ISTINYE UNIVERSITY BİLGİ PAKETİ / DERS KATALOĞU
| Molecular Oncology (DR) | |||||
| PhD | TR-NQF-HE: Level 8 | QF-EHEA: Third Cycle | EQF-LLL: Level 8 | ||
Course Introduction and Application Information
| Course Code: | MONK6005 | ||||
| Course Name: | Omix Technologies in Molecular Oncology | ||||
| Semester: | Spring | ||||
| 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: | E-Learning | ||||
| Course Coordinator: | Doç. Dr. HURİ DEDEAKAYOĞULLARI | ||||
| Course Lecturer(s): | Huri Bulut, Caner Geyik, Öykü Gönül Geyik, Murat Ekremoğlu, Yelda Birinci Kudu | ||||
| Course Assistants: |
Course Objective and Content
| Course Objectives: | Within the scope of this course, postgraduate students; It is aimed to gain theoretical experience in the research of biological effects and biomarkers by using OMİKS technologies. |
| Course Content: | Structural and functional research using Genome, Transcriptome, Proteome, Metabolome, Metagenome and Biomarker Concepts and OMIKS Technologies. |
Learning Outcomes
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The students who have succeeded in this course;
1) In this course, students know the historical process and types of omics technology, the basics of genomics, functional genomics and proteomics, their usage areas and current applications. 2) Student; Gain insight into deep learning used to predict genomic changes in cancer based on morphological features, Understands the importance of proteomics approaches in the whole of methods used in cancer diagnosis and treatment, Explain the methods used to detect RNA modifications, Gain knowledge about the isolation of protein complexes, Discuss the role and importance of glycans and glycosylated proteins in cancer, Explains the changes related to lipid metabolism in cancer, Recognizes the methods used in the determination of lipid metabolites, Discuss method principles and current developments in genomic technologies, Discuss method principles and current developments in metabolomics technologies, Learns the analysis of metabolites that differ physically and chemically by different chromatographic methods. |
Course Flow Plan
| Week | Subject | Related Preparation |
| 1) | Deep learning in cancer pathology: next generation clinical biomarkers | Computational solutions for omics data. Nat Rev Genet. 2013 May;14(5):333-46. doi: 10.1038/nrg3433. o Data Analysis for life sciences with R. Rafael Irizarry and Michael Love. (https://leanpub.com/dataanalysisforthelifesciences) |
| 2) | Proteomics in diagnosis and treatment approaches | Computational solutions for omics data. Nat Rev Genet. 2013 May;14(5):333-46. doi: 10.1038/nrg3433. |
| 3) | BN-PAGE method and applications | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 4) | genomic technologies | Sequencing technologies: the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46. doi: 10.1038/nrg2626. Epub 2009 Dec 8. Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016 May 17;17(6):333-51. |
| 5) | Epitranscriptomic analyzes and cancer | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 6) | STUDENT PRESENTATIONS | |
| 7) | Exam | |
| 8) | Lipidomic Analysis in Cancer | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 9) | Metabolomics technologies | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 10) | Chromatographic techniques in metabolomics | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 11) | Glycoproteomic technologies in cancer | Omics Technologies and Bio-engineering,Volume 1: Towards Improving Quality of Life, 1st Edition - December 1, 2017 Editors: Debmalya Barh, Vasco Azevedo |
| 12) | Current approaches in omics technologies (article analysis) | Current research articles |
| 13) | Student presentations | |
| 14) | Final exam |
Sources
| Course Notes / Textbooks: | Omics Technologies and Bio-engineering, Editors: Debmalya Barh, Vasco Azevedo, 1st Edition - December 1, 2017 |
| References: | o Sequencing technologies: the next generation. Nat Rev Genet. 2010 Jan;11(1):31-46. doi: 10.1038/nrg2626. Epub 2009 Dec 8. o Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet. 2016 May 17;17(6):333-51. doi: 10.1038/nrg.2016.49. o Bioinformatics: next-generation omics. Nat Rev Genet. 2012 May 2;13(6):378. doi: 10.1038/nrg3250. o Computational solutions for omics data. Nat Rev Genet. 2013 May;14(5):333-46. doi: 10.1038/nrg3433. o Data Analysis for life sciences with R. Rafael Irizarry and Michael Love. (https://leanpub.com/dataanalysisforthelifesciences) o Reference standards for next-generation sequencing. Nat Rev Genet. 2017; 18(8): 473-484. doi: 10.1038/nrg.2017.44. Epub 2017 Jun 19. o A survey of best practices for RNA-seq data analysis Genome Biol. 2016; 17: 13. doi: 10.1186/s13059-016-0881-8. o Genomic Data Science Specialization in Coursera https://www.coursera.org/specializations/genomic-data-science |
Course - Program Learning Outcome Relationship
| Course Learning Outcomes | 1 |
2 |
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|---|---|---|---|---|---|---|---|---|---|---|
| Program Outcomes | ||||||||||
| 1) To be able to define, evaluate and use current and advanced knowledge of cancer and molecular cancer | ||||||||||
| 2) To be able to research, comprehend and analyze a scientific and technological issue in the field of molecular cancer with a systematic approach. | ||||||||||
| 3) Ability to develop, design, adapt and implement new and complex ideas about the molecular mechanisms of cancer at an expert level with original thinking and/or research | ||||||||||
| 4) To be able to comprehend the interdisciplinary interaction with which the molecular cancer field is related, to develop a new method, design and/or application with a new idea or a known idea. | ||||||||||
| 5) To gain the ability to synthesize, analyze, interpret, question and criticize information about treatment approaches developed against cancer | ||||||||||
| 6) Tp develop new ideas and methods in the field by using high-level skills such as problem solving and decision making in their studies. | ||||||||||
| 7) To have good communication skills in their work and being able to critically examine and develop the norms that guide these relationships, and to manage actions to change them when necessary | ||||||||||
| 8) To have an awareness of ethical responsibility in their research and to be able to defend their findings by using advanced written, verbal and visual communication. | ||||||||||
| 9) To contribute to the solution of social, scientific, computational and ethical problems encountered in the field of molecular cancer and to support the development of these values. | ||||||||||
| 10) To be able to interpret research and study results and expand the limits of knowledge in the field by producing an original work. | ||||||||||
Course - Learning Outcome Relationship
| No Effect | 1 Lowest | 2 Average | 3 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | To be able to define, evaluate and use current and advanced knowledge of cancer and molecular cancer | 2 |
| 2) | To be able to research, comprehend and analyze a scientific and technological issue in the field of molecular cancer with a systematic approach. | 3 |
| 3) | Ability to develop, design, adapt and implement new and complex ideas about the molecular mechanisms of cancer at an expert level with original thinking and/or research | 3 |
| 4) | To be able to comprehend the interdisciplinary interaction with which the molecular cancer field is related, to develop a new method, design and/or application with a new idea or a known idea. | 3 |
| 5) | To gain the ability to synthesize, analyze, interpret, question and criticize information about treatment approaches developed against cancer | 2 |
| 6) | Tp develop new ideas and methods in the field by using high-level skills such as problem solving and decision making in their studies. | 2 |
| 7) | To have good communication skills in their work and being able to critically examine and develop the norms that guide these relationships, and to manage actions to change them when necessary | 2 |
| 8) | To have an awareness of ethical responsibility in their research and to be able to defend their findings by using advanced written, verbal and visual communication. | 2 |
| 9) | To contribute to the solution of social, scientific, computational and ethical problems encountered in the field of molecular cancer and to support the development of these values. | 3 |
| 10) | To be able to interpret research and study results and expand the limits of knowledge in the field by producing an original work. | 2 |
Assessment & Grading
| Semester Requirements | Number of Activities | Level of Contribution |
| Homework Assignments | 1 | % 40 |
| Seminar | 1 | % 60 |
| total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 100 | |
| PERCENTAGE OF FINAL WORK | % | |
| total | % 100 | |
Workload and ECTS Credit Calculation
| Activities | Number of Activities | Preparation for the Activity | Spent for the Activity Itself | Completing the Activity Requirements | Workload | ||
| Course Hours | 2 | 2 | 2 | 20 | 48 | ||
| Presentations / Seminar | 2 | 4 | 2 | 12 | |||
| Midterms | 1 | 5 | 5 | 15 | 25 | ||
| Final | 2 | 10 | 10 | 40 | |||
| Total Workload | 125 | ||||||