36685 Immunological Bioinformatics Course Program January 2018
Information for Course Attendees
The official course site can be found here
General Daily Schedule
- 09.00 - 12.00 Lectures
- 12.00 - 13.00 Lunch
- 13.00 - 17.00 Exercises
Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises (students are required to bring their own laptop). All literature will be available through DTU inside or this site.
Location
DTU Lyngby Campus, Building 208, room 062 (Down the stairs in the basement). Should you be new to DTU, a map can be found here.
Other
Please note, the course schedule 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!
Classes will be a mixture of lectures and group work. Most of the group work will consist of computer exercises. Students are required to bring their own laptop.
Course Program
Tuesday, January 2nd - Introduction, Immunology Brush-up and Databases
Reading list
Schedule
09.00 - 09.30 Introduction to the course, Leon Eyrich Jessen
09:30 - 10:15 Lecture: Basic Mechanisms of Immune Defense, Professor Søren Buus, University of Copenhagen
10.15 - 10.30 Coffee Break
10.30 - 11.15 Lecture: Antigen Capture and Presentation to T-lymphocytes, Professor Søren Buus, University of Copenhagen
11.15 - 12.00 Lecture: The Impact of Immunological Bioinformatics on Immunological Research (Slides 1, 2), Professor Søren Buus, University of Copenhagen
12.00 - 13.00 Lunch break
13.00 - 13.50 Group Formation and short quiz on immunology
14:00 - 16.00 Exercise: Databases and web resources in Immunological Bioinformatics
Wednesday, January 3rd - Bacterial Pathogenicity, Virulence and Phylogeny
Reading list
- CGE tool box, read the sections on pathogenFinder, resFinder and virulenceFinder
Schedule
09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen
09:15 - 09:45 Lecture: PathogenFinder, Johanne Ahrenfeldt
09:45 - 10:00 Coffee Break
10:00 - 11:00 Exercise: PathogenFinder, Johanne Ahrenfeldt
11:15 - 12:00 Lecture: VirulenceFinder, Johanne Ahrenfeldt
12:00 - 13:00 Lunch break
13:00 - 14:00 Lecture: Antibiotic Resistance and ResFinder(slides 1, 2), Johanne Ahrenfeldt
14:00 - 15:00 Exercise: VirulenceFinder and ResFinder, Johanne Ahrenfeldt
15:00 - 16:00 Lecture: Bacterial Phylogeny (slides 1, 2), Johanne Ahrenfeldt
Thursday, January 4th - B- and T-cell Receptors Genetics and Structure
Reading list
Schedule
09:00 - 09:15 Recap: Yesterdays exercises, Leon Eyrich Jessen
09:15 - 10:00 Lecture: TCR and BCR maturation, Leon Eyrich Jessen
10:00 - 10:15 Coffee Break
10:15 - 12:00 Exercise: Analysis of immunoglobulin gene rearrangements, Leon Eyrich Jessen
12:00 - 13:00 Lunch Break
13:00 - 14:00 Lecture: TCR and BCR structure, Kamilla Kjærgaard Jensen
14:00 - 16:00 Exercise: Antibody Structure Prediction and Analysis, Kamilla Kjærgaard Jensen
Friday, January 5th - B Cell Epitope Predictions
Reading list
- Paper: BepiPred 2.0
- Paper: B-cell epitope prediction
- Video: Simplified B-cell walkthrough (Nice and easy understandable explanation of B-cells)
- Resource: PDB 101: Introduction to PDB Data
- Optional: SigniSite paper and supplementary data
Schedule
09:00 - 09:15 Recap: Yesterdays exercises, Kamilla Kjærgaard Jensen
09:15 - 10:00 Lecture: Homology Modeling to Predict Antigen Structure, Kamilla Kjærgaard Jensen
10:00 - 10:15 Coffee Break
10:15 - 12:00 Exercise: Homology Modeling to Predict Antigen Structure, Kamilla Kjærgaard Jensen
12:00 - 13:00 Lunch Break
13:00 - 13:30 Lecture: Linear B cell epitope prediction, Martin Closter Jespersen
13:30 - 14:00 Lecture: Conformational B cell epitope prediction, Martin Closter Jespersen
14:00 - 15:00 Exercise: B cell epitope predictions, Martin Closter Jespersen
15:00 - 15:30 Lecture: SigniSite for Protein Level Geno-/Phenotype Correlation (slides 1, 2), Leon Eyrich Jessen
15:30 - 16:00 Exercise: Using SigniSite to identify resistance mutations, Leon Eyrich Jessen
Monday January 8th - T-cell Epitopes
Reading list
- Immunological Bioinformatics Chapter 3
- Immunological Bioinformatics Chapter 4
- Paper: Modeling the adaptive immune system: predictions and simulations
- Paper: Major histocompatibility complex class I binding predictions as a tool in epitope discovery
- Paper: MHC Class II epitope predictive algorithms.
Schedule
09:00 - 09:30 Recap: Yesterdays exercises, Leon Eyrich Jessen
09:30 - 10:15 Prediction of MHC peptide binding using data mining techniques (PSSM's and ANN), Morten Nielsen
10:15 - 10:30 Coffee Break
10:30 - 11:15 Rational epitope discovery using immunoinformatics, Morten Nielsen
11:15 - 12:00 A little on MHC class II binding, Morten Nielsen
Session materials: Slides [PDF], Logo handout, NN handout.
12:00 - 13:00: Lunch Break
13:00 - 16:00: Performance measures Exercise - Prediction of MHC:peptide binding using PSSM and ANN Morten Nielsen, Department of Bio and Health Informatics.
Tuesday, January 9th - Antigen Processing and Presentation, Supertypes, HLA Clustering, and Vaccine Design
Reading list
- Chapter 13
- Chapter 14
- Simultaneous alignment and clustering of peptide data using a Gibbs sampling approach
- Optional: A Quantitative Analysis of the Variables Affecting the Repertoire of T Cell Specificities Recognized after Vaccinia Virus Infection
- Optional: Identification and HLA-tetramer-validation of human CD4+ and CD8+ T cell responses against HCMV proteins IE1 and IE2
Schedule
09:00 - 09:30 Exercise round up, Morten Nielsen
09:30 - 10:00 Identifying multiple sequence motifs in large scale peptide data sets
10:00 - 10:30 Supertypes and functional clustering of MHC molecules, Morten Nielsen
10:30 - 10:45 Coffee Break
10:45 - 11:30 What defines a T cel epitope? Is there any thing beyond MHC binding?, Morten Nielsen
11:30 - 12:00 Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design, Morten Nielsen
12:00 - 13:00 Lunch Break
13:00 - 16:00 Exercises: Development of vaccines against HCV, Morten Nielsen
Wednesday, January 10th - Chimeric Antigen Receptor (CAR) Immunotherapy
Reading list
- Paper: Increasing the safety and efficacy of chimeric antigen receptor T cell therapy
- Article: The CAR T-Cell Race
Scedule
09:00 - 09:15 Recap: Yesterdays exercises, Morten Nielsen
09:15 - 10:00 Lecture: Antibody Humanization, Paolo Marcatili
10:00 - 10:30 Coffee Break
10:30 - 12:00 Exercise: Antibody Humanization, Paolo Marcatili
12:00 - 13:00 Lunch Break
13:00 - 14:00 Lecture: Humanization and deimmunazation for cancer T cell therapy molecules, Paolo Marcatili
14:00 - 16:00 Exercise: CAR T-cell humanisation and de-immunisation, Paolo Marcatili
Thursday, January 11th - Seminar on Cancer Immunotherapy by Invited Speakers
Scedule
09:00 - 09:45 Clinical Associate Professor, MD, PhD, Marco Donia, UCPH/Herlev-Gentofte Hospital: Cancer Immunotherapy
10:00 - 10:45 Professor Sine Reker Hadrup, DTU Vet: Interrogating the antigen specific T cell recognition of cancer
11:00 - 11:45 Associate Professor Lars Rønn Olsen, DTU Bioinformatics: Prediction of Immunotherapy Treatment Outcome
12:00 - 13:00 Lunch Break
13:00 - 14:00 Introduction to project work and exam, Leon Eyrich Jessen
Friday, January 12th - Thursday January 18th - Project Work
09.00 - 17.00: Group project work
Groups and projects 2018
- G01 - Line, Solveig and Monica: "Peptide Vaccine Design against Epstein-Barr Virus for Prevention of Nasopharyngeal Cancer"
- G02 - Mikael, Jacob and Kathrine: "Winter is coming - a bioinformatic approach to prepare for the next influenza virus"
- G03 - Sandra, Esteban, Narasimha and Taner: "Zika virus vaccine for Brazilian Population"
- G04 - Signe, Julie, Ina and Aimilia: "Identifying target epitopes for designing a vaccine against Acinetobacter baumannii"
- G05 - Christian, Mikkel and Frank: "HIV vaccine development for sub-saharian Africans"
- G06 - Keith, Nadia and Jeppe: "EViVa – Vaccine for EBV"
- G07 - Sofie, Natasja and Ulla: "Zika-virus Vaccine Development"
Friday, January 19th - Exams
08:00 - 16:00 Exam day, Morten Nielsen and Leon Eyrich Jessen
Exam schedule
Group 01
- 07:55 - 08:00 G01 - Setup
- 08:00 - 08:15 G01 - Presentation
- 08:15 - 08:25 Line
- 08:25 - 08:35 Solveig
- 08:35 - 08:45 Monica
- 08:45 - 08:50 Grading
Group 05
- 08:55 - 09:00 G05 - Setup
- 09:00 - 09:15 G05 - Presentation
- 09:15 - 09:25 Christian
- 09:25 - 09:35 Mikkel
- 09:35 - 09:45 Frank
- 09:45 - 09:50 Grading
Group 04
- 09:55 - 10:00 G04 - Setup
- 10:00 - 10:15 G04 - Presentation
- 10:15 - 10:25 Signe
- 10:25 - 10:35 Julie
- 10:35 - 10:45 Ina
- 10:45 - 10:55 Aimilia
- 10:55 - 11:00 Grading
Group 03
- 11:05 - 11:10 G03 - Setup
- 11:10 - 11:25 G03 - Presentation
- 11:25 - 11:35 Sandra
- 11:35 - 11:45 Esteban
- 11:45 - 11:55 Narasimha
- 11:55 - 12:05 Taner
- 12:05 - 12:10 Grading
12:10 - 12:55 Lunch
Group 02
- 12:55 - 13:00 G02 - Setup
- 13:00 - 13:15 G02 - Presentation
- 13:15 - 13:25 Mikael
- 13:25 - 13:35 Jacob
- 13:35 - 13:45 Kathrine
- 13:45 - 13:50 Grading
Group 06
- 13:55 - 14:00 G06 - Setup
- 14:00 - 14:15 G06 - Presentation
- 14:15 - 14:25 Keith
- 14:25 - 14:35 Nadia
- 14:35 - 14:45 Jeppe
- 14:45 - 14:50 Grading
Group 07
- 14:55 - 15:00 G07 - Setup
- 15:00 - 15:15 G07 - Presentation
- 15:15 - 15:25 Sofie
- 15:25 - 15:35 Natasja
- 15:35 - 15:45 Ulla
- 15:45 - 15:50 Grading