Genomes and Evolution (Biochem 4Y03/6Y03)

Dr Paul Higgs

Course Outline to download -   DOC

Schedule for Winter 2007: Thur, Mon 9.30; Tue 10.30 BSB318

This course will focus on key issues in molecular evolution, and will introduce the bioinformatics methods that are necessary to answer these questions. Now that hundreds of complete genomes are available, what have we learned? Which genes are shared between organisms? How do we build evolutionary trees? Is there a molecular clock? What are the evolutionary relationships between bacteria? How often does horizontal gene transfer occur? What are the origins of organelles and their genomes? How does the human genome compare with other species? What do microarray and proteomics experiments tells us about how organisms work at the whole genome level?

Prerequisites: BIOCHEM 2B03 or 3G03 Antirequisite: BIOLOGY 4DD3

Lecture Contents and Papers to Download

Lectures will be based on material included in the book "Bioinformatics and Molecular Evolution" by P.G.Higgs and T.K.Attwood. Chapter references below refer to this book.

1. What is bioinformatics? Data explosions. The relationship between molecular evolution and bioinformatics. The relevance of bioinformatics for genomics, microarrays and proteomics.

READ Chapter 1

2. Molecular Evolution and Population Genetics. Sequence variation within and between populations. Random drift and fixation. Neutral evolution and selection.

READ Chapter 3

3. Models for nucleic acid sequence evolution. Synonymous and non-synonymous substitutions.

READ Section 4.1

Additional information - Calculation of Synonymous and Non-synonymous substitutions DOC - Original paper by Nei and Gojobori (1986) PDF

4. Methods of molecular phylogenetics. Comparison of distance matrix, parsimony, maximum likelihood and Bayesian methods. Biological examples and controversies in phylogenetics. Mammalian orders. Animal Phyla. Major Eukaryotic groups. Molecular Clocks.

READ Chapter 8 and Section 11.3

Phylogenetics lecture notes PPT

5. Models for protein sequence evolution. Scoring systems for sequence alignment. Codon usage.

READ Sections 2.4 and 2.5

READ Sections 4.2 and 4.3

6. Sequence alignment. Database searching.

READ Chapter 6 and Section 7.1

7. Bacterial genome evolution. Horizontal transfer. The tree of life.

READ Section 12.1

8. Organellar genomes. The origin of mitochondria and chloroplasts. Gene transfer between nuclear and organellar genomes.

READ Section 12.2

Lectures on mitochondrial genomes - PPT

9. The transcriptome and the proteome. Microarray experiments and data analysis. Proteomics techniques. Protein-protein interaction networks.

READ Chapter 13

Thermodynamics of hybridization on microarrays. Carlon and Heim. (2006) - PDF

Assignments

Assignment 1 (worth 15%) Due by Thursday 1st Feb. - DOC

You will also need this paper for Assignment 1. Ingman et al. (2000) - PDF

Assignment 2 (worth 15%) Due by Monday 26th Feb. - DOC

You will also need this paper for Assignment 2. Subramanian and Kumar (2006) - PDF

Mid-term test (worth 15%) By popular demand, this will be on Monday 12th March. Note that you may bring a crib sheet of one side of paper with any notes on that you think will be helpful. The questions require short written answers - one or two paragraphs each. They are based on everything we covered in the lectures before the reading week. It is worth revising the sections marked READ above. Calculators should not be necessary, but you can use one if you want.

Assignment 3 (worth 15%) Due by Monday 2nd April ***NEW DATE*** - DOC

You will also need these two papers for Assignment 3. Hao and Golding (2007) - PDF - Blomme et al (2006) - PDF -

Final exam (worth 40%) Scheduled for Wednesday 18th April at 14.00. in IWC1. The questions will be on the whole course and will be of a similar format to the midterm.