27685 Course programme 2017
Immunological Bioinformatics - #27685
Information for participants
GENERAL DAILY SCHEDULE
Lectures will be from 9 - 12 am, Lunch from 12 - 13, Exercises from 13 - 17 pm.
PLACE: DTU Building 210 room 162
Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises (bring your own laptop).
Please note:
- The programme may change slightly along the way.
- The required readings for a class can be trusted one week in advance.
- The exact content of powerpoint slides and handouts may change up to the last minute!
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 All files and materials can be found on CampusNet
LITERATURE: All literature will be available through CampusNet or through this wiki page
Thursday, June 1
Introduction, immunology brush up, and databases
- BACKGROUND TEXTS: Introduction to Immunology
Optional reading: Immunological Bioinformatics, Chapter 4 p. 98-101
9.00 - 9.30: [Introduction to the course.]
Paolo Marcatili, CBS, DTU Systems Biology.
9:30-10:15: Basic mechanisms of immune defense, Søren Buus, KU 10.15 - 10.30: Coffee Break
10.30 - 11.15: Antigen presentation to T-Cells, Søren Buus, KU
11.15 - 12.00: The impact of Immunological Bioinformatics on immunological research, Søren Buus, KU
12.00 - 13.00: lunch break
13.00 - 13.50: Group Formation and Preliminary Test
14:00 - 16.00: Databases and web resources in Immunological Bioinformatics
Paolo Marcatili
Paolo Marcatili, CBS, DTU Systems Biology.
Friday, June 2
Immunological target identification
- BACKGROUND TEXTS:
CGE tool box: PDF Read the sections on PathogenFinder, VirulenceFinder and ResFinder
PathogenFinder paper: PDF
9:00 - 12:00: Bacterial pathogenicity and virulence
Johanne Ahrenfeldt, PhD Student DTU Bioinformatics
9:00 - 9:45 Presentation on PathogenFinder
Slides: File:PathogenFinder.pdf
10:00 - 11:00 Exercises
11:15-12:00 Presentation on VirulenceFinder
Slides: File:VirulenceFinder.pdf
12.00 - 13.00: lunch break
13:00 - 15:00: Antibiotic resistance
Johanne Ahrenfeldt, PhD Student DTU Bioinformatics
13:00 - 13:45 Presentation on ResFinder
Slides: File:ResFinder.pdf
14:00 - 15:00 Exercises in VirulenceFinder and ResFinder
Functional annotation of protein sequences
Lecture: Tools for sequence annotation
Exercise: Annotation of Bacterial Sequences
Tuesday, June 6
B- and T-cell receptors genetics and structure
BACKGROUND TEXTS: antibody repertoire,
antibody modeling,
TCR modeling
9.00 - 10.00: TCR and BCR maturation.
10.30 - 12.00: Analysis of immunoglobulin gene rearrangements
Paolo Marcatili, CBS, DTU Systems Biology.
12.00 - 13.00: Lunch Break
13.00 - 14.00: TCR and BCR structure
Paolo Marcatili
14.00 - 16.00: [Exercise on antibody structure prediction and analysis]
Paolo Marcatili, CBS, DTU Systems Biology.
Wednesday, June 7
B cell epitope predictions
- BACKGROUND TEXTS: Chapter 3 + BepiPred 2.0 + B-cell epitope prediction
- 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).
Video:Linear B cell epitope prediction slides
Video:Conformational B cell epitope prediction slides
10.00 - 12.00: Exercise: B cell epitope predictions.
Exercise: optional.
12.00 - 13.00: Lunch Break
13.00 - 13.15: Exercise round up
13:15- 13:30: Quiz
13.45 - 14.30: Antibody Humanization
14.30-16.00: Exercise on Antibody Humanization
Thursday June 8
T-cell Epitopes
- BACKGROUND TEXTS:
Optional readings: Immunological Bioinformatics, Chapter 4. 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.
9.00 - 9.30: Last Exercise round up
9.30 - 12.00: Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN)
Rational epitope discovery using immunoinformatics
A little on MHC class II binding
Coffee Break at some point around 10.30
Slides [PDF].
Logo handout.
Answer Logo handout.
NN handout.
Morten Nielsen, Department of Bio and Health Informatics .
12.00 - 13.00: Lunch Break
13.00 - 16.00: Performance measures
Exercise - Prediction of MHC:peptide binding using PSSM and ANN.
Answers: Prediction of MHC:peptide binding using PSSM and ANN.
Morten Nielsen, Department of Bio and Health Informatics.
Friday, June 9
Antigen processing and presentation, Supertypes, HLA clustering, and vaccine design
- BACKGROUND TEXTS: Capters 13-14.
Additional readings: A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection ; Identification of poxvirus CD8 T cell determinants to enable rational design and characterization of smallpox vaccines
9.00 - 9.30: Exercise round up
9.30 - 10.00:Supertypes and functional clustering of MHC molecules
Morten, CBS, Department of Bio and Health Informatics.
10.00 - 10.45: What defines a T cel epitope? Is there any thing beyond MHC binding?
10.45 - 11.00: Coffee Break
11.00 - 11.45: Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design
Morten Nielsen, Department of Bio and Health Informatics.
12.00 - 13.00: Lunch Break
13.00 - 16.00: Exercises: Development of vaccines against HCV.
Answers
Morten Nielsen, Department of Bio and Health Informatics.
Monday, June 12
9.00 - 9.20: Question and round up from last week
Quiz
9.20 - 10.05: Use of Mass-spec data for epitope identification
Mass-spec elution data and Gibbs Clustering
Morten Nielsen, Department of Bio and Health Informatics.
10.05 - 10.20: Coffee Break
10.20 - 12.00: Gibbs sampling approach for peptide clustering
The use of GibbsClustering for the analysis of ligand MS data
12.00 - 13.00: Lunch Break
13.00 - 16.00: Humanization and deimmunazation for cancer T cell therapy molecules
Exercise on CAR T-cell humanisation and de-immunisation
Tuesday, June 13
Cancer immunology
9.00 - 12.00 Seminars:
9.00 - 9.50: Cancer Genomics
Aron Charles Eklund, DTU Systems Biology
10.00 - 10.50: High-throughput identification of T cell epitopes
Lecture by Sine Reker Hadrup
Sine Reker Hadrup, DTU Vet
11.00 - 11.50: Cancer Immunotherapy
Marco Donia, KU and Herlev Hospital
12.00 - 13.00: Lunch Break
Introduction to project work Poster Example Paolo Marcatili, DTU Systems Biology
Wednesday, June 14 - June 20
9.00 - 17.00: Project work
Power point presentations are fine as well, but keep it short and to the point
Wednesday and Thursday, June 21-22
9.00 - 17.00: exams
For more information, please contact Paolo Marcatili
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