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Techniques in Molecular Biology and Bioinformatics course, Oxford University
Lectures for 14-15 October
Link to DNA Atlas pages
List of Prokaryotic Genomes at NCBI
 Thursday, 14 October, 2010 Introduction to genomics
- 9.30-10.15
- Sequences as Biological Information
Link to pdf file of lecture notes
- 10.15-10.30
- Break
- 10.30-11.15
- Sequencing Speed and the Human Genome Project
Link to pdf file of lecture notes
- 11.15-11.30
- Break
- 11.30-12.30
- Bacterial Genomics
Link to pdf file of lecture notes
- 13.00-14.00
- LUNCH Break
- 14.00-14.45
- Introduction to DNA Structural Atlases for visualization of bacterial chromosome sequences
Link to pdf file of lecture notes
- 14.45-15:00
- Break
- 15.00-15.30
- Nucleocomal 'position preference' as a predictive tool for chromatin-free regions of the chromosome, which might be highly expressed
Link to pdf file of lecture notes
- 15.30
- Assignment of Computer exercises (take home - to be done individually, report back on Friday morning).
Literature:
For more work from the Comparative Microbial Genomics group, have a look HERE for a list of publications
RNAmmer paper (Nucleic Acids Research, 35:3100-3108,(2007).)
Tools for Comparing Bacterial Genomes (book chapter from Microbiology of Hydrocarbons, Oils, Lipids, and Derived Compounds, (Springer-Verlag, Heidelberg, Germany, 2009).)
Genome Comparison of Bacterial Pathogens (Chapter 1 in Genome Dynamics, volume 6 - Microbial Pathogenomics, (Karger AG publishers, Basel, 2009).)
 Friday, 15 October, 2010 Gene Expression, Metagenomics, and Evolution
- 9.30-10.15
- rRNAs
Link to pdf file of lecture notes
- 10.15-10.30
- Break
- 10.30-11.15
- Gene Expression in Bacterial Genomes
Link to pdf file of lecture notes
- 11.15-11.30
- Break
- 11.30-12.00
- Brief explanation of how to make a "custom BLAST atlas"
- 12.00-14.00
- LUNCH Break
- 14.00-14.45
- Metagenomics of Bacterial Communities
Link to pdf file of lecture notes
- 14.45-15:00
- Break
- 15.00-16.00
- Evolution of Bacterial Communities
Link to pdf file of lecture notes
Literature:
Leaner and Meaner E. coli genomes (Genome Biology, 7:237,(2006).)
Origin of Replication in Circular Prokaryotic Chromosomes Environmental Microbiology, 8:353-361, (2006).
Other fun diversions (book reviews, etc.)
My review of Behe's "Edge of Evolution" book is now online on the BioLogos web pages... Here's a link!
A Biochemist's Response to 'The Biochemical Challenge to Evolution', originally published in Bios magazine (volume 70, pages 40-45, 1999).
"The Stealth Creationists" Skeptic, 8:72-74, (2001).
"The Purpose-Driven iPod" essay for Christian Century magazine (Sept. 2008).
"An Inordinate Fondness of Bacteria" - book review of Stephen Meyer's Signature of the Cell. This review will eventually be published (allegedly) in the Reports of the National Center for Science Education (RNCSE)
BioLogos web page where my review of "Edge of Evolution" will appear soon - and a link to PDF of full review is here.
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