Greetings, I gave this class for several semesters at Georgia State University, and I wanted to memorialize it here, as it was in Spring 2025.
Bioinformatics is an intersection between statistics, molecular biology, and computer science. Learning bioinformatics will have different meanings depending on your background. Advancing yourself in all three of these fields will aid in your success. However, many other skills will help you here, and so success can also come in the forms of learning other related skills.
In addition to bioinformatics, this course will also touch on how bioinformatics can aid in the study of infectious diseases. This will help give real life meaning to these academic exercises and will help you get real career skills in bioinformatics.
- Christensen, Introduction to Bioinformatics in Microbiology, 2023 (second edition)
- Rob Edward’s Computational Genomics Manual
- Website https://linsalrob.github.io/ComputationalGenomicsManual/
- Rob Edward’s YouTube playlist https://www.youtube.com/playlist?list=PLpPXw4zFa0uLMHwSZ7DMeLGjIUgo1IBbn
- Many more resources for the curious: https://github.com/lskatz/awesome-bioinformatics-education
This class requires the Linux command line.
You will be required to install the Linux command line. There are a few ways you can do this including:
- MacOS already has the command line.
- Ubuntu Linux already has the command line.
- Windows: WSL2 from the Microsoft app store.
Additionally, you might find it helpful to install a proper text editor. I recommend that you use the program VSCode.
Suggested readings refer to the Christensen textbook unless otherwise noted.
| Week | Title | Readings | Quiz | Recorded lecture1 |
|---|---|---|---|---|
| 01 | intro_to_the_course | Chapter 1, section 1 | - | |
| 02 | worldwide_databases | Chapter 3 | quiz | |
| 03 | introToLinux | Chapter 1, sections 3 through 5. UCDavis bootcamp. | quiz | Sep 8, 2022 |
| 04 | sequencing_formats | Chapter 2, section 4 | quiz | Sep 14, 2023 |
| 05 | installation_of_software | https://astrobiomike.github.io/unix/conda-intro | quiz | |
| 06 | sequencing_instruments | Chapter 2 | quiz | Oct 2, 2024 |
| 07 | assembly | Chapter 2, sections 2-3 | quiz | Feb 22, 2023 |
| 08 | Genome_annotation_2024_revised | Chapter 2, section 5 | quiz | Gene prediction - Feb 22, 2023 |
| 09 | sequence_querying | Chapter 4 | quiz | Nov 11, 2022 |
| 10 | multiple_sequence_alignment | Chapter 6 | quiz | |
| 11 | phylogeny | Chapter 4 | quiz | |
| 12 | genomic_epidemiology | Chapter 11; Stevens et al 2022 | quiz | |
| 13 | amplicon metagenomics [pptx not available] | Chapter 9 | quiz | |
| 14 | shotgun metagenomics | Chapter 9 | quiz | |
| 15 | Final exam [no pptx] | final | Apr 8, 2025 |
Fundamentals of Bioinformatics by Lee Katz is licensed under Creative Commons Attribution-NonCommercial 4.0 International
Footnotes
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Access given by request; the recording was not necessarily made at the same time of the slides, in 2025, and so material might be different. The playlist of recordings can be found at https://www.youtube.com/playlist?list=PL_G_azApeLUxLEdgw-TicGN83OlkmqnIb. ↩