| Cancer Biology and Pharmacology (Master) (with Thesis) | |||||
| Master | TR-NQF-HE: Level 7 | QF-EHEA: Second Cycle | EQF-LLL: Level 7 | ||
| Course Code: | KBY5011 | ||||
| Course Name: | Cancer Bioinformatics | ||||
| Semester: | Fall | ||||
| Course Credits: |
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| Language of instruction: | Turkish | ||||
| Course Condition: | |||||
| Does the Course Require Work Experience?: | No | ||||
| Type of course: | Departmental Elective | ||||
| Course Level: |
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| Mode of Delivery: | Face to face | ||||
| Course Coordinator: | Dr. Öğr. Üy. ASLI KUTLU | ||||
| Course Lecturer(s): | ASLI KUTLU | ||||
| Course Assistants: |
| Course Objectives: | The objective of this course for each student is summarized as using web-based bioinformatic tools in effective manner, performing mathematical modeling-based analysis, and interpreting the obtained results according to developed mathematical models. |
| Course Content: | The content of this course is the effective use of bioinformatics tools during cancer research and targeted drug design approaches. Another important content of the course is to convey basic information about the effective use of existing mathematical models during the experimental design phase and the interpretation of the results. The elements necessary for drug design will be emphasised with the multiple perspectives that will be gained to the students. |
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The students who have succeeded in this course;
1) Students who successfully complete this course; • Knows the concept of 'big data' in cancer, and uses this concept effectively 2) Knows the scope of mathematical models and assumptions 3) Can effectively use the bioinformatics tools used extensively in cancer 4) Masters the algorithm behind online bioinformatics tools, and can target algorithms and parameters used when needed 5) Performing effective variant analysis after next generation sequencing 6) Having a deep knowledge about gene, protein and miRNA interaction networks 7) Having a certain level of knowledge about models and tools used in cancer systems biology 8) Knows the whole of the methods of targeted drug design |
| Week | Subject | Related Preparation |
| 1) | Introduction to bioinformatics and main concepts | Presentations |
| 2) | Big data in cancer & How to use big data? | Presentations |
| 3) | NCBI-based web-tools and further analysis | Presentations |
| 4) | Performing variant analysis with NGS | Presentations |
| 5) | Gene-Gene, gene-miRNA & Gene-protein interaction networks | Presentations |
| 6) | The combination of transcriptomics and genomics for somatic mutation analysis | Presentations |
| 7) | Looking cancer from epigenetics | Presentations |
| 8) | Review week for midterm | |
| 9) | Mathematical modelings for cancer signal networks | Presentations |
| 10) | Cancer system biology and network analysis | Presentations |
| 11) | Drug development studies | Presentations |
| 12) | Identification of sub-types of tumor and sub-clones via statistical approaches | Presentations |
| 13) | Project presentations | Student presentations |
| 14) | Project presentations | Student presentations |
| Course Notes / Textbooks: | • Cancer system biology, bioinformatics and medicine. Springer. (Editors: Alfredo Cesario • Frederick B. Marcus) • Cancer Bioinformatics . Springer Protocols (Editor: Alexander Krasnitz) |
| References: | • Cancer system biology, bioinformatics and medicine. Springer. (Editors: Alfredo Cesario • Frederick B. Marcus) • Cancer Bioinformatics . Springer Protocols (Editor: Alexander Krasnitz) |
| Course Learning Outcomes | 1 |
2 |
3 |
4 |
5 |
6 |
7 |
8 |
|---|---|---|---|---|---|---|---|---|
| Program Outcomes | ||||||||
| 1) The ability to define basic concepts of Cancer Biology and Pharmacology, get information objectively about the related field within the scope of the program | 3 | 2 | 2 | 2 | 2 | 2 | 3 | 2 |
| 2) Having knowledge about the molecular mechanisms of cancer, learning the process of carcinogenesis at molecular level | 2 | 1 | 3 | 2 | 1 | 3 | 3 | 2 |
| 3) Learning of pharmacology and anti-cancer drug development, screening and relevant molecular/cellular techniques (cytotoxicity, etc.), get information about the postgraduate regulation related to cancer research and drug development, cooperation and experience share with institutions providing technological support | 3 | 3 | 2 | 1 | 2 | 3 | 3 | 3 |
| 4) The ability to synthesize, analyze, interpret, interrogate and criticize the relevant information on cancer biology and drug development | 3 | 3 | 3 | 1 | 1 | 2 | 3 | 3 |
| 5) The ability to use good communication skills and computer technology efficiently in their work | 3 | 1 | 1 | 2 | 1 | 1 | 3 | 3 |
| 6) The ability to convey/present the findings of the research and the results either verbally or in writing | 3 | 1 | 1 | 1 | 3 | 1 | 1 | 3 |
| 7) The ability to carry out professional and academic studies independently using accumulated knowledge and to work and take responsibility as a team member with other professions working in this field | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| 8) Having a sense of ethical responsibility in research | 3 | 3 | 3 | 3 | 3 | 3 | 3 | 3 |
| No Effect | 1 Lowest | 2 Average | 3 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | The ability to define basic concepts of Cancer Biology and Pharmacology, get information objectively about the related field within the scope of the program | 2 |
| 2) | Having knowledge about the molecular mechanisms of cancer, learning the process of carcinogenesis at molecular level | 3 |
| 3) | Learning of pharmacology and anti-cancer drug development, screening and relevant molecular/cellular techniques (cytotoxicity, etc.), get information about the postgraduate regulation related to cancer research and drug development, cooperation and experience share with institutions providing technological support | 3 |
| 4) | The ability to synthesize, analyze, interpret, interrogate and criticize the relevant information on cancer biology and drug development | 2 |
| 5) | The ability to use good communication skills and computer technology efficiently in their work | 3 |
| 6) | The ability to convey/present the findings of the research and the results either verbally or in writing | 2 |
| 7) | The ability to carry out professional and academic studies independently using accumulated knowledge and to work and take responsibility as a team member with other professions working in this field | 2 |
| 8) | Having a sense of ethical responsibility in research | 1 |
| Semester Requirements | Number of Activities | Level of Contribution |
| Midterms | 1 | % 40 |
| Final | 1 | % 60 |
| total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 40 | |
| PERCENTAGE OF FINAL WORK | % 60 | |
| total | % 100 | |
| Activities | Number of Activities | Workload |
| Course Hours | 14 | 28 |
| Study Hours Out of Class | 14 | 56 |
| Presentations / Seminar | 2 | 20 |
| Homework Assignments | 2 | 8 |
| Midterms | 1 | 10 |
| Final | 1 | 14 |
| Total Workload | 136 | |