Goals:

  1. Understanding of basics of genomics
  2. Enable students to browse current literature and gain exposure to research in this field
  3. Familiarise with main topics using available Simulation Tools

Textbooks:

No textbook is required for this course. However, the following resources are recommended.

  • Lesk, Arthur M. Introduction to genomics. Oxford University Press, 2017
  • Gusfield, Dan. Algorithms on strings, trees and sequences: computer science and computational biology. Cambridge University Press, 1997.
  • Durbin, Richard, ed. Biological sequence analysis: probabilistic models of proteins and nucleic acids. Cambridge university press, 1998.
  • Hein, Jotun, Mikkel Schierup, and Carsten Wiuf. Gene genealogies, variation and evolution: a primer in coalescent theory. Oxford university press, 2004.
  • Neil C. Jones and Pavel A. Pevzner, An Introduction to Bioinformatics Algorithms, The MIT Press, 2004

Pre-requisite:

  •  An Introduction to Bioinformatics

Syllabus:

  1. Basics — Mina Sadat Mahmoodi
    1. Genomics
    2. Content of genomes
    3. Functional genomics
    4. Evolution of genomes
    5. Sequencing technologies
  2. Sequence Analysis — Mustafa Tavassolipour
    1. Evolutionary models
    2. Homology
    3. Local and Global alignment
  3. NGS Data Analysis  — Amin Ghahramani
    1. Error modeling
    2. Read mapping
    3. Sequence assembly
    4. Phasing
  4. Comparative Genomics — Amir Hossein Saberi
    1. Genome evolution models
    2. Phylogenetic
    3. Phylogenomics
  5. Population Genetics —  Amir Najafi
    1. Hardy-Weinberg Principle
    2. Wright-Fisher Model
    3. Coalescent Theory
    4. Genome wide association study
    5. Cancer genetics
  6. Functional Genomics — Mojtaba Nikahd
    1. Gene expression data analysis
    2. Epigenomics
    3. eQTL
    4. Regulatory  networks
    5. Differential networks

Grade Distribution (Tentative):

  • Final 40%
  • Midterms 20%
  • HW 30%
  • Project 10%

Homework:

  • PS I
  • PS II
  • PS III
  • PS IV
  • PS V
  • PS VI

Course Handouts:

To be uploaded.

Projects:

    • Test