CS 618

This page will contain the course syllabus and plan for CS 618 Computational Biology for the summer of 2024. For now, it contains a list of topics that we will look at. The basic plan is to look at a number of projects that I have worked on in the past, and to look at key tools and algorithms used in computational biology and bioinformatics.

Projects

Gene expression - determining key genes from gene expression datasets. Project is in R, uses Shiny, Datatables, ShinyProxy, Docker. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-bartlett.pdf

Protein topology prediction - finding potential transmembrane proteins in genomes. Project is in Python, uses Javascript, NCBI, BLAST. Poster - https://cs.indstate.edu/info/posters/bd4isu2022-hoffman.pdf

Transcription factors - finding mutations to disable a transcription factor while still preserving others. Project is in Python, R, and/or C. Poster - https://cs.indstate.edu/info/posters/bd4isu2020-bennett.pdf

Gene expression - determining key genes in a particular dataset from fish. Poster - https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf

Mass spectrometry data - keeping a database of mass spec data and searching through databases for new samples. Potential new project.

Topics/Concepts

Central dogma of genetics

Biological data - different types of assays, etc. - how the data is produced, what the data looks like, etc.

Sequence alignment algorithms

Clustering techniques

Statistics