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DTU course #27104 The Scientific Communication of Comparative Genomics

Course Programme - Autumn 2012
Link to description of course in DTU course catalogue


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 56 in building 301, 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 (20%), a poster (20%), and a final written manuscript (60%). 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     

overview





O 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
Also recommended: "Bacteria: The Benign, the Bad, and the Beautiful" by Trudy Wassenaar.
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'





O 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)






O Wednesday, 12 September, 2012 lecture hall 056 in building 301      


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.
From Genome Sequence to Taxonomy - A Skeptic's View article, page proofs for chapter 8 in The Prokaryotes to be published by Springer, in November 2012.       amazon.com link






O Thursday, 13 September, 2012 building 208, room 062 (downstairs)


13.00-13.45
Chapter 9 from textbook - "ribosomal RNAs"
Link to pdf file of lecture notes
13.45-14.00
Break
14.00-17.00
Download genomes, calculate basic genomic statistic and construct 16S rRNA tree (Shinny)
Computer Exercise # 2
PDF of lecture notes


Class work - form groups, download a set of genomes for your group, find rRNAs.
List of Genomes for group projects
Links
CMG BioTools homepage   CMG BioTools Wiki page (useful information here...)
Link to RNAmmer prediction server web page at CBS

Literature: Chapter 9 (11 pages) in the textbook.
RNAmmer paper, Nucleic Acids Research, 35:3100-3108, (2007).       PubMed
From Genome Sequence to Taxonomy - A Skeptic's View article, page proofs for chapter 8 in The Prokaryotes to be published by Springer, in November 2012.       amazon.com link
Two novel methods for using genome sequences to infer taxonomy, Microbiology, 158:1414 (2012).





O Wednesday, 19 September, 2012 lecture hall 056 in building 301       Gene Finding & Basic Genome Statistics


8.30-9.15
Chapters 6, 7 from textbook - "Methods to Compare Bacterial genomes"
Link to pdf file of lecture notes
9.15-9.30
Break
9.30-9.50
Journal Club - Group # 1 - Vibrio cholera outbreak in Haiti - Helen, Henrike, Natalia, Vanessa
"Genomic diversity of 2010 Haitian cholera outbreak strains", PNAS, 109:E2010-2017, (2012).       Link to journal web page
9.50-10.00
Break
10.00-10.20
Journal Club - Group # 42 - Lactobacillus - David, Martin Christen, Søren Kaae, Daniel
"Comparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera", Microbial Ecology, 63:651-673, (2012).      Link to journal web page
10.30-12.00
Computer exercises - Gene finding and amino acid & codon usage (Shinny)
Computer Exercise # 3
PDF of lecture notes


Literature: Chapter 6 (9 pages) and Chapter 7 (21 pages) in the textbook,       Replication Origins Paper, Environmental Microbiology, 8:353-361 (2006).       Tools to Compare Genomes       Genome Comparison of Bacterial Pathogens





O Thursday, 20 September, 2012 building 208, room 062 (downstairs)

13.00-13.45
Chapter 11 from textbook - "Comparison of Bacterial Proteomes - BLAST matrices & BLAST atlases"
Link to pdf file of lecture notes for BLAST matrices (preliminary version, from CDC workshop, August, 2012)
Link to pdf file of lecture notes for BLAST atlases (preliminary version, from CDC workshop, August, 2012)
13.45-14.00
Break
14.00-14.20
Journal Club Group # 3 - Salmonella - Maria, Johanne, Jesper, Jeppe
"Assessment of Whole-Genome Mapping in a Well-Defined Outbreak of Salmonella enterica Serotype Saintpaul", Journal Clinical Microbiology, 50:3063-3065, (2012).      Link to journal web page
14.30-17.00
Computer exercises - BLAST matrices and BLAST atlases (Shinny)
Computer Exercise # 3
PDF of lecture notes
Literature: Chapter 11 (21 pages) in the textbook,       Proteomes Comparisons - BLAST Matrix paper       BLAST Atlas paper.





O Wednesday, 26 September, 2012 lecture hall056 in building 301       Pan-Genome properties


8.30-9.15
Chapters 12 from textbook - "Bacterial core- and pan-genomes"
Link to pdf file of lecture notes
9.15-9.30
Break
9.30-9.50
Journal Club - Group # 2 - Salmonella Mette, Louise, Emile, og Nick
"Genomic variation in Salmonella enterica core genes for epidemiological typing", BMC Genomics, 13:88, (2012).       Link to journal web page
9.50-10.00
Break
10.00-10.20
Journal Club - Group # 5 - Vibrio -Jesper, Simon, Lars, Mikkel
"High depth, whole-genome sequencing of cholera isolates from Haiti and the Dominican Republic", BMC Genomics, 13:568, (2012).      Link to journal web page
10.20-10.30
Break
10.30-10.50
Journal Club - Group # 6 - Mycobacterium tuberculosis - Morten, Nelson, Alexander, Nils
"Microevolution of extensively drug-resistant tuberculosis in Russia", Genome Research, 22:735-745 (2012).      Link to journal web page
10.50-11.00
Break
11.00-12.00
Computer exercises - continue work (Shinny)
Computer Exercise # 4a
PDF of lecture notes
Literature: Chapters 12 (15 pages) in the textbook.

Link to article "Is the pan-genome also a pan-selectome?"




O Thursday, 27 September, 2012 building 208, room 062 (downstairs)



13.00-13.45
Chapter 10 - from textbook - "Gene Expression"
Link to pdf file of lecture notes for BLAST matrices (preliminary version, from last year's lecture, September, 2011)
13.45-14.00
Break
14.00-14.20
Journal Club Group # 7 - Campylobacter - Athina, Panagiotis, Estella, Judy, Julia
"Genomic characterization of Campylobacter jejuni strain M1", PLoS ONE, 5(8):e12253. (2012).      Link to journal web page
14.20-14.30
Break
14.20-14.40
Journal Club Group # 8 - Staphylococcus - Athina, Panagiotis, Estella, Judy, Julia
"Rapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.", N Engl J Med., 366(8):2267-2675. (2012).      Link to journal web page
14.40-14.50
Break
Journal Club Group # 9 - Bifidobacterium - Joesephine, Rasmus, Katrine, og Tina
"Comparative genomics of the genus Bifidobacterium", Microbiology, 156:3243–3254 (2010).      Link to journal web page
14.50-16.10
Break
16.10-17.00
Computer exercises - continue work (Shinny)
Computer Exercise # 4b
PDF of lecture notes
Literature: Chapter 10 (20 pages) in the textbook.






O Wednesday, 3 October, 2012 no class today....




O Thursday, 4 October, 2012 no class today....




O Wednesday, 10 October, 2012 Work on Posters


8.30-9:15
Evolution and The Origins of Bacterial Species
Link to pdf file of lecture notes
9.15-9.30
Break
9.30-9.50
Lecture on data visualization - some tips for good presentation technique (for posters, papers)
by Thomas Dybdal Pedersen Link to the Circos page       Link to pdf file of lecture notes
Literature: Chapters 5 and 14 of the textbook
"Is the pan-genome also a pan-selectome?"
"A domain sequence approach to pangenomics: applications to Escherichia coli"

Link to Review of 'Evolution: A View from the 21st Century' by James Shapiro
Link to Review of 'Signature in the Cell' by Stephen C Meyer
BioLogos Video about 'Signature in the Cell'
"The Skeptical Biochemist" review of Mike Behe's book, "The Edge of Evolution"
Article about Mechanisms of Darwinian Evolution
Review of 'Darwin's Black Box' - note: very old - from 1997!




O Thursday, 11 October, 2012 Work on Posters


13.00-13.30
iGEM 2012 talk by Chris Workman
Link to iGEM web page
13.30-13.40
Break
13.40-14.00
POSTERS - An Overview of What is Expected....
Link to pdf file of lecture notes
14.00-17.00
Computer exercises - continue work
Literature: "Ten Simple Rules for a Good Poster Presentation" by Thomas C. Erren and Philip E. Bourne, PLoS Comput Biol 3(5): e102 (2007). doi:10.1371/journal.pcbi.0030102.









O Wednesday and Thursday, 17-18 October, 2012

Autumn Break










O Wednesday, 24 October, 2012 Submit Posters



O Thursday, 25 October, 2012 - POSTER Party!






O Wednesday, 31 October, 2012 - Work on Papers


8.30-9.30
Lecture on What is Expected for the final paper
link to pdf of lecture notes.

NOTE: students can arrange for individual meetings to discuss their papers (please see me after class or email me....)


O Thursday, 1 November, 2012 Work on Papers










O Wednesday, 7 November, 2012 Work on Papers



O Thursday, 8 November, 2012 Work on Papers










O Wednesday, 14 November, 2012 Work on Papers



O Thursday, 15 November, 2012 Work on Papers










O Wednesday, 21 November, 2012 Work on Papers



O Thursday, 22 November, 2012 Work on Papers


overview








O Wednesday, 28 November, 2012 Work on Papers



O Thursday, 29 November, 2012 Work on Papers







O Wednesday, 5 December, 2012 - Hand in papers for Critique in class








Course organiser: David W. Ussery