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Full-Text Articles in Bioinformatics
Protein Structure-Guided Approaches To Identify Functional Mutations In Cancer, Sohini Sengupta
Protein Structure-Guided Approaches To Identify Functional Mutations In Cancer, Sohini Sengupta
Arts & Sciences Electronic Theses and Dissertations
Distinguishing driver mutations from passenger mutations within tumor cells continues to be a major challenge in cancer genomics. Many computational tools have been developed to address this challenge; however, they rely heavily on primary protein sequence context and frequency/mutation rate. Rare driver mutations not found in many cancer patients may be missed with these traditional approaches. Additionally, the structural context of mutations on tertiary/quaternary protein structures is not taken into account and may play a more prominent role in determining phenotype and function. This dissertation first presents a novel computational tool called HotSpot3D, which identifies regions of protein structures that …
Multi-Omics Portraits Of Cancer, Kuan-Lin Huang
Multi-Omics Portraits Of Cancer, Kuan-Lin Huang
Arts & Sciences Electronic Theses and Dissertations
Precision oncology demands accurate portrayal of a disease at all molecular levels. However, current large-scale studies of omics are often isolated by data types. I have been developing computational tools to conduct integrative analyses of omics data, identifying unique molecular etiology in each tumor. Particularly, this dissertation presents the following contributions to the computational omics of cancer: (1) uncovering the predisposition landscape in 33 cancers and how germline genome collaborates with somatic alterations in oncogenesis; (2) pioneering methods to combine genomic and proteomic data to identify treatment opportunities; and (3) revealing selective phosphorylation of kinase-substrate pairs. These findings advance our …