GBE 407 | Course Introduction and Application Information

Course Name
Genomics and Proteomics
Code
Semester
Theory
(hour/week)
Application/Lab
(hour/week)
Local Credits
ECTS
GBE 407
Fall/Spring
2
2
3
6

Prerequisites
None
Course Language
English
Course Type
Elective
Course Level
-
Course Coordinator -
Course Lecturer(s)
Assistant(s) -
Course Objectives The aim of this course is to introduce the methods which are used in protein biochemistry, bioinformatics and functional genomics.\nIn the scope of this lecture, responses of eukaryotic organisms to biotic and abiotic stress in all genome levels will be analyzed and the importance of personalized drug applications will be discussed.
Learning Outcomes The students who succeeded in this course;
  • Identify genomic structures in various species.
  • Explain traditional and modern genomic techniques.
  • Apply comparative genomic applications.
  • Explain proteomic approaches which are used in investigation of protein structure and function.
  • Investigate application areas of genomics and proteomics.
Course Content Definition and application areas of genomics and proteomics approaches, structural genomics, functional genomics and usage of comparative genomic, analysis of genomes of livings, proteomic analyses.

 



Course Category

Core Courses
Major Area Courses
Supportive Courses
Media and Management Skills Courses
Transferable Skill Courses

 

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week Subjects Related Preparation
1 Definition of genomics and general overview Genomics: Essential Methods- Chapter 1
2 Introduction to prokaryotic and eukaryotic genome and comparative genomics Genomics: Essential Methods- Chapter 1
3 Techniques and experimental strategies which are used in functional genomics applications Genomics: Essential Methods- Chapter 1
4 Genomics applications in human genetic diseases Genomics: Essential Methods- Chapter 1
5 RNA based techniques Genomics: Essential Methods- Chapter 1
6 Gene transfer techniques and gene therapy Genomics: Essential Methods- Chapter 1
7 1.Midterm
8 Definition of proteomics and its relation with genomics and system biology. Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter 1
9 Separation and determination techniques in proteomics 1: gel based separation, visualization of proteins/peptides gel in gel Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter2
10 Separation and determination techniques in proteomics 2: separation techniques without gel, and chips in proteomic applications Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter2
11 Analysis of peptides/proteins with mass spectroscopy, fundamental principles of applications Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter3
12 2.Midterm
13 Evaluation and analyses of mass spectroscopy and proteomic data together Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter4
14 Bioinformatics approaches in mass spectrometric proteome data analyses, proteomics application strategies Introducing Proteomics: From Concepts to Sample Separation, Mass Spectrometry and Data Analysis- Chapter4
15 General review Lecture presentations and notes
16 Final exam

 

Course Textbooks Genomics: Essential Methods, Mike Starkey (Editor), RamnathElaswarapu (Editor), Wiley-Blackwell; 1 edition, 2004.
References Introducing Proteomics: From concepts to sample preparation, mass spectrometry and data analysis, josipLovric, Wiley-Blackwell, 2011

 

EVALUATION SYSTEM

Semester Requirements Number Percentage
Participation
Laboratory / Application
Field Work
Quizzes / Studio Critiques
3
15
Homework / Assignments
3
15
Presentation / Jury
Project
Seminar / Workshop
Portfolios
Midterms / Oral Exams
2
40
Final / Oral Exam
1
30
Total

Contribution of Semester Work to Final Grade
70
Contribution of Final Work to Final Grade
30
Total

ECTS / WORKLOAD TABLE

Activities Number Duration (Hours) Workload
Course Hours
Including exam week: 16 x total hours
16
4
64
Laboratory / Application Hours
Including exam week: 16 x total hours
16
Study Hours Out of Class
14
1
Field Work
Quizzes / Studio Critiques
3
5
Homework / Assignments
3
10
Presentation / Jury
Project
Seminar / Workshop
Portfolios
Midterms / Oral Exams
2
16
Final / Oral Exam
1
25
    Total
180

 

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#
Program Qualifications / Outcomes
* Level of Contribution
1
2
3
4
5
1

To have sufficient background in Mathematics, Basic sciences and Biomedical Engineering areas and the skill to use this theoretical and practical background in the problems of the Biomedical Engineering.

2

To identify, formulate and solve Biomedical Engineering-related problems by using state-of-the-art methods, techniques and equipment; to select and apply appropriate analysis and modeling methods for this purpose.

3

To analyze a complex system, system components or process, and to design with realistic limitations to meet the requirements using modern design techniques; to apply modern design techniques for this purpose.

4

To choose and use the required modern techniques and tools for analysis and solution of complex problems in Biomedical Engineering applications; to skillfully use information technologies.

5

To design and do simulation and/or experiment, collect and analyze data and interpret results for studying complex engineering problems or research topics of the discipline. 

6

To efficiently participate in intradisciplinary and multidisciplinary teams; to work independently.

7

To communicate both in oral and written form in Turkish; to have knowledge of at least one foreign language; to have the skill to write and understand reports, prepare design and production reports, present, give and receive clear instructions.

8

To recognize the need for lifelong learning; ability to access information, to follow developments in science and technology, and to continue to educate him/herself.

9

To behave ethically, to be aware of professional and ethical responsibilities; to have knowledge about the standards in Biomedical Engineering applications.

10

To have information about business life practices such as project management, risk management, and change management; awareness of entrepreneurship, innovation, and sustainable development.

11

To have knowledge about contemporary issues and the global and societal effects of engineering practices on health, environment, and safety; awareness of the legal consequences of Biomedical Engineering solutions.

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest