Difference between revisions of "CS 618"
(Created page with "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 ba...") |
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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. | 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 | + | =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 | + | ***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 |
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* 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 | * 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 | ||
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* 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 | * 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 | ||
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* Gene expression - determining key genes in a particular dataset from fish. Poster - https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf | * Gene expression - determining key genes in a particular dataset from fish. Poster - https://cs.indstate.edu/info/posters/bd4isu2021-gosnell.pdf | ||
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* Mass spectrometry data - keeping a database of mass spec data and searching through databases for new samples. Potential new project. | * Mass spectrometry data - keeping a database of mass spec data and searching through databases for new samples. Potential new project. | ||
Revision as of 22:11, 17 April 2024
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.
- Sequence alignment algorithms
- Clustering techniques
- Statistics
