Course Syllabus
Genomic Biology
The term ‘Genomics’ covers the advances that have been made in the development of tools and technologies that allow high-throughput mapping, sequencing and functional analysis of genes. The era of genomics started with the sequencing of the human genome and currently, the full genomic sequence of several eukaryotic organisms is available. The course will cover tools, applications and ethical concerns related to genomics. It will provide students with an insight into cutting edge technologies and how they are used to enhance our understanding of how genes function. The course is intended for students that have had a modern introduction to biology. We will make every attempt to accommodate students with different backgrounds, although the course will remain rigorous.
PBIO 3020
Katrien M. Devos
Fall 2006
Principal Course Assignments:
None
Specific Course Requirements for Grading:
Thu 19th Sept.:
Take-home assignment to be turned in Tue 26th September
Tue 10th Oct.:
Exam
Thu 9th Nov.:
Exam
Grading Policy:
The class includes three midterm assignments or exams, each of which will account for 20% of the total grade. Home assignments are expected to be submitted within 1 week.
The final exam will account for 40% of the grade.
Attendance Policy:
Class attendance will not be taken. It is the responsibility of the student to ensure that he/she is up-to-date with course materials. Please note that, although the slides presented in each class will be available on-line, both written and verbally covered materials are required knowledge for the exams. Furthermore, in-class exercises will be conducted to help students understand the materials and link different parts of the syllabus. Students are therefore strongly advised to attend classes and take copious notes.
Required Course Material Including Texts:
Tentative Syllabus
This syllabus is ‘tentative’ because it will no doubt require fine-tuning as we proceed. Some material may require more time and some less than originally anticipated. Your feedback and suggestions will be essential to arriving at a syllabus that is both rigorous and stimulating.
Thu 17th Aug.
1. Review: Genomes, DNA and Genes
Tue 22nd Aug.
2. Definition and technical foundations of genomics
- What is genomics?
- Recombinant DNA technology
- Library construction and screening
Thu 24th Aug.
2. Definition and technical foundations of genomics (cont.)
- DNA sequencing
- Polymerase chain reaction
- Class exercise
Tue 29th Aug.
3. The structure of genomes
- Genome size and C-value paradox
- Classes of repetitive DNA
Thu 31st Aug.
4. Mapping
- Markers (morphological, biochemical and DNA markers)
Tue 5th Sept
4. Mapping (cont.)
- Review of Mendelian genetics
- Class exercise
Thu 7th Sept.
4. Mapping (cont.)
- Genetic mapping
- Class exercise
Tue 12th Sept.
4. Mapping (cont.)
- Physical mapping
- Class exercise
Thu 14th Sept.
5. Sequencing
- Whole genome sequencing
- BAC by BAC approach
- Shotgun sequencing
- New sequencing method: 454 sequencing
Thu 19th Sept.
No class – Take-home assignment
Thu 21st Sept.
No class – Reading/reviewing of materials as per assignment
Tue 26th Sept.
5. Sequencing (cont.)
- Sequencing the gene space
- Expressed sequenced tags
- Other gene-enrichment techniques
- Genome annotation
- Displays and features of two completed genomes
Thu 28th Sept.
6. Bioinformatics
- Sequence databases: entries and access
- Sequence alignments
- Global and local alignments
- Alignment methods (dot matrix, blast, blat)
- Class exercises
Tue 3rd Oct.
7. Expression Analysis
- Individual genes
- Northern analysis
- Real-time PCR
Thu 5th Oct.
7. Expression Analysis (cont.)
- Genome-wide analysis
- Microarrays
- SAGE
- MPSS
Tue 10th Oct.
Exam
Thu 12th Oct.
8. High-throughput genetics
- Forward genetics
Tue 17th Oct.
8. High-throughput genetics (cont.)
- Reverse genetics
- Class exercise
Thu 19th Oct.
9. Comparative Genomics
- Techniques (chromosome painting, comparative mapping, comparative sequence analysis)
Tue 24th Oct.
9. Comparative Genomics (cont.)
- Aims of comparative studies
Thu 26th Oct. Fall break
Tue 31st Oct.
10. Microbial Genomics
Thu 2nd Nov.
10. Comparative and Microbial Genomics
- Class exercise
Thu 9th Nov.
Exam
Tue 14th Nov.
12. Genomics Applications
- Genomics and medicine
Thu 16th Nov.
12. Genomics Applications (cont.)
- Monogenic and complex disease traits
Tue 21st Nov.
12. Genomics Applications (cont.).
- Pharmacogenomics
Thu 23rd Nov. Thanksgiving holiday
Tue 28th Nov.
12. Genomics Applications (cont.)
- Genomics in agriculture
Thu 30th Nov.
13. Ethical issues of genomics
Thu 5th Dec.
13. Ethical issues of genomics (cont.)
- Discussion
14. Question time: time for students to ask questions/clarifications on course topics
Makeup Exam Policy:
Students that have a valid reason for missing an exam will be allowed to take an equivalent exam on another day.