36685 Immunological Bioinformatics Course Program January 2019
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Information for Course Attendees
Main page for course site can be found here. Please note, that the program can be subject to changes or updates. Make sure to reload the page, to get the newest version of the program.
Course responsible and main lecturers
- Postdoc Leon Eyrich Jessen, DTU Health Technology [LEJ]
- Associate Professor Paolo Marcatili, DTU Health Technology [PM]
- Professor Morten Nielsen, DTU Health Technology [MN]
Other lecturers
- PhD student Birkir Reynisson, DTU Health Technology [BR]
- Professor Søren Buus, Department of Immunology and Microbiology, University of Copenhagen [SB]
- Postdoc, MD, PhD, Troels Holz Borch, Center for Cancer Immune Therapy (CCIT), University of Copenhagen/Herlev-Gentofte Hospital
- Professor Sine Reker Hadrup, DTU Health Technology
- Associate Professor Lars Rønn Olsen, DTU Health Technology
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
Teaching and exam will be at DTU Lyngby Campus in Building 208, room 062 (Down the stairs in the basement). Should you be new to DTU, a map of DTU Lyngby Campus can be found here.
Course Schedule Overview
| Monday Jan. 7th | Tuesday Jan. 8th | Wednesday Jan. 9th | Thursday Jan. 10th | Friday Jan. 11th | Monday Jan. 14th | Tuesday Jan. 15th | Wednesday Jan. 16th | |
|---|---|---|---|---|---|---|---|---|
| Introduction, Basic Immunology and IEDB | Genetics and Repertoires of B- and T-Cell Receptors | Structure of B- and T- Cell Receptors and B-Cell Epitopes | T-Cell Epitopes | Antigen Processing and Presentation, HLA Clustering, and Vaccine Design | Humanization, B- and T-Cell Interaction Models and Repertoires | De-Immunization, Chimeric Antigen Receptor (CAR) Immunotherapy | Seminar on Cancer Immunotherapy by Invited Speakers | |
| 09.00 - 09.30 | Course Introduction [LEJ] | Exercise recap [BR] | Exercise recap [LEJ] | Exercise recap [PM] | Exercise recap [MN] | Exercise recap [MN] | Exercise recap [LEJ] | |
| 09.30 - 10.15 | Lecture: Basic Mechanisms of Immune Defence [SB] | Introduction [LEJ] | Lecture: TCR and BCR structure [PM] | Lecture: Prediction of MHC peptide binding using PSSMs and ANNs [MN]. Session materials: Slides [PDF], Logo handout, Answer Logo handout. NN handout. | Lecture: Identifying multiple sequence motifs in large scale peptide data sets [MN] | Lecture: [Antibody Humanization] [PM] | Lecture: Protein drug de-immunization [BR] | Clinical Research: Troels Holz Borch (MD, PhD, National Center for Cancer Immune Therapy, Herlev Hospital) |
| 10.15 - 10.30 | Coffee Break | Coffee Break | Coffee Break | Coffee Break | Coffee Break | Coffee Break | Coffee Break | Coffee Break |
| 10.30 - 11.15 | Lecture: Antigen Capture and Presentation to T-lymphocytes [SB] | Group work [LEJ] | Exercise: Antibody Structure Prediction and Analysis [PM] | Lecture: Rational epitope discovery using immunoinformatics [MN] | Lecture: Supertypes and functional clustering of MHC molecules [MN] | Exercise: Antibody Humanization [PM] | Exercise: Protein drug de-immunization [BR] | Wet lab molecular Research: Sine Reker Hadrup (Professor, PhD, DTU Health Technology) |
| 11.15 - 12.00 | Lecture: The Impact of Immunological Bioinformatics on Immunological Research [SB] | Group work [LEJ] | Lecture: Linear and Conformational B-cell epitope prediction [PM] | Lecture: MHC class II binding and Performance measures [MN] | Lecture: What defines a T cel epitope? Is there any thing beyond MHC binding?, and Selecting the one in a million. Strategies for selecting peptide subsets, and vaccine design [MN] | Lecture: Modelling TCR interactions (netTCR) [LEJ] | Lecture: [Humanization and deimmunization for cancer T cell therapy molecules] [PM] | Dry lab bioinformatics Research: Lars Rønn Olsen (Associate Professor, PhD, DTU Health Technology) |
| 12.00 - 13.00 | Lunch Break | Lunch Break | Lunch Break | Lunch Break | Lunch Break | Lunch Break | Lunch Break | Lunch Break |
| 13.00 - 17.00 | Exercise: Immune Epitope Database [BR] | Group work and presentations [LEJ] | Exercise: B cell epitope predictions [PM] | Exercise:Prediction of MHC:peptide binding using PSSM and ANN
Answers: Prediction of MHC:peptide binding using PSSM and ANN |
Exercise: Development of vaccines against HCV [MN] Answers | Exercise: Working with peptide data [LEJ] | Exercise: [CAR T-cell humanisation and de-immunisation] [PM] | Introduction to project work and exam [LEJ] |
| Background materials | None |
Optional Support materials:
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Project Period and Exam
Thursday, January 17th - Wednesday January 23rd - Project Work
Please note: The deadline for uploading the final project presentation will be Wednesday January 23rd at 23.59. It is a prerequisite for the exam to complete this assignment. Furthermore, please note, that you are responsible for all aspects of the group work and subsequent presentation
09.00 - 17.00: Group project work
Groups and Projects 2019
The following groups counting 36 students in total, have been formed:
- G01 - (4p): Andreas (s134890), Asbjørn (s143849), Galal (s154802), Chaza (s144491)
- G02 - (4p): Madeeha (s154213), Amera (s130076), Alla (s061664), Asma (s161091)
- G03 - (4p): Cirkeline (s133643), Dorthe (s175824), Milena (milvu), Kristine (s111518)
- G04 - (4p): Marie (s143921), Catrine (s136574), Mikkel (s183049), Mikkel (s190095)
- G05 - (4p): Anna M (s136582), Pernille (s144499), Helena (s144530), Sebastian (s163691)
- G06 - (3p): Steinunn (s182233), Hrafnhildur (s182471), Vladislav (s182333)
- G07 - (3p): Ricki (s134898), Maria (s134878), Anna-Lisa (s190228)
- G08 - (5p): Lasse (s134887), Lasse (s173158), Anna (s124062), Jacob (s163726), Jakob (s163698)
- G09 - (5p): Daniel (s181782), Juan (s182441), Shreya (s181330), Kent (s133497), Adrianna (s181311)
Exam Schedule, Thursday-Friday, January 24-25th
The exam will be in the same room as the teaching, i.e. building 208, room 062
09:00 - 16:00 Thursday January 24th, Exam day 1, Morten Nielsen and Leon Eyrich Jessen
Group 1
- 09:00 - 09:15 Presentation incl. questions
- 09:15 - 09:25 G01_1 Chaza (s144491)
- 09:25 - 09:35 G01_2 Asbjørn (s143849)
- 09:35 - 09:45 G01_3 Galal (s154802)
- 09:45 - 09:55 G01_4 Andreas (s134890)
- 09:55 - 10:00 Grading
Group 9
- 10:00 - 10:15 Presentation incl. questions
- 10:15 - 10:25 G09_1 Adrianna (s181311)
- 10:25 - 10:35 G09_2 Kent (s133497)
- 10:35 - 10:45 G09_3 Juan (s182441)
- 10:45 - 10:55 G09_4 Daniel (s181782)
- 10:55 - 11:05 G09_5 Shreya (s181330)
- 11:05 - 11:10 Grading
Group 4
- 11:10 - 11:25 Presentation incl. questions
- 11:25 - 11:35 G04_1 Marie (s143921)
- 11:35 - 11:45 G04_2 Mikkel (s183049)
- 11:45 - 11:55 G04_3 Mikkel (s190095)
- 11:55 - 12:05 G04_4 Catrine (s136574)
- 12:05 - 12:10 Grading
Lunch break
Group 2
- 13:00 - 13:15 Presentation incl. questions
- 13:15 - 13:25 G02_1 Madeeha (s154213)
- 13:25 - 13:35 G02_2 Asma (s161091)
- 13:35 - 13:45 G02_3 Amera (s130076)
- 13:45 - 13:55 G02_4 Alla (s061664)
- 13:55 - 14:00 Grading
Group 7
- 14:00 - 14:15 Presentation incl. questions
- 14:15 - 14:25 G07_1 Ricki (s134898)
- 14:25 - 14:35 G07_2 Anna-Lisa (s190228)
- 14:35 - 14:45 G07_3 Maria (s134878)
- 14:45 - 14:50 Grading
Break
Group 3
- 15:00 - 15:15 Presentation incl. questions
- 15:15 - 15:25 G03_1 Kristine (s111518)
- 15:25 - 15:35 G03_2 Cirkeline (s133643)
- 15:35 - 15:45 G03_3 Dorthe (s175824)
- 15:45 - 15:55 G03_4 Milena (milvu)
- 15:55 - 16:00 Grading
09:00 - 12:00 Friday January 25th, Exam day 2, Morten Nielsen and Leon Eyrich Jessen
Group 5
- 09:00 - 09:15 Presentation incl. questions
- 09:15 - 09:25 G05_1 Anna M (s136582)
- 09:25 - 09:35 G05_2 Sebastian (s163691)
- 09:35 - 09:45 G05_3 Helena (s144530)
- 09:45 - 09:55 G05_4 Pernille (s144499)
- 09:55 - 10:00 Grading
Group 8
- 10:00 - 10:15 Presentation incl. questions
- 10:15 - 10:25 G08_1 Jakob (s163726)
- 10:25 - 10:35 G08_2 Lasse (s134887)
- 10:35 - 10:45 G08_3 Lasse (s173158)
- 10:45 - 10:55 G08_4 Jakob (s163698)
- 10:55 - 11:05 G08_5 Anna (s124062)
- 11:05 - 11:10 Grading
Group 6
- 11:10 - 11:25 Presentation incl. questions
- 11:25 - 11:35 G06_1 Steinunn (s182233)
- 11:35 - 11:45 G06_2 Vladislav (s182333)
- 11:45 - 11:55 G06_3 Hrafnhildur (s182471)
- 11:55 - 12:00 Grading