CBS >> CBS Courses >> Immunological Bioinformatics >> Course Programme 2012

Immunological Bioinformatics - #27685

Information for participants

THIS PROGRAMME IS STILL PRELIMINARY AND MIGHT CHANGE BEFORE THE ACTUAL DATE!

GENERAL DAILY SCHEDULE
Lectures will be from 9 - 12 am,
Lunch from 12 - 13, and,
Exercises from 13 - 17 pm.

PLACE: DTU Building 204 room 243 (2nd floor)
LITTERATURE: All litterature will be available through CampusNet

PROGRAMS AND TOOLS

Flash 6 or better
For following the lectures you need a browser with Flash 6 or better. Flash is freeware and can be downloaded by clicking on the link above
UNIX - Beginner's Guide to UNIX is available on-line.
For doing some of the exercises on our server you must be able to connect to the server using Secure Shell (SSH) and tunnel X through the connection.
See informations on prerequisites on:
Tools for SSH and X11

Course Programme
Please note that the programme is updated on a daily basis - click the 'refresh' button once in a while to make sure that you have the most updated information

LITTERATURE: All litterature will be available through CampusNet

Monday, June 10

Introduction, immunology brush up, and Unix

BACKGROUND TEXTS: Tutorial Text pages 4-7.
Optional reading: Immunological Bioinformatics, Chapter 4 p. 98-101

9.00 - 9.30: Introduction to the course.; Ole Lund, CBS, DTU Systems Biology.
9:30-10:15: Basic mechanisms of immune defense; Susanne Brix Pedersen, CBS, DTU Systems Biology.
10.15 - 10.45: Coffee Break
10.45 - 12.00: Basic mechanisms of immune defense continued
12.00 - 13.00: lunch break
13.00 - 13.30: Computer setup
13.30 - 14.30: Introduction to Immunological Bioinformatics.; Ole Lund, CBS, DTU Systems Biology.
14.30 - 16.00: Exercises: Unix and awk, a crash course; Ole Lund, CBS, DTU Systems Biology.

Tuesday, June 11

Vaccines, antibodies, and epitopes

BACKGROUND TEXTS: Article1 Optional reading: Immunological Bioinformatics, Chapters 2, 10.

9.00 - 9.30: Yesterday's exercise round up
9.30 - 10.15: Adjuvants; Prof. Peter Heegaard, DTU-Vet
10.45 - 11.15: Antibodies and TCRs, development and selection.; Ole Lund, CBS, DTU Systems Biology.
11.15 - 12.00: lunch break
12.00 - 16.00: Molecular evolution; Molecular Evolution. Handout exercise
Anders Gorm Pedersen, CBS, DTU Systems Biology.

Wednesday, June 12

Vaccines, antibodies, and epitopes

9.00 - 12.00

Analysis of immunoglobolin gene rearrangements.

Ole Lund, CBS, DTU Systems Biology.

12.00 - 13.00

Lunch

13.00 - 14.00

Development of a subunit vaccine against TB

Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute

12.00 - 16.00

Exercises:

Databases and web resources in Immunological bioinformatics.
Ole Lund, CBS, DTU Systems Biology.

Thursday June 13

B cell epitope predictions

BACKGROUND TEXTS: Chapter 3 + Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. + Improved method for predicting linear B-cell epitopes.
SUPPLEMENTARY: Simplified B-cell walkthrough (Nice and easy understandable explanation of B-cells, also overview of other aspects of the immune system is available at this channel).

9.00 - 9.30: Exercise round up; Ole Lund, Center for Biological Sequence Analysis, DTU Systems Biology.
9.30 - 10.00: Prediction of B cell epitopes; Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
10.00 - 12.00: Exercise: B cell epitope predictions.; Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 13.15: Exercise round up
13.15 - 14.00: Peptide microarray-driven analysis of immune targets; Christian Skjødt Hansen, CBS, Systems Biology
14.00 - 14.30: Diagnostic biomarker discovery for parasitic diseases using high-density peptide microarrays; Santiago J Carmona, Institute for Biotechnology Research, University of San Martin, Buenos Aires, Argentina
14.45-16.00: SigniSite: Identification of residue-level genotype-phenotype correlations in protein multiple sequence alignments; Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.; Additional links; The SigniSite-2.0 Server; Abstract; Know Your Amino Acids

Friday, June 14

Next generation sequencing, FACS data analysis

BACKGROUND TEXTS: Sequencing techniques
SUPPLEMENTARY: Shiga toxin antibodies

9.00 - 9.30: DNA sequencing; Mette Voldby Larsen, CBS, Department of Systems Biology, DTU
9.30 - 10.00: Exercise: Assembling NGS data; Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
10.00 - 10.30: From DNA to protein; Mette Voldby Larsen, CBS, Department of Systems Biology, DTU
10.30 - 11.00: Exercise: Predicting genes using Prodigal; Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
11.00 - 11.30: PathogenFinder; Salvatore Cosentino, CBS, Department of Systems Biology, DTU
11.30 - 12.00: Exercise: PathogenFinder; Mette Voldby Larsen, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 14.00: Automated analysis of FACS data; Juliet Wairimu Fredriksen, PhD student, CBS, Department of Systems Biology, DTU
14.00 - 16.00: Exercise: Automated FACS data analysis
9.00 - 9.30: Exercise round up
9.30 - 10.00: Performance measures; Supertypes and functional clustering of MHC molecules; Morten, CBS, DTU Systems Biology.
10.00 - 10.30: What defines a T cel epitope? Is there any thing beyond MHC binding?
10.30 - 10.45: Coffee Break
10.45 - 11.25: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design; Morten Nielsen, CBS, DTU Systems Biology.
11.25 - 12.00: Identifying multiple sequence motifs in large scale peptide data sets
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises: Development of vaccines against HCV.
Morten Nielsen, CBS, DTU Systems Biology.