MVE130 Large Scale Genomics, Techniques and Analysis

Gothenburg, Spring 2011


Latest updates

May 10: Master projects meeting: May 12@15.15 Euler

May 4: Schedule changes for Friday May 6:

                             12.00-13.45 MVF21 Metagenomics, Eric Kristiansson

                             14.00-15.00 KC (Chemistry Building) Towards a knowledge-based Human Protein Atlas, Mathias Uhlén – Honorary Doctor Seminar



Teachers and topics

Main responsible teacher and examiner:

OlleNerman (nerman(at), work phone: 031-7723565, home phone: 031-880877



GouthamVemui (goutham(at), Biotechnology, Chalmers 



JoakimNorbeck (norbeck(at), Biotechnology, Chalmers


Gene Expression with microarrays:



Gene Expresssion with Real time PCR:                                                                                                                     

Anna Johnning (anna.johnning(at), Medical Physiology, GU


Clustering, principal components and discriminant analysis, expression profiling:



Next Generation Sequencing and Metagenomics:                                                                                     

Erik Kristiansson (erik.kristiansson(at), MV, Chalmers


Cancer Genomics and Systems Biology:

Sven Nelander (sven.nelander(at), Wallenberg Lab, GU


Statistical Genetics:                                                                                                                                

 Staffan Nilsson (staffan(at), MV, Chalmers


Home page and lab assistance:                                                                                                             

Marija Cvijovic (marija.cvijovic(at), MV, Chalmers



1. Obligatory hand in of two lab reports (done in group of max 3 students together) to be sent to Marija (marija.cvijovic(at) Deadline May 25


2. Hand in of three individually written essays with max 2 pages on each:

a) Metabolomics task: decided by Goutham Vemuri and OlleNerman (hand out 25 March, hand in 22 May)
b) Proteomics task: decided by Joachim Norbeck and OlleNerman  (hand out 1 April, hand in 5 May)
c) Microarray task:  decided by OlleNerman (hand out 15 April, hand in 16 May)


These essays will be marked together with the written exam, and will result in max 12 points (4 points each) out of a total of 30.


3.  The remaining 18 points will result from a conventionally set exam on all parts of the course besides the metabolomics and proteomics parts.

The limits for the marks 3, 4 and 5 will be 15, 20 and 25 respectively, and minimum 7 points on essays are required for passing.


Place and date for the regular examination:30/05-2011 am in  V-house


Preliminary Schedule MVE130

Week 12

Tuesday 22 March, 10.00-11.45 in MVF21                                                                                               

Introduction and course overview (OlleNerman)

Thursday 24 March, 10.00-11.45 in MVF21                                                                                                                                                      

Metabolomics 1 (GouthamVemuri)

Friday 25 March, 13.15-15.00 in MVF21
Metabolomics 2 (GouthamVemuri)

Week 13

Tuesday  29 March, 10.00-11.45 in MVF 21
Proteomics I (Joachim Norbeck)


Thursday 31 March, 10.00-11.45 in MV21
Introduction to microarrays 1 (OlleNerman)


Friday 1 April 9.15-11.45 in MVF25                                                                                                                      

Microarrays lab 1 Introduction to preprocessing of microarrays and to LIMMA  (OlleNerman+MarijaCvijovic)


Friday 1 April 13.15-15.00 in MVF21

Proteomics II (Joachim Norbeck)


Week 14

Tuesday 5 April 10.00-11.45 in MVF21

Introduction to Microarrays 2 (OlleNerman)


Thursday 7 April 10.00-11.45 in MVF21

Clustering and Discriminant Analysis 1 (OlleNerman)


Friday 8 April  9.00-11.45 in MVF25                                                                                                                                 

Microarrays lab 2: LIMMA and Profiling of Expression data (OlleNerman+MarijaCvijovic)


Friday 8 April 13.15-15.00 in MVF21                                                                                                                      

Real time PCR expression analysis (Anna Johnning)


Week 15

Tuesday 12 April 10.00-11.45 in MVF21                                                                                                                                 

Clustering and Discriminant Analysis 2 (OlleNerman)


Thursday 14 April 9.00-11.45 in MVF21                                                                                                                               

Principal Component Lab (OlleNerman+Marija Cvijovic)


Friday 15 April 9.00-10.45 in MVF25                                                                                                                             

Clustering and Discriminant Analysis  3(OlleNerman)


Friday 15 April 13.15-15.00 in Pascal                                                                                                                  

MSc thesis presentation


Week 18

Tuesday 3 May 10.00-11.45 in MVF21

Next generation sequencing  andmetagenomics 1(Erik Kristiansson)


Thursday 5 May 10.00-11.45 in MVF21

Next generation sequencing and Metagenomics2 (Erik Kristiansson)


Friday 6 May 9.00-11.45 in MVF25

Metagenomics lab (Erik Kristiansson)


Friday 6 May 13.15-15.00 in MVF21                                                                                                                 

Clustering and Discriminant Analysis 4 (OlleNerman)


Week 19

Tuesday 10 May 10.00-11.45 in MVF21                                                                                                               

Cancer genomics and systems biology  1 (Sven Nelander)


Thursday 12 May 10.00-11.45 in MVF21                                                                                                               

Cancer genomics and systems biology  2 (Sven Nelander)


Friday 13 May 9.00-11.45 in MVF25                                                                                                                      

Cancer genomics Lab (Sven Nelander+MarijaCvijovic)


Friday 13 May 13.15-15.00 in MVF21                                                                                                            

Clustering and discriminant analysis 5 (OlleNerman)



Week 20

Tuesday 17 May 10.00-11.45 in MVF21                                                                                                                                     

Statistical Genetics 1 (Staffan Nilsson)


Thursday 19 May 10.00-11.45 in MVF21                                                                                                            

Statistical Genetics 2 (Staffan Nilsson)


Friday 20 May 9.00-11.45 in MVF25                                                                                                                  

Statistical Genetics Lab (Staffan Nilsson)


Friday 20 May 13.15-15.00 in MVF21                                                                                                                     

Reserve time (OlleNerman)


All course material will be either handed out or linked to. If you use course homepage link for academic year 2009/2010 you will find much of the material that will be used in the course, but:


§  Essay questions will be new for this year.

§  You are not allowed to “copy and paste” in the essays. We will use a system that detects texts that are copies of websites, published papers, other student´s texts etc. to check your submitted texts. Main purpose of the essays is to train your general writing and English writing capacity, and of course also your capacity to read and understand scientific texts as they appear in journals.


Finally I wish to mention that we plan to have a couple of seminars in mid- May with suggestions for applied master thesis projects in various bioscience and medical environments.


I look forward to the course with great expectations.