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Year/Semester of Study | 1 / Fall Semester | ||||
Level of Course | 3rd Cycle Degree Programme | ||||
Type of Course | Optional | ||||
Department | MOLECULAR BIOLOGY AND GENETICS (PHD) | ||||
Pre-requisities and Co-requisites | None | ||||
Mode of Delivery | Face to Face | ||||
Teaching Period | 14 Weeks | ||||
Name of Lecturer | NAŞİT İĞCİ (nasitigci@nevsehir.edu.tr) | ||||
Name of Lecturer(s) | |||||
Language of Instruction | Turkish | ||||
Work Placement(s) | None | ||||
Objectives of the Course | |||||
To give a practical knowledge about the aims of bioinformatics approaches in the field of proteomics studies. |
Learning Outcomes | PO | MME | |
The students who succeeded in this course: | |||
LO-1 | can explain current bioinformatics strategies used in proteomics. |
PO-1 Have information about current issues in molecular biology and genetics. PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it |
Examination Presentation |
LO-2 | can perform some important bioinformatic analyses in proteomics. |
PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it |
Examination Presentation |
LO-3 | gains knowledge about proteomics databases and can explain when to use which database in researches. |
PO-1 Have information about current issues in molecular biology and genetics. PO-3 Make use of the knowledge they have in order to find a solution to problems by analyzing, comparing and questioning them and can carry out original research in the related field on their own PO-4 Evaluate the knowledge and skills in a critical way in every activity regarding the field, thereby guiding their learning PO-6 Ability to design a research project in the field of molecular biology and genetics and to evaluate and present the results related to it |
Examination Presentation |
PO: Programme Outcomes MME:Method of measurement & Evaluation |
Course Contents | ||
Current proteomics strategies, use of proteomics bioinformatics, analysis in gel-based expression studies, use of protein databases, mass spectrometry based proteomics experimental approaches and protein identification with bioinformatics tools, bioinformatics approaches in protein 3 dimensional structure model. | ||
Weekly Course Content | ||
Week | Subject | Learning Activities and Teaching Methods |
1 | Current strategies and data sources of proteomics. | Lecture, Discussion, Question Answer, Literature Search |
2 | The place of bioinformatics in proteomics and their applications. | Lecture, Discussion, Question Answer, Literature Search |
3 | Expression analysis with gel-based methods and evaluation and presentation of the results using softwares. | Lecture, Discussion, Question Answer, Literature Search |
4 | Introduction of protein databases and methods of obtaining amino acid sequences in databases. | Lecture, Discussion, Question Answer, Literature Search |
5 | The use of protein databases to achieve the desired knowledge and their use for specific purposes. | Lecture, Discussion, Question Answer, Literature Search |
6 | Mass spectrometers and their use in proteomics. | Lecture, Discussion, Question Answer, Literature Search |
7 | Structure and information of the spectrum obtained by mass spectrometry. | Lecture, Discussion, Question Answer, Literature Search |
8 | mid-term exam | |
9 | Protein identification by mass spectrometry I: Peptide Mass Fingerprint Analysis. | Lecture, Discussion, Question Answer, Literature Search, Computer Work |
10 | Protein identification by mass spectrometry II: Peptide Fragment Fingerprint Analysis. | Lecture, Discussion, Question Answer, Literature Search, Computer Work |
11 | Mass spectrometry based de novo amino acid sequencing and software that can be used for this purpose. | Lecture, Discussion, Question Answer, Literature Search |
12 | Uses and applications of Protein BLAST. | Lecture, Discussion, Question Answer, Literature Search, Computer Work |
13 | Methods used in quantitative proteomics. | Lecture, Discussion, Question Answer, Literature Search |
14 | Use of bioinformatic analyses in quantitative proteomics. | Lecture, Discussion, Question Answer, Literature Search |
15 | Determining of protein 3 dimensional structures, software used in modeling and homology based structure modeling. Use of artificial intelligence in this field. | Lecture, Discussion, Question Answer, Literature Search, Computer Work |
16 | final exam | |
Recommend Course Book / Supplementary Book/Reading | ||
1 | Hubbard SJ, Jones AR. 2010. Proteome Bioinformatics. Springer. | |
2 | Campbell AM, Heyer LJ. 2006. Discovering Genomics, Proteomics and Bioinformatics. Benjamin Cummings. | |
3 | Eidhammer I, Flikka K, Martens L, Mikalsen S-O. 2007. Computational Methods for Mass Spectrometry Proteomics. Wiley. | |
4 | Özel Demiralp F, İğci N, Peker S, Ayhan B. 2014. Temel Proteomik Stratejiler. Ankara Üniversitesi Yayınevi, Ankara. | |
Required Course instruments and materials | ||
Lecture notes, books, related articles, computer. |
Assessment Methods | |||
Type of Assessment | Week | Hours | Weight(%) |
mid-term exam | 8 | 2 | 20 |
Other assessment methods | |||
1.Oral Examination | |||
2.Quiz | |||
3.Laboratory exam | |||
4.Presentation | 15 | 2 | 20 |
5.Report | |||
6.Workshop | |||
7.Performance Project | |||
8.Term Paper | |||
9.Project | |||
final exam | 16 | 2 | 60 |
Student Work Load | |||
Type of Work | Weekly Hours | Number of Weeks | Work Load |
Weekly Course Hours (Theoretical+Practice) | 3 | 14 | 42 |
Outside Class | |||
a) Reading | 3 | 14 | 42 |
b) Search in internet/Library | 3 | 14 | 42 |
c) Performance Project | 0 | ||
d) Prepare a workshop/Presentation/Report | 2 | 7 | 14 |
e) Term paper/Project | 0 | ||
Oral Examination | 0 | ||
Quiz | 0 | ||
Laboratory exam | 0 | ||
Own study for mid-term exam | 2 | 7 | 14 |
mid-term exam | 2 | 1 | 2 |
Own study for final exam | 2 | 7 | 14 |
final exam | 2 | 1 | 2 |
0 | |||
0 | |||
Total work load; | 172 |