INTERNATIONAL BURCH UNIVERSITY
Faculty of Engineering and Natural Sciences
Department of Genetics and Bioengineering
2017-2018

SYLLABUS
Code Name Level Year Semester
GBE 335 Genomics and Proteomics Undergraduate 3 Spring
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
5 66 English

Instructor Assistant Coordinator
Şenol Doğan, Assist. Prof. Dr. Şenol Doğan, Assist. Prof. Dr. Şenol Doğan, Assist. Prof. Dr.
[email protected] [email protected] no email

This course is organized as an integrated presentation of genome organization, genome sequencing and characterization, comparative genomics, and introductory genomic data analysis. It covers the basic terms, such as genome, transcriptome, and proteome, as well as more advanced concepts, for example, genome sequencing, gene activity regulation, evolution and phylogeny, epigenomics, and organelle genomics. This course is taken concurrently with a lab course which teaches students how to analyze genomes in silico using various bioinformatics tools.

COURSE OBJECTIVE
The cognitive, affective and behavioral objectives of this course are following:
• Introduction to the structure, organization, function and evolution of the genome.
• Familiarizing students with the functioning of the genome
• Explaining the analysis of the evolution of higher structural organisms.
• Explaining gene and cDNA libraries, microchips, and statistical processes of gene expression as well as gene and genome databases.

COURSE CONTENT
Week
Topic
  1. Introduction to Genomics
  2. DNA Sequencing
  3. Next Generation Sequencing
  4. Single Nucleotide Polymorphisms
  5. Copy Number Variations
  6. Genomic Variations and Anthropology
  7. Genome-wide Association Studies
  8. MIDTERM EXAM
  9. Chronic Myelogenous Leukemia
  10. Genomics and Drug Therapy
  11. Genetic Variation in Somatic Human Tissues
  12. Genomic Studies and Bioinformatic Tools
  13. Whole Genome Sequencing as Genetic Diagnostic Tool
  14. Student Presentations
  15. FINAL EXAM

LABORATORY/PRACTICE PLAN
Week
Topic
  1. Classical sequencing methods: Maxam-Gilbert and Sanger (two articles to discuss and presentation)
  2. DNA Sequencing Discussion
  3. Next Generation Sequencing Use in Genomics Discussion
  4. Single Nucleotide Polymorphisms and Disease
  5. GWAS; SNPs and CNVs (two articles to discuss and presentation; studying genes in OMIM)
  6. Use of Genomics in Population Studies Discussion

  1. NGS: Metagenomics (computer project and presentation about NGS methods)
  2. MIDTERM EXAM
  3. NGS: RNA-Seq data analysis (computer project)
  4. Mutations in genes; Ensembl and UCSC Search
  5. Ensembl and UCSC Search for SLC35A2 Gene Variations
  6. Comparative genomics (computer project)
  7. Epigenomics and pharmacogenomics (two articles to discuss and presentation)
  8. Protein analysis: domain and motif search and PPIs (either computer projects only or computer project and an article about PPIs to discuss; prepare a handout with all basic information)
  9. FINAL EXAM

TEACHING/ASSESSMENT
Description
  • Interactive Lectures
  • Presentation
  • Discussions and group work
Description (%)
Method Quantity Percentage (%)
Midterm Exam(s)120
Laboratory130
Attendance110
Final Exam140
Total: 100
Learning outcomes
  • General information about DNA and its structure
  • DNA related structures
  • Gene-protein association
  • Genomic Data, microRNA, Methylation, snRNA
  • Genetic Famliy Tree
  • Genomic Disease
  • Markers and potential diseases
  • Analyze of genomic data
TEXTBOOK(S)

    ECTS (Allocated based on student) WORKLOAD
    Activities Quantity Duration (Hour) Total Work Load
    Lecture (14 weeks x Lecture hours per week)14228
    Laboratory / Practice (14 weeks x Laboratory/Practice hours per week)14228
    Midterm Examination (1 week)122
    Final Examination(1 week)122
    Preparation for Midterm Examination122
    Preparation for Final Examination144
    Assignment / Homework/ Project 0
    Seminar / Presentation 0
    Total Workload: 66
    ECTS Credit (Total workload/25): 3