BİL623 Biomedical Informatics


Hasan OĞUL


Objective: The course is designed to make the students familier with the basic molecular biology concepts, computational biology problems and fundemental computer approaches used for modeling biological processes and associating them with clinical applications.

Instructor: Hasan Oğul, Assoc.Prof.Dr.,

Textbook: No main textbook, but the following are useful:

Fundamental Concepts of Bioinformatics, D.E. Krane, M.L. Raymer, 2003, Benjamin Cummings

Algorithms on strings, trees and sequences, D. Gusfield, 1997, Cambridge Univ. Press

Computational Molecular Biology, Clote & Backofen, 2000, Wiley


Bioinformatics; Journal of Computational Biology; BMC Bioinformatics; PLOS Computational Biology; Computational Biology and Chemistry; Current Bioinformatics; Computers in Biology and Medicine; Computer Methods and Programs in Biomedicine; Biosystems, FEBS Letters; Journal of Molecular Biology; Journal of Molecular Modeling; Proteins: Structure, Function and Bioinformatics.


Class activity (Participation, HWs, Presentations) 1/3

Midterm exam 1/3

Final exam 1/3


Week 1 No class    
Week 2 Cell-DNA-RNA-Protein  (Slides)  
Week 3 Protein Structure  (Slides)  
Week 4 Sequence Alignment  (Slides)  
Week 5 Alignment in Real Life


23 Oct. Progressive Multiple Aligment Berke clustal
  BLAST Berkay  
  Large Sequence Alignment Serkan mummer
Week 6 Sequence Classification    
30 Oct. Whole Sequence Classification Ahmet ESLpred
  Partial Sequence Classification Erhan exon
  Residue Classification Gökhan secondary
Week 7 Markov Modeling    
6 Nov. Probabilistic Suffix Tree Levent pst
  microRNA Target Prediction Deniz mirpred
  Hidden Markov Modeling of Proteins   hmm
Week 9 Microarray and related technologies    
Week 10 Gene Expression Analysis    
Week 11 Network Analysis and Diseases    
4 Dec. Data-Driven View of Disease Biology Berkay PLOS CB
  Protein Interactions and Disease Levent PLOS CB
  Network Biology Approach to Complex Diseases Ahmet PLOS CB
Week 12 Biological Knowledge Discovery & Management    
11 Dec. Pharmacogenomics Serkan PLOS CB
  Biological Knowledge Assembly and Interpretation Erhan PLOS CB
  Analyses Using Disease Ontologies Berke PLOS CB
Week 13 Other Data in Clinical Applications    
17 Dec. Mining Genome-Wide Genetic Markers   PLOS CB
  Text Mining for Translational Bioinformatics Deniz PLOS CB
  Bioimage Informatics for Systems Pharmacology Gökhan PLOS CB
Week 14 Project Discussions    






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