BIOL 338:
Introduction to Genomics: W2017 draft syllabus
Prerequisite: BIOL 233 or 234, or FRST 302
Instructors:
Keith
Adams Jae-Hyeok Lee
321
Biodiversity Research Centre 2327
Biological Sciences Building
Meeting times:
- Lectures: 10:00 – 10:50 on
Monday, Wednesday, and Friday
- Tutorial: Tutorials are required (not optional help
sessions) and contain new material related to the lecture topics.
T03: 12:30 – 2:00
Wednesdays in Woodward G41
T01: 11:00 – 12:30
Thursdays in Woodward B75
T02: 12:30 – 2:00 Thursdays
in Woodward B75
Course overview:
This course will provide students with an introduction to the
relatively new and cutting‐edge discipline of genomics. It will be
organized into five sections: Contents, organization, and dynamics of genomes;
genome sequencing and annotation; genomics approaches to studying gene
expression; genome analysis and comparative genomics; research in genomics.
Applications of genomics to human health and disease, crop plant improvement,
and other applied situations will be included. Tutorials will consist of
computer labs to introduce students to web resources in genomics, along with
group discussions of genomics research papers and timely topics in genomics.
Course learning outcomes:
Achieve a working knowledge of concepts and recent discoveries in
genomics
Explain how technological advances have led to conceptual advances in
genomics
Relate
concepts and discoveries in genomics to human disease, crop plant improvement, and
other
applied situations
Utilize major web resources in genomics
Identify
the main results from a genomics research study and interpret figures from a
primary
research paper
Evaluation:
Midterm exam 1 - 18%
Midterm exam 2 - 18%
Final exam – cumulative -
35%
Tutorial exercises – 18% (1.5%
per tutorial)
Pre-reading quizzes – 6%
Clicker questions/attendance –
5%
Reading:
No textbook. Readings will consist of literature review articles from
journals and other materials to give an introduction to the lecture topics.
Readings for tutorials will consist of primary research papers and other
materials. Readings will be posted on the course Connect site. There will be a
pre-reading quiz approximately once per week.
Required materials:
A
laptop computer or tablet is needed for computer exercises in certain
tutorials. Clickers are needed for all lectures.
Lecture schedule
Section
1: Contents, organization, and dynamics of genomes (Adams)
Jan.
4 – Course introduction, introduction to genomics
Jan.
6, 9 - Chromatin structure and methylation
Jan.
9, 11 - Transposable elements: types and their abundance in genomes
Jan.
13, 16 - Repetitive DNA: satellites and microsatellites
Jan. 18, 20 - Centromeres and telomeres
Jan.
23 - 27 – Sex chromosomes
Jan.
30 – midterm exam #1
Section
2: Resource building - Genome sequencing and annotation (Lee)
Feb. 1 - Promises and advances in genomics
Feb. 3 - Research questions in genomics
Feb. 6 – Next generation sequencing-enabled research
applications
Feb. 8 -10 - Basics and practice of genome assembly (focused on Human
genome assembly by CVI)
Feb. 13 - Family day, no class
Feb. 15-17 - Genome annotation: Chromosome mapping, gene structure,
and gene content
Section 3: Genomics approaches to studying gene expression (Adams)
Feb. 27 – March 1 – Transcriptomics
March 3 - 6 – Proteomics
March 8 - Uses of NGS in evolution studies
March 10 - Midterm exam #2
Section 4: Genomics-enabled biology: mutation profiling and
comparative genomics (Lee)
March 13 - System genomics as an integrated research tool
March 15-17 - Targeted sequencing: Exome
sequencing for mutational profiling and functional genomics approaches
March 20-22 - Population-level genomics: 1000 genome projects and
genome wide association studies (GWAS)
March 24 - Personalized genomics: survey, introduction, and discussion
March 27-29 - Comparative genomes (focused on Human Evolution and
Macroevolution)
Section 5: Research in genomics (Adams and Lee)
Mar-31 - Current topics in genomics: CRISPR system, genomics to combat
infectious diseases
April 3 - Research presentation (Adams Lab)
April 5 - Research presentation (Lee Lab)
Tutorials, indicated by weeks
[Jan. 9] 1. Research
paper discussion: transposable elements
[Jan. 16] 2. Computer
exercise: GenBank gene and chromosome records, BLAST
searching
[Jan. 23] 3. Research
paper discussion: sex chromosomes
[Jan. 30] 4. Peer
teaching and discussion: pros and cons of various NGS platforms (interactive)
[Feb. 6] 5. Research
paper discussion: NGS-based genome assembly (Klebsormidium
genome, as a review of the key concepts in genome assembly) - The need
for long-reads?
[Feb. 13] 6. Computer exercise:
Annotation of a protein-encoding gene (Computer algorithms and public
databases)
[Feb. 27] 7. Computer exercise:
Gene expression and human genomics databases
[March 6] 8. Research
paper discussion: Proteomics
[March 13] 9. Research
paper discussion: exome sequencing (Mendelian genetic disorder, as a review of the key concepts
in the exome study) - The statistical power of exome-reads?
[March 20] 10. Survey on
public views about personalized medicine (Briefing of their homework in class -no
tutorial sessions per se)
[March 27] 11. Research paper
discussion: comparative genomics study (Human specific traits, focused on
comparative techniques)
[April 3] 12. Paper discussion:
CRISPR system