the genome to perform a variety of cellular functions, rather than merely acting as information carriers for protein synthesis. These RNAs are usually referred to as the non-coding RNAs (ncRNAs). The versatile regulation mechanisms and functionalities of the ncRNAs contribute to the amazing complexity of the biological system. The ncRNAs perform their biological functions by folding into specific structures. In this case, the comparative study of the ncRNA structures is key to the inference of their molecular and cellular functions. We are especially interested in …