• Basic information
• Learning outcomes
• Contents
• Assessment
• Workload

Learning outcomes

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

1. get acquainted with sate of the art high throughput (HT) technologies such as genomics, proteomics, transcriptomics, etc., and next generation sequencing (NGS) platforms and their use in core research, and become familiar with the programs used to handle HT data produced from these HT platforms.

   Contribution to Program Outcomes

   1. To be able to define the structure-function relationship at the molecular level in cells and organisms.
   2. To be able to follow current scientific and technological innovations with the awareness of continuous learning and to apply them in the field.

   Method of assessment

   1. Written exam
2. Understands and analyze the high throughput data obtained from omics studies that may include the microarray or RNA-seq generated transcriptome data and LCMSMS based proteomics data sets. Acquires basic knowledge of the CRISPR Cas9 applications in various area of molecular sciences. Use Glaxy program to analyze at the basics level various omics data stored in publicly available in the databanks. Understand the basics and the use of conventional methodologies (Macromolecular interactions, subcellular localization of proteins, Mass spectrometry, 2D-PAGE, and etc.,) in Functional Genomics studies.

   Contribution to Program Outcomes

   1. To be able to define general concepts and problems related to Molecular Biology and Genetics and to produce solutions.
   2. To be able to define the structure-function relationship at the molecular level in cells and organisms.
   3. To be able to explain the genetic information flow in organisms and populations.

   Method of assessment

   1. Written exam
3. develop ability to comprehend and interpret 'omics' based HT data frequently come across in the scientific literature

   Contribution to Program Outcomes

   1. To be able to define general concepts and problems related to Molecular Biology and Genetics and to produce solutions.
   2. To be able to define the structure-function relationship at the molecular level in cells and organisms.
   3. To be able to explain the genetic information flow in organisms and populations.

   Method of assessment

   1. Written exam

Contents
Week 1:	Functional genomics: Introduction and brief history
Week 2:	In vitro cellular systems and animal models for functional genomic studies
Week 3:	Introduction to Next Generation DNA/RNA sequencing, Overview of Different NGS platforms
Week 4:	Gene Expression Studies I: DNA and RNA based Microarrays and data analysis (Software and Programs used: Galaxy, GenPattern and Bioconductor)
Week 5:	Gene Expression Studies II: RNA sequencing
Week 6:	Gene Expression Studies III: (Serial analysis of gene expression) SAGE and similar methodologies for transcriptome level expression studies
Week 7:	Mid-term Exam: RNAi and CRISPR based functional screens for functional Genomic studies
Week 8:	Proteomics I: introduction to mass spectrometry (LCMS and LCMSMS) and applications in Life sciences
Week 9:	Proteomics II: 2-D PAGE and DIGE applications
Week 10:	Genome and Gene modifications: CRISPR technology and its use in basic research and future perspective in human genome editing
Week 11:	Introduction to Next Generation Sequencing Technologies I: İllumina, İontorent, Pac bio and Oxford Nanopor platforms
Week 12:	Interactome studies: Protein Protein, Protein Nucleic acid interaction detection methodologies including IPs, IPMS, Turbo ID-MS, Yeast two Hybrid
Week 13:	Proteins subcellular localization: Confocal Imaging.
Week 14:	Protein Structure and Functional Relationship: Protein 3D structures. ( introduction to Deep View Program for in slico analyses of protein structure)
Week 15*:	From Genotype to Phenotype : Single nucleotide polymorphisms (SNPs), Genome Wide Association studies.
Week 16*:	Paper discussion in Functional Genomics: A recent scientific research paper in related subjects is assigned to all students a week in advance for critical review in the lecture.
Textbooks and materials:	Bioinformatic and Functional Genomics 3rd eddition J Pevsner. ISBN-13: 978-1118581780 A Primer of Genome Science by Greg Gibson, Spencer V. Muse 3rd. Edition Discovering Genomics, Proteomics and Bioinformatics, A. Malcolm Campbell, Davidson College Laurie J. Heyer, Davidson College. 2nd Edition
Recommended readings:	Functional Genomics: A Practical Approach by Stephen P. Hunt and Rick Livesey; Functional Genomics (Methods in Molecular Biology) Michael J. Brownstein, Arkady Khodursky; Proteomics in Functional Genomics: Protein Struture analysis, P. Jolles, Hans Jörnvall
	* Between 15th and 16th weeks is there a free week for students to prepare for final exam.

Assessment
Method of assessment	Week number	Weight (%)
Mid-terms:	0	0
Other in-term studies:	0	0
Project:	0	0
Homework:	7	50
Quiz:	0	0
Final exam:	16	50
	Total weight:	(%)

Workload
Activity	Duration (Hours per week)	Total number of weeks	Total hours in term
Courses (Face-to-face teaching):	3	14
Own studies outside class:	2	14
Practice, Recitation:	0	0
Homework:	0	0
Term project:	0	0
Term project presentation:	0	0
Quiz:	0	0
Own study for mid-term exam:	2	6
Mid-term:	3	1
Personal studies for final exam:	3	6
Final exam:	3	1
		Total workload:
		Total ECTS credits:	*
	* ECTS credit is calculated by dividing total workload by 25. (1 ECTS = 25 work hours)