BIFX 550 Functional Genomics: Sequence Analysis and Structural Bioinformatics

Prerequisite: Completion of BIFX 504 or instructor permission. 

This course will use sequence and structural information to solve biological disease-centered problems. BIFX550 will provide the knowledge to study both individual and collections of genes/proteins (NGS data) with the goal of modeling the functional impact of genomic variants. Functional genomics has applications in several areas of health sciences including drug-discovery. This course serves as an intermediate level class for graduate students who plan to work in the areas of computational biology or bioinformatics using available applications and/or interested in developing custom R or Linux-based pipeline(s)/script(s). In BIFX550, students will work on a semester-long functional genomics (find-a-gene) project where students will apply the knowledge gained in the classes to identify a novel gene. While completing the project, students will gain a theoretical understanding of common bioinformatics tasks and learn to effectively apply the relevant software applications (ex. NCBI's sequence comparison software, BLAST) to solve problems. BIFX550, will introduce the essential mathematics and statistics before introducing each application. Protein function depends on its 3D structure/folding. BIFX550 will help students make the connection from 1D DNA/RNA sequence to their corresponding 3D protein(s). To address the shifting trends in computational genomics research from the High-Performance-Computing/CPU-dependent platforms to Tensor-Processing-Unit/cloud-based solutions, this course will teach how to install/use important software, develop SHELL scripts in Linux-based environments and learn web-based (Galaxy; NCBI) resources.