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Syllabus ( BSB 617 )


   Basic information
Course title: Systems Biology of Pathogen-Host Interactions
Course code: BSB 617
Lecturer: Dr. Öğr. Üyesi Saliha DURMUŞ TEKİR
ECTS credits: 7.5
GTU credits: 3 (3+0+0)
Year, Semester: 1/2, Spring
Level of course: Second Cycle (Master's)
Type of course: Area Elective
Language of instruction: English
Mode of delivery: Face to face
Pre- and co-requisites: None
Professional practice: No
Purpose of the course:
   Learning outcomes Up

Upon successful completion of this course, students will be able to:

  1. Have knowledge on infectious diseases in terms of causes, outcomes and global impacts

    Contribution to Program Outcomes

    1. Acquire scientific knowledge and work independently
    2. Develop an awareness of continuous learning in relation with modern technology

    Method of assessment

    1. Written exam
    2. Homework assignment
    3. Seminar/presentation
  2. Have knowledge on the current understanding of infection mechanisms, current therapeutics, drug-resistant pathogens and new strategies to fight drug resistance

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Identify the changes in cellular and molecular mechanisms in health and disease from the perspective of bioinformatics and systems biology.
    3. Acquire scientific knowledge and work independently

    Method of assessment

    1. Written exam
    2. Homework assignment
  3. Have knowledge on the recent studies on infection mechanisms through pathogen-host interactions using experimental and computational systems biology approaches

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Apply modelling approaches to cellular networks.
    3. Identify the changes in cellular and molecular mechanisms in health and disease from the perspective of bioinformatics and systems biology.

    Method of assessment

    1. Written exam
    2. Homework assignment
  4. Know the available bioinformatics tools for studies of infection mechanisms through pathogen-host molecular interactions

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Apply modelling approaches to cellular networks.
    3. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
    4. Work effectively in multi-disciplinary research teams

    Method of assessment

    1. Term paper
  5. Investigate infection mechanisms through pathogen-host protein-protein interactions using bioinformatics tools via systems biology approaches

    Contribution to Program Outcomes

    1. Identify the changes in cellular and molecular mechanisms in health and disease from the perspective of bioinformatics and systems biology.
    2. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
    3. Review the literature critically pertaining to his/her research projects, and connect the earlier literature to his/her own results.
    4. Develop an awareness of continuous learning in relation with modern technology
    5. Effectively express his/her research ideas and findings both orally and in writing
    6. Grasp the importance of bioinformatics and systems biology based viewpoint in the analysis and interpretation of working principles of the cell.

    Method of assessment

    1. Written exam
    2. Seminar/presentation
    3. Term paper
   Contents Up
Week 1: Infectious diseases, pathogens and the infectious threats to humans in the 21st century
Homework I
Week 2: Types of pathogenic microorganisms and their different infection strategies
Week 3: - Current anti-infective therapeutics and drug resistance mechanisms
- Pathogen-host interaction systems as underlying mechanisms of infections
- Next-generation anti-infectives against drug resistant pathogens
Homework II
Week 4: Review of recent studies of infection mechanisms through pathogen-host interactions using experimental and computational systems biology approaches
Week 5: Current bioinformatics tools for studies of infection mechanisms through pathogen-host interactions
Quiz I
Week 6: Investigation of literature examples for computational analysis of bacteria-human protein-protein interaction networks
Homework III
Week 7: Investigation of literature examples for computational analysis of virus-human protein-protein interaction networks
Week 8: Computational techniques for analysis of large scale pathogen-human protein-protein interaction networks I: Analysis of pathogen-targeted human proteins in terms of their topological properties within the human own protein interaction network
Homework IV
Week 9: Computational techniques for analysis of large scale pathogen-human protein-protein interaction networks II: Analysis of targeted human proteins in terms of their functional properties within the human own protein interaction network
Quiz II
Week 10: Computational techniques for analysis of large scale pathogen-human protein-protein interaction networks III: Analysis of bi-partite interaction graphs between pathogen and human proteins in terms of topological properties
Week 11: Computational techniques for analysis of large scale pathogen-human protein-protein interaction networks IV: Investigation of combined pathogen-human protein-protein interactions integrated with interactions within human proteins and also within pathogen proteins
Week 12: Mid-project presentations
Week 13: - Summary of the computational analysis techniques
- Proposing further experimental studies and potential therapeutic mechanisms against pathogens based on the analysis results
Week 14: Finding orthologous pathogen-human protein-protein interactions interaction data for pathogens lacking experimental data
Week 15*: General overview
Week 16*: Project presentations
Textbooks and materials: 1. Edda Klipp, Wolfram Liebermeister, Cristoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig. “Systems Biology”, Wiley-Blackwell, 2009.
Recommended readings: 1. Reinhard Guthke, Saliha Durmuş, Tunahan Çakır, Emrah Nikerel, Arzucan Özgür (editors), Special issue: “Computational systems biology of pathogen-host interactions”, Frontiers in Microbiology, Vol. 6, 2015.

2. Reinhard Guthke, Marc Thilo Figge (editors), Special issue: “Systems biology of microbial infection”, Frontiers in Microbiology, Vol. 3, 2012.
  * Between 15th and 16th weeks is there a free week for students to prepare for final exam.
Assessment Up
Method of assessment Week number Weight (%)
Mid-terms: 0
Other in-term studies: 0
Project: 7 40
Homework: 1, 3, 6, 8 40
Quiz: 5, 9 20
Final exam: 0
  Total weight:
(%)
   Workload Up
Activity Duration (Hours per week) Total number of weeks Total hours in term
Courses (Face-to-face teaching): 3 14
Own studies outside class: 3 14
Practice, Recitation: 3 3
Homework: 7 4
Term project: 7 9
Term project presentation: 2 2
Quiz: 1 2
Own study for mid-term exam: 0 0
Mid-term: 0 0
Personal studies for final exam: 0 0
Final exam: 0 0
    Total workload:
    Total ECTS credits:
*
  * ECTS credit is calculated by dividing total workload by 25.
(1 ECTS = 25 work hours)
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