COURSE UNIT TITLE

: BIOENFORMATIC

DEGREE PROGRAMMES

Description of Individual Course Units

Course Unit Code Course Unit Title Type Of Course D U L ECTS
BIY 2025 BIOENFORMATIC COMPULSORY 2 0 0 5

Offered By

Biology

Level of Course Unit

First Cycle Programmes (Bachelor's Degree)

Course Coordinator

PROFESSOR DOCTOR ÇETIN ILGAZ

Offered to

Biology

Course Objective

This course is designed to introduce future biologists to bioinformatics tools and analysis methods. Upon completion of the course, students should be more comfortable working with the vast amounts of genomic data and online tools that will be relevant to their work in the coming decades.

Learning Outcomes of the Course Unit

1   Have a solid understanding of the field of bioinformatics sequence analysis and many topics of molecular biology
2   Have a good skill set and extensive experience using common sequence analysis tools and databases
3   Have a good exposure to a variety of sequence analysis problems and understand how to solve them
4   Be able to address their own sequence analysis problems or design sequence analysis software
5   Know how to convey what they have learned in clearly composed documents or brief demonstrations

Mode of Delivery

Face -to- Face

Prerequisites and Co-requisites

None

Recomended Optional Programme Components

None

Course Contents

Week Subject Description
1 Introduction
2 Genomic sequences
3 Sequence alignment
4 Database searching; BLAST.
5 Advanced BLAST: PSI-BLAST, Genomic DNA. Find-a-gene project
6 Multiple sequence alignment
7 Midterm exam
8 mRNA and gene expression introduction
9 Statistics for differential expression, multiple testing.
10 Sequence variation, phenologs, comparative genomics
11 Molecular phylogeny and evolution
12 Journal article discussion
13 Journal article discussion
14 Journal article discussion
15 Final exam

Recomended or Required Reading

Lesk, A.M. 2002. Introduction to Bioinformatics. Oxford University Press. Orengo, C., Jones, D. and Thornton, J. 2003. Bioinformatics: Genes, Proteins and Computers. Garland Science/BIOS Scientific Publishers, New York. Krawetz, S.A. and Womble, D.D. 2003. Introduction to Bioinformatics: a Theoretical and Practical Approach. Claveria JM, Notredame C, Bioinformatic for dummies. 2007. Willey publishing Humana Press, Totowa, New Jersey.Irizarry, R. A. (2017). Data analysis for the life sciences with R. Boca Raton, CRC Press, Taylor & Francis Group. Gentleman, R. (2009). R programming for bioinformatics. Boca Raton, CRC Press. Sinha, P. P. (2014). Bioinformatics with R Cookbook. Packt Publishing Ltd.

Planned Learning Activities and Teaching Methods

Lecture, question-answer

Assessment Methods

SORTING NUMBER SHORT CODE LONG CODE FORMULA
1 VZ Vize
2 FN Final
3 BNS BNS VZ * 0.40 + FN * 0.60
4 BUT Bütünleme Notu
5 BBN Bütünleme Sonu Başarı Notu VZ * 0.40 + BUT * 0.60


Further Notes About Assessment Methods

None

Assessment Criteria

Student will be evaluated with midterm and final examinations.

Language of Instruction

Turkish

Course Policies and Rules

Attendance to at least 80% for the lectures is an essential requirement of this course and is the responsibility of the student. It is necessary that attendance to the lecture and homework delivery must be on time. Any unethical behavior that occurs either in presentations or in exams will be dealt with as outlined in school policy

Contact Details for the Lecturer(s)

cetin.ilgaz@deu.edu.tr

Office Hours

will be announced.

Work Placement(s)

None

Workload Calculation

Activities Number Time (hours) Total Work Load (hours)
Lectures 14 2 28
Preparations before/after weekly lectures 14 3 42
Preparation for midterm exam 1 20 20
Preparation for final exam 1 20 20
Midterm 1 2 2
Final 1 2 2
TOTAL WORKLOAD (hours) 114

Contribution of Learning Outcomes to Programme Outcomes

PO/LOPO.1PO.2PO.3PO.4PO.5PO.6PO.7PO.8PO.9PO.10PO.11PO.12PO.13PO.14
LO.145555555
LO.25555555
LO.355555
LO.45555555
LO.545555

CONTACT INFORMATION
Dokuz Eylül Üniversitesi Cumhuriyet Bulvarı No: 144 35210 Alsancak / İZMİR
Phone: +90(232) 412 12 12 - Fax: +90 (232) 464 81 35

Copyright 2015 DEÜ. BİD

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