36685 Immunological Bioinformatics Course Program January 2018

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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

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

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

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

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
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