INTERNATIONAL BURCH UNIVERSITY
Graduate Study - Faculty of Engineering and Natural Sciences
Genetics and Bioengineering PhD
2012-2013

SYLLABUS
Code Name Level Year Semester
GBE 620 Functional Genomics Graduate 1 Fall
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
Area Elective 7.5 3 0 English

Instructor Assistant Coordinator
Lada Lukić-Bilela, Assist. Prof. Dr. Lada Lukić-Bilela, Assist. Prof. Dr.
change@a.com no email

COURSE OBJECTIVE
A Primary Course Objective:
Understanding the relationship between an organism\\\'s genome and its phenotype. Functional genomics focuses on the dynamic aspects such as gene transcription, translation, and protein–protein interactions, as opposed to the static aspects of the genomic information such as DNA sequence or structures.

General Course Objectives:
Upon completion of this course, the student will be familiar with:
 how genomic sequencing is done
 comparison of genes by using various databases
mutagenesis
various RNA types
using different DNA segments, such as SNPs, for particular purposes
importance of the systematic approach

COURSE CONTENT
Week
Topic
  1.  Course introduction  Introduction to syllabus
  2.  Functional vs. Comparative Genomic  Genome Architecture and Organization
  3.  At the DNA level: Genetic interaction mapping; Genome Mapping and Organization; The ENCODE Project
  4.  At the DNA level: Genome Sequencing Projects; Human Epigenome Project; Assembling Genome Sequences; Computational Tools
  5.  At the RNA level: Transcriptome profiling; Serial Analysis of Gene Expression (SAGE)
  6.  At the RNA level: cDNA Microarrays, Oligonucleotide Microarrays, Regulation of Gene Expression
  7.  At the protein level: protein–protein interactions - Yeast two-hybrid system; AP/MS
  8.  Functional annotations for genes: Differential Display, Gene Discovery – Expressed Sequence Tags (ESTs)
  9.  Functional annotations for genes: Sequence Polymorphisms in Genomes and SNPs; Applications
  10.  Metabolomics: Non-targeted analysis and Targeted analysis
  11.  Loss-of-function techniques: Site-directed Mutagenesis: Kunkel\\\\\\\\\\\\\\\\
  12.  Loss-of-function techniques: Forward and Reverse Genetics, RNAi-mediated Gene Silencing, Gene Knockouts, Micro-RNAs and Small RNAs

  1.  Functional genomics and bioinformatics
  2.  Application of Functional Genomics in Medicine, Forensic, Agriculture and Population Studies  From Functional Genomics to System Biology

LABORATORY/PRACTICE PLAN
Week
Topic

    TEACHING/ASSESSMENT
    Description
    • Lectures
    • Presentation
    • Seminar
    • Project
    • Case Studies
    Description (%)
    Method Quantity Percentage (%)
    Homework5
    Project15
    Midterm Exam(s)30
    Presentation10
    Final Exam140
    Total: 100
    Learning outcomes
    • Critical Thinking and Quantitative Reasoning in GBE
    • Genetic and Bioengineering Application
    • Genetic and Bioengineering Management
    • Genetic and Bioengineering Professional Practice
    • Genetic and Bioengineering Systems and Theory Practice
    TEXTBOOK(S)
    • Required
    • 1.Pevsner, Jonathan (2009) Bioinformatics and Functional Genomics. 2nd edition, Wiley-Blackwell, 2009, New Jersey, USA.
    • 2.Functional Genomics (Methods in Molecular Biology), Humana Press, Softcover reprint of hardcover 1st ed. 2003. (dec. 9, 2010).

    ECTS (Allocated based on student) WORKLOAD
    Activities Quantity Duration (Hour) Total Work Load
    Lecture (14 weeks x Lecture hours per week)480
    Laboratory / Practice (14 weeks x Laboratory/Practice hours per week) 0
    Midterm Examination (1 week) 0
    Final Examination(1 week) 0
    Preparation for Midterm Examination 0
    Preparation for Final Examination7.50
    Total Workload: 0
    ECTS Credit (Total workload/25): 0