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DTU course #27105 Comparative Microbial Genomics

Course Programme - Summer 2014
Link to description of course in DTU course catalogue


The three week summer course meets daily (kl. 9.00-17), and will start on Wednesday, 4 June, 2014 at 09:00. In general lectures will be in the mornings, and group projects based on a select set of bacterial genomes will be in the afternoons. The course will take place in room 259 in building 325, at the Technical University of Denmark, Lyngby.

Performance will be evaluated an oral presentation of group projects on the last day of the course. 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     





O Wednesday, 4 June, 2014      Introduction to bioinformatics and comparative genomics


9.00-9.45
Chapter 1 from textbook - "Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Chapter 2 from textbook - "Introduction to Bioinformatics"
Link to pdf file of lecture notes
10.45-11.00
Break
11.00-17.00
Group formation, discussion of possible projects, selection of genomes
List of Genomes at NCBI
Initial sign-up for teams of four students for computer exercises and genome projects
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 'Evolution: A View from the 21st Century' by James Shapiro
Link to 'The Skeptical Biochemist' a review of Michael Behe's book The Edge of Evolution
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'

Link to Anders Gorm's CBS course on Molecular Evolution
Computational Molecular Evolution, now offered on Coursera





O Friday, 6 June, 2014      Introduction to bioinformatics and comparative genomics


9.00-9.45
Chapter 3 from textbook - "3 Generations of DNA Sequencing"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Special - "Detecting and Identifying New Outbreaks Using Real-time Monitoring with 3rd Generation Genomic Sequencing"
Link to pdf file of lecture notes
10.45-11.00
Break
11.00-17.00
Group work on genome 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 Tuesday, 10 June, 2014      Project overview


9.00-9.45
Inspirational Lecture - Henrik Bjørn Nielson "Quantitative MetaGenomics"
9.45-10.00
Break
10.00-10.30
Overview of the week; introduction to computer exercises
Overview
Introduction to Unix
Introduction to Computer Exercises
10.30-17.00
Group work on genome projects





O Wednesday, 11 June, 2014      Databases


9.00-9.45
Inspirational Lecture - Ole Lund "SNP trees for Bacterial Genomes"
9.45-10.00
Break
10.00-10.30
Lecture on Databases; introduction to computer exercises
Databases - lecture notes
Introduction to Computer Exercises
10.30-17.00
Group work on genome projects





O Thursday, 12 June, 2014      Calculating Genome Statistics


9.00-9.45
Lecture by Oksana - Basic genome statistics, Amino acid and Codon Usage
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.30
Introduction to computer exercises
Introduction to Computer Exercises
10.30-17.00
Group work on genome projects

O Friday, 13 June, 2014      Ribosomal RNA


9.00-9.45
Lecture by Oksana - RNA Comparison
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Introduction to computer exercises
Introduction to Computer Exercises
10.45-11.00
Break
11.00-17.00
Group work on genome 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 Chapter 8 (pages 209-227)in The Prokaryotes Springer (2013).
Two novel methods for using genome sequences to infer taxonomy       PubMed, Microbiology, 158:1414 (2012).









O Monday, 16 June, 2014      Genome Atlases


9.00-9.45
Chapters 3 and 7 from textbook - "Introduction to DNA Atlases - Part 1: DNA Structures"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.30
Chapter 7 from textbook - "Introduction to DNA Atlases - Part 2: Repeats and Genome Atlases"
Link to pdf file of lecture notes
10.30-10.45
Break
10.45-11.30
Chapter 7 from textbook - "Comparison of Genome Properties - with an emphasis on AT content"
Link to pdf file of lecture notes
11.30-17.00
Group Exercises: Genome Atlases
Links
CBS genomeatlas pages   Link to CBS web page with zoomable atlases


Literature: Chapters 3 and 7 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 Tuesday, 17 June, 2014      BLAST Atlases


9.00-9.45
Chapter 8 from textbook - "Introduction to DNA Atlases - Part 3: BLAST Atlases"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Chapter 10 from textbook - "Gene Regulation"
Link to pdf file of lecture notes
10.45-11.00
Break
11.00-17.00
Group Exercises: BLAST Atlases
Link
Link to CBS web page with zoomable atlases

Literature: Chapters 8 and 10 in the textbook.
Peter F. Hallin, Tim T. Binnewies and David W. Ussery, "The genome BLASTatlas-a GeneWiz extension for visualization of whole-genome homology", Molecular BioSystems, 4:363-371 (2008).        [PubMed]        PDF

Peter F. Hallin, Hans Henrik Staerfeldt, Eva Rotenberg, Tim T. Binnewies, Craig J. Benham, David Wayne Ussery, "GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes", Standards in Genomic Sciences, 1:204-215, (2009.)        [PubMed]        Link to SIGS Journal page        PDF





O Wednesday, 18 June, 2014      Comparative Proteomics


9.00-9.45
Chapter 11 from textbook - "A Brief History of E. coli Proteomics"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Chapter 11 from textbook - "BLAST Matrices"
Link to pdf file of lecture notes
10.45-11.00
Break
11.00-17.00
Group Exercises: BLAST Matrices

Literature: Chapter 11 in the textbook.

Lars Juhl Jensen, Marie Skovgaard, Thomas Sicheritz-Ponten, Niclas Tu Hansen, Helle Johansson, Merete Kjær Jørgensen, Kristoffer Kiil, Peter F. Hallin and David Ussery, "Comparative genomics of four Pseudomonas species"
Chapter 5 in THE PSEUDOMONADS VOL I. GENOMICS, LIFE STYLE AND MOLECULAR ARCHITECTURE (Juan L. Ramos, editor), Kluwer Academic / Plenum Publishers, New York, pages 139-164.        PDF file 
Microbiology "Genome Update" #12 January, 2005
Tim T. Binnewies, Peter F. Hallin, Hans-Henrik Stærfeldt, David W. Ussery, "Genome Update: Proteome Comparisons"
Microbiology, 151:1-3, 2005.         [PubMed]        PDF file 

Tim T. Binnewies, Yair Motro, Peter F. Hallin, Ole Lund, David Dunn, Tom La, David J. Hampson, Matthew Bellgard, Trudy M. Wassenaar, and David W. Ussery, "Ten years of bacterial genome sequencing: comparative-genomics-based discoveries",
Functional and Integrative Genomics 6:165-185, (2006).         [PubMed]        PDF file 

Hanni Willenbrock, Anne Petersen, Camilla Sekse, Kristoffer Kiil, Yngvild Wasteson, and David W. Ussery, "Design of a 7 Genomes Escherichia coli Microarray for Comparative Genomic Profiling ",
Journal of Bacteriology 188:7713-7721, (2006).        [PubMed]        PDF file

Oksana Lukjancenko, Trudy M. Wassenaar, and David W. Ussery, "Comparison of 61 Sequenced Escherichia coli Genomes",
Microbial Ecology, 60:708-720, (2010). [DOI: 10.1007/s00248-010-9717-3]        Link to Microbial Ecology Journal page        [PubMed]        PDF file

Rolf S Kaas, Carsten Friis, David W Ussery and Frank M Aarestrup, "Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes",
BMC Genomics, 13:577 (2012). doi:10.1186/1471-2164-13-577        [PubMed]        Link to BMC Genomics Journal page        PDF file

Lars-Gustav Snipen and David W Ussery, "A domain sequence approach to pangenomics: applications to Escherichia coli",
F1000 Research, 1:19 (2012). doi: 10.3410/f1000research.1-19.v1        Link to F1000 Research page -->        PDF file

Helen Cook and David Ussery, "Sigma Factors in a Thousand Escherichia coli genomes", Environmental Microbiology, 15:3121-2139 (2013). doi: 10.1111/1462-2920.12236        [PubMed]        Link to Environmental Microbiology Journal page        PDF file





O Thursday, 19 June, 2014      Pan- and Core-Genomes


9.00-9.45
Chapter 12 from textbook - "Bacterial Pan- and Core-genomnes"
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-10.45
Chapter 14 from textbook - "Evolution in Bacterial Genomes"
Link to pdf file of lecture notes
10.45-11.00
Break
11.00-17.00
Group Exercises - Pan- and Core-genome plots; pan-genome family trees

Literature: Chapters 12 and 14 in the textbook.


Francisco Rodriguez-Valera and David W Ussery, "Is the pan-genome also a pan-selectome?", F1000 Research, 1:16 (2012). doi: 10.3410/f1000research.1-16.v1        Link to F1000 Research page -->        PDF file

Lars Snipen, and David W. Ussery, "Standard operating procedure for computing pangenome trees", Standards in Genomic Sciences, 2:135-141, (2010).        Link to SIGS Journal page        PDF file

Lars Snipen, T. Alm°y, David W. Ussery, "Microbial comparative pan-genomics using binomial mixture models", BMC Genomics, 10:385, (2009).        [PubMed]        PDF file

Link to 'The Skeptical Biochemist' a review of Michael Behe's book The Edge of Evolution
Link to Review of 'Evolution: A View from the 21st Century' by James Shapiro
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'

Link to Anders Gorm's CBS course on Molecular Evolution
Computational Molecular Evolution, now offered on Coursera





O Friday, 20 June, 2014      Using comparative genomics for epidemiological typing of Salmonella


9.00-9.45
Lecture by Shinny "Using comparative genomics for epidemiological typing of Salmonella"
9.45-10.00
Break
10.00-17.00
Group Exercises - finish Pan- and Core-genome plots; pan-genome family trees







O Monday, 23 June, 2014      Group Project work


9.00-9.45
Example paper #1 Oksana's "61 E. coli genomes" paper
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-17.00
Group work on genome projects
Literature:
Oksana Lukjancenko, Trudy M. Wassenaar, and David W. Ussery, "Comparison of 61 Sequenced Escherichia coli Genomes",
Microbial Ecology, 60:708-720, (2010). [DOI: 10.1007/s00248-010-9717-3]        Link to Microbial Ecology Journal page        [PubMed]        PDF file





O Tuesday, 24 June, 2014      Group Project work


9.00-9.45
Example paper #2 Shinny's "Salmonella core gene epidemiology" paper
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-17.00
Group work on genome projects
Literature:
Pimlapas Leekitcharoenphon, Oksana Lukjancenko, Carsten Friis, Frank M Aarestrup and David W Ussery, "Genomic variation in Salmonella enterica core genes for epidemiological typing",
BMC Genomics, 13:88 doi:10.1186/1471-2164-13-88 (March, 2012).        [PubMed]        Link to BMC Genomics Journal page        PDF file





O Wednesday, 25 June, 2014      Group Project work


9.00-9.45
Example paper #3 Asli's "Azotobacter" paper
Link to pdf file of lecture notes
9.45-10.00
Break
10.00-17.00
Group work on genome projects
Literature:
Asli I. Ozen and David W. Ussery, "Defining the Pseudomonas Genus: Where Do We Draw the Line with Azotobacter?",
Microbial Ecology, 63:239-248, (2012). [DOI: 10.1007/s00248-011-9914-8]        [PubMed]        Link to Microbial Ecology Journal page        PDF file





O Thursday, 26 June, 2014      BLAST Matrices


9.00-9.30
Group Presentation Bacillus group
9.30-9.45
Break
9.35-10.30
Group Presentation Salmonella group
10.30-10.45
Break
10.45-11.15
Group Presentation Streptococcus group
11.15-11.30
Break
11.30-12.00
Group Presentation Escherichia coli group





Course organiser: David W. Ussery