Bioinformatics Algorithms
Undergraduate and Master's Course, Istanbul Aydın University, Department of Software Engineering, 2019
I taught this course at both the undergraduate and master’s levels every Spring semester at Istanbul Aydın University.
The course focused on core bioinformatics algorithms and the application of R programming for the analysis of biological data. Students developed pipelines to handle gene expression data and biomarker discovery projects.
Course Level:
- Undergraduate (SEN 426)
- Graduate (Bioinformatics for Master’s students)
Years Taught:
- Spring 2019
- Spring 2020
- Spring 2021
- Spring 2022
Topics Covered:
- Sequence alignment algorithms (global/local: Needleman-Wunsch, Smith-Waterman)
- FASTA and BLAST tools for sequence similarity searching
- Phylogenetic tree construction (e.g., UPGMA, neighbor-joining)
- Hidden Markov Models (HMMs) for gene prediction and sequence modeling
- Differential gene expression (microarray and RNA-Seq)
Tools & Languages:
- R (Bioconductor, limma, edgeR, ggplot2)