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Comparative Microbial Genomics Workshop

16 - 20 October 2006, Oslo, Norway

Organized by Dave Ussery at the Center for Biological Sequence Analysis, Technical University of Denmark and Torbjørn Rognes at the Centre for Molecular Biology and Neruroscience, Rikshospitalet-Radiumhospitalet Medical Centre and University of Oslo, with help from Kristoffer Kiil, Karin Lagesen, Morten Mattingsdal, Birgit Eliassen, Per Eystein Sæbø and Jon Myrseth.

Dave Ussery is also associate professor II at CMBN, UiO, funded by FUGE East.

For additional information about the course, please contact Torbjørn Rognes by email to torbjorn DOT rognes AT medisin DOT uio DOT no.


Due to the massive availability of sequences of genomes of microbes and other organisms, comparative genomics has gained recognition as a powerful tool for deciphering biological processes both through sequence comparisons and comparative regulation. It helps us understand the genetic basis of diversity and evolutions in organisms, leading to the insight understanding into how living things evolved through stressed environments to the pathogenesis of pathogens, including identification novel drug targets and development of novel drug candidates. Moreover, it presents promising opportunities to identify new genes that are difficult to elucidate by classic experimental methods, thereby offering potential genetic resources for basic research and also for medical and biotechnological uses.

The workshop is designed to enable participants to use comparative genomic tools through lectures and hands-on practical to extract biological meanings and discover novel genes from the vast amount of genomic data and solving problems of their research interest. The workshop will also serve as a platform for participants to establish multidisciplinary collaborations in comparative genomics research among various groups of scientists and researchers at national and international level.


Who should attend

The aim of the workshop is to bring participants from different backgrounds and research interests to work together in cooperation. Thus, the workshop is suitable for all students and researchers in medical science, biological science, computer science, bioinformatics, biotechnology and related fields. The participants should have a basic knowledge in molecular biology and some background in statistics. Those who are from the computer science related will be introduced to basic molecular biology to be able to perform the hands-on exercise.

Participants will have the opportunity to work in groups consist of colleagues from different disciplines. Moreover, participants will be able to take the workshop as a forum to share and exchange their experiences and also to discuss and identify practical problems and solutions with the experts in the field of comparative microbial genomics and bioinformatics.



Please register no later than 8 October 2006 by sending an email to kristin DOT bernhus AT medisin DOT uio DOT no, including the following information:

  • your full name
  • your email address
  • your full workplace or study address
  • your scientific background (biology, computer science, medicine)
  • which (if any) study programmes you are enrolled into (Master, PhD, ...) at which department or faculty (medicine, biology, ...) at which institution (UiO, UMB, ...)

The number of participants is restricted to 24. A limited number of participants will allow the opportunity for the participants to access to all the facility and to work closely with the experts, or to work on their own data (if any). Participants will be selected on a first-come, first-served basis, provided a reasonable background.

There is no fee, but the participants will need to bring or pay for their own lunch. There is a small canteen in the building where the course is taking place.

Please note that all attendees are required to bring their own laptop computer in order to be able to carry out the exercises. All computers need to be connected to the UiO network (wired or wireless). Limited technical assistance will be provided.


Lectures and exercises

The course will consist of lectures and computer exercises, where the students will be introduced to a range of computational methods used in the field.

Lectures will take place in seminar room 408 in "Veglaboratoriet", University of Oslo, Gaustadalleen 25. As far as possible, we will put up the lecture notes on this course web page. Lecture notes will be in PDF format and will in many cases be preliminary, ie. the lecturer will provide the final notes after the talk and these will then replace the preliminary notes.

Exercises will be performed in groups of two and supervised by one or more instructors.

Exam: There will be an exam at the end of the course. The exam consists of an exercise that should be presented in a report. The exam is presented here. The exam must be carried out individually by each student.

Study points: To be determined. Details will be provided later.



Monday 16 October 2006
09:00 - 12:00

Introduction to microbial genomics
Lecture 1: Sequences as information and related Nobel prizes
Lecture 2: An Introduction to genomics
Coffee break
Chromosomal DNA Structures
Lecture 3: DNA structures from A- to Z

12:00 - 13:00


13:00 - 17:00

Lecture 4: Replication-strand specific oligomer bias in bacterial genomes
Coffee break
Methods to Compare Microbial Genomes
Lecture 5: 20 Methods to Compare Microbial Genomes

Tuesday 17 October 2006
09:00 - 12:00

Lecture 6: Non-messenger RNAs
Coffee break
Lecture 7: Prediction of pathogenicity networks in bacterial proteomes

12:00 - 13:00


13:00 - 17:00

Exercise 1: Introduction to UNIX and Biological Information exercise
Coffee break
Exercise 2: DNA structures exercise – Replication origin

Wednesday 18 October 2006
09:00 - 12:00

Gene Regulation in Microbial Genomes
Lecture 8: DNA curvature, melting, and flexibility
Coffee break
Lecture 9: Gene Expression - A Global, Chromosomal View

12:00 - 13:00 Lunch
13:00 - 17:00

Exercise 3: AT content, codon usage
Coffee break
Exercise 4: Gene regulation exercise – Sigma and transcription factors


19 October 2006

09:00 - 12:00

Protein function, localization and networks
Lecture 10: Protein function and localisation
Lecture 11: Protein networks
Coffee break
Lecture 12: Proteome comparison

12:00 - 13:00


13:00 - 17:00

Exercise: 2-D comparison Blast Matrix Blast Atlas

Friday 20 October 2006
09:00 - 12:00

Metagenomics and pangenomics
Lecture 13: Meta-genomics
Coffee break
Lecture 14: Opening the pan-genomics box for E. coli - Comparison of 20 sequenced Escherichia coli genomes

12:00 - 13:00


13:00 - 17:00

Presentation of the format of the report for the exam
Lecture 15: Summary
Course wrapup with pizza


Please see the following pages for similar earlier workshops:

E.coli structur atlas
Centre for Molecular Biology and Neuroscience (CMBN)
PO Box 1105 Blindern, NO-0317 Oslo, Norway. Tel: +47 22851528. Fax: +47 22851488