CSE 5400-20 / 4510-10  (Summer 2020)
COMPUTATIONAL VIROLOGY: MACHINE LEARNING PERSPECTIVE
CRN: 60745 / 60744

May 18 - July 10, 2020  (Timing: First meeting on May 18, Monday, 4:30pm)

Learning Objectives:
* Genomics basics: with focus on virus and immune systems 			[NCBI, GISAID databases]
* Sequence alignment with hierarchical clustering for Phylogeny construction 	[Nextstrain system] 
* Sequence to Protein, Structures, Domains and Motifs				[NY Times article]
* Gene expression with microarrays and bi-clustering

The course will be mostly self-motivated overview of computational challenges and open questions in virology
and immunology. The following are a few sample project concepts:
* Topological analysis of SARS-COV-1 and -2 sequences
* Phylogeny construction of immune sequences, possible data from COVID-19
* Exploring simulation of molecular dynamics tools
* Exploring usages of deep learning in virology and immunology

No biology prerequisites are needed. GOOD GPA and a HIGH PROFICIENCY in programming in Python, Matlab, or any 
high-level language should be sufficient. Good background in Data structures & Algorithms (CSE 2010/5210) helps 
in understanding and implementing the algorithms. Students from Biological science and other sciences are welcome.