CBS >> CBS Courses >> Immunological Bioinformatics >> Course Programme 2011

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: 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 6

Introduction, immunology brush up, and Unix

BACKGROUND TEXTS: Book Chapter 4 p. 98-101, Tutorial Text pages 4-7.

9.00 - 9.30: Introduction to the course.; Claus Lundegaard, CBS, DTU Systems Biology.; Project description; Introduction to project work
As Slides; Recording.
9:30-10:15: 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 7

T-cell Epitopes

BACKGROUND TEXTS: Tutorial Text pages 11-13, Book 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 round up
9.30 - 12.00: Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN); MHC polymorphism, sequences, and population data.; Allele-specific versus pan-specific prediction methods; Does processing matter?; Rational epitope discovery using immunoinformatics; A little on MHC class II binding; Morten Nielsen, CBS, DTU Systems Biology; Coffee Break at some point around 10.30; Prediction of MHC peptide binding Powerpoint slides. PDF.; Morten Nielsen, CBS, DTU Systems Biology.; Recording 2 --- Recording 1
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercise:; Prediction of MHC:peptide binding using PSSM and ANN.; Morten Nielsen, CBS, DTU Systems Biology.

Wednesday, June 8

Vaccines, antibodies, and epitopes

BACKGROUND TEXTS: Chapters 2, 10. Article1, Article 2

9.00 - 9.30: Yesterdays exercise round up.; Recording
9.30 - 10.15: Vaccines and epitope dicovery.; Claus Lundegaard, CBS, DTU Systems Biology; Recording; Adjuvants; Prof. Peter Heggaard, DTU-Vet; Recording
10.45 - 11.15: Antibodies and TCRs, development and selection.; Claus Lundegaard, CBS, DTU Systems Biology.; Recording 1; Recording 2
11.15 - 12.00: lunch break
12.00 - 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.

Thursday, June 9

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: Yesterday's exercise round up recording; Yesterday's exrcise 2 round up.
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.; 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 10

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: Yesterdays exercise round up.; NetMHCpan sheet; NetMHCIIpan sheet; Recording.; Claus Lundegaard, Center for Biological Sequence Analysis, DTU Systems Biology.
9.30 - 10.00: Prediction of B cell epitopes; Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.; Recording
10.00 - 12.00: Exercise: B cell epitope predictions.; Leon Jessen, Center for Biological Sequence Analysis, DTU Systems Biology.; Jens Kringelum, Center for Biological Sequence Analysis, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 13.45 NOTE: Prof. Doherty could not make it this year, so we will watch the recording from last year.: Development of a subunit vaccine against TB; Prof. T. Mark Doherty, Coordinator, Research and Strategy, Infectious Disease Immunology, Statens Serum Institute; Recording.
13.45-: Project work; Claus Lundegaard, Center for Biological Sequence Analysis, DTU Systems Biology.

Tuesday, June 14

Evolution and viral pathogens

BACKGROUND TEXTS: Chapter 3

9.00 - 9.30: Friday's exercise round up.; Recording.
9.30 - 10.15: Prediction of immunogenicuty of therapeutic proteins; Jens Vindahl Kringelum, M.Sc., CBS
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.