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DTU course #27104 The Scientific Communication of Comparative Genomics

Course Programme - Autumn 2010
Link to description of course in DTU course catalogue

The course meets on Wednesday mornings (kl. 8-12) and Thursday afternoons, (kl. 13-17), and will start on Wednesday, 1 September, 2010 at 08:00. Lectures, journal clubs and exercises will take place in lecture hall 060 (downstairs) in building 208, 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 Prokaryotic Genomes at NCBI

Wednesday, 1 September, 2010 Introduction to the course

8.00-8.45: Introduction to the course - some 'housekeeping details'
An overview of the course, working groups, computer exercises, what is expected from this course.
8.45-9.00: Break
9.00-9.45: Chapter 3 from textbook - "Comparative Microbial Genomics: A Brief Overview"
Link to pdf file of lecture notes
9.45-10.00: Break
10.00-11.00: Chapter 1 from textbook - "Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics"
Link to pdf file of lecture notes; Assignment to teams of four students for computer exercises and papers

Literature: Chapters 1 and 3 in the textbook

Thursday, 2 September, 2010 Introduction to Unix

13.00-17.00: Exercise 1 Introduction to Unix & computer exercises
Link to pdf of assigned student groups, including organism names and Journal Club dates

Wednesday, 8 September, 2010 rRNAs and the tree of life

8.30-9.00: Chapter 2 from textbook - "Introduction to Bioinformatics"
Link to pdf file of lecture notes
9.00-9.30: Chapter 4 from textbook - "Genomic Databases"
Link to pdf file of lecture notes
9.30-9.45: Break
9.45-10.30: Chapter 9 from textbook - "non-coding RNA genes"
Link to pdf file of lecture notes
9.45-10.00: Break
10.00 - 12.00: Exercise 2 - making 16S rRNA trees

Literature: Chapters 2 and 9 of textbook. 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).)

Chlamydiae / Verrucomicrobia group. Link to list of names. Link to list of NCBI Project IDs.

Clostridia group. Link to list of names. Link to list of NCBI Project IDs.

Cyanobacteria group. Link to list of names. Link to list of NCBI Project IDs.

DeltaProteobacteria group. Link to list of names. Link to list of NCBI Project IDs.

EpsilonProteobacteria group. Link to list of names. Link to list of NCBI Project IDs.

Spirochaetes group. Link to list of names. Link to list of NCBI Project IDs.

Thermotogae / Chloroflexi group. Link to list of names. Link to list of NCBI Project IDs.

Thursday, 9 September, 2010 Finding rRNAs


13.00-13.30: Example Journal Club: "rRNA Operon Visualization" paper, presented by Dave
13.30-13.45: Break
13.45-17.00: Exercise 2 Continue - Fetching genomes, extracting 16S rRNA, building trees

Literature: Chapter 4 in the textbook Vibrio Genomes review article (Nature Reviews Microbiology, 4:697-704,(2006). Note in particular Figure 2.) Genome Atlas Resource In: Computational Systems Biology and Bioinformatics. International Conference on Computational Systems-Biology and Bioinformatics (CSBio 2010), Proceedings. CCIS, vol. 115, pp. 149-158. Springer, Heidelberg (2010).

Today's Journal Club Reference

rRNA operon visualization
"Visualization of ribosomal RNA operon copy number distribution.",
BMC Microbiology, 9:208, (2009) [PubMed] BMC Microbiology link
Link to pdf of Journal Club Presentation

Wednesday, 15 September, 2010 Comparative Genomics

Methods to Compare Genomes

8.30-9.00: Chapters 5,6 from textbook - "Comparing Genomes - Human Genome Project"
Link to pdf file of lecture notes
9.00-9.30: Chapter 6 from textbook - "Comparing Genomes - Bacterial Genomics"
Link to pdf file of lecture notes
9.30-9.45: Break
9.45-10.45: Chapter 6 from textbook - "Comparing Genomes - An Introduction to DNA structural Atlases"
Link to pdf file of lecture notes
10.45-11.00: Break
11.00-12.00: Computer Exercises - Zoomable atlases; Computer Exercises - Predicting Protein-encoding genes

Literature: Chapters 5 and 6

Thursday, 16 September, 2010 - Chlamydiae / Verrucomicrobia Journal Clubs

Chlamydiae / Verrucomicrobia group. Link to list of names. Link to list of NCBI Project IDs.

13.00-13.30: Journal Club: "Novel Chlamydia strains" paper, presented by Group 5
Anders Mosborg Aggestrup, Charlotte Henszelman Joersbo, Kristian Thorsen, and Paula Hansen
Link to pdf file of Journal Club
13.30-13.45: Break
13.45-14.15: Journal Club: "Koala Chlamydia genome" paper, presented by Group 13
Ana Rems, Christina Spuur Noedvig, and Frederik Otzen Bagger
Link to pdf file of Journal Club
14.15-14.30: Break
14.30-17.00: Computer Exercises - Pan- Core-genome plots (Scroll down in the Exercises for the second part, about today's exercises.)

Literature: Chapter 12 in the textbook

Today's Journal Club References

Novel Chlamydia strains
"Novel Chlamydiales strains isolated from a water treatment plant.",
Environmental Microbiologyy, 11:188-200, (2009) [PubMed] link to pdf of paper.

Koala Chlamydia genome
"Comparison of koala LPCoLN and human strains of Chlamydia pneumoniae highlights extended genetic diversity in the species.",
BMC Genomics, 11:442, (2010) doi:10.1186/1471-2164-11-442 [PubMed] BMC Microbiology link link to pdf of paper.

Wednesday, 22 September, 2010 - Cyanobacteria Journal Clubs

Cyanobacteria group. Link to list of names. Link to list of NCBI Project IDs.

8.30-9:00: How to make a poster, and Chapter 7 from textbook - "Comparing Genomes - DNA structural Atlases, part 2 - position preference"
Some Example Posters Feature Plots Poster Clostridium Poster Codon Usage Poster Staph. aureus Poster
Link to pdf file of lecture notes
9.00-10.00: Break and work on catching up from computer exercises from last week - NOTE! New, updated links.; Some hepful hints on copying files to and from your computer; Exercise 4 - Using Prodigal to find genes; Exercise 5 - Making Pan- core-genome plots
10.00-10.30: Journal Club: "Streamlining in Cyanobacteria" paper, presented by Group 1
Janni Nielsen, Kim Ngo, Martin Mortensen, and Tasja Buschhardt
Link to pdf file of Journal Club
10.30-10.45: Break
10.45-11.15: Journal Club: "CyanoClust tool" paper, presented by Group 6
Eilsa Popescu, Gabriel Durac, Stine Soerensen, Tsonko Tsonkov and Visanu Wanchai
Link to pdf file of Journal Club
11.15-12.00: Chapter 12 from textbook - "Pan- / core-genome plots"
Link to pdf file of lecture notes

Literature: Chapters 7 and 12 in the textbook "Ten Simple Rules for Good Poster Presentation" Link to a good web page about preparing posters.
"The Role of Nucleosome Positioning in the Evolution of Gene Regulation" , PLoS Biology, 8(7): e1000414, (2010). doi:10.1371/journal.pbio.1000414
"Prediction of highly expressed genes in microbes based on chromatin accessibility" , BMC Molecular Biology, 8:11, (2007). doi:10.1186/1471-2199-8-11.
"Three Views of Bacterial Genomes", Res. Microbiol., 150773-777, (1999).
"A DNA Structural Atlas for Escherichia coli", J. Mol. Biol., 299907-930, (2000). doi:10.1006/jmbi.2000.3787

Today's Journal Club References

Streamlining in Cyanobacteria
"No evidence for elemental-based streamlining of prokaryotic genomes",
Trends in Ecology and Evolution, 25:319-320, (2010) [PubMed] link to pdf of paper supplemental paper # 1 supplemental paper # 2

CyanoClust tool
"CyanoClust: comparative genome resources of cyanobacteria and plastids",
DATABASE, 2010:bap025, (2010) doi:10.1093/database/bap025 [PubMed] DATABASE journal link link to pdf of paper.

Thursday, 23 September, 2010 - BLAST Matrices and Salmonella Journal Club

13.00-13.30: Journal Club - "Salmonella small RNAs" paper, presented by Group 3
Anja Stausgaard, Hanne Jensen, and Maria Hansen
Link to pdf file of Journal Club
13.30-13.45: Break
13.45-14.30: Chapter 11 from textbook - "Comparing Proteomes" - with emphasis on BLAST Matrices
Link to pdf file of lecture notes
14.30-17.00: computer exercises - "BLAST Matrix"; Exercise 6 - BLAST Matrices; Some hepful hints on copying files to and from your computer; Exercise 4 - Using Prodigal to find genes; Exercise 5 - Making Pan- core-genome plots

Literature: Chapter 11 in the textbook
"Microbial comparative pan-genomics using binomial mixture models" paper in BMC genomics (2009).
Today's Journal Club References

Salmonella small RNAs
"sRNAscanner: a computational tool for intergenic small RNA detection in bacterial genomes",
PLoS One, 5:e11970, (2010) doi:10.1371/journal.pone.0011970 [PubMed] PLoS ONE journal link link to pdf of paper link to pdf of paper about small RNAs in Salmonella.

Wednesday, 29 September, 2010 - Clostridia Journal Clubs

Clostridia group. Link to list of names. Link to list of NCBI Project IDs.

8.00-8.45: Chapter 10 from textbook
Link to pdf file of lecture notes
8.45-9.00: Break
9.00-9.45: Chapter 13 from textbook
Link to pdf file of lecture notes
9.45-10.00: Break
10.00-10.30: Journal Club: ~~"Clostridium carboxidivorans strain P7 genome"~~ paper, presented by Group 4
"Comparative genomic analysis of a neurotoxigenic Clostridiumi> species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism"
Camilla Hoejer, Lisa Iversen, Sofie Asmussen, and Susanne Hannibal
10.30-10.45: Break
10.45-11.15: Journal Club: "Evolution of Clostridium difficile" paper, presented by Group 7
Christian Lundin and Henrik Frandsen
11.15-11.45: Discuss posters (due 28 Oktober) - what is expected

Literature: Chapters 10 and 13 of textbook.
Today's Journal Club References

Clostridium carboxidivorans strain P7 genome
"Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7",
Journal of Bacteriology, in the press: (2010)        [PubMed]        J. Bact. journal link        link to pdf of paper (original - but not used!).
"Comparative genomic analysis of a neurotoxigenic Clostridiumi> species using partial genome sequence: Phylogenetic analysis of a few conserved proteins involved in cellular processes and metabolism",
link to pdf of paper chosen by Group 4.        [PubMed] for new article

Evolution of Clostridium difficile
"Evolutionary dynamics of Clostridium difficile over short and long time scales",
PNAS, 107:7527-7532, (2010)   doi: 10.1073/pnas.0914322107 [PubMed]        PNAS journal link        link to pdf of paper.

Thursday, 30 September, 2010

13.00-17.00
Computer Exercises - BLAST atlases

Wednesday, 6 October, 2010 - DeltaProteobacteria Journal Clubs

DeltaProteobacteria group. Link to list of names. Link to list of NCBI Project IDs.

10.45-11.15
Journal Club - "Geobacter 6x" paper, presented by Group 8
Karina Madsen, Lousie Brogaard, Mark Nygaard, and Per Nielsen

Today's Journal Club Reference

Geobacter 6x paper
"Evolution of electron transfer out of the cell: comparative genomics of six Geobacter genomes",
BMC Genomics, 11:40, (2010)   doi:10.1186/1471-2164-11-40 [PubMed]        BMC Genomics journal link        link to pdf of paper.

Thursday, 7 October, 2010

13.00-17.00
Computer Exercises

Wednesday, 13 October, 2010 - EpsilonProteobacteria Journal Club

EpsilonProteobacteria group. Link to list of names. Link to list of NCBI Project IDs.

8.30-9.30: Chapter 14 from textbook - "Evolution of Bacterial Genomes"
Link to pdf file of lecture notes
9.30-9:45: Break
9.45-10.15

Today's Journal Club References

Deferribacter desulfuricans strain SSM1 genome
"Bacterial Lifestyle in a Deep-sea Hydrothermal Vent Chimney Revealed by the Genome Sequence of the Thermophilic Bacterium Deferribacter desulfuricans SSM1",
DNA Research, 17:123-137, (2010) doi:10.1093/dnares/dsq005 [PubMed] DNA Research journal link link to pdf of paper.

Campylobacter pan-genome paper
"Evolutionary Dynamics of Complete Campylobacter Pan-Genomes and the Bacterial Species Concept",
Genome Biol Evol., 2:646-655, (2010) doi:10.1186/1471-2164-11-40 [PubMed] Genome Biol Evol. journal link link to pdf of paper.

Literature: Chapters 10 and 13 of textbook.

Thursday, 14 October, 2010


13.00-17.00: Computer exercises

Wednesday and Thursday, 20-21 October, 2010

Autumn Break

Wednesday, 27 October, 2010 - Spirochaetes Journal Clubs

Spirochaetes group. Link to list of names. Link to list of NCBI Project IDs.

8.30-10.00: Informal group help / discussions on posters (due next week!) and figures for paper
10.00-10.30: Journal Club - "Brachyspira pilosicoli strain 95/1000 genome" paper, presented by Group 10
Agne Zebryte, Alireza Kashanipour, Anders Noergaard, and Claes Ahlberg
10.30-10.45: Break
10.45-11.15: Journal Club - "Treponema pallidum subsp. pallidum Chicago Strain" paper, presented by Group 11
Emil Nielsen, Kosai Al-Nakeeb, and Sigmar Stefansson

Today's Journal Club References

Brachyspira pilosicoli strain 95/1000 genome paper
"The Complete Genome Sequence of the Pathogenic Intestinal Spirochete Brachyspira pilosicoli and Comparison with Other Brachyspira Genomes",
PLoS ONE, 5(7): e11455, (2010) doi:10.1371/journal.pone.0011455 [PubMed] PLoS ONE journal link link to pdf of paper.

Treponema pallidum subsp. pallidum Chicago Strain
"Complete Genome Sequence and Annotation of the Treponema pallidum subsp. pallidum Chicago Strain",
J. Bact., 192:2645-2646, (2010) doi:10.1128/JB.00159-10 [PubMed] J. Bact. journal link link to pdf of paper.

Thursday, 28 October, 2010

13.00-17.00
Computer Exercise - discuss posters - due next week!!

Wednesday, 3 November, 2010 - Thermotogae / Chloroflexi Journal Clubs

Thermotogae / Chloroflexi group. Link to list of names. Link to list of NCBI Project IDs.

9.00-9.45
Lecture on "how to write a paper" - Outline
Link to pdf file of lecture notes

9.45-10.00
Break
10.00-10.30
Journal Club - "4 Thermotogales genomes" paper, presented by Group 12
Rolf Mortensen, Simon Koplev, Stine Persson, and Yongguang Pei
10.30-10.45
Break
10.45-11.15
Journal Club - "Listeria genomes" paper, presented by Group 32
Roberto Ferro and Carlotta Ronda
Literature: Ten Simple Rules for Getting Published Today's Journal Club References

4 Thermotogales genomes
"On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales",
PNAS, 106:5865-5870, (2009)   doi: 10.1073/pnas.0901260106 [PubMed]        PNAS journal link        link to pdf of paper.

Listeria pan-genome
"Probing the pan-genome of Listeria monocytogenesi>: new insights into intraspecific niche expansion and genomic diversification.",
BMC Genomics, 11:500, (2010)   doi:10.1186/1471-2164-11-500 [PubMed]        BMC Genomics journal link

Thursday, 4 November, 2010

POSTERS due!!!!

Wednesday, 10 November, 2010

9.00-12.00
no class - work on manuscript for publication

Thursday, 11 November, 2010

13.00-17.00
no class - work on manuscript for publication

Wednesday, 17 November, 2010

9.00-10.00
work on manuscript for publication

10.00-10.45
Guest Lecture

10.45-12.00
work on manuscript for publication

Thursday, 18 November, 2010

13.00-17.00
no class - work on manuscript for publication

Wednesday, 24 November, 2010

no class today

Thursday, 25 November, 2010

13.00-17.00
13.00-15.00
Guest lecture

15.00-17.00
work on manuscript for publication

Wed/Thurs, 1-2 December, 2009

Papers due no later than kl. 12.00 on TUESDAY, 30 November - the final papers will then be copied and distributed in class, and we will together referee them and hand them back to the groups for final grade, and revision if necessary.

The, final, revised papers and all work must be finished and handed in no later than 12:00 noon on 10 December
But of course, groups are encouraged to hand them in anytime before then - in principle, a well-written paper can even be submitted for final grading on the evening of 26 November (or even earlier!), provided that it is so good that neither the other student referees nor the course teacher finds any mistakes!

Coourse organiser: David W. Ussery

This file was last modified Monday 29th of August 2011 21:35:53 GMT

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