Computational Biology


Meeting times             : Tuesday 9:45, 10:45, 11:45

Instructor                   : Bilge Karaçalı, PhD

Office                          : EEE Building Room 219

Phone                         : 6534

E-mail                         :



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.



Midterm           20%

Final                 30%

Homework       20%

Project             30%


Term Project



Homework 1

Homework 2

Homework 3










Week 1: Introduction to computational biology


Week 2: Nucleic acid and protein structure


Week 3: Evolution mechanism through mutations


Week 4: Probabilistic sequence evolution models


Week 5: Simulating sequence evolution


Week 6: Gene and protein databases


Week 7: Sequence alignment


Week 8: Searching sequence databases


Week 9: Inter-species evolutionary relationships via phylogenetic trees


Week 10: Optimality criteria in phylogenetic tree construction


Week 11: Pattern searching in functional protein groups: Sequence motifs


Week 12: Bioinformatics


Week 13: Microarray data analysis


Week 14: Readings on systems biology


Data files