| MATHEMATICS (TURKISH, PHD) | |||||
| PhD | TR-NQF-HE: Level 8 | QF-EHEA: Third Cycle | EQF-LLL: Level 8 | ||
| Course Code | Course Name | Semester | Theoretical | Practical | Credit | ECTS |
| CMP4131 | Bioinformatics | Fall | 3 | 0 | 3 | 6 |
| The course opens with the approval of the Department at the beginning of each semester |
| Language of instruction: | En |
| Type of course: | Departmental Elective |
| Course Level: | |
| Mode of Delivery: | Face to face |
| Course Coordinator : | Dr. Öğr. Üyesi TARKAN AYDIN |
| Course Objectives: | The course aims to teach the fundamental computational problems in molecular biology and genomics, the types and sources of data available for bioinformatics, a core set of widely used algorithms in bioinformatics. |
|
The students who have succeeded in this course; I. Defining the fundamental computational problems in molecular biology and genomics II. Understanding the types and sources of data available for bioinformatics III. Implementing a core set of widely used algorithms in bioinformatics IV. Understanding and comparing global, local and semi-global pairwise alignments. V. Understanding and comparing PAM vs. BLOSSUM scoring matrices. VI. Analyzing gene expression data. VII. Recognizing protein folding problem VIII. Analyzing protein-protein interaction networks. IX. Implementing a set of algorithms that have important applications in bioinformatics, but which have key applications outside of biology as well. |
| This course covers computational techniques for mining the large amount of information produced by recent advances in molecular biology, such as genome sequencing and microarrray technologies. The methods by which computers are used to manipulate and analyze sequences and structures will also be taught. The outline of the course is arranged to give fundamental concepts of bioinformatics to the students. |
| Week | Subject | Related Preparation | |
| 1) | Review | ||
| 1) | Introduction: Molecular Biology and Computer Science a) The organization of DNA, proteins, cell. b) In silico biology | ||
| 2) | Pairwise alignment of biomolecular sequences and search for similarities: Global alignment of two sequences. | ||
| 3) | Local alignment, Semi-global alignment. | ||
| 4) | Scoring similarity matrices: BLOSSUM | ||
| 5) | PAM similarity matrices | ||
| 6) | Multiple sequence alignment a) Iterative Methods b) Structure Based Methods | ||
| 7) | Scoring multiple alignments | ||
| 8) | Bioinformatics approaches to gene expression, detecting differential expression | ||
| 9) | Multiple hypothesis testing and false-discovery-rate methods for gene expression data. | ||
| 10) | Protein Folding Problem: Simulated Annealing Algorithms | ||
| 11) | Threading, Homology Modeling for Protein Folding Problem | ||
| 12) | Protein-protein and protein/DNA interactions, Gene/Protein networks, pathways | ||
| 13) | Construction and analysis of large scale biological networks | ||
| 15) | Final | ||
| 16) | Final | ||
| Course Notes: | Pevsner J., Bioinformatics and Functional Genomics, Wiley-Liss, 2009. |
| References: | Mount D.W., Bioinformatics: Sequence and Genome Analysis (2nd edition), Cold Spring Harbor Laboratory Press, 2004. Krane D.E., Raymer M.L., Fundamental Concepts of Bioinformatics, Benjamin Cummings, 2003. |
| Semester Requirements | Number of Activities | Level of Contribution |
| Attendance | % 0 | |
| Laboratory | % 0 | |
| Application | % 0 | |
| Field Work | % 0 | |
| Special Course Internship (Work Placement) | % 0 | |
| Quizzes | % 0 | |
| Homework Assignments | 2 | % 10 |
| Presentation | % 0 | |
| Project | 1 | % 25 |
| Seminar | % 0 | |
| Midterms | 1 | % 30 |
| Preliminary Jury | % 0 | |
| Final | 1 | % 35 |
| Paper Submission | % 0 | |
| Jury | % 0 | |
| Bütünleme | % 0 | |
| Total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 40 | |
| PERCENTAGE OF FINAL WORK | % 60 | |
| Total | % 100 | |
| Activities | Number of Activities | Duration (Hours) | Workload |
| Course Hours | 14 | 3 | 42 |
| Laboratory | 0 | 0 | 0 |
| Application | 0 | 0 | 0 |
| Special Course Internship (Work Placement) | 0 | 0 | 0 |
| Field Work | 0 | 0 | 0 |
| Study Hours Out of Class | 14 | 6 | 84 |
| Presentations / Seminar | 0 | 0 | 0 |
| Project | 0 | 0 | 0 |
| Homework Assignments | 0 | 0 | 0 |
| Quizzes | 0 | 0 | 0 |
| Preliminary Jury | 0 | ||
| Midterms | 1 | 2 | 2 |
| Paper Submission | 0 | ||
| Jury | 0 | ||
| Final | 1 | 2 | 2 |
| Total Workload | 130 | ||
| No Effect | 1 Lowest | 2 Low | 3 Average | 4 High | 5 Highest |
| Program Outcomes | Level of Contribution |