Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

CBS >> CBS Courses >> Comparative Microbial Genomics Workshop >> Course Programme

Description

The course will be held at KMUTT (King Mongkut's University of Technology Thonburi) in Bangkok, Thailand. This is the fourth workshop on Comparative Microbial Genomics held in Thailand. (The previous three workshops were held in 2005, 2008 and in 2010). The workshop will focus on methods to compare bacterial genomes, and is a one-week version of the DTU course 27104 taught in Denmark. The general format is lectures in the morning, and computer exercises in the afternoon. The workshop will be presented by Dave Ussery, leader for the Comparative Microbial Genomics group [link to publications], and the computer exercises will be assisted by Oksana.

Course outline

  Monday, 20 June Tuesday, 21 June Wednesday, 22 June Thursday, 23 June Friday, 24 June
9:30-10:30
Introduction to Genomics
E. coli O104 as an example
3 Generations of Genome Sequencing
Pan- and Core-genomics
Analysis of pan- and core-genomes
Summary
10:30-11:00
(Coffee Break)
 
11:00-12:00
Sequences as biological information
BLAST matrices and atlases
Finding Conserved 'Core-genes' in Bacterial Genomes
Designing Pan- and Core-genome Microarrays
Group presentations
12:00-13:00
(Lunch break)
 
13:00-15:00
Introduction to UNIX
BLAST matrices
Pan-core genome plots
Finding core-gene families
Group presentations
15:00-15:30
(Coffee break)
 
15:30-17:00
Construction of 16S rRNA trees
BLAST atlases
Pan-genome family trees
Species-specific Microarray chip design
Group presentations, certificate presentation, closing


Book Cover The textbook is written specifically for this course:
COMPUTING FOR COMPARATIVE GENOMICS: Bioinformatics for Microbiologists
by David W. Ussery, Stefano Borini, and Trudy M. Wassenaar

Springer, published in spring, 2009.       Link to Amazon.com



Monday, 20 June, 2011: DNA, RNA and Genomics

9:30-10:30Lecture: Introduction to Genomics     PDF of Talk    Quiz
10:30-11:00Coffee break
11:00-12:00Lecture: Sequences as biological information     PDF of Talk    Quiz
12:00-13:00Lunch break
13:00-17:00Introduction to UNIX,    and Exercise 1


Literature: Chapters 1-6 of textbook
Link to PDF of "RNAmmer" paper (PMID 17452365)
"Comparison of 61 Sequenced E. coli Genomes", Microbial Ecology, 60:708-720, (2010).
"Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream", Nature Biotechnology, 27:627-632, (2009).





Tuesday, 21 June, 2011: Proteins and Proteomics


9:30-10:30Lecture: 3 Generations of Sequencing Technology     PDF of Talk  
10:30-11:00Coffee break
11:00-12:00Lecture: BLAST Matrices, Atlases     PDF of Talk  
12:00-13:00Lunch break
13:00-17:00Computer Exercises - Part 2: Prediction of Protein-encoding Genes; Construction of a BLAST Matrix, and a BLAST Atlas


Literature: Chapters 7-9 of textbook
Link to PDF of "BLAST Atlas" paper (PMID 18414733)
Link to PDF of "BLAST Matrix" paper (PMID 15632419)





Wednesday, 22 June, 2011: Conserved genes within a group of bacteria


9:30-10:30Lecture: Pan- and Core-genomics     PDF of Talk
10:30-11:00Coffee break
11:00-12:00Lecture: Finding Conserved 'Core-genes' in Bacterial Genomes     PDF of Talk
12:00-13:00Lunch break
13:00-17:00Computer Exercises - Part 3: Pan- and Core-Genome trees


Literature: Chapters 10-14 of textbook
Link to "Standard operating procedure for computing pangenome trees" paper (PMID 21304685)
Link to "Microbial comparative pan-genomics using binomial mixture models." paper (PMID 19691844)
Link to "The Salmonella enterica Pan-genome." paper (PMID 21643699)





Thursday, 23 June, 2011: Designing Genus-specific Microarrays

(Oksana Lukjancenko)


9:30-10:30Lecture: Introduction to Genome-Based Microarrays     PDF of talk
10:30-11:00Coffee break
11:00-12:00Lecture: Design of an Enterobacteriaceae pan-genome microarray     PDF of talk
12:00-13:00Lunch break
13:00-17:00Computer Exercises - Part 4: Designing Genome-specific Microarrays


Literature: Link to Lancet about the E. coli O104 outbreak in Germany     Article in today's New York Times about the same thing.
Link to Oksana's paper on "designing an enteric chip"
Link to Oksana's paper on "Comparison of 61 E. coli Genomes"     (PMID 20623278)





Friday, 24 June, 2011: Student Presentations


9:30-10:15Presentations from Groups 1-4
Group 1 - Escherichia (stud137)   Group 3 - Cyanobacteria (stud139)     Group 4 - Bifidobacterium (stud140)
10:30-11:00Coffee break
11:00-11:45Presentations from Groups 5-8
Group 5 - Lactic Acid Bacteria (stud141)   Group 6 - Bacteroidetes (stud143)     Group 7 - Chlorobi (stud144)
12:00-13:00Lunch break
13:00-14:00Presentations from Groups 9-12
Group 9 - Bacillus (stud146)    Group 10 - Mycobacterium (stud147)     Group 11 - Archaea (stud148)     Group 12 - Brucella (stud149)
14:00-14:30Break
14:30-15:15Presentations from Groups 13-15
Group 13 - Pseudomonas (stud150)    Group 14 - Rhodobacter and Rhizobium (stud151)     Group 15 - Staphylococcus (stud152)
15:15-16:15Certificate Presentations and Closing







This file was last modified Tuesday 21st of June, 2011 17:25:26