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The course meets on Wednesday mornings (kl. 8.30-12) and Thursday afternoons, (kl. 13-17), and will start on Wednesday, 5 September, 2012 at 08:30. Lectures and group projects will take place on Wednesday mornings in lecture hall 98 in building 306, computer exercises will take place Thursday afternoons in building 208, room 062 (downstairs), at the Technical University of Denmark, Lyngby.
Performance will be evaluated as described on the course overview page. Briefly, the grade is determined by a journal club report (25%), a poster (25%), and a final written manuscript (50%). The aims and learning objectives for this course are as described on the course webpage and also in the DTU course catalog.
Link to DNA Atlas pages
List of Genomes at NCBI
 Wednesday, 5 September, 2012 lecture hall 98 in building 306 Introduction to bioinformatics and databases
- 8.30-9.15
- Chapter 1 from textbook - "Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics"
Link to pdf file of lecture notes
- 9.15-9.30
- Break
- 9.30-10.15
- Chapter 2 from textbook - "Introduction to Bioinformatics"
Link to pdf file of lecture notes
- 10.15-10.30
- Break
- 10.30-11.30
- Journal Clubs and Posters - a brief overview
List of Genomes at NCBI
- Initial sign-up for teams of four students for computer exercises and papers
Links
NCBI Genomes page (a bit slow in loading, but a good source for all the current genomes in GenBank)
Link to CBS web page with zoomable atlases GenomeAtlas web pages (version 3)
Literature:
Chapters 1-2 of the textbook
Draft of chapters from a new textbook "Bacterial Genetics and Molecular Biology - a Genomics Perspective" - feel free to read and give me any comments...
DNA Structures from A- to Z from Encyclopedia of Life Sciences
"Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream", Nature Biotechnology, 27:627-632, (2009).
Tools for Comparing Bacterial Genomes
Link to Review of 'Signature in the Cell'
BioLogos Video about 'Signature in the Cell'
Article about Mechanisms of Darwinian Evolution
Review of 'Darwin's Black Box'
 Thursday, 6 September, 2012 building 208, room 062 (downstairs)
- 13.00-13.45
- Chapter 7 from textbook - "Chromosomal Atlases"
Link to pdf file of lecture notes
- 13.45-14.00
- Break
- 14.00-17.00
- Install VirtualBox and set-up CMG BioTools (Shinny)
Computer Exercise # 1
PDF of lecture notes
Virtual Box and CMG BioTools Installation Instructions Introduction to UNIX
Link to picture guide for installing Virtual Box and CMG BioTools
Class work - download the following 5 genome sequences: CP000030 AE016879 CP000814 AE014075 AE014613
Construct a 'genomeatlas' for at least one of these genomes...
List of Genomes for group projects
Links
CMG BioTools homepage CMG BioTools Wiki page (useful information here...)
Literature:
Chapter 7 (21 pages) in the textbook.
Physical Maps of Chromosomes from Encyclopedia of Life Sciences
Three Views of Bacterial Genomes ('Genome Atlas' paper, 1999
A DNA Structural Atlas for Escherichia coli (JMB, 2000)
Visualization of Pathogenicity Islands in Bacterial Genomes (2000)
Wednesday, 12 September, 2012 lecture hall 98 in building 306
- 8.30-9.15
- Lecture - Three Generations of DNA Sequencing
Link to pdf file of lecture notes
- 9.15-9.30
- Break
- 9.30-10.00
- Lecture - From Genome Sequence to Taxonomy - A Skeptic's View
Link to pdf file of lecture notes
- 10.00-12.00
- Introduction to Journal Clubs
Literature:
Chapters 3 (14 pages) and 4 (12 pages) in the textbook.
Thursday, 13 September, 2012 building 208, room 062 (downstairs)
-
- 13.00-13.45
- Lecture
- 13.45-14.00
- Break
- 14.00-14.30
- Example Journal Club - "Defining the Pseudomonas Genus"
- 14.30-16.30
- Computer exercises - Week 1.
Literature:
Chapter 6 (9 pages) in the textbook
Wednesday, 19 September, 2012 lecture hall 98 in building 306 Gene Finding & Basic Genome Statistics
- 8.30-9.15
- Chapters 7, 8 from textbook - "Genomic Properties"
- 9.15-9.30
- Break
- 9.30-10.00
- Journal Club # 1 - Acinetobacter - Linda, Monica, Malene, Isa
- 10.00-10.15
- Break
- 10.15-10.45
- Journal Club # 2 - Lactobacillus - Linda, Dilek, Catharina
- 10.45-12.00
- Computer exercises - Week 2, day 1.
other files - updated 14 September, 2011...
Literature:
Chapter 7 (21 pages) and Chapter 8 (11 pages) in the textbook, , .
Thursday, 20 September, 2012 building 208, room 062 (downstairs)
- 13.00-13.45
- Chapter 9 from textbook - "Transcriptomics"
- 13.45-14.00
- Break
- 14.00-14.30
- Journal Club # 3 - Salmonella - Martin, Tanni, Sandra, Sebastian, Julie
- 14.30-14.45
- Break
- 14.45-15.15
- Journal Club # 4 - Bifidobacterium - Stine, Dan, Lene, Sufia
- 15.15-17.00
Literature:
Chapter 9 (12 pages) in the textbook, , .
Wednesday, 26 September, 2012 lecture hall 98 in building 306 Ribosomal sequence analysis, basic phylogenetics
- 8.30-9:30
- Computer exercises - Week 3, day 1.
- 9.30-10.15
- Chapter 13 from textbook - "Metagenomics" - special guest lecture by Professor Francisco Rodriguez-Valera, Universidad Miguel Hernandez, San Juan de Alicante, Spain
- 10.15-10.30
- Break
- 10.30-11.00
- Journal Club # 5 - Brucella - Ola, Una, Michael, Maja
- 11.00-11.15
- Break
- 11.15-11.45
- Journal Club # 6 - Escherichia - Yongguang, Katarzyna, Jing, Boryana
Literature:
Chapters 13 (14 pages) in the textbook, , .
Thursday, 27 September, 2012 building 208, room 062 (downstairs)
- 13.00-13.45
- Chapter 10 from textbook - "Expression of Genes and Proteins"
- 13.45-14.00
- Break
- 14.00-14.30
- Chapter 11 from textbook - "Of Proteins, Genomes, and Proteomes"
- 14.30-14.45
- Break
- 14.45-15.15
- Journal Club # 7 - Vibrio - Iliana, Susan, Kasper, Dominika
- 15.15-15.30
- Break
- 15.30-16.00
- Journal Club # 8 - Staphylococcus - Henrik, Marc, Athansios, Rasmus, Marwa
- 16.00-17.00
- Computer exercises - Week 3, day 2.
Literature:
Chapters 10 (19 pages) and 11 (15 pages) in the textbook, , .
Wednesday, 3 October, 2012 lecture hall 98 in building 306 Proteome comparisons
- 8.00-8.45
- Chapter 12 from textbook - "Microbial Communities"
- 8.45-9.00
- Break
- 9.00-9.45
- Chapter 14 from textbook
- 9.45-10.00
- Break
- 10.00-10.30
- Journal Club # 9 - Bacillus - Tine, Martin, Niels, Sabine
- 10.30-12.00
- Computer exercises.
Literature:
Chapters 12 and 14 of the textbook,
Thursday, 4 October, 2012 building 208, room 062 (downstairs)
-
- 13.00-17.00
- Computer exercises.
 Wednesday and Thursday, 10-11 October, 2012
Autumn Break
Wednesday, 17 October, 2012 Work on Posters
- 10.00-10:30
- Lecture on posters - some tips of what to include, and what makes a good poster
Link to page for zoomable atlases Link to PDF of zoomable atlas paper describing method
Thursday, 18 October, 2012 Work on Posters
Wednesday, 24 October, 2012 Submit Posters
Thursday, 25 October, 2012 - POSTER Party!
Wednesday, 31 October, 2012 - Work on Papers
Thursday, 1 November, 2012 Work on Papers
Wednesday, 7 November, 2012 Work on Papers
Thursday, 8 November, 2012 Work on Papers
Wednesday, 14 November, 2012 Work on Papers
Thursday, 15 November, 2012 Work on Papers
-
- 13.00-14.00
- Lecture on What is Expected for the final paper
link to pdf of lecture notes.
Wednesday, 21 November, 2012 Work on Papers
Thursday, 22 November, 2012 Work on Papers
Wednesday, 28 November, 2012 - Hand in papers for Critique in class
Thursday, 29 November, 2012 Referee papers
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