Syllabus BIOL-UA 124 Fundamentals of Bioinformatics

BIOLOGY COURSE SYLLABUS

Course Number & Title: BIOL-UA 124 Fundamentals of Bioinformatics

Instructor(s): S. Carol Huang, Manpreet S. Katari

Course Description: The course has a lecture and a recitation component. During the recitation the students will use popular software packages to analyze publicly available data from genome projects and high-throughput experiments. The course is divided into three sections:

1) Genomics – students will learn about different DNA-sequencing technologies and the challenges behind analyzing the sequences. Students will learn the concepts behind aligning sequences and predicting where genes reside in sequences.

2) Structural Bioinformatics – students will learn the concepts behind predicting RNA and protein structures.

3) Functional Genomics – students will learn about gene expression analysis and how it can be used to identify changes in genome structure and gene activity.

Pre-requisites: BIOL-UA 21 Molecular and Cell Biology I.

Textbook(s): Recommended:

(UB) Understanding Bioinformatics, Marketa J Zvelebil, Jeremy O. Baum. Garland Science.

Grading Information: Course grades will be based on the following: • 20% Assignments • 20% Midterm 1 • 20% Midterm 2 • 30% Final • 10% Attendance/Participation

Lecture Topics and Readings Topics Covered Readings

Introduction to Sequence Technologies https://www.ncbi.nlm.nih.gov/books/N BK21117/ Sequence Assembly and Alignment https://www.ncbi.nlm.nih.gov/books/N BK21116/ Pairwise Sequence alignment (BLAST) UB Chapter 4 & 5 & PSI BLAST

Multiple Sequence Alignment and UB Chapter 6 Protein Motif and Domain predictions

Phylogenetics and Tree Building UB Chapter 7 & 8

Gene Structure Prediction UB Chapter 9 & 10 https://www.ncbi.nlm.nih.gov/books/N BK21136/#A6613

Domains and Secondary Structure UB Chapter 11 & 12 predictions

Tertiary Protein Structure prediction UB Chapter 13 & 14

RNA and miRNA structure Prediction Practical Aspects of microRNA Target Prediction, T.M Witkos, E Koscianska, and W.J Krzyzosiak

Gene Expression Analysis UB Chapter 15

Clustering UB Chapter 16

Proteome sequence and expression UB Chapter 15 Analysis

Protein Interactions UB Chapter 17

Systems Biology & Gene networks UB Chapter 17