EE550
Computational Biology
Meeting times : Tuesday 13:30, 14:30, 15:30
Instructor : Bilge Karaçalı, PhD
Office : EEE Building Room K1-32
E-mail : bilge@iyte.edu.tr
Summary
This course will begin with a broad description of cellular organization in a molecular biology perspective including nucleic acid and protein structure. Computational methods for pattern detection and clustering will be introduced in the analysis of amino acid sequences of proteins. Probabilistic models of genetic evolution will be developed along with sequence alignment and motif detection algorithms. RNA and DNA analysis with microarrays will be discussed. Dynamic modelling of gene transcription networks will be introduced.
Make-up
lecture scheduled for TODAY
Grading
Midterm 20%
Final 30%
Homework 20%
Project 30%
Homework Assignments
Homework #1 (due 22.03.2022)
Homework #2 (due 29.03.2022)
Homework #3 (due 12.04.2022)
Homework #4 (due 24.05.2022)
Tests
Midterm (due 25.04.2022)
Final (due 10.06.2022)
Material
Week 1: Introduction to computational biology
Week 2: Nucleic acid and protein structure
Week 3: Evolution mechanism through mutations
Week 4: Probabilistic amino acid sequence evolution models
Week 5: Gene and protein databases
Week 7: Searching sequence databases
Week 8: Inter-species evolutionary relationships via phylogenetic trees
Week 9: Optimality criteria in phylogenetic tree construction
Week 10: Pattern searching in functional protein groups: Sequence motifs
Week 12: Microarray data analysis
Week 13: Systems biology – Gene transcription networks
Week 14: Regulation of gene transcription
Data files