Other Computer Engineering Commons^™

A Novel Computational Network Methodology For Discovery Of Biomarkers And Therapeutic Targets, Qing Ye

Graduate Theses, Dissertations, and Problem Reports

Lung cancer has the second highest cancer incidence rate and the top cancer-related mortality worldwide. An estimate from the American Cancer Society shows that, in 2022, there will be about 236,740 lung cancer cases (117,910 men and 118,830 women) in the US. To date, there are no prognostic/predictive biomarkers to select chemotherapy, immunotherapy, and radiotherapy in individual non-small cell lung cancer (NSCLC) patients. There is an unmet clinical need to identify patients with early-stage NSCLC who are likely to develop recurrence and to predict their therapeutic responses. This dissertation developed a novel computational methodology for modeling molecular gene association networks …

Scalable Profiling And Visualization For Characterizing Microbiomes, Camilo Valdes

FIU Electronic Theses and Dissertations

Metagenomics is the study of the combined genetic material found in microbiome samples, and it serves as an instrument for studying microbial communities, their biodiversities, and the relationships to their host environments. Creating, interpreting, and understanding microbial community profiles produced from microbiome samples is a challenging task as it requires large computational resources along with innovative techniques to process and analyze datasets that can contain terabytes of information.

The community profiles are critical because they provide information about what microorganisms are present in the sample, and in what proportions. This is particularly important as many human diseases and environmental disasters …

Genet-Cnv: Boolean Implication Networks For Modeling Genome-Wide Co-Occurrence Of Dna Copy Number Variations, Salvi Singh

Graduate Theses, Dissertations, and Problem Reports

Lung cancer is the leading cause of cancer-related death in the world. Lung cancer can be categorized as non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). NSCLC makes up about 80% to 85% of lung cancer cases diagnosed, whereas SCLC is responsible for 10% to 15% of the cases. It remains a challenge for physicians to identify patients who shall benefit from chemotherapy. In such a scenario, identifying genes that can facilitate therapeutic target discoveries and better understanding disease mechanisms and their regulation in different stages of lung cancer, remains an important topic of research.

In this …

Efficient Alignment Algorithms For Dna Sequencing Data, Nilesh Vinod Khiste

Electronic Thesis and Dissertation Repository

The DNA Next Generation Sequencing (NGS) technologies produce data at a low cost, enabling their application to many ambitious fields such as cancer research, disease control, personalized medicine etc. However, even after a decade of research, the modern aligners and assemblers are far from providing efficient and error free genome alignments and assemblies respectively. This is due to the inherent nature of the genome alignment and assembly problem, which involves many complexities. Many algorithms to address this problem have been proposed over the years, but there still is a huge scope for improvement in this research space.

Many new genome …