| ECONOMICS | |||||
| Bachelor | TR-NQF-HE: Level 6 | QF-EHEA: First Cycle | EQF-LLL: Level 6 | ||
| Course Code | Course Name | Semester | Theoretical | Practical | Credit | ECTS |
| MBG2004 | Computation for Biological Sciences II | Fall | 2 | 2 | 3 | 7 |
| This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester. |
| Language of instruction: | English |
| Type of course: | Non-Departmental Elective |
| Course Level: | Bachelor’s Degree (First Cycle) |
| Mode of Delivery: | Face to face |
| Course Coordinator : | Assist. Prof. CEMALETTİN BEKPEN |
| Course Lecturer(s): |
Prof. Dr. SÜREYYA AKYÜZ |
| Course Objectives: | This class intended to provide advanced information to computational tools for biology. This course covers the methods and tools for learning foundations of computational biology combining theory with practice. We cover both foundational topics in computational biology, and current research frontiers. We study fundamental techniques, recent advances in the field, and work directly with current large-scale biological datasets. |
|
The students who have succeeded in this course; • Genomes: Biological sequence analysis, comparative genomics, RNA structure, sequence alignment, • Pathways and Network analysis: Gene expression, clustering / classification, motifs, Bayesian networks, microRNAs, regulatory genomics, epigenomics • Molecular Evolution: Gene / species trees, phylogenomics, coalescent, personal genomics, population genomics, human ancestry, recent selection, disease mapping • Comparative Genomics/Transcriptomics: Compare current NGS mapping methodologies and genomes both theoretically and practically, • Genome Assembly: With the advances in sequencing technologies it has become much more feasible, and affordable, to assemble and annotate the genomic sequence of most organisms, including large eukaryote genomes. However, high quality genome assembly and annotation still represent a major challenge. In this class, we will discuss current methods and technologies to perform best assembly. • Current advances in systems and integrative biology (Review) |
| Advanced level sequence data, searching and alignment, structural data, genome sequencing, genome analysis, genetic variation, gene and protein expression, and biological networks and pathways. We will evaluate the results of these analyzes by using advances functional genomics, transcriptomics, enrichment methods |
| Week | Subject | Related Preparation |
| 1) | Introduction | Read the Syllabus and Describe Project Details |
| 2) | Advanced Comparative Genomics | |
| 3) | Human Genomic Variations (Population Genetics approach) | Practical Lab Assignment 1 by using https://usegalaxy.org/ |
| 4) | Variant Detection and Methods Single Nucleotide Variations (SNPs) Annotation | |
| 5) | SNP Genotyping Methods and Micro Array Analyses | Practical Lab Assignment 2 by using https://usegalaxy.org |
| 6) | Advanced Variant Detection and Methods Structural Variations (SVs) Copy Number Variation (CNVs) | |
| 7) | Gene Ontology and Gene Annotation | Practical Lab Assignment 3 by using https://usegalaxy.org/ |
| 8) | Advance Transcriptomics (RNA-Seq) Gene set enrichment analysis | |
| 9) | Midterm Review | Midterm Sınavı |
| 10) | Genome/Transcriptomics Assembly and Annotation | Practical Lab Assignment 4 by using https://usegalaxy.org/ |
| 11) | Advance Molecular Phylogenetics/Phylogenomics | |
| 12) | Molecular Evolution/PaleoGenomics | Final Project by using https://usegalaxy.org/ |
| 13) | MetaGenomics | |
| 14) | Review “Current advances in systems and integrative biology? ” | Final Project submission and Final Project Exam |
| Course Notes / Textbooks: | Ders notları haftalık olarak verilecektir. Course material will be provided weekly. |
| References: | 1) Durbin, Richard, Sean R. Eddy, Anders Krogh, et al. Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge University Press, 1998. 2) Jones, Neil C., and Pavel Pevzner. An Introduction to Bioinformatics Algorithms. MIT Press, 2004. ISBN: 9780262101066. |
| Semester Requirements | Number of Activities | Level of Contribution |
| Project | 1 | % 40 |
| Midterms | 1 | % 20 |
| Final | 1 | % 40 |
| Total | % 100 | |
| PERCENTAGE OF SEMESTER WORK | % 20 | |
| PERCENTAGE OF FINAL WORK | % 80 | |
| Total | % 100 | |
| Activities | Number of Activities | Duration (Hours) | Workload |
| Course Hours | 14 | 4 | 56 |
| Study Hours Out of Class | 14 | 7 | 98 |
| Project | 5 | 4 | 20 |
| Midterms | 1 | 2 | 2 |
| Final | 1 | 2 | 2 |
| Total Workload | 178 | ||
| No Effect | 1 Lowest | 2 Low | 3 Average | 4 High | 5 Highest |
| Program Outcomes | Level of Contribution | |
| 1) | As a world citizen, she is aware of global economic, political, social and ecological developments and trends. | 2 |
| 2) | He/she is equipped to closely follow the technological progress required by global and local dynamics and to continue learning. | 2 |
| 3) | Absorbs basic economic principles and analysis methods and uses them to evaluate daily events. | 2 |
| 4) | Uses quantitative and statistical tools to identify economic problems, analyze them, and share their findings with relevant stakeholders. | 2 |
| 5) | Understands the decision-making stages of economic units under existing constraints and incentives, examines the interactions and possible future effects of these decisions. | 1 |
| 6) | Comprehends new ways of doing business using digital technologies. and new market structures. | 2 |
| 7) | Takes critical approach to economic and social problems and develops analytical solutions. | 1 |
| 8) | Has the necessary mathematical equipment to produce analytical solutions and use quantitative research methods. | 2 |
| 9) | In the works he/she contributes, observes individual and social welfare together and with an ethical perspective. | 2 |
| 10) | Deals with economic problems with an interdisciplinary approach and seeks solutions by making use of different disciplines. | 1 |
| 11) | Generates original and innovative ideas in the works she/he contributes as part of a team. | 2 |