CBS >> CBS Courses >> Immunological Bioinformatics >> Course Programme 2010

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 208 room 060 (in the basement)
LITTERATURE: Immunological Bioinformatics, Lund et al., MIT Press 2005. (can be purchased at discount in CBS build. 208) + additional publications

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: Immunological Bioinformatics, Lund et al., MIT Press 2005 can be purchased at discount in CBS build. 208

Monday, June 7

Introduction, immunology brush up, and Unix

BACKGROUND TEXTS: Textbook Chapter 1, Tutorial Text page 6

9.00 - 9.20: Introduction to the course.; Claus Lundegaard, CBS, DTU Systems Biology.
9:20-10:15: Basic mechanisms of immune defense; Susanne Brix Pedersen, CBS, DTU Systems Biology.; Recording (including breaks...Sorry!)
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: Training and evaluation of predictive methods.; Claus Lundegaard, CBS, DTU Systems Biology.; Recording; Handout
13.30 - 16.00: Exercises: Unix and awk, a crash course; Claus Lundegaard, CBS, DTU Systems Biology.

Tuesday, June 8

Vaccines, antibodies, and epitopes

BACKGROUND TEXTS: Chapters 2, 10. Article1, Article 2
Only recording of Dr. Fomsgaard

9.00 - 9.30: Yesterday's exercise round up
9.30 - 10.15: Vaccines and epitope dicovery.; Claus Lundegaard, CBS, DTU Systems Biology
10.15 - 10.45: Coffee Break
10.45 - 11.15: Antibodies and TCRs, development and selection.; Claus Lundegaard, CBS, DTU Systems Biology.
11.15 - 12.00: DNA Vaccines, plasmids and design; Anders Fomsgaard, MD, DMSc, Chief of Molecular Virology Laboratory, Department of Virology, Statens Serum Institut; Recording.
12.00 - 13.00: lunch break
13.00 - 15.30: Exercises:
: Databases and web resources in Immunological bioinformatics.
Claus Lundegaard, CBS, DTU Systems Biology.
: Analysis of immunoglobolin gene rearrangements.; Claus Lundegaard, CBS, DTU Systems Biology.

Wednesday, June 9

T-cell Epitopes

BACKGROUND TEXTS: Chapters 6-8.
Additional readings: Modeling the adaptive immune system: predictions and simulations A consensus epitope prediction approach identifies the breadth of murine TCD8+-cell responses to vaccinia virus, Major histocompatibility complex class I binding predictions as a tool in epitope discovery, MHC Class II epitope predictive algorithms.
No recordings of this days lectures

9.00 - 9.30: Yesterday's exercise 1 round up Yesterday's exrcise 2 round up.
9.30 - 10.00: MHC polymorphism, sequences, and population data.; Claus Lundegaard, CBS, DTU Systems Biology
10.00 - 10.30: Coffee Break
10.30 - 12.00: Prediction of MHC peptide binding.; Claus Lundegaard, CBS, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercise:; Prediction of MHC:peptide binding using PSSM and ANN.; Claus Lundegaard, CBS, DTU Systems Biology.

Thursday, June 10

Supertypes, HLA clustering, and integration

BACKGROUND TEXTS: Capters 13-14.
Additional readings: Antigen processing influences HIV-specific cytotoxic T lymphocyte immunodominance ; Identification of poxvirus CD8 T cell determinants to enable rational design and characterization of smallpox vaccines

9.00 - 9.30: Yesterdays exercise round up.; Recording.
9.30 - 10.15: Supertypes and Clustering; Claus Lundegaard, CBS, DTU Systems Biology.; Recording.
10.15 - 10.45: Coffee Break
10.45 - 11.30: Prediction of proteasome processing and TAP binding; The Class I Pathway.; Handout.; Claus Lundegaard, CBS, DTU Systems Biology.; Recording
11.30 - 12.00: Integration of predictions.; Claus Lundegaard, CBS, DTU Systems Biology.; Recording.
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises: Development of vaccines against HCV.
Claus Lundegaard, CBS, DTU Systems Biology.

Friday, June 11

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.

9.00 - 9.30: Yesterdays exercise round up.; Recording.
9.30 - 10.00: Prediction of B cell epitopes; Claus Lundegaard, CBS, DTU Systems Biology.; Recording
10.00 - 12.00: Exercise: B cell epitope predictions.; Claus Lundegaard + Bent Petersen, CBS, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 13.45: Development of a subunit vaccine against TB; Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute; Recording.
13.45-14.30: Project initiation; Introduction to project work
As Slides; Recording.

Monday, June 14

Evolution and viral pathogens

BACKGROUND TEXTS: Chapter 3

9.00 - 9.30: Friday's exercise round up.; Recording.
9.30 - 10.15: Mathhematical simulations of HIV infection; Nicolas Rapin, Ph.D., BRIC; Recording.
10.15 - 10.30: Coffee Break
10.30 - 12.00: Molecular Evolution. Handout exercise
Anders Gorm Pedersen, CBS, DTU Systems Biology.; Recording1.; Recording2.
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises: Viral Evolution
Anders Gorm Pedersen and Claus Lundegaard, CBS, DTU Systems Biology.; Recording.

Tuesday, June 15

Symposium with invited speakers

9.30 - 10.00: Yesterdays Exercise roundup; Anders Gorm Petersen, CBS, DTU Systems Biology.
10.00 - 10.30: Coffee Break
10.30 - 11.15
: TBA; Magnus Strandh, Symphogen A/S
11.15 - 12.00: MHC Dextramers for detection of antigen specific T-cells; Jørgen Schøller, Ph.D., CSO, Co-founder, Immudex A/S
12.00 - 13.00: Lunch Break
13.00 - 13.45: Epitope grafting and antibody engineering - the molecular basis of the allergic reaction; Kaare Lund, PhD, Manager, Experimental Immunology, ALK-Abello A/S
14.00 - 14.45: Adjuvants in vaccine formulations; Prof. Peter Heegaard, DTU-Vet

Friday, June 16 to Tuesday, June 22:

Project work

Wednesday, June 23

Quiz and exercise exam

10.00 - 14.00: Exam 2010.; Quiz and exercize exam.

Thursday, June 24: Poster Presentations

Poster Day

9.30 - 10.15: Coffee (10.00) and poster setup
10.15 - 10.45: Prediction of MHC II loading of tissue restricted antigens
10.45 - 11.15: Prediction of Immunogenic Peptides in Ebola- and Marburgvirus
11.15 - 11.45: Constructing a Vaccine Against Human Papillomavirus
12.00 - 13.00: Lunch Break
13.00 - 13.30: Constructing a Vaccine Against Human Papillomavirus; Hepatitis C Virus
13.30 - 14.00: VACCINE FOR THE ZAIRE EBOLAVIRUS
14.00 - 14.30: Mycobacterium tuberculosis
14.30 - 15.00: Course round up

For more information, please contact Claus Lundegaard.

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This file was last modified Wednesday 23rd 2010f June 2010 14:56:53 GMT

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