Instructor: Reza Rezazadegan
Venue: Shiraz University, Department of Mathematics and Computer Science, Spring 2025
Course webpage: www.dreamintelligent.com/bioinformatics-course
Course Github: https://github.com/rezareza007/bioinformatics/
Prerequisites
- Molecular biology
- Python programming
- Data structures and algorithms
- Probability and statistics
References
- Xiong, Essential Bioinformatics
- Baum, Zvelebil, Understanding Bioinformatics
- Compeau, Pevtzner, Bioinformatics Algorithms
- BioPython Reference Manual
Course Evaluation:
- Workshop: 2.5 points
- Presentation: 2.5 points
- Midterm: 8. Midterm date: Azar 5
- Final: 7 points
Syllabus
Chapter 1- Introduction to Bioinformatics and its applications
Xiong 1, Baum 1
Chapter 2-Bioinformatics Databases
Xiong 2, Baum 3
Chapter 3-Pairwise Sequence Alignment Unveiling Evolutionary Stories from Biological Sequences
Xiong 3, Baum 4,5
Chapter 4 – Database Similarity Search for Sequences- Hunting for Homologs in the Genomic World
Xiong 4, 5
Chapter 5-Multiple sequence alignment and profiles- Unveiling Conserved Patterns in Protein Families
Xiong 5,6, Baum 6
Chapter 6-Evolution and Phylogenetics – Unraveling the Tree of Life
Xiong 10,11, Baum 7,8
Chapter 7-Gene prediction
Xiong 8,9, Baum 9, 10
Chapter 8-Protein secondary structure, comparison and classification
Xiong 12,13, Baum 2
Chapter 9-Protein secondary structure prediction
Xiong 14, Baum 11, 12
Chapter 10-Protein Tertiary structure
Xiong 15, Baum 13, 14
Chapter 11-RNA secondary structure
Xiong 16
Chapter 12- Genom Analysis
Xiong 17, 18, 19, Baum 15
Chapter 13-Applications of bioinformatics in diagnosing special diseases
Workshop
Students demonstrate experimentations using the BioPython library
Optional:
Code Challenges: Students implement algorithms discussed in class using Python. Platforms like Rosalind (http://rosalind.info) can automatically test your implementations, providing immediate feedback.
Student Presentation Topics
– Bioinformatics Algorithms Chapters
– Network biology
– Transcriptomics
– Multi-omics
– Drug design
– Transformers for understanding biological data
– Origin of life
– Transcription factors