Gene Expression and Cell Models, Spring 2007

This course, KMB026 Gene Expression and Cell Models (5cu), is part of Chalmers International Master's Programme in Bioinformatics.
Examiner: Olle Nerman ,  Mathematical Statistics Chalmers, phone: 7723565  mail: nerman@math.chalmers.se. I will be assisted by Peter Gennemark , Computing Science Chalmers, phone: 7725334, mail:  peterg@cs.chalmers.se

The Schedule is still preliminary. More information than found below will be announced weekly during the course on this webpage!

Literature

A number of hand-outs and web-based resources will be used.

Some background material

• The Chipping Forecast I, Nature Genetics, volume 21 , supplement, 1999.
  
• The Chipping Forecast II, Nature Genetics, volume 32, supplement, 2002.
• The Chipping Forecast III, Nature Genetics, volume 37 supplement, 2005
  
• Whole-istic Biology, Science, volume 295, no. 5560, March 2002.
  
• Master Theses: Image Analysis of Affymetrix-type Microarray Images.
  
• Origins of Individual Swimming Behavior in Bacteria, Levin D L et al, Bioph. J. 74-1998.
  
• Data Clustering: A Review, Jain A.K. et al, ACM Comp. Surveys, 31-3, 1999.
  
• Discriminant Analysis and Clustering, Statistical Science 4-1,1989 p.44-69.Bookversion
  

A book on genomics, with biological perspective:

A Primer of Genome Science. Gibson G, Spencer M. Second edition. Sinauer. ISBN 0-87893-232-1

Examination

The exam for this course will consist of 5 essays to be handed in during the course. The questions will be of a general nature and quite open, and you are supposed to write an essay-type answer, in printed text, and paper format, where the text should be maximum two pages per question, and in the end of each question you should indicate your sources. Work individually in the writing process, use your own words, and do not copy (neither each other nor from electronic sources).

Participation in the computer practicals is compulsory. There will be final course marks, as usual in the scale 3, 4 or 5 (where 5 is the best).

Schedule for essay questions

All essays should be handed in to me, Olle Nerman, either at the lecture on the handin date, or, at that date, put in the box outside the door of my office 3056. DO NOT SUBMIT ELECTRONICALLY!

Shedule

References and details

Week 12 Tuesday March 20: Talk by Sven Nelander, slides

Week 13
Monday March 26: Introduction to pathways modelling, Signal transduction lab. Peter Gennemark

Week 16
Monday and Tuesday: Proteomics, Anders Blomberg

Week 17
Modelling with Systems biology toolbox, FCC, Henning Schmidt and others.

Week 18

Week 19

Week 20

Week 21